RLID	Gene_ID	Gene_Name	Link	Aliases	RNA_category	Organism	PMID	Subcellular_Localization	tissue	Methods	Description
RLID00000001	100003563	stmn2b	http://www.ncbi.nlm.nih.gov/gene/?term=100003563	"scg10, scgn10, stmn2, zgc:110132 "	mRNA	Danio rerio	24089481	Axon	Embryoneuron	Whole mount in situ hybridization	"Here, we provide direct evidence of the presence of mRNAs of the tubb5, nefma, and stmnb2 genes in several types of axons in the developing zebrafish (Danio rerio) embryo, with frequent accumulation at the growth cone. We further show that axonal localization of mRNA is a specific property of a subset of genes, as mRNAs of the huc and neurod genes, abundantly expressed in neurons, were not found in axons. "
RLID00000002	100008586	GAGE12F	http://www.ncbi.nlm.nih.gov/gene/?term=100008586		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000003	100008588	RNA18S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008588	RN18S1	rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00000004	100008588	RNA18S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008588	RN18S1	rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00000005	100008589	RNA28S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008589	RN28S1	rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00000006	100008589	RNA28S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008589	RN28S1	rRNA	Homo sapiens	16178658	Endoplasmic reticulum	HDF cell	Fluorescence in situ hybridization	"Extensive control studies are performed, including the use of fluorescence in-situ hybridization (FISH), negative-control beacons, and the detection of colocalization of 28S ribosomal RNA with the rough endoplasmic reticulum (ER), suggesting that the mRNA localization and colocalization patterns observed in our study are true and specific. "
RLID00000007	100008589	RNA28S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008589	RN28S1	rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000008	100008589	RNA28S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008589	RN28S1	rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000009	100008589	RNA28S5	http://www.ncbi.nlm.nih.gov/gene/?term=100008589	RN28S1	rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00000010	100009667	POU5F1P5	http://www.ncbi.nlm.nih.gov/gene/?term=100009667	Oct4-pg5	lncRNA	Homo sapiens	21151833	Nucleus	Breast cancer cell	qRT-PCR	We next analyzed nuclear run-on samples using primers specific for Oct4 transcript variant 2 and Oct4 pseudogene 4 and we observed a significant increase in transcription of both these RNA species (Fig. 3B and C). Data are collected from Figure 3.
RLID00000011	10000	AKT3	http://www.ncbi.nlm.nih.gov/gene/?term=10000	"MPPH, MPPH2, PKB-GAMMA, PKBG, PRKBG, RAC-PK-gamma, RAC-gamma, STK-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000012	10000	AKT3	http://www.ncbi.nlm.nih.gov/gene/?term=10000	"MPPH, MPPH2, PKB-GAMMA, PKBG, PRKBG, RAC-PK-gamma, RAC-gamma, STK-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000013	100019	Mdn1	http://www.ncbi.nlm.nih.gov/gene/?term=100019	"4833432B22Rik, A130070M06, AA958993, D4Abb1e, Gm135 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000014	10001	MED6	http://www.ncbi.nlm.nih.gov/gene/?term=10001	"ARC33, NY-REN-28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000015	100034733	2610305J24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100034733		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000016	100034739	Gm17762	http://www.ncbi.nlm.nih.gov/gene/?term=100034739		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000017	100036887	ppp1r2	http://www.ncbi.nlm.nih.gov/gene/?term=100036887		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000018	100037236	grip2	http://www.ncbi.nlm.nih.gov/gene/?term=100037236	"grip2.1, xgrip2 "	mRNA	Xenopus laevis	17320814	Germ plasm	Embryo	In situ hybridization	"Using a large-scale in situ hybridization screening, we found that the mRNA coding for Xenopus glutamate receptor interacting protein 2 (XGRIP2) was localized to the germ plasm of Xenopus laevis. "
RLID00000019	100037236	grip2	http://www.ncbi.nlm.nih.gov/gene/?term=100037236	"grip2.1, xgrip2 "	mRNA	Xenopus laevis	17924960	Mitochondrion	Oocyte	In situ hybridization	Grip2 mRNA is present in the mitochondrial cloud of late pre-vitellogenic oocytes and then in the germ plasm through oogenesis and early development until tailbud tadpole stages.
RLID00000020	100037236	grip2	http://www.ncbi.nlm.nih.gov/gene/?term=100037236	"grip2.1, xgrip2 "	mRNA	Xenopus laevis	17924960	Germ plasm	Oocyte	In situ hybridization	Grip2 mRNA is present in the mitochondrial cloud of late pre-vitellogenic oocytes and then in the germ plasm through oogenesis and early development until tailbud tadpole stages.
RLID00000021	100037236	grip2	http://www.ncbi.nlm.nih.gov/gene/?term=100037236	"grip2.1, xgrip2 "	mRNA	Xenopus laevis	21788733	Mitochondrion	Oocyte	RNA localization assays	"Here, we demonstrate that the 3'-UTR of XGrip2.1 contains a 211 nucleotide RNA signal sequence that promotes localization to the mitochondrial cloud via the early localization pathway upon injection into stage I oocytes. "
RLID00000022	100037236	grip2	http://www.ncbi.nlm.nih.gov/gene/?term=100037236	"grip2.1, xgrip2 "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000023	100037417	DDTL	http://www.ncbi.nlm.nih.gov/gene/?term=100037417	KB-226F1.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000024	100038259	sulf1	http://www.ncbi.nlm.nih.gov/gene/?term=100038259	"XtSulf-1, XtSulf1, hsulf-1, sulf-1 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000025	100038470	Gm10808	http://www.ncbi.nlm.nih.gov/gene/?term=100038470	ENSMUSG00000075047	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000026	100038555	Gm10578	http://www.ncbi.nlm.nih.gov/gene/?term=100038555	ENSMUSG00000073800	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000027	100038570	Gm11744	http://www.ncbi.nlm.nih.gov/gene/?term=100038570	"OTTMUSG00000003947, Prcd "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000028	100038589	Gm10744	http://www.ncbi.nlm.nih.gov/gene/?term=100038589	ENSMUSG00000074683	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000029	100038630	Gm10727	http://www.ncbi.nlm.nih.gov/gene/?term=100038630	ENSMUSG00000074599	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000030	100038644	Gm10667	http://www.ncbi.nlm.nih.gov/gene/?term=100038644	ENSMUSG00000074318	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000031	100038687	Gm10577	http://www.ncbi.nlm.nih.gov/gene/?term=100038687	ENSMUSG00000073789	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000032	100038723	Sox5it	http://www.ncbi.nlm.nih.gov/gene/?term=100038723	"ENSMUSG00000072677, Gm10396 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000033	100039795	Ildr2	http://www.ncbi.nlm.nih.gov/gene/?term=100039795	"2810478N18Rik, 3110063L10Rik, AI852300, D1Ertd471e, Dbsm1, ENSMUSG00000040612, Ll "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000034	100040322	3830408C21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100040322		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000035	100040529	Gm2824	http://www.ncbi.nlm.nih.gov/gene/?term=100040529		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000036	100040736	Foxd2os	http://www.ncbi.nlm.nih.gov/gene/?term=100040736	9130206I24Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000037	100040972	Tceal7	http://www.ncbi.nlm.nih.gov/gene/?term=100040972	1110018P05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000038	100041143	Gm3161	http://www.ncbi.nlm.nih.gov/gene/?term=100041143		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000039	100041286	Snhg15	http://www.ncbi.nlm.nih.gov/gene/?term=100041286	"Gm11974, OTTMUSG00000005115 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000040	100041734	4930522L14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100041734		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000041	100041806	LOC100041806	http://www.ncbi.nlm.nih.gov/gene/?term=100041806		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000042	100041932	Gm3579	http://www.ncbi.nlm.nih.gov/gene/?term=100041932	H3097D08	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000043	100042056	9130019P16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100042056	"6430501H15Rik, OTTMUSG00000023151 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000044	100042166	Gm3704	http://www.ncbi.nlm.nih.gov/gene/?term=100042166		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000045	100042192	Gm3715	http://www.ncbi.nlm.nih.gov/gene/?term=100042192	5033421C21Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000046	100042198	Gm3716	http://www.ncbi.nlm.nih.gov/gene/?term=100042198	Gm1683	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000047	100042480	Nhsl2	http://www.ncbi.nlm.nih.gov/gene/?term=100042480	"1110062M06Rik, 6430511F03, AI225852, AW488865, EG621083, ENSMUSG00000073037, Gm10456 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000048	100042770	Gm4022	http://www.ncbi.nlm.nih.gov/gene/?term=100042770		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000049	100043034	Rex2	http://www.ncbi.nlm.nih.gov/gene/?term=100043034	"Gm13138, OTTMUSG00000010655 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000050	100043040	1110002L01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100043040		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000051	100043089	Gm4221	http://www.ncbi.nlm.nih.gov/gene/?term=100043089		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000052	100043600	Gm4544	http://www.ncbi.nlm.nih.gov/gene/?term=100043600		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000053	100043636	AI662270	http://www.ncbi.nlm.nih.gov/gene/?term=100043636	AW496474	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000054	100043902	Six3os1	http://www.ncbi.nlm.nih.gov/gene/?term=100043902	"D17Mgi26, E130112H22Rik, Rncr1, Six3os "	lncRNA	Mus musculus	15703187	Nucleus	Embryonic tissue	In situ hybridization|RT-PCR	"We detected the expression in adult retina (postnatal day 30, P30) of Six3OS, Six6OS, Otx2OS, CrxOS and RaxOS (Fig. 3 and data not shown). In general, these transcripts were all expressed at higher levels in the inner nuclear layer (INL) and in the ganglion cell layer (GCL).  "
RLID00000055	100043911	Ppp4r1l-ps	http://www.ncbi.nlm.nih.gov/gene/?term=100043911	"1700007P14Rik, 5830403E09Rik, C030010B13Rik, Ppp4r1l "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000056	100048912	CDKN2B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100048912	"ANRIL, CDKN2B-AS, CDKN2BAS, NCRNA00089, PCAT12, p15AS "	lncRNA	Homo sapiens	25690653	Nucleus	P493-6 cell	qRT-PCR	"To validate the isolation of nuclear and cytoplasmic fractions, the enrichment of 3 nuclear (ANRIL, MIAT, XIST) and 3 cytoplasmic (RPPH1, DANCR, tRNA-Lys) RNAs was analyzed by qRT-PCR. "
RLID00000057	100048912	CDKN2B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100048912	"ANRIL, CDKN2B-AS, CDKN2BAS, NCRNA00089, PCAT12, p15AS "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00000058	100049226	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=100049226	"glh-1, olvas "	mRNA	Oryzias latipes	24814190	Germ plasm	Germ cell	Light|Microscopy	Germ cells of diverse animal species have a unique membrane-less organelle called germ plasm (GP). GP is usually associated with mitochondria and contains RNA binding proteins and mRNAs of germ genes such as vasa.
RLID00000059	100049418	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=100049418		mRNA	Oryzias latipes	23439406	Mitochondrion	Oocyte	In situ hybridization	"Here we report in the fish medaka (Oryzias latipes) that RNAs encoding microphthalmia-associated transcription factor (Mitf) are prominent components of the BB. By fluorescence in situ hybridization on ovarian section, we revealed that the transcripts of both mitf1 and mitf2 genes concentrated in the BB, in which they co-localized with the dazl RNA, a definitive BB marker highly conserved in vertebrates.  "
RLID00000060	100049571	Ancr-1	http://www.ncbi.nlm.nih.gov/gene/?term=100049571		lncRNA	Apis mellifera	15208441	Nucleus	Brain neurons	In situ hybridization	"In the present study, we identified another novel gene, termed AncR-1, whose transcripts were localized to nuclei in the whole cortex region of the honeybee brain, as a candidate novel noncoding nuclear RNA gene. "
RLID00000061	100049572	Ks-1	http://www.ncbi.nlm.nih.gov/gene/?term=100049572		lncRNA	Apis mellifera	12088150	Nucleus	Kenyon cell	In situ hybridization	"Furthermore, fluorescent in situ hybridization revealed that Ks-1 transcripts are located in the nuclei of the neural cells, accumulating in some scattered spots. These findings demonstrate that Ks-1 encodes a novel class of noncoding nuclear RNA and is possibly involved in the regulation of neural functions. "
RLID00000062	100049613	TRK-TTT3-4	http://www.ncbi.nlm.nih.gov/gene/?term=100049613	"TRK-TTT3-3, TRNAK3 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000063	10005	ACOT8	http://www.ncbi.nlm.nih.gov/gene/?term=10005	"HNAACTE, NAP1, PTE-1, PTE-2, PTE1, PTE2, hACTE-III, hTE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000064	10005	ACOT8	http://www.ncbi.nlm.nih.gov/gene/?term=10005	"HNAACTE, NAP1, PTE-1, PTE-2, PTE1, PTE2, hACTE-III, hTE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000065	100061	Lrrc19	http://www.ncbi.nlm.nih.gov/gene/?term=100061	"9130022A01Rik, AI314124, AL022954, AW261791 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000066	100061	Lrrc19	http://www.ncbi.nlm.nih.gov/gene/?term=100061	"9130022A01Rik, AI314124, AL022954, AW261791 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000067	10006	ABI1	http://www.ncbi.nlm.nih.gov/gene/?term=10006	"ABI-1, ABLBP4, E3B1, NAP1BP, SSH3BP, SSH3BP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000068	10006	ABI1	http://www.ncbi.nlm.nih.gov/gene/?term=10006	"ABI-1, ABLBP4, E3B1, NAP1BP, SSH3BP, SSH3BP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000069	10007	GNPDA1	http://www.ncbi.nlm.nih.gov/gene/?term=10007	"GNP1, GNPDA, GNPI, GPI, HLN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000070	10007	GNPDA1	http://www.ncbi.nlm.nih.gov/gene/?term=10007	"GNP1, GNPDA, GNPI, GPI, HLN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000071	10007	GNPDA1	http://www.ncbi.nlm.nih.gov/gene/?term=10007	"GNP1, GNPDA, GNPI, GPI, HLN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000072	10007	GNPDA1	http://www.ncbi.nlm.nih.gov/gene/?term=10007	"GNP1, GNPDA, GNPI, GPI, HLN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000073	100093630	SNHG8	http://www.ncbi.nlm.nih.gov/gene/?term=100093630	"LINC00060, NCRNA00060 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000074	100101685	cnksr2	http://www.ncbi.nlm.nih.gov/gene/?term=100101685	"cnk2, ksr2 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000075	10010	TANK	http://www.ncbi.nlm.nih.gov/gene/?term=10010	"I-TRAF, ITRAF, TRAF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000076	10010	TANK	http://www.ncbi.nlm.nih.gov/gene/?term=10010	"I-TRAF, ITRAF, TRAF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000077	10010	TANK	http://www.ncbi.nlm.nih.gov/gene/?term=10010	"I-TRAF, ITRAF, TRAF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000078	100113378	SNORD119	http://www.ncbi.nlm.nih.gov/gene/?term=100113378		snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00000079	100113378	SNORD119	http://www.ncbi.nlm.nih.gov/gene/?term=100113378		snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000080	100113378	SNORD119	http://www.ncbi.nlm.nih.gov/gene/?term=100113378		snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000081	100113379	SNORD121A	http://www.ncbi.nlm.nih.gov/gene/?term=100113379		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000082	100113380	SNORD125	http://www.ncbi.nlm.nih.gov/gene/?term=100113380		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000083	100113382	SNORD105B	http://www.ncbi.nlm.nih.gov/gene/?term=100113382		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000084	100113382	SNORD105B	http://www.ncbi.nlm.nih.gov/gene/?term=100113382		snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00000085	100113382	SNORD105B	http://www.ncbi.nlm.nih.gov/gene/?term=100113382		snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00000086	100113386	UCKL1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100113386	"UCKL1-AS, UCKL1AS, UCKL1OS "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000087	100113391	SNORD126	http://www.ncbi.nlm.nih.gov/gene/?term=100113391	"MIR1201, MIRN1201 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000088	100113392	SNORD11B	http://www.ncbi.nlm.nih.gov/gene/?term=100113392		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000089	100113393	SNORD12B	http://www.ncbi.nlm.nih.gov/gene/?term=100113393		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000090	100113402	SNORD111B	http://www.ncbi.nlm.nih.gov/gene/?term=100113402	MIR3647	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000091	100113407	TMEM170B	http://www.ncbi.nlm.nih.gov/gene/?term=100113407		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000092	100113407	TMEM170B	http://www.ncbi.nlm.nih.gov/gene/?term=100113407		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000093	10011	SRA1	http://www.ncbi.nlm.nih.gov/gene/?term=10011	"SRA, SRAP, STRAA1, pp7684 "	lncRNA	Homo sapiens	17170069	Cytoplasm	S91|3T3|MCF-7|LNCaP cell	In situ hybridization|RT-PCR	"As shown in Fig. 5B, hSRA was cytoplasmic in the majority of cells (90%), but in the remainder it was localized in the nucleus in a distinctly speckled pattern, suggesting that hSRA is organized in yet another nuclear subcompartment. "
RLID00000094	10011	SRA1	http://www.ncbi.nlm.nih.gov/gene/?term=10011	"SRA, SRAP, STRAA1, pp7684 "	lncRNA	Homo sapiens	17170069	Nucleus	S91|3T3|MCF-7|LNCaP cell	In situ hybridization|RT-PCR	"As shown in Fig. 5B, hSRA was cytoplasmic in the majority of cells (?90%), but in the remainder it was localized in the nucleus in a distinctly speckled pattern, suggesting that hSRA is organized in yet another nuclear subcompartment. "
RLID00000095	10011	SRA1	http://www.ncbi.nlm.nih.gov/gene/?term=10011	"SRA, SRAP, STRAA1, pp7684 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000096	100121	Tdrd7	http://www.ncbi.nlm.nih.gov/gene/?term=100121	"5730495N10Rik, AI447470, PCTAIRE2BP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000097	100124412	FAM138E	http://www.ncbi.nlm.nih.gov/gene/?term=100124412	F379	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00000098	100124516	SNORD58C	http://www.ncbi.nlm.nih.gov/gene/?term=100124516	U58	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00000099	100124516	SNORD58C	http://www.ncbi.nlm.nih.gov/gene/?term=100124516	U58	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000100	100124516	SNORD58C	http://www.ncbi.nlm.nih.gov/gene/?term=100124516	U58	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000101	100124534	SNORA84	http://www.ncbi.nlm.nih.gov/gene/?term=100124534		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000102	100124536	SNORA38B	http://www.ncbi.nlm.nih.gov/gene/?term=100124536		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000103	100124539	SNORA11B	http://www.ncbi.nlm.nih.gov/gene/?term=100124539		snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000104	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072 "	lncRNA	Homo sapiens	21963238	Nucleus	Breast cancer cell	qRT-PCR|Chip-seq	"HOTAIR binding sites occur on multiple chromosomes and are enriched in genic regions, notably regions annotated as enhancers and introns (Fig. 5A). "
RLID00000105	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072 "	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00000106	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072 "	lncRNA	Homo sapiens	23133536	Nucleus	Breast cancer cell	In situ hybridization	"Of note, single molecule RNA FISH against HOTAIR in primary lung and foot fibroblast cells showed both nuclear and cytoplasmic localization [16], and recent chromatin immunoprecipitation experiments have localized HOTAIR in conjunction with PRC2 complex on chromatin in cancer cells "
RLID00000107	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072 "	lncRNA	Homo sapiens	23133536	Cytoplasm	Breast cancer cell	In situ hybridization	"Of note, single molecule RNA FISH against HOTAIR in primary lung and foot fibroblast cells showed both nuclear and cytoplasmic localization [16], and recent chromatin immunoprecipitation experiments have localized HOTAIR in conjunction with PRC2 complex on chromatin in cancer cells "
RLID00000108	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072 "	lncRNA	Homo sapiens	19571010	Nucleus	HFF|HLF|HeLa cell	Fluorescence in situ hybridization	"Figure 3b: Subcellular localization analysis of lincRNAs by RNA FISH demonstrates localization of lincRNAs to the nucleus. Each panel represents the in situ hybridization of �0 fluorescently labeled DNA oligos with complementarity to the interrogated lincRNA. RNA FISH experiments were performed in male hFF for each represented lincRNA (XIST, HOTAIR, TUG-1, lincMKLN-1, lincFOXF1, and lincSFPQ), and also in female hLF for XIST (XX). White “speckles�indicate the subcellular localization of each lincRNA. The nuclear compartment is demarked by DAPI staining (purple). "
RLID00000109	100125288	ZGLP1	http://www.ncbi.nlm.nih.gov/gene/?term=100125288	"GATAD3, GLP-1, GLP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000110	100126243	A030001D20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100126243	1110025D03Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000111	100126364	Floury1	http://www.ncbi.nlm.nih.gov/gene/100126364	GRMZM2G094532	mRNA	Zea mays	11910012	Endoplasmic reticulum	Endosperm	In situ hybridization	"We analyzed the distribution of mRNAs encoding the 22-kD alpha-zein and the 27-kD gamma-zein proteins on cisternal and protein body rough endoplasmic reticulum membranes. In situ hybridization revealed similar frequencies of the mRNAs in both regions of the endoplasmic reticulum, indicating that the transcripts are distributed more or less randomly. "
RLID00000112	100126476	TRNAL-CAA	http://www.ncbi.nlm.nih.gov/gene/?term=100126476		tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000113	100126798	SNAR-A1	http://www.ncbi.nlm.nih.gov/gene/?term=100126798	SNAR-A53113498	lncRNA	Homo sapiens	20935053	Cytoplasm	HeLa cell	qRT-PCR	"To approach their function, we examined the subcellular distribution of snaR-A. Fractionation of 293, 293T and HeLa cells revealed snaR-A to be predominantly cytoplasmic (Figure 6A, upper panel).  "
RLID00000114	100126798	SNAR-A1	http://www.ncbi.nlm.nih.gov/gene/?term=100126798	SNAR-A53113498	lncRNA	Homo sapiens	20935053	Ribosome	HeLa cell	qRT-PCR	"SnaR-A is up-regulated in transformed and immortalized human cells, and is stably bound to ribosomes in HeLa cells. "
RLID00000115	100127243	ddx59	http://www.ncbi.nlm.nih.gov/gene/?term=100127243	centroid	mRNA	Xenopus laevis	17939116	Mitochondrion	Oocyte	In situ hybridization	"We found that centroid mRNA is localized in Xenopus oocytes by a combination of early and late pathways, a pattern of localization that is very similar to the intermediate pathway localization of fatvg mRNA, another germ-plasm-localized RNA in Xenopus oocytes. Also, centroid mRNA is present in the mitochondrial cloud and in the germ plasm at the surface of germinal granules. "
RLID00000116	100127243	ddx59	http://www.ncbi.nlm.nih.gov/gene/?term=100127243	centroid	mRNA	Xenopus laevis	17939116	Germ plasm	Oocyte	In situ hybridization	"We found that centroid mRNA is localized in Xenopus oocytes by a combination of early and late pathways, a pattern of localization that is very similar to the intermediate pathway localization of fatvg mRNA, another germ-plasm-localized RNA in Xenopus oocytes. Also, centroid mRNA is present in the mitochondrial cloud and in the germ plasm at the surface of germinal granules. "
RLID00000117	100128108	LOC100128108	http://www.ncbi.nlm.nih.gov/gene/?term=100128108		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000118	100128385	FAM225B	http://www.ncbi.nlm.nih.gov/gene/?term=100128385	"C9orf110, LINC00256B, NCRNA00256B "	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000119	100128731	OST4	http://www.ncbi.nlm.nih.gov/gene/?term=100128731		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000120	100128731	OST4	http://www.ncbi.nlm.nih.gov/gene/?term=100128731		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000121	100128881	VPS9D1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100128881		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000122	100129196	MATN1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100129196		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000123	100129482	ZNF37BP	http://www.ncbi.nlm.nih.gov/gene/?term=100129482	"KOX21, ZNF37B "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000124	100129550	LOC100129550	http://www.ncbi.nlm.nih.gov/gene/?term=100129550		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000125	100129550	LOC100129550	http://www.ncbi.nlm.nih.gov/gene/?term=100129550		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000126	100130581	LINC00910	http://www.ncbi.nlm.nih.gov/gene/?term=100130581		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000127	100130865	LOC100130865	http://www.ncbi.nlm.nih.gov/gene/?term=100130865		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000128	100130967	C6orf99	http://www.ncbi.nlm.nih.gov/gene/?term=100130967	yR211F11.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000129	100131017	ZNF316	http://www.ncbi.nlm.nih.gov/gene/?term=100131017	"ENST00000305834, MZF-3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000130	100131187	TSTD1	http://www.ncbi.nlm.nih.gov/gene/?term=100131187	KAT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000131	100131801	PET100	http://www.ncbi.nlm.nih.gov/gene/?term=100131801	C19orf79	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000132	100132399	GAGE12D	http://www.ncbi.nlm.nih.gov/gene/?term=100132399	GAGE-12B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000133	100132596	XGY2	http://www.ncbi.nlm.nih.gov/gene/?term=100132596	"XG, XGPY, XGPY2 "	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00000134	100133050	LOC100133050	http://www.ncbi.nlm.nih.gov/gene/?term=100133050		lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00000135	100134938	UPK3BL	http://www.ncbi.nlm.nih.gov/gene/?term=100134938	UPLP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000136	100134938	UPK3BL	http://www.ncbi.nlm.nih.gov/gene/?term=100134938	UPLP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000137	10013	HDAC6	http://www.ncbi.nlm.nih.gov/gene/?term=10013	"CPBHM, HD6, JM21, PPP1R90 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000138	10013	HDAC6	http://www.ncbi.nlm.nih.gov/gene/?term=10013	"HD6, JM21, CPBHM, PPP1R90 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00000139	100141515	C17orf99	http://www.ncbi.nlm.nih.gov/gene/?term=100141515	UNQ464	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000140	100144748	KLLN	http://www.ncbi.nlm.nih.gov/gene/?term=100144748	"CWS4, KILLIN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000141	100144748	KLLN	http://www.ncbi.nlm.nih.gov/gene/?term=100144748	"CWS4, KILLIN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000142	10014	HDAC5	http://www.ncbi.nlm.nih.gov/gene/?term=10014	"HD5, NY-CO-9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000143	10014	HDAC5	http://www.ncbi.nlm.nih.gov/gene/?term=10014	"HD5, NY-CO-9 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00000144	100151683	RNU4ATAC	http://www.ncbi.nlm.nih.gov/gene/?term=100151683	"MOPD1, RFMN1, TALS, U4ATAC, RNU4ATAC "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000145	100151683	RNU4ATAC	http://www.ncbi.nlm.nih.gov/gene/?term=100151683	"MOPD1, RFMN1, TALS, U4ATAC, RNU4ATAC "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000146	100151684	RNU6ATAC	http://www.ncbi.nlm.nih.gov/gene/?term=100151684	"RNU6ATAC1, U6ATAC "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000147	100151688	RNU6ATAC5P	http://www.ncbi.nlm.nih.gov/gene/?term=100151688		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000148	100152093	PENK	http://www.ncbi.nlm.nih.gov/gene/?term=100152093		mRNA	Cavia porcellus	8269474	Endoplasmic reticulum	Neuron	In situ hybridization	"Proenkephalin mRNAs were clearly localized within circumscribed cytoplasmic compartments. The immunoprecipitates were mainly observed within the rough endoplasmic reticulum, especially at the periphery of the cell. "
RLID00000149	100158262	SCARNA9L	http://www.ncbi.nlm.nih.gov/gene/?term=100158262		snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00000150	100158262	SCARNA9L	http://www.ncbi.nlm.nih.gov/gene/?term=100158262		snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00000151	100158262	SCARNA9L	http://www.ncbi.nlm.nih.gov/gene/?term=100158262		snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"On the other hand, sdRNAs of only three Cajal body snoRNAs (SCARNA6, SCARNA15, SCARNA9L2) were represented in the subcellular libraries. "
RLID00000152	100158449	magi1	http://www.ncbi.nlm.nih.gov/gene/?term=100158449	"aip3, baiap1, bap1, magi-1, tnrc19, wwp3 "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000153	10015	PDCD6IP	http://www.ncbi.nlm.nih.gov/gene/?term=10015	"AIP1, ALIX, DRIP4, HP95 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000154	10015	PDCD6IP	http://www.ncbi.nlm.nih.gov/gene/?term=10015	"AIP1, ALIX, DRIP4, HP95 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000155	10015	PDCD6IP	http://www.ncbi.nlm.nih.gov/gene/?term=10015	"AIP1, ALIX, DRIP4, HP95 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000156	100169751	RNA5S1	http://www.ncbi.nlm.nih.gov/gene/?term=100169751	RN5S1	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000157	100169751	RNA5S1	http://www.ncbi.nlm.nih.gov/gene/?term=100169751	RN5S1	rRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00000158	100169751	RNA5S1	http://www.ncbi.nlm.nih.gov/gene/?term=100169751	RN5S1	rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000159	100169751	RNA5S1	http://www.ncbi.nlm.nih.gov/gene/?term=100169751	RN5S1	rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000160	100169753	RNA5S2	http://www.ncbi.nlm.nih.gov/gene/?term=100169753	RN5S2	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000161	100169754	RNA5S3	http://www.ncbi.nlm.nih.gov/gene/?term=100169754	RN5S3	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000162	100169754	RNA5S3	http://www.ncbi.nlm.nih.gov/gene/?term=100169754	RN5S3	rRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00000163	100169755	RNA5S4	http://www.ncbi.nlm.nih.gov/gene/?term=100169755	RN5S4	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000164	100169756	RNA5S5	http://www.ncbi.nlm.nih.gov/gene/?term=100169756	RN5S5	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000165	100169757	RNA5S6	http://www.ncbi.nlm.nih.gov/gene/?term=100169757	RN5S6	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000166	100169758	RNA5S7	http://www.ncbi.nlm.nih.gov/gene/?term=100169758	RN5S7	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000167	100169759	RNA5S8	http://www.ncbi.nlm.nih.gov/gene/?term=100169759	RN5S8	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000168	100169761	RNA5S10	http://www.ncbi.nlm.nih.gov/gene/?term=100169761	RN5S10	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000169	100169762	RNA5S11	http://www.ncbi.nlm.nih.gov/gene/?term=100169762	RN5S11	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000170	100169763	RNA5S12	http://www.ncbi.nlm.nih.gov/gene/?term=100169763	RN5S12	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000171	100169764	RNA5S13	http://www.ncbi.nlm.nih.gov/gene/?term=100169764	RN5S13	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000172	100169765	RNA5S14	http://www.ncbi.nlm.nih.gov/gene/?term=100169765	RN5S14	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000173	100169766	RNA5S15	http://www.ncbi.nlm.nih.gov/gene/?term=100169766	RN5S15	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000174	100169767	RNA5S16	http://www.ncbi.nlm.nih.gov/gene/?term=100169767	RN5S16	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000175	100169768	RNA5S17	http://www.ncbi.nlm.nih.gov/gene/?term=100169768	RN5S17	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000176	100169879	Gm11117	http://www.ncbi.nlm.nih.gov/gene/?term=100169879	ENSMUSG00000079441	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000177	100169	Phactr4	http://www.ncbi.nlm.nih.gov/gene/?term=100169	"3110001B12Rik, AI527228, AW495572, C330013F19Rik, N28169, mKIAA4120 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000178	10016	PDCD6	http://www.ncbi.nlm.nih.gov/gene/?term=10016	"ALG-2, ALG2, PEF1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000179	100170550	ano1	http://www.ncbi.nlm.nih.gov/gene/?term=100170550	"dog1, oraov2, taos2, tmem16a "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000180	100177	Zmym6	http://www.ncbi.nlm.nih.gov/gene/?term=100177	"9330177P20Rik, AI593204, AI661340, D4Wsu24e, Zfp258 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000181	10017	BCL2L10	http://www.ncbi.nlm.nih.gov/gene/?term=10017	"BCL-B, Boo, Diva, bcl2-L-10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000182	100188986	TRH-GTG1-7	http://www.ncbi.nlm.nih.gov/gene/?term=100188986	"TRH-GTG1-5, TRNAH1 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000183	100188987	TRH-GTG1-5	http://www.ncbi.nlm.nih.gov/gene/?term=100188987	"TRH-GTG1-8, TRNAH3 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000184	100188988	TRH-GTG1-8	http://www.ncbi.nlm.nih.gov/gene/?term=100188988	"TRH-GTG1-6, TRNAH2 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000185	100188991	TRH-GTG1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100188991	TRNAH4	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000186	100188993	TRV-TAC1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100188993	TRNAV11	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000187	100189015	TRX-CAT1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189015	TRNAM3	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000188	100189030	TRE-TTC2-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189030	TRNAE7	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000189	100189040	TRX-CAT1-4	http://www.ncbi.nlm.nih.gov/gene/?term=100189040	"TRNAM4, TRX-CAT1-5 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000190	100189063	TRE-TTC2-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189063	TRNAE11	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000191	100189065	TRH-GTG1-9	http://www.ncbi.nlm.nih.gov/gene/?term=100189065	"TRH-GTG1-7, TRNAH6 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000192	100189094	TRX-CAT1-3	http://www.ncbi.nlm.nih.gov/gene/?term=100189094	"TRNAM6, TRX-CAT1-4 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000193	100189120	TRD-GTC2-5	http://www.ncbi.nlm.nih.gov/gene/?term=100189120	TRNAD5	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000194	100189122	TRK-TTT3-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189122	TRNAK16	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000195	100189134	TRD-GTC2-4	http://www.ncbi.nlm.nih.gov/gene/?term=100189134	TRNAD6	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000196	100189144	TRC-GCA1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189144	TRNAC10	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000197	100189151	TRL-TAG2-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189151	TRNAL15	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000198	100189158	TRD-GTC2-6	http://www.ncbi.nlm.nih.gov/gene/?term=100189158	"TRD-GTC2-10, TRNAD8 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000199	100189160	TRG-GCC1-4	http://www.ncbi.nlm.nih.gov/gene/?term=100189160	TRNAG15	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000200	100189174	TRH-GTG1-4	http://www.ncbi.nlm.nih.gov/gene/?term=100189174	TRNAH7	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000201	100189191	TRV-TAC1-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189191	TRNAV19	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000202	100189207	TRD-GTC1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189207	TRNAD10	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000203	100189230	TRG-GCC1-3	http://www.ncbi.nlm.nih.gov/gene/?term=100189230	TRNAG21	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000204	100189231	TRG-CCC2-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189231	"TRG-CCC2-2, TRNAG22 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000205	100189234	TRK-TTT3-3	http://www.ncbi.nlm.nih.gov/gene/?term=100189234	"TRK-TTT3-5, TRNAK22 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000206	100189235	TRD-GTC2-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189235	TRNAD11	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000207	100189237	TRL-CAA1-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189237	TRNAL22	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000208	100189239	TRD-GTC2-8	http://www.ncbi.nlm.nih.gov/gene/?term=100189239	"TRD-GTC2-6, TRNAD12 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000209	100189243	TRR-ACG1-3	http://www.ncbi.nlm.nih.gov/gene/?term=100189243	"TRNAR21, TRR-ACG1-1 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000210	100189252	TRG-GCC1-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189252	TRNAG23	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000211	100189255	TRX-CAT1-8	http://www.ncbi.nlm.nih.gov/gene/?term=100189255	"TRNAM14, TRX-CAT1-2 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000212	100189283	TRV-TAC2-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189283	TRNAV23	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000213	100189284	TRG-GCC1-5	http://www.ncbi.nlm.nih.gov/gene/?term=100189284	TRNAG27	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000214	100189286	TRP-TGG1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189286	TRNAP17	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000215	100189290	TRD-GTC2-3	http://www.ncbi.nlm.nih.gov/gene/?term=100189290	TRNAD13	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000216	100189292	TRD-GTC2-7	http://www.ncbi.nlm.nih.gov/gene/?term=100189292	"TRD-GTC2-11, TRNAD14 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000217	100189297	TRX-CAT1-6	http://www.ncbi.nlm.nih.gov/gene/?term=100189297	"TRNAM15, TRX-CAT1-7 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000218	100189307	TRH-GTG1-3	http://www.ncbi.nlm.nih.gov/gene/?term=100189307	TRNAH9	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000219	100189313	TRL-TAA1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189313	TRNAL29	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000220	100189315	TRX-CAT1-7	http://www.ncbi.nlm.nih.gov/gene/?term=100189315	"TRNAM17, TRX-CAT1-8 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000221	100189333	TRE-TTC1-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189333	"TRE-TTC1-1, TRNAE20 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000222	100189334	TRH-GTG1-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189334	TRNAH10	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000223	100189343	TRD-GTC2-9	http://www.ncbi.nlm.nih.gov/gene/?term=100189343	"TRD-GTC2-7, TRNAD15 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000224	100189345	TRX-CAT1-5	http://www.ncbi.nlm.nih.gov/gene/?term=100189345	"TRNAM18, TRX-CAT1-6 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000225	100189347	TRD-GTC2-10	http://www.ncbi.nlm.nih.gov/gene/?term=100189347	"TRD-GTC2-8, TRNAD16 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000226	100189366	TRG-GCC1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189366	TRNAG30	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000227	100189383	TRD-GTC2-11	http://www.ncbi.nlm.nih.gov/gene/?term=100189383	"TRD-GTC2-9, TRNAD17 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000228	100189396	TRR-ACG1-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189396	"TRNAR26, TRR-ACG1-2 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000229	100189412	TRD-GTC2-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189412	TRNAD18	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000230	100189416	TRV-CAC3-1	http://www.ncbi.nlm.nih.gov/gene/?term=100189416	TRNAV32	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000231	100189425	TRK-TTT3-2	http://www.ncbi.nlm.nih.gov/gene/?term=100189425	TRNAK34	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000232	10019	SH2B3	http://www.ncbi.nlm.nih.gov/gene/?term=10019	"IDDM20, LNK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000233	10019	SH2B3	http://www.ncbi.nlm.nih.gov/gene/?term=10019	"IDDM20, LNK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000234	10019	SH2B3	http://www.ncbi.nlm.nih.gov/gene/?term=10019	"IDDM20, LNK "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000235	1001	CDH3	http://www.ncbi.nlm.nih.gov/gene/?term=1001	"CDHP, HJMD, PCAD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000236	1001	CDH3	http://www.ncbi.nlm.nih.gov/gene/?term=1001	"CDHP, HJMD, PCAD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000237	100206	Adprhl2	http://www.ncbi.nlm.nih.gov/gene/?term=100206	"AI836109, Arh3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000238	10020	GNE	http://www.ncbi.nlm.nih.gov/gene/?term=10020	"DMRV, GLCNE, IBM2, NM, Uae1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000239	10020	GNE	http://www.ncbi.nlm.nih.gov/gene/?term=10020	"DMRV, GLCNE, IBM2, NM, Uae1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000240	10020	GNE	http://www.ncbi.nlm.nih.gov/gene/?term=10020	"DMRV, GLCNE, IBM2, NM, Uae1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000241	10020	GNE	http://www.ncbi.nlm.nih.gov/gene/?term=10020	"DMRV, GLCNE, IBM2, NM, Uae1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000242	100210	Gpn2	http://www.ncbi.nlm.nih.gov/gene/?term=100210	"AI838661, Atpbd1b, R74630 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000243	100216200	pld2	http://www.ncbi.nlm.nih.gov/gene/?term=100216200		mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000244	100216343	Gm17501	http://www.ncbi.nlm.nih.gov/gene/?term=100216343		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000245	10023	FRAT1	http://www.ncbi.nlm.nih.gov/gene/?term=10023		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000246	10024	TROAP	http://www.ncbi.nlm.nih.gov/gene/?term=10024	TASTIN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000247	10024	TROAP	http://www.ncbi.nlm.nih.gov/gene/?term=10024	TASTIN	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000248	10024	TROAP	http://www.ncbi.nlm.nih.gov/gene/?term=10024	TASTIN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000249	10025	MED16	http://www.ncbi.nlm.nih.gov/gene/?term=10025	"DRIP92, THRAP5, TRAP95 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000250	10026	PIGK	http://www.ncbi.nlm.nih.gov/gene/?term=10026	GPI8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000251	10026	PIGK	http://www.ncbi.nlm.nih.gov/gene/?term=10026	GPI8	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000252	10026	PIGK	http://www.ncbi.nlm.nih.gov/gene/?term=10026	GPI8	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000253	100272147	CMC4	http://www.ncbi.nlm.nih.gov/gene/?term=100272147	"C6.1B, MTCP1, MTCP1B, MTCP1NB, p8, p8MTCP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000254	100272219	AA543186	http://www.ncbi.nlm.nih.gov/gene/?term=100272219		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000255	100273	Osbpl9	http://www.ncbi.nlm.nih.gov/gene/?term=100273	"2600011I06Rik, AU015843, Orp-9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000256	100287314	LINC00941	http://www.ncbi.nlm.nih.gov/gene/?term=100287314		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000257	100287314	LINC00941	http://www.ncbi.nlm.nih.gov/gene/?term=100287314		lncRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00000258	100287314	LINC00941	http://www.ncbi.nlm.nih.gov/gene/?term=100287314		lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00000259	100287569	LINC00173	http://www.ncbi.nlm.nih.gov/gene/?term=100287569	NCRNA00173	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000260	100288142	NBPF20	http://www.ncbi.nlm.nih.gov/gene/?term=100288142		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000261	100288798	LOC100288798	http://www.ncbi.nlm.nih.gov/gene/?term=100288798		lncRNA	Homo sapiens	26670263	Cytoplasm	HeLa cell	Next-generation sequencing|qRT-PCR	"The minor spliced LOC100288798 isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. "
RLID00000262	100288798	LOC100288798	http://www.ncbi.nlm.nih.gov/gene/?term=100288798		lncRNA	Homo sapiens	26670263	Nucleus	HeLa cell	Next-generation sequencing|qRT-PCR	"The minor spliced LOC100288798 isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. "
RLID00000263	100288798	LOC100288798	http://www.ncbi.nlm.nih.gov/gene/?term=100288798		lncRNA	Homo sapiens	26670263	Cytoplasm	KBM7 cell	Next-generation sequencing|qRT-PCR	"The minor spliced LOC100288798 isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. "
RLID00000264	100288798	LOC100288798	http://www.ncbi.nlm.nih.gov/gene/?term=100288798		lncRNA	Homo sapiens	26670263	Nucleus	KBM7 cell	Next-generation sequencing|qRT-PCR	"The minor spliced LOC100288798 isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. "
RLID00000265	100288801	FRG2C	http://www.ncbi.nlm.nih.gov/gene/?term=100288801		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000266	100288801	FRG2C	http://www.ncbi.nlm.nih.gov/gene/?term=100288801		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000267	100289635	ZNF605	http://www.ncbi.nlm.nih.gov/gene/?term=100289635		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000268	100302634	Astx6	http://www.ncbi.nlm.nih.gov/gene/?term=100302634	"Gm14949, OTTMUSG00000018579 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000269	100302738	RNU6-21P	http://www.ncbi.nlm.nih.gov/gene/?term=100302738	RNU6-21	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000270	100302741	RNU6-15P	http://www.ncbi.nlm.nih.gov/gene/?term=100302741	RNU6-15	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000271	100302742	RNU6-42P	http://www.ncbi.nlm.nih.gov/gene/?term=100302742	RNU6-42	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000272	100302743	SNORA80B	http://www.ncbi.nlm.nih.gov/gene/?term=100302743	ACA67B	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000273	100303755	PET117	http://www.ncbi.nlm.nih.gov/gene/?term=100303755	CSRP2BP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000274	100306951	PITPNA-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100306951		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000275	100329140	Mettl5os	http://www.ncbi.nlm.nih.gov/gene/?term=100329140	4930550G17Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000276	100337591	SNORA70F	http://www.ncbi.nlm.nih.gov/gene/?term=100337591	U70F	snoRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000277	100361269	Snrpa1	http://www.ncbi.nlm.nih.gov/gene/100361269		mRNA	Rattus norvegicus	11861124	Dendrite	Peptidergic neuron	In situ hybridization	"28S rRNA, initiator tRNA(Met), and poly(A) mRNA were revealed extending into proximal and middle parts of dendrites where intensely reactive punctate structures were common. 28S rRNA could be detected in the distal parts of the dendrites. "
RLID00000278	10036	CHAF1A	http://www.ncbi.nlm.nih.gov/gene/?term=10036	"CAF-1, CAF1, CAF1B, CAF1P150, P150 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000279	10036	CHAF1A	http://www.ncbi.nlm.nih.gov/gene/?term=10036	"CAF-1, CAF1, CAF1B, CAF1P150, P150 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000280	100379295	RNY4P8	http://www.ncbi.nlm.nih.gov/gene/?term=100379295		lncRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00000281	100379571	BACE1-AS	http://www.ncbi.nlm.nih.gov/gene/?term=100379571	"BACE1-AS1, BACE1AS, NCRNA00177 "	lncRNA	Homo sapiens	18587408	Cytoplasm	Brain	Knockdown	"Exposure of the SH-SY5Y cells to conditioned media from CHO-7PA2 cells, but not conditioned media from control parental CHO cells resulted in an increase in cytoplasmic concentrations of BACE1-AS transcript (Fig. 4b).  "
RLID00000282	100380046	atrx	http://www.ncbi.nlm.nih.gov/gene/?term=100380046	rad54	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000283	100381270	ZBED6	http://www.ncbi.nlm.nih.gov/gene/?term=100381270	MGR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000284	10038	PARP2	http://www.ncbi.nlm.nih.gov/gene/?term=10038	"ADPRT2, ADPRTL2, ADPRTL3, ARTD2, PARP-2, pADPRT-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000285	1003	CDH5	http://www.ncbi.nlm.nih.gov/gene/?term=1003	"7B4, CD144 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000286	10040	TOM1L1	http://www.ncbi.nlm.nih.gov/gene/?term=10040	SRCASM	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000287	100416706	Zfp729b	http://www.ncbi.nlm.nih.gov/gene/?term=100416706	AA987127	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000288	10042	HMGXB4	http://www.ncbi.nlm.nih.gov/gene/?term=10042	"HMG2L1, HMGBCG, THC211630 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000289	10042	HMGXB4	http://www.ncbi.nlm.nih.gov/gene/?term=10042	"HMG2L1, HMGBCG, THC211630 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000290	100434	Slc44a1	http://www.ncbi.nlm.nih.gov/gene/?term=100434	"2210409B22Rik, 4833416H08Rik, AW547365, CHTL1, CTL1, Cdw92 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000291	10043	TOM1	http://www.ncbi.nlm.nih.gov/gene/?term=10043		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000292	10045	SH2D3A	http://www.ncbi.nlm.nih.gov/gene/?term=10045	NSP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000293	100462953	MINOS1P1	http://www.ncbi.nlm.nih.gov/gene/?term=100462953	"CG012, N4BP2L2-IT, N4BP2L2-IT1, N4BP2L2IT1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000294	100462977	MTRNR2L1	http://www.ncbi.nlm.nih.gov/gene/?term=100462977	HN1	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000295	100462981	MTRNR2L2	http://www.ncbi.nlm.nih.gov/gene/?term=100462981	HN2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000296	100462981	MTRNR2L2	http://www.ncbi.nlm.nih.gov/gene/?term=100462981	HN2	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00000297	100463482	MTRNR2L6	http://www.ncbi.nlm.nih.gov/gene/?term=100463482	HN6	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000298	100463486	MTRNR2L8	http://www.ncbi.nlm.nih.gov/gene/?term=100463486	HN8	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000299	100463486	MTRNR2L8	http://www.ncbi.nlm.nih.gov/gene/?term=100463486	HN8	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00000300	100463488	MTRNR2L10	http://www.ncbi.nlm.nih.gov/gene/?term=100463488	HN10	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000301	100465	Mob3c	http://www.ncbi.nlm.nih.gov/gene/?term=100465	"AW822253, D130076I06Rik, Mobkl2c "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000302	100479	BB131254	http://www.ncbi.nlm.nih.gov/gene/?term=100479		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000303	100487162	fam109a	http://www.ncbi.nlm.nih.gov/gene/?term=100487162		mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000304	100491386	fam65a	http://www.ncbi.nlm.nih.gov/gene/?term=100491386		mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000305	100491926	mov10	http://www.ncbi.nlm.nih.gov/gene/?term=100491926		mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000306	100495373	grip2	http://www.ncbi.nlm.nih.gov/gene/?term=100495373	"XGRIP2, Xgrip2.1 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000307	100496435	armc5	http://www.ncbi.nlm.nih.gov/gene/?term=100496435		mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000308	100498314	nat6	http://www.ncbi.nlm.nih.gov/gene/?term=100498314	"fus-2, fus2 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00000309	100499638	LOC100499638	http://www.ncbi.nlm.nih.gov/gene/?term=100499638	"GLYMA_13G101900, PIN2a "	mRNA	Solanum americanum	11785934	Cytoplasm	Phloem	Immunohistochemical localization|Immunoelectron microscopy	"Immunohistochemical localization, using these antibodies, revealed SaPIN2a expression in external and internal phloem of stem. Immunoelectron microscopy of stem, root and leaf sections further localized SaPIN2a to the CC and predominantly to the SE, particularly the parietal cytoplasm adjacent to the cell wall, the lumen and the sieve-area pores. "
RLID00000310	10049	DNAJB6	http://www.ncbi.nlm.nih.gov/gene/?term=10049	"DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000311	10049	DNAJB6	http://www.ncbi.nlm.nih.gov/gene/?term=10049	"DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000312	10049	DNAJB6	http://www.ncbi.nlm.nih.gov/gene/?term=10049	"DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000313	100500713	9530027J09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100500713		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000314	100502700	AV039307	http://www.ncbi.nlm.nih.gov/gene/?term=100502700		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000315	100502841	Epg5	http://www.ncbi.nlm.nih.gov/gene/?term=100502841	"4732475F16, 5430411K18Rik, AI661957, AW456499, mKIAA1632 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000316	100502898	Gm19440	http://www.ncbi.nlm.nih.gov/gene/?term=100502898		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000317	100503120	A930006K02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100503120		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000318	100503199	5430416N02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100503199	"100041797, Adapt33, Gm3514 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000319	100503380	Snhg4	http://www.ncbi.nlm.nih.gov/gene/?term=100503380	Gm17457	lncRNA	Mus musculus	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/snhg4/
RLID00000320	100503380	Snhg4	http://www.ncbi.nlm.nih.gov/gene/?term=100503380	Gm17457	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000321	100503463	AI256396	http://www.ncbi.nlm.nih.gov/gene/?term=100503463		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000322	100503470	Gm16619	http://www.ncbi.nlm.nih.gov/gene/?term=100503470		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000323	100503670	Rpl5	http://www.ncbi.nlm.nih.gov/gene/?term=100503670	U21RNA	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000324	100503690	Gm19835	http://www.ncbi.nlm.nih.gov/gene/?term=100503690		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000325	100503754	Gm11725	http://www.ncbi.nlm.nih.gov/gene/?term=100503754	OTTMUSG00000003731	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000326	100503859	1110015O18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100503859		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000327	100503871	4833432E10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100503871		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000328	100504070	Gm20043	http://www.ncbi.nlm.nih.gov/gene/?term=100504070		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000329	100504178	Dhrs13os	http://www.ncbi.nlm.nih.gov/gene/?term=100504178	"A030003K02Rik, AA682085 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000330	100504262	A730020E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100504262		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000331	100504455	Gm15834	http://www.ncbi.nlm.nih.gov/gene/?term=100504455	"C130065N10Rik, OTTMUSG00000026620 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000332	100504527	Gm10374	http://www.ncbi.nlm.nih.gov/gene/?term=100504527	ENSMUSG00000072593	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000333	100504663	Atg14	http://www.ncbi.nlm.nih.gov/gene/?term=100504663	"4832427M01L, D14Ertd114e, D14Ertd436e, Atg14 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000334	100505641	FGD5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505641		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000335	100505761	RPARP-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505761		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000336	100505817	LOC100505817	http://www.ncbi.nlm.nih.gov/gene/?term=100505817		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000337	100505876	CEBPZOS	http://www.ncbi.nlm.nih.gov/gene/?term=100505876	CEBPZ-AS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000338	100505894	TMEM161B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505894	linc-POLR3G-8	lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00000339	100505989	LINC01207	http://www.ncbi.nlm.nih.gov/gene/?term=100505989		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000340	100506054	RNASEH1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506054		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000341	100506190	LINC00963	http://www.ncbi.nlm.nih.gov/gene/?term=100506190		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000342	100506233	RAB30-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506233		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000343	100506233	RAB30-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506233		lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00000344	100506233	RAB30-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506233		lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00000345	100506365	OTUD6B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506365	GS1-251I9.4	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000346	100506385	LINC01426	http://www.ncbi.nlm.nih.gov/gene/?term=100506385	lincRNA-uc002yug.2	lncRNA	Homo sapiens	25486427	Nucleus	TE-1|Eca-109	Fluorescence in situ hybridization	"It revealed that most of the lincRNA-uc002yug.2 was detected in the nuclear fraction (Figure 2a). RNA fluorescence in situ hybridization (RNA FISH) using specific probes for lincRNA-uc002yug.2 transcript (red) and RUNX1 pre-mRNA (green) in Eca-109 (Supplementary Figure 2A) and TE-1 (Figure 2c) cells showed the localization of lincRNA-uc002yug.2 transcript and RUNX1 pre-mRNA, and lincRNA-uc002yug.2 was predominantly present in the nucleus. "
RLID00000347	100506668	NRAV	http://www.ncbi.nlm.nih.gov/gene/?term=100506668	"DYNLL1-AS1, DYNLL1AS1 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000348	100506714	NUP50-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506714		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000349	100507246	SNHG16	http://www.ncbi.nlm.nih.gov/gene/?term=100507246	ncRAN	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000350	100507303	SNHG19	http://www.ncbi.nlm.nih.gov/gene/?term=100507303	SNORD60HG	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000351	100507316	MINCR	http://www.ncbi.nlm.nih.gov/gene/?term=100507316	LINC01604	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000352	100507428	LINC00458	http://www.ncbi.nlm.nih.gov/gene/?term=100507428	LncRNA-ES3	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"By means of RNA fractionation followed by quantitative PCR (qPCR), we found that lncRNA_ES1, lncRNA_ES2 and lncRNA_ES3 were preferentially retained in the nucleus (Figure 5A). "
RLID00000353	100507436	MICA	http://www.ncbi.nlm.nih.gov/gene/?term=100507436	"MIC-A, PERB11.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000354	100507436	MICA	http://www.ncbi.nlm.nih.gov/gene/?term=100507436	"MIC-A, PERB11.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000355	100507436	MICA	http://www.ncbi.nlm.nih.gov/gene/?term=100507436	"MIC-A, PERB11.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000356	100515	Zfp518b	http://www.ncbi.nlm.nih.gov/gene/?term=100515	"6820424L24Rik, AA410078, AI661722, Znf518b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000357	10051	SMC4	http://www.ncbi.nlm.nih.gov/gene/?term=10051	"CAP-C, CAPC, SMC-4L1, hCAP-C, SMC4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000358	10051	SMC4	http://www.ncbi.nlm.nih.gov/gene/?term=10051	"CAP-C, CAPC, SMC-4L1, hCAP-C, SMC4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000359	10051	SMC4	http://www.ncbi.nlm.nih.gov/gene/?term=10051	"CAP-C, CAPC, SMC-4, SMC4L1, hCAP-C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000360	10052	GJC1	http://www.ncbi.nlm.nih.gov/gene/?term=10052	"CX45, GJA7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000361	10052	GJC1	http://www.ncbi.nlm.nih.gov/gene/?term=10052	"CX45, GJA7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000362	10052	GJC1	http://www.ncbi.nlm.nih.gov/gene/?term=10052	"CX45, GJA7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000363	100532	Rell1	http://www.ncbi.nlm.nih.gov/gene/?term=100532	AA536743	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000364	100534641	Gm13856	http://www.ncbi.nlm.nih.gov/gene/?term=100534641	OTTMUSG00000014774	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000365	10053	AP1M2	http://www.ncbi.nlm.nih.gov/gene/?term=10053	"AP1-mu2, HSMU1B, MU-1B, MU1B, mu2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000366	10054	UBA2	http://www.ncbi.nlm.nih.gov/gene/?term=10054	"ARX, HRIHFB2115, SAE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000367	10055	SAE1	http://www.ncbi.nlm.nih.gov/gene/?term=10055	"AOS1, HSPC140, SUA1, UBLE1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000368	100568459	Bc1	http://www.ncbi.nlm.nih.gov/gene/?term=100568459	Gm24367	lncRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	"Figure 8: Within synaptoneurosomes, BC1 RNA and mature miR-124a are predominantly soluble components. Data are collected from Figure 8. "
RLID00000369	10057	ABCC5	http://www.ncbi.nlm.nih.gov/gene/?term=10057	"ABC33, EST277145, MOAT-C, MOATC, MRP5, SMRP, pABC11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000370	10057	ABCC5	http://www.ncbi.nlm.nih.gov/gene/?term=10057	"ABC33, EST277145, MOAT-C, MOATC, MRP5, SMRP, pABC11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000371	10059	DNM1L	http://www.ncbi.nlm.nih.gov/gene/?term=10059	"DLP1, DRP1, DVLP, DYMPLE, EMPF, HDYNIV "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000372	10059	DNM1L	http://www.ncbi.nlm.nih.gov/gene/?term=10059	"DLP1, DRP1, DVLP, DYMPLE, EMPF, HDYNIV "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000373	10059	DNM1L	http://www.ncbi.nlm.nih.gov/gene/?term=10059	"DLP1, DRP1, DVLP, DYMPLE, EMPF, HDYNIV "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000374	100609	Nsun5	http://www.ncbi.nlm.nih.gov/gene/?term=100609	"9830109N13Rik, AI326939, Nol1r, Wbscr20, Wbscr20a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000375	10061	ABCF2	http://www.ncbi.nlm.nih.gov/gene/?term=10061	"ABC28, EST133090, HUSSY-18, HUSSY18 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000376	10061	ABCF2	http://www.ncbi.nlm.nih.gov/gene/?term=10061	"ABC28, EST133090, HUSSY-18, HUSSY18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000377	10062	NR1H3	http://www.ncbi.nlm.nih.gov/gene/?term=10062	"LXR-a, LXRA, RLD-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000378	10062	NR1H3	http://www.ncbi.nlm.nih.gov/gene/?term=10062	"LXR-a, LXRA, RLD-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000379	10063	COX17	http://www.ncbi.nlm.nih.gov/gene/?term=10063		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000380	10063	COX17	http://www.ncbi.nlm.nih.gov/gene/?term=10063		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000381	10063	COX17	http://www.ncbi.nlm.nih.gov/gene/?term=10063		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000382	100642175	SPRY4-IT1	http://www.ncbi.nlm.nih.gov/gene/?term=100642175	SPRIGHTLY	lncRNA	Homo sapiens	21558391	Cytoplasm	Melanoma cell	In situ hybridization	"RNA-FISH analysis showed that SPRY4-IT1 is predominantly localized in the cytoplasm of melanoma cells, and SPRY4-IT1 RNAi knockdown results in defects in cell growth, differentiation, and higher rates of apoptosis in melanoma cell lines. "
RLID00000383	100652748	TIMM23B	http://www.ncbi.nlm.nih.gov/gene/?term=100652748	"TIMM23, bA592B15.7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000384	100652781	SNX29P1	http://www.ncbi.nlm.nih.gov/gene/?term=100652781	"RUNDC2B, RUNDC2L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000385	100652781	SNX29P1	http://www.ncbi.nlm.nih.gov/gene/?term=100652781	"RUNDC2B, RUNDC2L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000386	10066	SCAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=10066		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000387	10066	SCAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=10066		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000388	10066	SCAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=10066		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000389	10067	SCAMP3	http://www.ncbi.nlm.nih.gov/gene/?term=10067	C1orf3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000390	10067	SCAMP3	http://www.ncbi.nlm.nih.gov/gene/?term=10067	C1orf3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000391	10067	SCAMP3	http://www.ncbi.nlm.nih.gov/gene/?term=10067	C1orf3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000392	100682913	PI4K2B	http://www.ncbi.nlm.nih.gov/gene/?term=100682913		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000393	100683775	RPS15A	http://www.ncbi.nlm.nih.gov/gene/?term=100683775		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000394	100683	Trrap	http://www.ncbi.nlm.nih.gov/gene/?term=100683	AI481500	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000395	100684006	DNAJC24	http://www.ncbi.nlm.nih.gov/gene/?term=100684006		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000396	100685242	UBE2G1	http://www.ncbi.nlm.nih.gov/gene/?term=100685242		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000397	100686016	POLR1D	http://www.ncbi.nlm.nih.gov/gene/?term=100686016		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000398	100686627	RYR3	http://www.ncbi.nlm.nih.gov/gene/?term=100686627		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000399	100687033	NDUFB6	http://www.ncbi.nlm.nih.gov/gene/?term=100687033		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000400	100687634	IDI1	http://www.ncbi.nlm.nih.gov/gene/?term=100687634		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000401	100687992	HOXD8	http://www.ncbi.nlm.nih.gov/gene/?term=100687992		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000402	100688743	TAF13	http://www.ncbi.nlm.nih.gov/gene/?term=100688743		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000403	100689050	Adapt15	http://www.ncbi.nlm.nih.gov/gene/?term=100689050	Gadd7	lncRNA	Cricetulus griseus	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/Gadd7/
RLID00000404	100689062	Xbp1	http://www.ncbi.nlm.nih.gov/gene/?term=100689062	"I79_012500, Xbp-1 "	mRNA	Cricetulus griseus	16644724	Cytoplasm	Ovary cell	RT-PCR|Northern blot	"Using cell lines that continuously or transiently express these reporter constructs, we show that cytoplasmic unspliced XBP1 mRNA is efficiently spliced by activated IRE1alpha and requires ongoing cellular transcription but not active translation. Analysis of nuclear and cytoplasmic RNA fractions demonstrated that XBP1 mRNA splicing occurs in the cytoplasm. The results show that 5�capped and 3�poly(A)-tailed XBP1 mRNAs directly delivered into the cytoplasm can be efficient substrates for UPR-dependent XBP1 intron removal. "
RLID00000405	100689062	Xbp1	http://www.ncbi.nlm.nih.gov/gene/?term=100689062	"I79_012500, Xbp-1 "	mRNA	Cricetulus griseus	16644724	Nucleus	Ovary cell	RT-PCR|Northern blot	"FIGURE 5. XBP1 mRNA splicing occurs in the cytoplasm. CHO/mXBP1ΔC(un)-d2EGFP reporter cells were treated with Tm for 4 h and then RNAs were isolated from total (T), nuclear (N), and cytoplasmic (C) fractions and used for RT-PCR analysis (A). To demonstrate the quality of the fractionation, nucleoplasmic (N) and cytoplasmic (C) RNAs were monitored by Northern blot analysis for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (B), tRNALys (C), and U6 small nuclear RNA (D). All RNAs shown were isolated from the same experiment. GADPH is shown as a loading control (E). The image of RNA stained with ethidium bromide in a formaldehyde/agarose gel demonstrates the quality of the RNA. N.B. indicates Northern blot. "
RLID00000406	100689703	9330133O14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100689703		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000407	10069	RWDD2B	http://www.ncbi.nlm.nih.gov/gene/?term=10069	"C21orf6, GL011 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000408	1006	CDH8	http://www.ncbi.nlm.nih.gov/gene/?term=1006	Nbla04261	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000409	100710	Pds5b	http://www.ncbi.nlm.nih.gov/gene/?term=100710	"AI646570, AS3, AW212954, Aprin, mKIAA0979 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000410	10071	MUC12	http://www.ncbi.nlm.nih.gov/gene/?term=10071	"MUC-11, MUC-12, MUC11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000411	10072	DPP3	http://www.ncbi.nlm.nih.gov/gene/?term=10072	DPPIII	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000412	100736557	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=100736557	"I79_001391, GAPD "	mRNA	Cricetulus griseus	16644724	Nucleus	Ovary cell	RT-PCR|Northern blot	"FIGURE 5. XBP1 mRNA splicing occurs in the cytoplasm. CHO/mXBP1ΔC(un)-d2EGFP reporter cells were treated with Tm for 4 h and then RNAs were isolated from total (T), nuclear (N), and cytoplasmic (C) fractions and used for RT-PCR analysis (A). To demonstrate the quality of the fractionation, nucleoplasmic (N) and cytoplasmic (C) RNAs were monitored by Northern blot analysis for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (B), tRNALys (C), and U6 small nuclear RNA (D). All RNAs shown were isolated from the same experiment. GADPH is shown as a loading control (E). The image of RNA stained with ethidium bromide in a formaldehyde/agarose gel demonstrates the quality of the RNA. N.B. indicates Northern blot. "
RLID00000413	100736557	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=100736557	"I79_001391, GAPD "	mRNA	Cricetulus griseus	16644724	Cytoplasm	Ovary cell	RT-PCR|Northern blot	"FIGURE 5. XBP1 mRNA splicing occurs in the cytoplasm. CHO/mXBP1ΔC(un)-d2EGFP reporter cells were treated with Tm for 4 h and then RNAs were isolated from total (T), nuclear (N), and cytoplasmic (C) fractions and used for RT-PCR analysis (A). To demonstrate the quality of the fractionation, nucleoplasmic (N) and cytoplasmic (C) RNAs were monitored by Northern blot analysis for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (B), tRNALys (C), and U6 small nuclear RNA (D). All RNAs shown were isolated from the same experiment. GADPH is shown as a loading control (E). The image of RNA stained with ethidium bromide in a formaldehyde/agarose gel demonstrates the quality of the RNA. N.B. indicates Northern blot. "
RLID00000414	100737	Dcun1d4	http://www.ncbi.nlm.nih.gov/gene/?term=100737	AI836376	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000415	10073	SNUPN	http://www.ncbi.nlm.nih.gov/gene/?term=10073	"KPNBL, RNUT1, Snurportin1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000416	10073	SNUPN	http://www.ncbi.nlm.nih.gov/gene/?term=10073	"KPNBL, RNUT1, Snurportin1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000417	100750237	TG	http://www.ncbi.nlm.nih.gov/gene/?term=100750237		mRNA	Capra hircus	272676	Cytoplasm	Thyroids	Next-generation sequencing|qRT-PCR	"In regard to subcellular distribution, the relative amount of the thyroglobulin mRNA sequences from the goiter in nuclear RNA was 42% of normal, in cytoplasmic RNA was 7% of normal, and in the membrane fraction was only 1-2% of normal. Our results suggest that the lack of thyroglobulin in these goiters is due to a defect in thyroglobulin mRNA which leads to aberrant processing and/or transport of it from its site of synthesis to the endoplasmic reticulum. "
RLID00000418	100750237	TG	http://www.ncbi.nlm.nih.gov/gene/?term=100750237		mRNA	Capra hircus	272675	Nucleus	Thyroids	Next-generation sequencing|qRT-PCR	"In regard to subcellular distribution, the relative amount of the thyroglobulin mRNA sequences from the goiter in nuclear RNA was 42% of normal, in cytoplasmic RNA was 7% of normal, and in the membrane fraction was only 1-2% of normal. Our results suggest that the lack of thyroglobulin in these goiters is due to a defect in thyroglobulin mRNA which leads to aberrant processing and/or transport of it from its site of synthesis to the endoplasmic reticulum. "
RLID00000419	10075	HUWE1	http://www.ncbi.nlm.nih.gov/gene/?term=10075	"ARF-BP1, HECTH9, HSPC272, Ib772, LASU1, MULE, URE-B1, UREB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000420	10075	HUWE1	http://www.ncbi.nlm.nih.gov/gene/?term=10075	"ARF-BP1, HECTH9, HSPC272, Ib772, LASU1, MULE, URE-B1, UREB1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000421	10075	HUWE1	http://www.ncbi.nlm.nih.gov/gene/?term=10075	"ARF-BP1, HECTH9, HSPC272, Ib772, LASU1, MULE, URE-B1, UREB1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000422	100763	Ube3c	http://www.ncbi.nlm.nih.gov/gene/?term=100763	"AI853514, mKIAA0010 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000423	10076	PTPRU	http://www.ncbi.nlm.nih.gov/gene/?term=10076	"FMI, PCP-2, PTP, PTP-J, PTP-PI, PTP-RO, PTPPSI, PTPRO, PTPU2, R-PTP-PSI, R-PTP-U, hPTP-J "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000424	10077	TSPAN32	http://www.ncbi.nlm.nih.gov/gene/?term=10077	"ART1, PHEMX, PHMX, TSSC6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000425	10078	TSSC4	http://www.ncbi.nlm.nih.gov/gene/?term=10078		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000426	10081	PDCD7	http://www.ncbi.nlm.nih.gov/gene/?term=10081	"ES18, HES18 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000427	100825	AU022245	http://www.ncbi.nlm.nih.gov/gene/?term=100825		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000428	10082	GPC6	http://www.ncbi.nlm.nih.gov/gene/?term=10082	OMIMD1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000429	10083	USH1C	http://www.ncbi.nlm.nih.gov/gene/?term=10083	"AIE-75, DFNB18, DFNB18A, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, PDZD7C, ush1cpst "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000430	10084	PQBP1	http://www.ncbi.nlm.nih.gov/gene/?term=10084	"MRX2, MRX55, MRXS3, MRXS8, NPW38, RENS1, SHS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000431	10085	EDIL3	http://www.ncbi.nlm.nih.gov/gene/?term=10085	DEL1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000432	100861531	Rn45s	http://www.ncbi.nlm.nih.gov/gene/?term=100861531		rRNA	Mus musculus	16874305	Nucleus	Fibroblast	qRT-PCR|Northern blot	"In contrast, the nuclear localized 45S rRNA shows a mean nuclear/cytoplasmic ratio of 621:1 (Figure 6A). "
RLID00000433	100861532	RNA45S5	http://www.ncbi.nlm.nih.gov/gene/?term=100861532	RN45S	rRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000434	100861535	Rn28s	http://www.ncbi.nlm.nih.gov/gene/100861535		rRNA	Rattus norvegicus	11861124	Dendrite	Peptidergic neuron	In situ hybridization	"28S rRNA, initiator tRNA(Met), and poly(A) mRNA were revealed extending into proximal and middle parts of dendrites where intensely reactive punctate structures were common. 28S rRNA could be detected in the distal parts of the dendrites. "
RLID00000435	100861766	Gm16755	http://www.ncbi.nlm.nih.gov/gene/?term=100861766		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000436	100861869	Gm21283	http://www.ncbi.nlm.nih.gov/gene/?term=100861869		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000437	100873336	RNA5-8SP6	http://www.ncbi.nlm.nih.gov/gene/?term=100873336	RN5-8S6	rRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00000438	100873740	RNU6-31P	http://www.ncbi.nlm.nih.gov/gene/?term=100873740	"RNU6-31, RNU6-6 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000439	100873745	RNU6-10P	http://www.ncbi.nlm.nih.gov/gene/?term=100873745	RNU6-10	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000440	100873746	RNU6-14P	http://www.ncbi.nlm.nih.gov/gene/?term=100873746	RNU6-14	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000441	100873747	RNU6-30P	http://www.ncbi.nlm.nih.gov/gene/?term=100873747	RNU6-30	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000442	100873748	RNU6-33P	http://www.ncbi.nlm.nih.gov/gene/?term=100873748	RNU6-33	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000443	100873749	RNU6-34P	http://www.ncbi.nlm.nih.gov/gene/?term=100873749	RNU6-34	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000444	100873750	RNU6-35P	http://www.ncbi.nlm.nih.gov/gene/?term=100873750	RNU6-35	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000445	100873753	RNU6-16P	http://www.ncbi.nlm.nih.gov/gene/?term=100873753	RNU6-16	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000446	100873754	RNU6-19P	http://www.ncbi.nlm.nih.gov/gene/?term=100873754	RNU6-19	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000447	100873755	RNU6-23P	http://www.ncbi.nlm.nih.gov/gene/?term=100873755	RNU6-23	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000448	100873756	RNU6-28P	http://www.ncbi.nlm.nih.gov/gene/?term=100873756	RNU6-28	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000449	100873757	RNU6-36P	http://www.ncbi.nlm.nih.gov/gene/?term=100873757	RNU6-36	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000450	100873758	RNU6-39P	http://www.ncbi.nlm.nih.gov/gene/?term=100873758	RNU6-39	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000451	100873759	RNU6-45P	http://www.ncbi.nlm.nih.gov/gene/?term=100873759	RNU6-45	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000452	100873760	RNU6-46P	http://www.ncbi.nlm.nih.gov/gene/?term=100873760	RNU6-46	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000453	100873767	RNU6-59P	http://www.ncbi.nlm.nih.gov/gene/?term=100873767	RNU6-59	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000454	100873767	RNU6-59P	http://www.ncbi.nlm.nih.gov/gene/?term=100873767	RNU6-59	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000455	100873814	RNU1-17P	http://www.ncbi.nlm.nih.gov/gene/?term=100873814		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000456	100873815	RNU1-18P	http://www.ncbi.nlm.nih.gov/gene/?term=100873815		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000457	100873824	RNU2-7P	http://www.ncbi.nlm.nih.gov/gene/?term=100873824		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000458	100873825	RNU2-6P	http://www.ncbi.nlm.nih.gov/gene/?term=100873825		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000459	100873829	RNU5E-4P	http://www.ncbi.nlm.nih.gov/gene/?term=100873829		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000460	100873830	RNU5A-2P	http://www.ncbi.nlm.nih.gov/gene/?term=100873830		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000461	100873841	RNU5D-2P	http://www.ncbi.nlm.nih.gov/gene/?term=100873841		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000462	100873860	RNU1-16P	http://www.ncbi.nlm.nih.gov/gene/?term=100873860	U1.64	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000463	100873861	RNU1-19P	http://www.ncbi.nlm.nih.gov/gene/?term=100873861		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000464	100873862	RNU1-21P	http://www.ncbi.nlm.nih.gov/gene/?term=100873862		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000465	100873863	RNU1-22P	http://www.ncbi.nlm.nih.gov/gene/?term=100873863		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000466	100874051	LZTS1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874051		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000467	100874054	FALEC	http://www.ncbi.nlm.nih.gov/gene/?term=100874054	"FAL1, LINC00568, ncRNA-a1 "	lncRNA	Homo sapiens	22955988	Nucleus	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00000468	100874323	HOXA10-AS	http://www.ncbi.nlm.nih.gov/gene/?term=100874323	HOXA-AS4	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000469	10087	COL4A3BP	http://www.ncbi.nlm.nih.gov/gene/?term=10087	"CERT, CERTL, GPBP, MRD34, STARD11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000470	10087	COL4A3BP	http://www.ncbi.nlm.nih.gov/gene/?term=10087	"CERT, CERTL, GPBP, MRD34, STARD11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000471	100885779	LINC-ROR	http://www.ncbi.nlm.nih.gov/gene/?term=100885779	"ROR, lincRNA-RoR "	lncRNA	Homo sapiens	23208419	Cytoplasm	Breast|Colon	In situ hybridization	"Furthermore, in situ hybridization (ISH) revealed that RoR is mainly present in the cytoplasm (Supplementary information, Figure S8A).  "
RLID00000472	100885779	LINC-ROR	http://www.ncbi.nlm.nih.gov/gene/?term=100885779	"ROR, lincRNA-RoR "	lncRNA	Homo sapiens	23541921	Cytoplasm	Embryonic stem cell	In situ hybridization	"Employing a fluorescence in situ hybridization (FISH) assay, we found that the linc-RoR transcripts were abundant in the cytoplasm of self-renewing hESC cells (H1, 40 passages; X-01, 30 passages) ( Figure 1A), which supports the hypothesis that linc-RoR interacted with miRNAs in the cytoplasm.  "
RLID00000473	100887744	RNU6-48P	http://www.ncbi.nlm.nih.gov/gene/?term=100887744	RNU6-48	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000474	100887755	TRERNA1	http://www.ncbi.nlm.nih.gov/gene/?term=100887755	"LINC00651, treRNA "	lncRNA	Homo sapiens	23974796	Cytoplasm	A549 cell	qRT-PCR	"Nuclear and cytoplasm fractionation was isolated from A549 cells, and the expression of endogenous treRNA was quantified by qRT-PCR. Approximately 75% of spliced treRNA was located in the cytoplasm (Supplementary Figure S10). Data are collected from Figure S10. "
RLID00000475	100887755	TRERNA1	http://www.ncbi.nlm.nih.gov/gene/?term=100887755	"LINC00651, treRNA "	lncRNA	Homo sapiens	23974796	Nucleus	A549 cell	qRT-PCR	"Nuclear and cytoplasm fractionation was isolated from A549 cells, and the expression of endogenous treRNA was quantified by qRT-PCR. Approximately 75% of spliced treRNA was located in the cytoplasm (Supplementary Figure S10). Data are collected from Figure S10. "
RLID00000476	10092	ARPC5	http://www.ncbi.nlm.nih.gov/gene/?term=10092	"ARC16, dJ127C7.3, p16-Arc "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000477	10092	ARPC5	http://www.ncbi.nlm.nih.gov/gene/?term=10092	"ARC16, dJ127C7.3, p16-Arc "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000478	10092	ARPC5	http://www.ncbi.nlm.nih.gov/gene/?term=10092	"ARC16, dJ127C7.3, p16-Arc "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000479	10093	ARPC4	http://www.ncbi.nlm.nih.gov/gene/?term=10093	"ARC20, P20-ARC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000480	10093	ARPC4	http://www.ncbi.nlm.nih.gov/gene/?term=10093	"ARC20, P20-ARC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000481	10093	ARPC4	http://www.ncbi.nlm.nih.gov/gene/?term=10093	"ARC20, P20-ARC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000482	10094	ARPC3	http://www.ncbi.nlm.nih.gov/gene/?term=10094	"ARC21, p21-Arc "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000483	10094	ARPC3	http://www.ncbi.nlm.nih.gov/gene/?term=10094	"ARC21, p21-Arc "	mRNA	Homo sapiens	23452202	Cell leading edge	Lung fibroblast	qRT-PCR	Our data have shown that mRNA encoding WAVE-Arp2/3-associated proteins is co-localized with foci enriched with active protein synthesis at the leading edge during cell migration (Figure 4).
RLID00000484	10095	ARPC1B	http://www.ncbi.nlm.nih.gov/gene/?term=10095	"ARC41, p40-ARC, p41-ARC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000485	10095	ARPC1B	http://www.ncbi.nlm.nih.gov/gene/?term=10095	"ARC41, p40-ARC, p41-ARC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000486	10095	ARPC1B	http://www.ncbi.nlm.nih.gov/gene/?term=10095	"ARC41, p40-ARC, p41-ARC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000487	10096	ACTR3	http://www.ncbi.nlm.nih.gov/gene/?term=10096	ARP3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000488	100978	Nfxl1	http://www.ncbi.nlm.nih.gov/gene/?term=100978	"1700012H24Rik, AW538212, D430033A06Rik, DNABF, GCF, Gm1058, TCF9 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000489	10097	ACTR2	http://www.ncbi.nlm.nih.gov/gene/?term=10097	ARP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000490	100986	Akap9	http://www.ncbi.nlm.nih.gov/gene/?term=100986	"5730481H23Rik, AKAP-9, AKAP450, AW545847, C79026, G1-448-15, PRKA9, mKIAA0803, mei2-5, repro12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000491	10098	TSPAN5	http://www.ncbi.nlm.nih.gov/gene/?term=10098	"NET-4, NET4, TM4SF9, TSPAN-5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000492	10098	TSPAN5	http://www.ncbi.nlm.nih.gov/gene/?term=10098	"NET-4, NET4, TM4SF9, TSPAN-5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000493	100996579	LOC100996579	http://www.ncbi.nlm.nih.gov/gene/?term=100996579		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000494	10099	TSPAN3	http://www.ncbi.nlm.nih.gov/gene/?term=10099	"TM4-A, TM4SF8, TSPAN-3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000495	10099	TSPAN3	http://www.ncbi.nlm.nih.gov/gene/?term=10099	"TM4-A, TM4SF8, TSPAN-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000496	10101	NUBP2	http://www.ncbi.nlm.nih.gov/gene/?term=10101	"CFD1, NBP 2, NUBP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000497	10102	TSFM	http://www.ncbi.nlm.nih.gov/gene/?term=10102	"EFTS, EFTSMT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000498	10102	TSFM	http://www.ncbi.nlm.nih.gov/gene/?term=10102	"EFTS, EFTSMT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000499	10103	TSPAN1	http://www.ncbi.nlm.nih.gov/gene/?term=10103	"NET1, TM4C, TM4SF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000500	101056138	Gm20619	http://www.ncbi.nlm.nih.gov/gene/?term=101056138		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000501	10105	PPIF	http://www.ncbi.nlm.nih.gov/gene/?term=10105	"CYP3, CyP-M, Cyp-D, CypD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000502	10105	PPIF	http://www.ncbi.nlm.nih.gov/gene/?term=10105	"CYP3, CyP-M, Cyp-D, CypD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000503	10106	CTDSP2	http://www.ncbi.nlm.nih.gov/gene/?term=10106	"OS4, PSR2, SCP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000504	10109	ARPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10109	"ARC34, PNAS-139, PRO2446, p34-Arc "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000505	10109	ARPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10109	"ARC34, PNAS-139, PRO2446, p34-Arc "	mRNA	Homo sapiens	23452202	Lamellipodium	Lung fibroblast	Fluorescence in situ hybridization	"Rac1, ArpC2 and β-actin mRNAs co-localize with actively translating ribosomes on lamellipodia. "
RLID00000506	10109	ARPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10109	"ARC34, PNAS-139, PRO2446, p34-Arc "	mRNA	Homo sapiens	23452202	Cell leading edge	Lung fibroblast	qRT-PCR	Our data have shown that mRNA encoding WAVE-Arp2/3-associated proteins is co-localized with foci enriched with active protein synthesis at the leading edge during cell migration (Figure 4).
RLID00000507	10109	ARPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10109	"ARC34, PNAS-139, PRO2446, p34-Arc "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000508	101100	Ttll3	http://www.ncbi.nlm.nih.gov/gene/?term=101100	"4833441J24Rik, AI450050 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000509	10110	SGK2	http://www.ncbi.nlm.nih.gov/gene/?term=10110	"H-SGK2, dJ138B7.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000510	101118	Tmem168	http://www.ncbi.nlm.nih.gov/gene/?term=101118	"5730526F17Rik, 8430437G11Rik, AI462344, AI504145 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000511	10111	RAD50	http://www.ncbi.nlm.nih.gov/gene/?term=10111	"NBSLD, RAD502, hRad50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000512	101122	Rpusd3	http://www.ncbi.nlm.nih.gov/gene/?term=101122	AI527266	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000513	10112	KIF20A	http://www.ncbi.nlm.nih.gov/gene/?term=10112	"MKLP2, RAB6KIFL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000514	10113	PREB	http://www.ncbi.nlm.nih.gov/gene/?term=10113	SEC12	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000515	10113	PREB	http://www.ncbi.nlm.nih.gov/gene/?term=10113	SEC12	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000516	101148	B630005N14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=101148	AI666701	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000517	10114	HIPK3	http://www.ncbi.nlm.nih.gov/gene/?term=10114	"DYRK6, FIST3, PKY, YAK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000518	10114	HIPK3	http://www.ncbi.nlm.nih.gov/gene/?term=10114	"DYRK6, FIST3, PKY, YAK1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000519	101154644	LINCMD1	http://www.ncbi.nlm.nih.gov/gene/?term=101154644	"LINC-MD1, MIR133BHG "	lncRNA	Homo sapiens	22000014	Cytoplasm	Myoblast	RT-PCR	Linc-MD1 is a long noncoding cytoplasmic RNA expressed during myoblast differentiation
RLID00000520	101163732	LOC101163732	http://www.ncbi.nlm.nih.gov/gene/?term=101163732	Mitf2	mRNA	Oryzias latipes	23439406	Mitochondrion	Oocyte	In situ hybridization	"Here we report in the fish medaka (Oryzias latipes) that RNAs encoding microphthalmia-associated transcription factor (Mitf) are prominent components of the BB. By fluorescence in situ hybridization on ovarian section, we revealed that the transcripts of both mitf1 and mitf2 genes concentrated in the BB, in which they co-localized with the dazl RNA, a definitive BB marker highly conserved in vertebrates.  "
RLID00000521	101165733	mitf	http://www.ncbi.nlm.nih.gov/gene/?term=101165733		mRNA	Oryzias latipes	23439406	Mitochondrion	Oocyte	In situ hybridization	"Here we report in the fish medaka (Oryzias latipes) that RNAs encoding microphthalmia-associated transcription factor (Mitf) are prominent components of the BB. By fluorescence in situ hybridization on ovarian section, we revealed that the transcripts of both mitf1 and mitf2 genes concentrated in the BB, in which they co-localized with the dazl RNA, a definitive BB marker highly conserved in vertebrates.  "
RLID00000522	10116	FEM1B	http://www.ncbi.nlm.nih.gov/gene/?term=10116	"F1A-ALPHA, F1AA, FEM1-beta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000523	101179	6430519N07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=101179	"AI848395, AW554807 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000524	101185	Pot1a	http://www.ncbi.nlm.nih.gov/gene/?term=101185	"1500031H18Rik, AI851169, Pot1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000525	101187	Parp11	http://www.ncbi.nlm.nih.gov/gene/?term=101187	"5330431N24Rik, AI851877, ARTD11, HIN1L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000526	101206	Tada3	http://www.ncbi.nlm.nih.gov/gene/?term=101206	"1110004B19Rik, ADA3, AI987856l, Tada3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000527	10120	ACTR1B	http://www.ncbi.nlm.nih.gov/gene/?term=10120	"ARP1B, CTRN2, PC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000528	101214	Tra2a	http://www.ncbi.nlm.nih.gov/gene/?term=101214	"1500010G04Rik, AL022798, G430041M01Rik, mAWMS1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000529	10121	ACTR1A	http://www.ncbi.nlm.nih.gov/gene/?term=10121	"ARP1, Arp1A, CTRN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000530	10121	ACTR1A	http://www.ncbi.nlm.nih.gov/gene/?term=10121	"ARP1, Arp1A, CTRN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000531	10121	ACTR1A	http://www.ncbi.nlm.nih.gov/gene/?term=10121	"ARP1, Arp1A, CTRN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000532	101234261	LSINCT5	http://www.ncbi.nlm.nih.gov/gene/?term=101234261		lncRNA	Homo sapiens	21532345	Nucleus	Breast cancer cell|Ovarian cancer cell	qRT-PCR	"In this report, we demonstrate that LSINCT5 is a 2.6 Kb polyadenylated, long stress-induced non-coding transcript that is on the negative strand, localized in the nucleus and potentially transcribed by RNA polymerase III. "
RLID00000533	10123	ARL4C	http://www.ncbi.nlm.nih.gov/gene/?term=10123	"ARL7, LAK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000534	101240	Wdr91	http://www.ncbi.nlm.nih.gov/gene/?term=101240	"9530020G05Rik, AI987683, AU018665 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000535	101243555	PTENP1-AS	http://www.ncbi.nlm.nih.gov/gene/?term=101243555	"PTENP1as, PTENpg1-asRNA "	lncRNA	Homo sapiens	23435381	Cytoplasm	Eembryonic kidney cell	qRT-PCR	"Cellular fractionation showed that the spliced α and β isoforms were expressed at high levels in the cytoplasm, whereas the unspliced PTENpg1 asRNA α isoform was exclusively found in the nuclear fraction (Supplementary Fig. 2d-e). "
RLID00000536	101243555	PTENP1-AS	http://www.ncbi.nlm.nih.gov/gene/?term=101243555	"PTENP1as, PTENpg1-asRNA "	lncRNA	Homo sapiens	23435381	Nucleus	Eembryonic kidney cell	qRT-PCR	"Cellular fractionation showed that the spliced α and β isoforms were expressed at high levels in the cytoplasm, whereas the unspliced PTENpg1 asRNA α isoform was exclusively found in the nuclear fraction (Supplementary Fig. 2d-e). "
RLID00000537	10124	ARL4A	http://www.ncbi.nlm.nih.gov/gene/?term=10124	ARL4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000538	10126	DNAL4	http://www.ncbi.nlm.nih.gov/gene/?term=10126	"MRMV3, PIG27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000539	10127	ZNF263	http://www.ncbi.nlm.nih.gov/gene/?term=10127	"FPM315, ZKSCAN12, ZSCAN44 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000540	10127	ZNF263	http://www.ncbi.nlm.nih.gov/gene/?term=10127	"FPM315, ZKSCAN12, ZSCAN44 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000541	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"CLONE-23970, GP130, LRP130, LSFC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000542	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"LSFC, GP130, LRP130, CLONE-23970 "	mRNA	Homo sapiens	15081402	Nucleus	HeLa cell	In situ hybridization	"To further analyze the subcellular localization of LRP130, a nuclear/ER fraction was fractionated into the nucleoplasm (NP) and nuclear envelope (NE)/ER, and the latter was further separated into outer nuclear membrane (ONM)/ER and inner nuclear membrane (INM) by treatment with Triton X-100. LRP130 was detectable in all three fractions, and the distribution pattern was in good accordance with that known for ONM/ER proteins. Interestingly, immunostaining of HeLa cells demonstrated nuclear rim staining of LRP130, specifically at the outside of the NE and also at ER, and association of LRP130 with poly(A)(+) RNA was restricted only to the ONM/ER fraction. "
RLID00000543	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"LSFC, GP130, LRP130, CLONE-23970 "	mRNA	Homo sapiens	15081402	Endoplasmic reticulum	HeLa cell	In situ hybridization	"To further analyze the subcellular localization of LRP130, a nuclear/ER fraction was fractionated into the nucleoplasm (NP) and nuclear envelope (NE)/ER, and the latter was further separated into outer nuclear membrane (ONM)/ER and inner nuclear membrane (INM) by treatment with Triton X-100. LRP130 was detectable in all three fractions, and the distribution pattern was in good accordance with that known for ONM/ER proteins. Interestingly, immunostaining of HeLa cells demonstrated nuclear rim staining of LRP130, specifically at the outside of the NE and also at ER, and association of LRP130 with poly(A)(+) RNA was restricted only to the ONM/ER fraction. "
RLID00000544	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"CLONE-23970, GP130, LRP130, LSFC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000545	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"CLONE-23970, GP130, LRP130, LSFC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000546	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"CLONE-23970, GP130, LRP130, LSFC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000547	10128	LRPPRC	http://www.ncbi.nlm.nih.gov/gene/?term=10128	"CLONE-23970, GP130, LRP130, LSFC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000548	10130	PDIA6	http://www.ncbi.nlm.nih.gov/gene/?term=10130	"ERP5, P5, TXNDC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000549	10131	TRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10131	"HSP 75, HSP75, HSP90L, TRAP-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000550	10131	TRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10131	"HSP 75, HSP75, HSP90L, TRAP-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000551	101340252	SNORD121B	http://www.ncbi.nlm.nih.gov/gene/?term=101340252		snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000552	10134	BCAP31	http://www.ncbi.nlm.nih.gov/gene/?term=10134	"6C6-AG, BAP31, CDM, DDCH, DXS1357E "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000553	10134	BCAP31	http://www.ncbi.nlm.nih.gov/gene/?term=10134	"6C6-AG, BAP31, CDM, DDCH, DXS1357E "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000554	10134	BCAP31	http://www.ncbi.nlm.nih.gov/gene/?term=10134	"6C6-AG, BAP31, CDM, DDCH, DXS1357E "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000555	101351	Eogt	http://www.ncbi.nlm.nih.gov/gene/?term=101351	"A130022J15Rik, AI447490, AW214473, AW259391, Aer61 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000556	10135	NAMPT	http://www.ncbi.nlm.nih.gov/gene/?term=10135	"1110035O14Rik, PBEF, PBEF1, VF, VISFATIN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000557	10136	CELA3A	http://www.ncbi.nlm.nih.gov/gene/?term=10136	"ELA3, ELA3A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000558	10137	RBM12	http://www.ncbi.nlm.nih.gov/gene/?term=10137	"HRIHFB2091, SWAN "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000559	10138	YAF2	http://www.ncbi.nlm.nih.gov/gene/?term=10138		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000560	10139	ARFRP1	http://www.ncbi.nlm.nih.gov/gene/?term=10139	"ARL18, ARP, Arp1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000561	10139	ARFRP1	http://www.ncbi.nlm.nih.gov/gene/?term=10139	"ARL18, ARP, Arp1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000562	101401	Adamts9	http://www.ncbi.nlm.nih.gov/gene/?term=101401	"1810011L16Rik, 8430403M15Rik, AW743315, E030027K14Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000563	10140	TOB1	http://www.ncbi.nlm.nih.gov/gene/?term=10140	"APRO6, PIG49, TOB, TROB, TROB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000564	10140	TOB1	http://www.ncbi.nlm.nih.gov/gene/?term=10140	"APRO6, PIG49, TOB, TROB, TROB1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000565	10140	TOB1	http://www.ncbi.nlm.nih.gov/gene/?term=10140	"APRO6, PIG49, TOB, TROB, TROB1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000566	101410538	MMP24-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101410538		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000567	10142	AKAP9	http://www.ncbi.nlm.nih.gov/gene/?term=10142	"AKAP-9, AKAP350, AKAP450, CG-NAP, HYPERION, LQT11, MU-RMS-40.16A, PPP1R45, PRKA9, YOTIAO "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000568	101434	Ceacam15	http://www.ncbi.nlm.nih.gov/gene/?term=101434	"AA407838, C430002N04Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000569	10146	G3BP1	http://www.ncbi.nlm.nih.gov/gene/?term=10146	"G3BP, HDH-VIII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000570	10146	G3BP1	http://www.ncbi.nlm.nih.gov/gene/?term=10146	"G3BP, HDH-VIII "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000571	10146	G3BP1	http://www.ncbi.nlm.nih.gov/gene/?term=10146	"G3BP, HDH-VIII "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000572	101476	Plekha1	http://www.ncbi.nlm.nih.gov/gene/?term=101476	"AA960558, C920009D07Rik, TAPP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000573	10147	SUGP2	http://www.ncbi.nlm.nih.gov/gene/?term=10147	SFRS14	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000574	10147	SUGP2	http://www.ncbi.nlm.nih.gov/gene/?term=10147	SFRS14	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000575	10148	EBI3	http://www.ncbi.nlm.nih.gov/gene/?term=10148	"IL-27B, IL27B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000576	101490	Inpp5f	http://www.ncbi.nlm.nih.gov/gene/?term=101490	"5830435P03Rik, AI115354, AW561896, SAC2, cI-27, mKIAA0966 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000577	101502	Hsd3b7	http://www.ncbi.nlm.nih.gov/gene/?term=101502	"AI195443, BB098564 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000578	10150	MBNL2	http://www.ncbi.nlm.nih.gov/gene/?term=10150	"MBLL, MBLL39, PRO2032 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000579	10150	MBNL2	http://www.ncbi.nlm.nih.gov/gene/?term=10150	"MBLL, MBLL39, PRO2032 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000580	10152	ABI2	http://www.ncbi.nlm.nih.gov/gene/?term=10152	"ABI-2, ABI2B, AIP-1, AblBP3, SSH3BP2, argBP1, argBPIA, argBPIB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000581	10152	ABI2	http://www.ncbi.nlm.nih.gov/gene/?term=10152	"ABI-2B, AIP-1, AblBP3, SSH3BP2, argBP1, argBPIA, argBPIB, ABI2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000582	10153	CEBPZ	http://www.ncbi.nlm.nih.gov/gene/?term=10153	"CBF, CBF2, HSP-CBF, NOC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000583	10153	CEBPZ	http://www.ncbi.nlm.nih.gov/gene/?term=10153	"CBF, CBF2, HSP-CBF, NOC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000584	101544	Zfp575	http://www.ncbi.nlm.nih.gov/gene/?term=101544	"AI326876, Znf575 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000585	10155	TRIM28	http://www.ncbi.nlm.nih.gov/gene/?term=10155	"KAP1, PPP1R157, RNF96, TF1B, TIF1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000586	10155	TRIM28	http://www.ncbi.nlm.nih.gov/gene/?term=10155	"KAP1, PPP1R157, RNF96, TF1B, TIF1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000587	101565	Ccp110	http://www.ncbi.nlm.nih.gov/gene/?term=101565	"6330503K22Rik, AA415922, AI427129, AW557948, CP110 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000588	10157	AASS	http://www.ncbi.nlm.nih.gov/gene/?term=10157	"LKR/SDH, LKRSDH, LORSDH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000589	10157	AASS	http://www.ncbi.nlm.nih.gov/gene/?term=10157	"LKR/SDH, LKRSDH, LORSDH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000590	101592	Efl1	http://www.ncbi.nlm.nih.gov/gene/?term=101592	"4932434J20Rik, 6030468D11Rik, AI451340, AU019507, AU022896, D7Ertd791e, Eftud1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000591	10159	ATP6AP2	http://www.ncbi.nlm.nih.gov/gene/?term=10159	"APT6M8-9, ATP6IP2, ATP6M8-9, ELDF10, HT028, M8-9, MRXE, MRXSH, MSTP009, PRR, RENR, XMRE, XPDS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000592	1015	CDH17	http://www.ncbi.nlm.nih.gov/gene/?term=1015	"CDH16, HPT-1, HPT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000593	101602	AI467606	http://www.ncbi.nlm.nih.gov/gene/?term=101602		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000594	10160	FARP1	http://www.ncbi.nlm.nih.gov/gene/?term=10160	"CDEP, FARP1-IT1, PLEKHC2, PPP1R75 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000595	10160	FARP1	http://www.ncbi.nlm.nih.gov/gene/?term=10160	"CDEP-IT1, PLEKHC2, PPP1R75, FARP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000596	101613	Nlrp6	http://www.ncbi.nlm.nih.gov/gene/?term=101613	"AI504961, Avr, Nalp6, Navr, Navr/Avr, Non-AVR, Pypaf5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000597	10162	LPCAT3	http://www.ncbi.nlm.nih.gov/gene/?term=10162	"C3F, LPCAT, LPLAT 5, LPSAT, MBOAT5, OACT5, nessy "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000598	10162	LPCAT3	http://www.ncbi.nlm.nih.gov/gene/?term=10162	"C3F, LPCAT, LPLAT 5, LPSAT, MBOAT5, OACT5, nessy "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000599	10162	LPCAT3	http://www.ncbi.nlm.nih.gov/gene/?term=10162	"C3F, LPCAT, LPLAT 5, LPSAT, MBOAT5, OACT5, nessy "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000600	10162	LPCAT3	http://www.ncbi.nlm.nih.gov/gene/?term=10162	"C3F, LPCAT, LPLAT 5, LPSAT, MBOAT5, OACT5, nessy "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000601	101631	Pwwp2b	http://www.ncbi.nlm.nih.gov/gene/?term=101631	"AI594893, D7Ertd517e, D930023J19Rik, Pwwp2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000602	10163	WASF2	http://www.ncbi.nlm.nih.gov/gene/?term=10163	"IMD2, SCAR2, WASF4, WAVE2, dJ393P12.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000603	10163	WASF2	http://www.ncbi.nlm.nih.gov/gene/?term=10163	"IMD2, SCAR2, WASF4, WAVE2, dJ393P12.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000604	101646	B830008H07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=101646	AI662092	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000605	10165	SLC25A13	http://www.ncbi.nlm.nih.gov/gene/?term=10165	"ARALAR2, CITRIN, CTLN2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000606	10166	SLC25A15	http://www.ncbi.nlm.nih.gov/gene/?term=10166	"D13S327, HHH, ORC1, ORNT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000607	101685	Spty2d1	http://www.ncbi.nlm.nih.gov/gene/?term=101685	"5830435K17Rik, AI852426, P16H6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000608	10169	SERF2	http://www.ncbi.nlm.nih.gov/gene/?term=10169	"4F5REL, FAM2C, H4F5REL, HsT17089 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000609	10169	SERF2	http://www.ncbi.nlm.nih.gov/gene/?term=10169	"4F5REL, FAM2C, H4F5REL, HsT17089 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000610	101706	Numa1	http://www.ncbi.nlm.nih.gov/gene/?term=101706	"6720401E04Rik, AA764025, AL022610, AU014979 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000611	101715	AL023008	http://www.ncbi.nlm.nih.gov/gene/?term=101715		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000612	10171	RCL1	http://www.ncbi.nlm.nih.gov/gene/?term=10171	"RNAC, RPCL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000613	10171	RCL1	http://www.ncbi.nlm.nih.gov/gene/?term=10171	"RNAC, RPCL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000614	101739	Psip1	http://www.ncbi.nlm.nih.gov/gene/?term=101739	"AA408851, AU015605, Dfs70, Ledgfa, Ledgfb, Psip2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000615	10174	SORBS3	http://www.ncbi.nlm.nih.gov/gene/?term=10174	"SCAM-1, SCAM1, SH3D4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000616	101752218	ARPC5L	http://www.ncbi.nlm.nih.gov/gene/?term=101752218	null	mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00000617	10175	CNIH1	http://www.ncbi.nlm.nih.gov/gene/?term=10175	"CNIH, CNIH-1, CNIL, TGAM77 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000618	10175	CNIH1	http://www.ncbi.nlm.nih.gov/gene/?term=10175	"CNIH, CNIH-1, CNIL, TGAM77 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000619	10178782	CG31808	http://www.ncbi.nlm.nih.gov/gene/?term=10178782	"Dmel_ BcDNA:RE70695, CR31808, Dmel\CG31808, Dmel_CR31808, MRE33, RE70695 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00000620	10178964	CR42862	http://www.ncbi.nlm.nih.gov/gene/?term=10178964	"Dmel_ BcDNA:GH06422, CG13878, CG16971, CG32477, CR32477, Dmel\CR42862, Dmel_CG16971, Dmel_CR32477, anon-EST:fe1H7 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00000621	10178964	CR42862	http://www.ncbi.nlm.nih.gov/gene/?term=10178964	"Dmel_ BcDNA:GH06422, CG13878, CG16971, CG32477, CR32477, Dmel\CR42862, Dmel_CG16971, Dmel_CR32477, anon-EST:fe1H7 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00000622	10179	RBM7	http://www.ncbi.nlm.nih.gov/gene/?term=10179		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000623	1017	CDK2	http://www.ncbi.nlm.nih.gov/gene/?term=1017	"CDKN2, p33(CDK2) "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000624	101805488	CCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=101805488	"LINC00873, NCCP1 "	lncRNA	Homo sapiens	25677908	Nucleus	TE1 cell|KYSE410 cell	qRT-PCR	"CCAT2 was mostly upregulated in KYSE410 cell (24.7-fold upregulation) when normalized to normal esophageal epithelium cell line (HEEC) and most CCAT2 transcripts were located in nucleus (>95 %). Finally, with respect to the subcellular location, in TE1 and KYSE410 cell lines, CCAT2 was mostly located in nucleus (more than 95 %, shown in Fig. 2d). "
RLID00000625	10180	RBM6	http://www.ncbi.nlm.nih.gov/gene/?term=10180	"3G2, DEF-3, DEF3, HLC-11, NY-LU-12, g16 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000626	10181	RBM5	http://www.ncbi.nlm.nih.gov/gene/?term=10181	"G15, H37, LUCA15, RMB5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000627	10181	RBM5	http://www.ncbi.nlm.nih.gov/gene/?term=10181	"G15, H37, LUCA15, RMB5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000628	10184	LHFPL2	http://www.ncbi.nlm.nih.gov/gene/?term=10184		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000629	10188	TNK2	http://www.ncbi.nlm.nih.gov/gene/?term=10188	"ACK, ACK-1, ACK1, p21cdc42Hs "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000630	10189	ALYREF	http://www.ncbi.nlm.nih.gov/gene/?term=10189	"ALY, ALY/REF, BEF, REF, THOC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000631	10190	TXNDC9	http://www.ncbi.nlm.nih.gov/gene/?term=10190	"APACD, PHLP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000632	101926933	LOC101926933	http://www.ncbi.nlm.nih.gov/gene/?term=101926933		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000633	101927167	GATA2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101927167		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000634	101927746	LOC101927746	http://www.ncbi.nlm.nih.gov/gene/?term=101927746		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000635	101928464	LOC101928464	http://www.ncbi.nlm.nih.gov/gene/?term=101928464		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000636	101928483	NALT1	http://www.ncbi.nlm.nih.gov/gene/?term=101928483	"LINC01573, MIR4674HG, NALT "	lncRNA	Homo sapiens	26330272	Cytoplasm	T-lymphoma cell	RT-PCR	"We found that NALT was obviously existed in both cytoplasm and nucleus, and the expression of NALT in the nucleus was higher than that in the cytoplasm (Fig. 4B).  "
RLID00000637	101928483	NALT1	http://www.ncbi.nlm.nih.gov/gene/?term=101928483	"LINC01573, MIR4674HG, NALT "	lncRNA	Homo sapiens	26330272	Nucleus	T-lymphoma cell	RT-PCR	"We found that NALT was obviously existed in both cytoplasm and nucleus, and the expression of NALT in the nucleus was higher than that in the cytoplasm (Fig. 4B).  "
RLID00000638	10193	RNF41	http://www.ncbi.nlm.nih.gov/gene/?term=10193	"FLRF, NRDP1, SBBI03 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000639	10194	TSHZ1	http://www.ncbi.nlm.nih.gov/gene/?term=10194	"CAA, NY-CO-33, SDCCAG33, TSH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000640	101954264	RNVU1-4	http://www.ncbi.nlm.nih.gov/gene/?term=101954264	"RNU1-102, RNU1-50, RNVU1-5, vU1.4, vU1.5 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000641	101954266	RNVU1-14	http://www.ncbi.nlm.nih.gov/gene/?term=101954266	"RNU1-37, vU1.14 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000642	101954267	RNVU1-15	http://www.ncbi.nlm.nih.gov/gene/?term=101954267	"RNU1-121, RNU1-66, RNVU1-16, vU1.15, vU1.16 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000643	101954269	RNVU1-17	http://www.ncbi.nlm.nih.gov/gene/?term=101954269	"RNU1-127, vU1.17 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000644	101954271	RNU6-9	http://www.ncbi.nlm.nih.gov/gene/?term=101954271	U6-9	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000645	101954272	RNVU1-3	http://www.ncbi.nlm.nih.gov/gene/?term=101954272	"RNU1-113, RNU1-151, RNVU1-12, vU1.12, vU1.3 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000646	101954273	RNVU1-1	http://www.ncbi.nlm.nih.gov/gene/?term=101954273	"RNU1-10P, RNU1-53, RNU1P100, U1.4, U1P14, vU1.1, vU1.10, RNVU1-1 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000647	101954275	RNU6-7	http://www.ncbi.nlm.nih.gov/gene/?term=101954275	U6-7	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000648	101954276	RNVU1-6	http://www.ncbi.nlm.nih.gov/gene/?term=101954276	"RNU1-99, vU1.6 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000649	101954277	RNVU1-19	http://www.ncbi.nlm.nih.gov/gene/?term=101954277	"RNU1-126, RNU1-147, RNVU1-13, vU1.13, vU1.19 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000650	101954278	RNU6-8	http://www.ncbi.nlm.nih.gov/gene/?term=101954278	U6-8	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000651	10195	ALG3	http://www.ncbi.nlm.nih.gov/gene/?term=10195	"CDG1D, CDGS4, CDGS6, D16Ertd36e, NOT56L, Not56, not "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000652	10196	PRMT3	http://www.ncbi.nlm.nih.gov/gene/?term=10196	HRMT1L3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000653	10197	PSME3	http://www.ncbi.nlm.nih.gov/gene/?term=10197	"HEL-S-283, Ki, PA28-gamma, PA28G, PA28gamma, REG-GAMMA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000654	10197	PSME3	http://www.ncbi.nlm.nih.gov/gene/?term=10197	"HEL-S-283, Ki, PA28-gamma, PA28G, PA28gamma, REG-GAMMA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000655	101985	Usb1	http://www.ncbi.nlm.nih.gov/gene/?term=101985	AA960436	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000656	10198	MPHOSPH9	http://www.ncbi.nlm.nih.gov/gene/?term=10198	"MPP-9, MPP9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000657	101994	Champ1	http://www.ncbi.nlm.nih.gov/gene/?term=101994	"AA675043, AI116001, D8Ertd457e, D8Ertd569e, Zfp828, Znf828, mKIAA1802 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000658	10199	MPHOSPH10	http://www.ncbi.nlm.nih.gov/gene/?term=10199	"CT90, MPP10, MPP10P, PPP1R106 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000659	1019	CDK4	http://www.ncbi.nlm.nih.gov/gene/?term=1019	"CMM3, PSK-J3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000660	1019	CDK4	http://www.ncbi.nlm.nih.gov/gene/?term=1019	"CMM3, PSK-J3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000661	101	ADAM8	http://www.ncbi.nlm.nih.gov/gene/?term=101	"CD156, CD156a, MS2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000662	10200	MPHOSPH6	http://www.ncbi.nlm.nih.gov/gene/?term=10200	"MPP, MPP-6, MPP6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000663	10200	MPHOSPH6	http://www.ncbi.nlm.nih.gov/gene/?term=10200	"MPP, MPP-6, MPP6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000664	10200	MPHOSPH6	http://www.ncbi.nlm.nih.gov/gene/?term=10200	"MPP, MPP-6, MPP6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000665	10201	NME6	http://www.ncbi.nlm.nih.gov/gene/?term=10201	"IPIA-ALPHA, NDK 6, NM23-H6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000666	10202	DHRS2	http://www.ncbi.nlm.nih.gov/gene/?term=10202	"HEP27, SDR25C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000667	10204	NUTF2	http://www.ncbi.nlm.nih.gov/gene/?term=10204	"NTF2, PP15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000668	10204	NUTF2	http://www.ncbi.nlm.nih.gov/gene/?term=10204	"NTF-2, NTF2, PP15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000669	10204	NUTF2	http://www.ncbi.nlm.nih.gov/gene/?term=10204	"NTF-2, NTF2, PP15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000670	10205	MPZL2	http://www.ncbi.nlm.nih.gov/gene/?term=10205	"EVA, EVA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000671	10205	MPZL2	http://www.ncbi.nlm.nih.gov/gene/?term=10205	"EVA, EVA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000672	102060	Gadd45gip1	http://www.ncbi.nlm.nih.gov/gene/?term=102060	"2310040G17Rik, AI425883, Crif1, MRP-L59, Plinp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000673	10206	TRIM13	http://www.ncbi.nlm.nih.gov/gene/?term=10206	"CAR, DLEU5, LEU5, RFP2, RNF77 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000674	10206	TRIM13	http://www.ncbi.nlm.nih.gov/gene/?term=10206	"CAR, DLEU5, LEU5, RFP2, RNF77 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000675	10206	TRIM13	http://www.ncbi.nlm.nih.gov/gene/?term=10206	"CAR, DLEU5, LEU5, RFP2, RNF77 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000676	10207	PATJ	http://www.ncbi.nlm.nih.gov/gene/?term=10207	"Cipp, INADL, InaD-like, hINADL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000677	10208	USPL1	http://www.ncbi.nlm.nih.gov/gene/?term=10208	"C13orf22, D13S106E, bA121O19.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000678	10208	USPL1	http://www.ncbi.nlm.nih.gov/gene/?term=10208	"C13orf22, D13S106E, bA121O19.1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000679	102093	Phkb	http://www.ncbi.nlm.nih.gov/gene/?term=102093	AI463271	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000680	10209	EIF1	http://www.ncbi.nlm.nih.gov/gene/?term=10209	"A121, EIF-1, EIF1A, ISO1, SUI1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000681	10209	EIF1	http://www.ncbi.nlm.nih.gov/gene/?term=10209	"A121, EIF-1A, ISO1, SUI1, EIF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000682	10209	EIF1	http://www.ncbi.nlm.nih.gov/gene/?term=10209	"A121, EIF-1A, ISO1, SUI1, EIF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000683	1020	CDK5	http://www.ncbi.nlm.nih.gov/gene/?term=1020	"LIS7, PSSALRE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000684	1020	CDK5	http://www.ncbi.nlm.nih.gov/gene/?term=1020	"LIS7, PSSALRE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000685	1020	CDK5	http://www.ncbi.nlm.nih.gov/gene/?term=1020	"LIS7, PSSALRE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000686	102103	Mtus1	http://www.ncbi.nlm.nih.gov/gene/?term=102103	"AI481402, ATBP135, Atip1, B430010I23Rik, B430305I03Rik, C85752, Cctsg1-440, MD44, MTSG1, mKIAA1288 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000687	10210	TOPORS	http://www.ncbi.nlm.nih.gov/gene/?term=10210	"LUN, P53BP3, RP31, TP53BPL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000688	10211	FLOT1	http://www.ncbi.nlm.nih.gov/gene/?term=10211		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000689	102124	Enkd1	http://www.ncbi.nlm.nih.gov/gene/?term=102124	"AI606951, E130303B06Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000690	10212	DDX39A	http://www.ncbi.nlm.nih.gov/gene/?term=10212	"BAT1, BAT1L, DDX39, DDXL, URH49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000691	10213	PSMD14	http://www.ncbi.nlm.nih.gov/gene/?term=10213	"PAD1, POH1, RPN11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000692	10213	PSMD14	http://www.ncbi.nlm.nih.gov/gene/?term=10213	"PAD1, POH1, RPN11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000693	10213	PSMD14	http://www.ncbi.nlm.nih.gov/gene/?term=10213	"PAD1, POH1, RPN11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000694	102141	Snx25	http://www.ncbi.nlm.nih.gov/gene/?term=102141	"AI661919, Gm1699, Gm173, Sbbi31 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000695	10214	SSX3	http://www.ncbi.nlm.nih.gov/gene/?term=10214	CT5.3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000696	102152026	HNRNPA1	http://www.ncbi.nlm.nih.gov/gene/?term=102152026		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00000697	10217	CTDSPL	http://www.ncbi.nlm.nih.gov/gene/?term=10217	"C3orf8, HYA22, PSR1, RBSP3, SCP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000698	10217	CTDSPL	http://www.ncbi.nlm.nih.gov/gene/?term=10217	"C3orf8, HYA22, PSR1, RBSP3, SCP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000699	1021	CDK6	http://www.ncbi.nlm.nih.gov/gene/?term=1021	"MCPH12, PLSTIRE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000700	1021	CDK6	http://www.ncbi.nlm.nih.gov/gene/?term=1021	"MCPH12, PLSTIRE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000701	1021	CDK6	http://www.ncbi.nlm.nih.gov/gene/?term=1021	"MCPH12, PLSTIRE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000702	10220	GDF11	http://www.ncbi.nlm.nih.gov/gene/?term=10220	"BMP-11, BMP11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000703	102216341	LINC01109	http://www.ncbi.nlm.nih.gov/gene/?term=102216341	lncRNA-N1	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00000704	102216342	LINC01108	http://www.ncbi.nlm.nih.gov/gene/?term=102216342	LncRNA-ES1	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"By means of RNA fractionation followed by quantitative PCR (qPCR), we found that lncRNA_ES1, lncRNA_ES2 and lncRNA_ES3 were preferentially retained in the nucleus (Figure 5A). "
RLID00000705	10221	TRIB1	http://www.ncbi.nlm.nih.gov/gene/?term=10221	"C8FW, GIG-2, GIG2, SKIP1, TRB-1, TRB1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000706	10223	GPA33	http://www.ncbi.nlm.nih.gov/gene/?term=10223	A33	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000707	10223	GPA33	http://www.ncbi.nlm.nih.gov/gene/?term=10223	A33	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000708	10225	CD96	http://www.ncbi.nlm.nih.gov/gene/?term=10225	TACTILE	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000709	10225	CD96	http://www.ncbi.nlm.nih.gov/gene/?term=10225	TACTILE	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000710	10226	PLIN3	http://www.ncbi.nlm.nih.gov/gene/?term=10226	"M6PRBP1, PP17, TIP47 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000711	10226	PLIN3	http://www.ncbi.nlm.nih.gov/gene/?term=10226	"M6PRBP1, PP17, TIP47 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000712	10227	MFSD10	http://www.ncbi.nlm.nih.gov/gene/?term=10227	"TETRAN, TETTRAN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000713	10227	MFSD10	http://www.ncbi.nlm.nih.gov/gene/?term=10227	"TETRAN, TETTRAN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000714	10228	STX6	http://www.ncbi.nlm.nih.gov/gene/?term=10228		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000715	10228	STX6	http://www.ncbi.nlm.nih.gov/gene/?term=10228		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000716	10229	COQ7	http://www.ncbi.nlm.nih.gov/gene/?term=10229	"CAT5, CLK-1, CLK1, COQ10D8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000717	10229	COQ7	http://www.ncbi.nlm.nih.gov/gene/?term=10229	"CAT5, CLK-1, CLK1, COQ10D8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000718	10229	COQ7	http://www.ncbi.nlm.nih.gov/gene/?term=10229	"CAT5, CLK-1, CLK1, COQ10D8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000719	1022	CDK7	http://www.ncbi.nlm.nih.gov/gene/?term=1022	"CAK1, CDKN7, HCAK, MO15, STK1, p39MO15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000720	10230	NBR2	http://www.ncbi.nlm.nih.gov/gene/?term=10230	NCRNA00192	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000721	102334	Ankrd10	http://www.ncbi.nlm.nih.gov/gene/?term=102334	"4833425P12Rik, AW549277 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000722	10233	LRRC23	http://www.ncbi.nlm.nih.gov/gene/?term=10233	LRPB7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000723	10234	LRRC17	http://www.ncbi.nlm.nih.gov/gene/?term=10234	P37NB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000724	10236	HNRNPR	http://www.ncbi.nlm.nih.gov/gene/?term=10236	"HNRPR, hnRNP-R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000725	10236	HNRNPR	http://www.ncbi.nlm.nih.gov/gene/?term=10236	"HNRPR, hnRNP-R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000726	10237	SLC35B1	http://www.ncbi.nlm.nih.gov/gene/?term=10237	UGTREL1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000727	10237	SLC35B1	http://www.ncbi.nlm.nih.gov/gene/?term=10237	UGTREL1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000728	10237	SLC35B1	http://www.ncbi.nlm.nih.gov/gene/?term=10237	UGTREL1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000729	10238	DCAF7	http://www.ncbi.nlm.nih.gov/gene/?term=10238	"AN11, HAN11, SWAN-1, WDR68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000730	10238	DCAF7	http://www.ncbi.nlm.nih.gov/gene/?term=10238	"AN11, HAN11, SWAN-1, WDR68 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000731	10238	DCAF7	http://www.ncbi.nlm.nih.gov/gene/?term=10238	"AN11, HAN11, SWAN-1, WDR68 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000732	10238	DCAF7	http://www.ncbi.nlm.nih.gov/gene/?term=10238	"AN11, HAN11, SWAN-1, WDR68 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000733	102392528	IGF1	http://www.ncbi.nlm.nih.gov/gene/?term=102392528	IGF-1	mRNA	Bubalus bubalis	25304995	Cytoplasm	Endothelial cell	RT-PCR	"A relatively high mRNA expression of IGF-I and IGF-II in early, mid- and late luteal phases with immunoreactivity mostly restricted to cytoplasm of large luteal cells indicates their autocrine role, whereas very weak immunoreactivity in endothelial cells during the mid-luteal phase indicates their paracrine role. "
RLID00000734	102395378	IGF2	http://www.ncbi.nlm.nih.gov/gene/?term=102395378	IGF-II	mRNA	Bubalus bubalis	25304995	Cytoplasm	Endothelial cell	RT-PCR	"A relatively high mRNA expression of IGF-I and IGF-II in early, mid- and late luteal phases with immunoreactivity mostly restricted to cytoplasm of large luteal cells indicates their autocrine role, whereas very weak immunoreactivity in endothelial cells during the mid-luteal phase indicates their paracrine role. "
RLID00000735	10239	AP3S2	http://www.ncbi.nlm.nih.gov/gene/?term=10239	"AP3S3, sigma3b "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000736	10239	AP3S2	http://www.ncbi.nlm.nih.gov/gene/?term=10239	"AP3S3, sigma3b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000737	10239	AP3S2	http://www.ncbi.nlm.nih.gov/gene/?term=10239	"AP3S3, sigma3b "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000738	10239	AP3S2	http://www.ncbi.nlm.nih.gov/gene/?term=10239	"AP3S3, sigma3b "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000739	102402	AA414992	http://www.ncbi.nlm.nih.gov/gene/?term=102402		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000740	10241	CALCOCO2	http://www.ncbi.nlm.nih.gov/gene/?term=10241	NDP52	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000741	10244	RABEPK	http://www.ncbi.nlm.nih.gov/gene/?term=10244	"RAB9P40, bA65N13.1, p40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000742	10244	RABEPK	http://www.ncbi.nlm.nih.gov/gene/?term=10244	"RAB9P40, bA65N13.1, p40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000743	10244	RABEPK	http://www.ncbi.nlm.nih.gov/gene/?term=10244	"RAB9P40, bA65N13.1, p40 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000744	10245	TIMM17B	http://www.ncbi.nlm.nih.gov/gene/?term=10245	"DXS9822, JM3, TIM17B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000745	10245	TIMM17B	http://www.ncbi.nlm.nih.gov/gene/?term=10245	"DXS9822, JM3, TIM17B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000746	10247	RIDA	http://www.ncbi.nlm.nih.gov/gene/?term=10247	"HRSP12, P14.5, PSP, UK114 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000747	10247	RIDA	http://www.ncbi.nlm.nih.gov/gene/?term=10247	"HRSP12, P14.5, PSP, UK114 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000748	10247	RIDA	http://www.ncbi.nlm.nih.gov/gene/?term=10247	"HRSP12, P14.5, PSP, UK114 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000749	10248	POP7	http://www.ncbi.nlm.nih.gov/gene/?term=10248	"0610037N12Rik, RPP2, RPP20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000750	10248	POP7	http://www.ncbi.nlm.nih.gov/gene/?term=10248	"0610037N12Rik, RPP2, RPP20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000751	1024	CDK8	http://www.ncbi.nlm.nih.gov/gene/?term=1024	K35	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000752	10250	SRRM1	http://www.ncbi.nlm.nih.gov/gene/?term=10250	"160-KD, POP101, SRM160 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000753	10253	SPRY2	http://www.ncbi.nlm.nih.gov/gene/?term=10253	"IGAN3, hSPRY2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000754	10253	SPRY2	http://www.ncbi.nlm.nih.gov/gene/?term=10253	"IGAN3, hSPRY2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000755	10254	STAM2	http://www.ncbi.nlm.nih.gov/gene/?term=10254	"Hbp, STAM2A, STAM2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000756	10254	STAM2	http://www.ncbi.nlm.nih.gov/gene/?term=10254	"HbpA, STAM2B, STAM2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000757	10254	STAM2	http://www.ncbi.nlm.nih.gov/gene/?term=10254	"HbpA, STAM2B, STAM2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000758	10256	CNKSR1	http://www.ncbi.nlm.nih.gov/gene/?term=10256	"CNK, CNK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000759	102577426	LOC102577426	http://www.ncbi.nlm.nih.gov/gene/?term=102577426		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000760	10257	ABCC4	http://www.ncbi.nlm.nih.gov/gene/?term=10257	"MOAT-B, MOATB, MRP4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000761	102596	AI842136	http://www.ncbi.nlm.nih.gov/gene/?term=102596		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000762	1025	CDK9	http://www.ncbi.nlm.nih.gov/gene/?term=1025	"C-2k, CDC2L4, CTK1, PITALRE, TAK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000763	1025	CDK9	http://www.ncbi.nlm.nih.gov/gene/?term=1025	"TAK, C-2k, CTK1, CDC2L4, PITALRE "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00000764	1025	CDK9	http://www.ncbi.nlm.nih.gov/gene/?term=1025	"C-2k, CDC2L4, CTK1, PITALRE, TAK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000765	1025	CDK9	http://www.ncbi.nlm.nih.gov/gene/?term=1025	"C-2k, CDC2L4, CTK1, PITALRE, TAK "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00000766	102606465	LOC102606465	http://www.ncbi.nlm.nih.gov/gene/?term=102606465		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000767	102607	Snx19	http://www.ncbi.nlm.nih.gov/gene/?term=102607	"3526401K03Rik, AI195321, AI848208, mKIAA0254 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000768	10260	DENND4A	http://www.ncbi.nlm.nih.gov/gene/?term=10260	"IRLB, MYCPBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000769	102614	Rpp25	http://www.ncbi.nlm.nih.gov/gene/?term=102614	AI851155	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000770	10262	SF3B4	http://www.ncbi.nlm.nih.gov/gene/?term=10262	"AFD1, Hsh49, SAP49, SF3b49 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000771	102631772	Gm30025	http://www.ncbi.nlm.nih.gov/gene/?term=102631772		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000772	102631810	Gm30052	http://www.ncbi.nlm.nih.gov/gene/?term=102631810		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000773	102631915	Gm30127	http://www.ncbi.nlm.nih.gov/gene/?term=102631915		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000774	102632457	Gm30524	http://www.ncbi.nlm.nih.gov/gene/?term=102632457		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000775	102632462	Gm30529	http://www.ncbi.nlm.nih.gov/gene/?term=102632462		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000776	102632567	Gm30606	http://www.ncbi.nlm.nih.gov/gene/?term=102632567		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000777	102632947	Gm15731	http://www.ncbi.nlm.nih.gov/gene/?term=102632947	OTTMUSG00000025798	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000778	102632	Acad11	http://www.ncbi.nlm.nih.gov/gene/?term=102632	"5730439E10Rik, AI987948 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000779	102633271	Gm31135	http://www.ncbi.nlm.nih.gov/gene/?term=102633271		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000780	102633311	Gm31169	http://www.ncbi.nlm.nih.gov/gene/?term=102633311		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000781	102633563	Gm31359	http://www.ncbi.nlm.nih.gov/gene/?term=102633563		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000782	102633666	LOC102633666	http://www.ncbi.nlm.nih.gov/gene/?term=102633666		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000783	102633824	Gm13261	http://www.ncbi.nlm.nih.gov/gene/?term=102633824	OTTMUSG00000011193	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000784	102634034	Gm31718	http://www.ncbi.nlm.nih.gov/gene/?term=102634034		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000785	102634543	Gm29128	http://www.ncbi.nlm.nih.gov/gene/?term=102634543		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000786	102634550	Gm27166	http://www.ncbi.nlm.nih.gov/gene/?term=102634550		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000787	102634913	Gm16070	http://www.ncbi.nlm.nih.gov/gene/?term=102634913	OTTMUSG00000029756	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000788	102635567	Gm32865	http://www.ncbi.nlm.nih.gov/gene/?term=102635567		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000789	102635787	Gm33035	http://www.ncbi.nlm.nih.gov/gene/?term=102635787		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000790	102635935	Gm12320	http://www.ncbi.nlm.nih.gov/gene/?term=102635935	OTTMUSG00000006074	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000791	102636202	Gm33337	http://www.ncbi.nlm.nih.gov/gene/?term=102636202		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000792	102636638	Gm13799	http://www.ncbi.nlm.nih.gov/gene/?term=102636638	OTTMUSG00000014516	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000793	102636700	LOC102636700	http://www.ncbi.nlm.nih.gov/gene/?term=102636700		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000794	102638129	Gm11587	http://www.ncbi.nlm.nih.gov/gene/?term=102638129	OTTMUSG00000002370	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000795	102638153	Gm34785	http://www.ncbi.nlm.nih.gov/gene/?term=102638153		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000796	102638523	Gm35066	http://www.ncbi.nlm.nih.gov/gene/?term=102638523		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000797	102638742	Gm35234	http://www.ncbi.nlm.nih.gov/gene/?term=102638742		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000798	102639053	Gm16222	http://www.ncbi.nlm.nih.gov/gene/?term=102639053	OTTMUSG00000031874	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000799	102639404	Gm26839	http://www.ncbi.nlm.nih.gov/gene/?term=102639404		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000800	102639566	Ptgs2os2	http://www.ncbi.nlm.nih.gov/gene/?term=102639566	"Gm26687, Linc-cox2, Lincrna-cox2 "	lncRNA	Mus musculus	23907535	Cytosol	Dendritic cell	qRT-PCR	hnRNP-A/B and hnRNP-A2/B1 were identified as specific binding partners for lincRNA-Cox2 in both the nuclear and cytosolic fractions.
RLID00000801	102639566	Ptgs2os2	http://www.ncbi.nlm.nih.gov/gene/?term=102639566	"Gm26687, Linc-cox2, Lincrna-cox2 "	lncRNA	Mus musculus	23907535	Nucleus	Dendritic cell	qRT-PCR	hnRNP-A/B and hnRNP-A2/B1 were identified as specific binding partners for lincRNA-Cox2 in both the nuclear and cytosolic fractions.
RLID00000802	102639608	Gm16725	http://www.ncbi.nlm.nih.gov/gene/?term=102639608		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000803	10263	CDK2AP2	http://www.ncbi.nlm.nih.gov/gene/?term=10263	"DOC-1R, p14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000804	10263	CDK2AP2	http://www.ncbi.nlm.nih.gov/gene/?term=10263	"DOC-1R, p14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000805	102640287	Gm36394	http://www.ncbi.nlm.nih.gov/gene/?term=102640287		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000806	102640338	Gm26782	http://www.ncbi.nlm.nih.gov/gene/?term=102640338		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000807	102640479	Gm36529	http://www.ncbi.nlm.nih.gov/gene/?term=102640479		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000808	102640577	Gm28515	http://www.ncbi.nlm.nih.gov/gene/?term=102640577		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000809	102640765	Gm36757	http://www.ncbi.nlm.nih.gov/gene/?term=102640765		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000810	102640816	Gm36794	http://www.ncbi.nlm.nih.gov/gene/?term=102640816		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000811	102640900	Gm28231	http://www.ncbi.nlm.nih.gov/gene/?term=102640900		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000812	102641805	LOC102641805	http://www.ncbi.nlm.nih.gov/gene/?term=102641805		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000813	102642321	Gm38604	http://www.ncbi.nlm.nih.gov/gene/?term=102642321		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000814	102642641	LOC102642641	http://www.ncbi.nlm.nih.gov/gene/?term=102642641		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000815	102657	Cd276	http://www.ncbi.nlm.nih.gov/gene/?term=102657	"6030411F23Rik, AU016588, B7RP-2, B7h3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000816	10267	RAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=10267		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000817	10267	RAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=10267		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000818	10269	ZMPSTE24	http://www.ncbi.nlm.nih.gov/gene/?term=10269	"FACE-1, FACE1, HGPS, PRO1, STE24, Ste24p "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000819	10269	ZMPSTE24	http://www.ncbi.nlm.nih.gov/gene/?term=10269	"FACE-1, FACE1, HGPS, PRO1, STE24, Ste24p "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000820	10269	ZMPSTE24	http://www.ncbi.nlm.nih.gov/gene/?term=10269	"FACE-1, FACE1, HGPS, PRO1, STE24, Ste24p "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000821	1026	CDKN1A	http://www.ncbi.nlm.nih.gov/gene/?term=1026	"CAP20, CDKN1, CIP1, MDA-6, P21, SDI1, WAF1, p21CIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000822	1026	CDKN1A	http://www.ncbi.nlm.nih.gov/gene/?term=1026	"CAP20, CDKN1, CIP1, MDA-6, P21, SDI1, WAF1, p21CIP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000823	1026	CDKN1A	http://www.ncbi.nlm.nih.gov/gene/?term=1026	"CAP20, CDKN1, CIP1, MDA-6, P21, SDI1, WAF1, p21CIP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000824	10270	AKAP8	http://www.ncbi.nlm.nih.gov/gene/?term=10270	"AKAP 95, AKAP-8, AKAP-95, AKAP95 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000825	102724473	GAGE10	http://www.ncbi.nlm.nih.gov/gene/?term=102724473	GAGE-10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000826	102725100	LOC102725100	http://www.ncbi.nlm.nih.gov/gene/?term=102725100		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000827	10272	FSTL3	http://www.ncbi.nlm.nih.gov/gene/?term=10272	"FLRG, FSRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000828	10273	STUB1	http://www.ncbi.nlm.nih.gov/gene/?term=10273	"CHIP, HSPABP2, NY-CO-7, SCAR16, SDCCAG7, UBOX1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000829	10273	STUB1	http://www.ncbi.nlm.nih.gov/gene/?term=10273	"CHIP, HSPABP2, NY-CO-7, SCAR16, SDCCAG7, UBOX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000830	10273	STUB1	http://www.ncbi.nlm.nih.gov/gene/?term=10273	"CHIP, HSPABP2, NY-CO-7, SCAR16, SDCCAG7, UBOX1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000831	10274	STAG1	http://www.ncbi.nlm.nih.gov/gene/?term=10274	"SA1, SCC3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000832	10274	STAG1	http://www.ncbi.nlm.nih.gov/gene/?term=10274	"SA1, SCC3A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000833	10276	NET1	http://www.ncbi.nlm.nih.gov/gene/?term=10276	"ARHGEF8, NET1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000834	10276	NET1	http://www.ncbi.nlm.nih.gov/gene/?term=10276	"ARHGEF8A, NET1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000835	10276	NET1	http://www.ncbi.nlm.nih.gov/gene/?term=10276	"ARHGEF8A, NET1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000836	102774	Bbs4	http://www.ncbi.nlm.nih.gov/gene/?term=102774	"AW537059, AW742241, D9Ertd464e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000837	10277	UBE4B	http://www.ncbi.nlm.nih.gov/gene/?term=10277	"E4, HDNB1, UBOX3, UFD2, UFD2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000838	10277	UBE4B	http://www.ncbi.nlm.nih.gov/gene/?term=10277	"E4, HDNB1, UBOX3, UFD2, UFD2A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000839	10277	UBE4B	http://www.ncbi.nlm.nih.gov/gene/?term=10277	"E4, HDNB1, UBOX3, UFD2, UFD2A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000840	10279	PRSS16	http://www.ncbi.nlm.nih.gov/gene/?term=10279	TSSP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000841	10279	PRSS16	http://www.ncbi.nlm.nih.gov/gene/?term=10279	TSSP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000842	1027	CDKN1B	http://www.ncbi.nlm.nih.gov/gene/?term=1027	"CDKN4, KIP1, MEN1B, MEN4, P27KIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000843	1027	CDKN1B	http://www.ncbi.nlm.nih.gov/gene/?term=1027	"CDKN4, KIP1, MEN1B, MEN4, P27KIP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000844	1027	CDKN1B	http://www.ncbi.nlm.nih.gov/gene/?term=1027	"CDKN4, KIP1, MEN1B, MEN4, P27KIP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000845	102800311	TP53COR1	http://www.ncbi.nlm.nih.gov/gene/?term=102800311	"TRP53COR1, linc-p21, lincRNA-p21 "	lncRNA	Homo sapiens	20673990	Nucleus	Lung tumor cell	qRT-PCR	"To test this, we first performed nuclear fractionation experiments and confirmed that lincRNA-p21 is enriched in the nucleus (Figure S5A).  "
RLID00000846	102800311	TP53COR1	http://www.ncbi.nlm.nih.gov/gene/?term=102800311	"TRP53COR1, linc-p21, lincRNA-p21 "	lncRNA	Homo sapiens	22841487	Cytoplasm	HeLa cell	qRT-PCR	LincRNA-p21 was moderately more abundant in the cytoplasm than in the nucleus of fractionated HeLa cells and its levels increased proportionately after silencing HuR (Fig. 2A).
RLID00000847	102800311	TP53COR1	http://www.ncbi.nlm.nih.gov/gene/?term=102800311	"TRP53COR1, linc-p21, lincRNA-p21 "	lncRNA	Homo sapiens	22841487	Nucleus	HeLa cell	qRT-PCR	LincRNA-p21 was moderately more abundant in the cytoplasm than in the nucleus of fractionated HeLa cells and its levels increased proportionately after silencing HuR (Fig. 2A).
RLID00000848	10280	SIGMAR1	http://www.ncbi.nlm.nih.gov/gene/?term=10280	"ALS16, DSMA2, OPRS1, SIG-1R, SR-BP, SR-BP1, SRBP, hSigmaR1, sigma1R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000849	10280	SIGMAR1	http://www.ncbi.nlm.nih.gov/gene/?term=10280	"ALS16, DSMA2, OPRS1, SIG-1R, SR-BP, SR-BP1, SRBP, hSigmaR1, sigma1R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000850	10281	DSCR4	http://www.ncbi.nlm.nih.gov/gene/?term=10281	"DCRB, DSCRB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000851	10282	BET1	http://www.ncbi.nlm.nih.gov/gene/?term=10282	HBET1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000852	10282	BET1	http://www.ncbi.nlm.nih.gov/gene/?term=10282	HBET1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000853	10282	BET1	http://www.ncbi.nlm.nih.gov/gene/?term=10282	HBET1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000854	10284	SAP18	http://www.ncbi.nlm.nih.gov/gene/?term=10284	"2HOR0202, SAP18P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000855	10284	SAP18	http://www.ncbi.nlm.nih.gov/gene/?term=10284	"2HOR0202P, SAP18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000856	10285	SMNDC1	http://www.ncbi.nlm.nih.gov/gene/?term=10285	"SMNR, SPF30, TDRD16C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000857	10285	SMNDC1	http://www.ncbi.nlm.nih.gov/gene/?term=10285	"SMNR, SPF30, TDRD16C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000858	10286	BCAS2	http://www.ncbi.nlm.nih.gov/gene/?term=10286	"DAM1, SPF27, Snt309 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000859	10289	EIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=10289	GC20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000860	10289	EIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=10289	GC20	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000861	1028	CDKN1C	http://www.ncbi.nlm.nih.gov/gene/?term=1028	"BWCR, BWS, KIP2, WBS, p57, p57Kip2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000862	10291	SF3A1	http://www.ncbi.nlm.nih.gov/gene/?term=10291	"PRP21, PRPF21, SAP114, SF3A120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000863	10291	SF3A1	http://www.ncbi.nlm.nih.gov/gene/?term=10291	"PRP21, PRPF21, SAP11420, SF3A1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000864	10293	TRAIP	http://www.ncbi.nlm.nih.gov/gene/?term=10293	"RNF206, SCKL9, TRIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000865	10293	TRAIP	http://www.ncbi.nlm.nih.gov/gene/?term=10293	"RNF206, SCKL9, TRIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000866	10294	DNAJA2	http://www.ncbi.nlm.nih.gov/gene/?term=10294	"CPR3, DJ3, DJA2, DNAJ, DNJ3, HIRIP4, PRO3015, RDJ2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000867	10294	DNAJA2	http://www.ncbi.nlm.nih.gov/gene/?term=10294	"CPR3, DJ3, DJA2, DNAJ, DNJ3, HIRIP4, PRO3015, RDJ2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000868	10295	BCKDK	http://www.ncbi.nlm.nih.gov/gene/?term=10295	"BCKDKD, BDK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000869	10296	MAEA	http://www.ncbi.nlm.nih.gov/gene/?term=10296	"EMLP, EMP, GID9, HLC-10, PIG5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000870	10296	MAEA	http://www.ncbi.nlm.nih.gov/gene/?term=10296	"EMLP, EMP, GID9, HLC-10, PIG5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000871	10296	MAEA	http://www.ncbi.nlm.nih.gov/gene/?term=10296	"EMLP, EMP, GID9, HLC-10, PIG5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000872	10298	PAK4	http://www.ncbi.nlm.nih.gov/gene/?term=10298		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000873	10299	MARCH6	http://www.ncbi.nlm.nih.gov/gene/?term=10299	"DOA10, MARCH-VI, RNF176, TEB4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000874	1029	CDKN2A	http://www.ncbi.nlm.nih.gov/gene/?term=1029	"ARF, CDK4I, CDKN2, CMM2, INK4, INK4A, MLM, MTS-1, MTS1, P14, P14ARF, P16, P16-INK4A, P16INK4, P16INK4A, P19, P19ARF, TP16 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000875	1029	CDKN2A	http://www.ncbi.nlm.nih.gov/gene/?term=1029	"ARF, CDK4I, CDKN2, CMM2, INK4, INK4A, MLM, MTS-1, MTS1, P14, P14ARF, P16, P16-INK4A, P16INK4, P16INK4A, P19, P19ARF, TP16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000876	102	ADAM10	http://www.ncbi.nlm.nih.gov/gene/?term=102	"AD10, AD18, CD156c, HsT18717, MADM, RAK, kuz "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000877	102	ADAM10	http://www.ncbi.nlm.nih.gov/gene/?term=102	"AD10, AD18, CD156c, CDw156, HsT18717, MADM, RAK, kuz "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000878	10300	KATNB1	http://www.ncbi.nlm.nih.gov/gene/?term=10300	"KAT, LIS6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000879	10300	KATNB1	http://www.ncbi.nlm.nih.gov/gene/?term=10300	"KAT, LIS6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000880	10300	KATNB1	http://www.ncbi.nlm.nih.gov/gene/?term=10300	"KAT, LIS6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000881	103012	Firre	http://www.ncbi.nlm.nih.gov/gene/?term=103012	"5830467J12Rik, 6720401G13Rik, AW048145 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000882	103012	Firre	http://www.ncbi.nlm.nih.gov/gene/?term=103012	"5830467J12Rik, 6720401G13Rik, AW048145 "	lncRNA	Mus musculus	25887447	Nucleolus	Embryo	Fluorescence in situ hybridization	The X-linked lncRNA Firre helps to position the inactive X chromosome near the nucleolus and to preserve one of its main epigenetic features. The Firre locus on the Xi but not the Xa (active X) was found to be located adjacent to the nucleolus. 
RLID00000883	10301	DLEU1	http://www.ncbi.nlm.nih.gov/gene/?term=10301	"BCMS, BCMS1, DLB1, DLEU2, LEU1, LEU2, LINC00021, NCRNA00021, XTP6 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000884	10302	SNAPC5	http://www.ncbi.nlm.nih.gov/gene/?term=10302	SNAP19	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000885	10302	SNAPC5	http://www.ncbi.nlm.nih.gov/gene/?term=10302	SNAP19	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000886	10307	APBB3	http://www.ncbi.nlm.nih.gov/gene/?term=10307	"FE65L2, SRA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000887	103080	Sept10	http://www.ncbi.nlm.nih.gov/gene/?term=103080	"4921515A04Rik, 9430099J10Rik, AA408298, AI874685 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000888	103098	Slc6a15	http://www.ncbi.nlm.nih.gov/gene/?term=103098	"AA536730, AI326450, AI326451, v7-3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000889	10309	CCNO	http://www.ncbi.nlm.nih.gov/gene/?term=10309	"CCNU, CILD29, UDG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000890	10311	DSCR3	http://www.ncbi.nlm.nih.gov/gene/?term=10311	"DCRA, DSCRA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000891	10311	DSCR3	http://www.ncbi.nlm.nih.gov/gene/?term=10311	"DCRA, DSCRA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000892	10311	DSCR3	http://www.ncbi.nlm.nih.gov/gene/?term=10311	"DCRA, DSCRA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000893	10312	TCIRG1	http://www.ncbi.nlm.nih.gov/gene/?term=10312	"ATP6N1C, ATP6V0A3, Atp6i, OC-116kDa, OC116, OPTB1, Stv1, TIRC7, Vph1, a3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000894	103135	Pan2	http://www.ncbi.nlm.nih.gov/gene/?term=103135	"1200014O24Rik, AI047843, AW742773, Usp52, mKIAA0710 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000895	10313	RTN3	http://www.ncbi.nlm.nih.gov/gene/?term=10313	"ASYIP, HAP, NSPL2, NSPLII, RTN3-A1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000896	10313	RTN3	http://www.ncbi.nlm.nih.gov/gene/?term=10313	"ASYIP, HAP, NSPL2, NSPLII-A1, RTN3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000897	10313	RTN3	http://www.ncbi.nlm.nih.gov/gene/?term=10313	"ASYIP, HAP, NSPL2, NSPLII-A1, RTN3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000898	10314	LANCL1	http://www.ncbi.nlm.nih.gov/gene/?term=10314	"GPR69A, p40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000899	10314	LANCL1	http://www.ncbi.nlm.nih.gov/gene/?term=10314	"GPR69A, p40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000900	10314	LANCL1	http://www.ncbi.nlm.nih.gov/gene/?term=10314	"GPR69A, p40 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000901	10318	TNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10318	"ABIN-1, NAF1, VAN, nip40-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000902	1031	CDKN2C	http://www.ncbi.nlm.nih.gov/gene/?term=1031	"INK4C, p18, p18-INK4C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000903	1031	CDKN2C	http://www.ncbi.nlm.nih.gov/gene/?term=1031	"INK4C, p18, p18-INK4C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000904	1031	CDKN2C	http://www.ncbi.nlm.nih.gov/gene/?term=1031	"INK4C, p18, p18-INK4C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000905	10320	IKZF1	http://www.ncbi.nlm.nih.gov/gene/?term=10320	"Hs.54452, IK1, IKAROS, LYF1, LyF-1, PPP1R92, PRO0758, ZNFN1A1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000906	10321	CRISP3	http://www.ncbi.nlm.nih.gov/gene/?term=10321	"Aeg2, CRISP-3, CRS3, SGP28, dJ442L6.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000907	10322	SMYD5	http://www.ncbi.nlm.nih.gov/gene/?term=10322	"NN8-4AG, RAI15, RRG1, ZMYND23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000908	103236	Csnk1g2	http://www.ncbi.nlm.nih.gov/gene/?term=103236	"2810429I12Rik, AI463719 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000909	10325	RRAGB	http://www.ncbi.nlm.nih.gov/gene/?term=10325	"RAGB, bA465E19.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000910	10327	AKR1A1	http://www.ncbi.nlm.nih.gov/gene/?term=10327	"ALDR1, ALR, ARM, DD3, HEL-S-6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000911	10328	EMC8	http://www.ncbi.nlm.nih.gov/gene/?term=10328	"C16orf2, C16orf4, COX4NB, FAM158B, NOC4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000912	10328	EMC8	http://www.ncbi.nlm.nih.gov/gene/?term=10328	"C16orf2, C16orf4, COX4NB, FAM158B, NOC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000913	10328	EMC8	http://www.ncbi.nlm.nih.gov/gene/?term=10328	"C16orf2, C16orf4, COX4NB, FAM158B, NOC4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000914	10329	TMEM5	http://www.ncbi.nlm.nih.gov/gene/?term=10329	"HP10481, MDDGA10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000915	10329	TMEM5	http://www.ncbi.nlm.nih.gov/gene/?term=10329	"HP10481, MDDGA10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000916	10329	TMEM5	http://www.ncbi.nlm.nih.gov/gene/?term=10329	"HP10481, MDDGA10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000917	1032	CDKN2D	http://www.ncbi.nlm.nih.gov/gene/?term=1032	"INK4D, p19, p19-INK4D "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000918	10330	CNPY2	http://www.ncbi.nlm.nih.gov/gene/?term=10330	"HP10390, MSAP, TMEM4, ZSIG9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000919	10330	CNPY2	http://www.ncbi.nlm.nih.gov/gene/?term=10330	"HP10390, MSAP, TMEM4, ZSIG9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000920	10331	B3GNT3	http://www.ncbi.nlm.nih.gov/gene/?term=10331	"B3GAL-T8, B3GN-T3, B3GNT-3, HP10328, TMEM3, beta3Gn-T3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000921	10335	MRVI1	http://www.ncbi.nlm.nih.gov/gene/?term=10335	"IRAG, JAW1L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000922	10335	MRVI1	http://www.ncbi.nlm.nih.gov/gene/?term=10335	"IRAG, JAW1L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000923	10336	PCGF3	http://www.ncbi.nlm.nih.gov/gene/?term=10336	"DONG1, RNF3, RNF3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000924	1033	CDKN3	http://www.ncbi.nlm.nih.gov/gene/?term=1033	"CDI1, CIP2, KAP, KAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000925	1033	CDKN3	http://www.ncbi.nlm.nih.gov/gene/?term=1033	"CDI1, CIP2, KAP, KAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000926	1033	CDKN3	http://www.ncbi.nlm.nih.gov/gene/?term=1033	"CDI1, CIP2, KAP, KAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000927	10342	TFG	http://www.ncbi.nlm.nih.gov/gene/?term=10342	"HMSNP, SPG57, TF6, TRKT3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000928	10342	TFG	http://www.ncbi.nlm.nih.gov/gene/?term=10342	"HMSNP, SPG57, TF6, TRKT3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000929	10342	TFG	http://www.ncbi.nlm.nih.gov/gene/?term=10342	"HMSNP, SPG57, TF6, TRKT3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000930	10345	TRDN	http://www.ncbi.nlm.nih.gov/gene/?term=10345	"CPVT5, TDN, TRISK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000931	103468	Nup107	http://www.ncbi.nlm.nih.gov/gene/?term=103468	"AW541137, C76801 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000932	10346	TRIM22	http://www.ncbi.nlm.nih.gov/gene/?term=10346	"GPSTAF50, RNF94, STAF50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000933	10347	ABCA7	http://www.ncbi.nlm.nih.gov/gene/?term=10347	"ABCA-SSN, ABCX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000934	10347	ABCA7	http://www.ncbi.nlm.nih.gov/gene/?term=10347	"ABCA-SSN, ABCX "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00000935	10347	ABCA7	http://www.ncbi.nlm.nih.gov/gene/?term=10347	"ABCA-SSN, ABCX "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000936	103504742	MT-LIPCAR	http://www.ncbi.nlm.nih.gov/gene/?term=103504742	"LIPCAR, uc022bqs.1 "	lncRNA	Homo sapiens	24663402	Mitochondrion	Heart	Microarray	The mitochondrial long noncoding RNA uc022bqs.1 (LIPCAR) was downregulated early after myocardial infarction but upregulated during later stages.
RLID00000937	103514	BB165335	http://www.ncbi.nlm.nih.gov/gene/?term=103514		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000938	10351	ABCA8	http://www.ncbi.nlm.nih.gov/gene/?term=10351		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000939	10352	WARS2	http://www.ncbi.nlm.nih.gov/gene/?term=10352	TrpRS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000940	103551	E130012A19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=103551	"AA409164, AI413509, AW539173, E13, esPRC2p48 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000941	103554	Psme4	http://www.ncbi.nlm.nih.gov/gene/?term=103554	"AA409398, AU041366, TEMO, mKIAA0077 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000942	103573	Xpo1	http://www.ncbi.nlm.nih.gov/gene/?term=103573	"AA420417, Crm1, Exp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000943	103583	Fbxw11	http://www.ncbi.nlm.nih.gov/gene/?term=103583	"2310065A07Rik, AA536858, BTRC2, BTRCP2, Fbxw1b, HOS "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000944	10360	NPM3	http://www.ncbi.nlm.nih.gov/gene/?term=10360	"PORMIN, TMEM123 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000945	103625684	RNU6-2	http://www.ncbi.nlm.nih.gov/gene/?term=103625684	U6-2	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000946	10362	HMG20B	http://www.ncbi.nlm.nih.gov/gene/?term=10362	"BRAF25, BRAF35, HMGX2, HMGXB2, PP7706, SMARCE1r, SOXL, pp8857 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000947	10362	HMG20B	http://www.ncbi.nlm.nih.gov/gene/?term=10362	"BRAF25, BRAF35, HMGX2, HMGXB2, PP7706, SMARCE1r, SOXL, pp8857 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000948	10363	HMG20A	http://www.ncbi.nlm.nih.gov/gene/?term=10363	"HMGX1, HMGXB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000949	10365	KLF2	http://www.ncbi.nlm.nih.gov/gene/?term=10365	LKLF	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000950	10367	MICU1	http://www.ncbi.nlm.nih.gov/gene/?term=10367	"CALC, CBARA1, EFHA3, MPXPS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000951	10367	MICU1	http://www.ncbi.nlm.nih.gov/gene/?term=10367	"CALC, CBARA1, EFHA3, MPXPS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000952	10370	CITED2	http://www.ncbi.nlm.nih.gov/gene/?term=10370	"ASD8, MRG-1, MRG1, P35SRJ, VSD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000953	10370	CITED2	http://www.ncbi.nlm.nih.gov/gene/?term=10370	"ASD8, MRG-1, MRG1, P35SRJ, VSD2 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00000954	103711	Pnpo	http://www.ncbi.nlm.nih.gov/gene/?term=103711	AI415282	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000955	10371	SEMA3A	http://www.ncbi.nlm.nih.gov/gene/?term=10371	"COLL1, HH16, Hsema-I, Hsema-III, SEMA1, SEMAD, SEMAIII, SEMAL, SemD, coll-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000956	10371	SEMA3A	http://www.ncbi.nlm.nih.gov/gene/?term=10371	"COLL1, HH16, Hsema-I, Hsema-III, SEMA1, SEMAD, SEMAIII, SEMAL, SemD, coll-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000957	103724	Tbc1d10a	http://www.ncbi.nlm.nih.gov/gene/?term=103724	"AI447804, EPI64, Tbc1d10, mFLJ00288 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000958	103742	Mien1	http://www.ncbi.nlm.nih.gov/gene/?term=103742	"1810046J19Rik, AI463380, Rdx12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000959	10376	TUBA1B	http://www.ncbi.nlm.nih.gov/gene/?term=10376	K-ALPHA-1	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000960	10376	TUBA1B	http://www.ncbi.nlm.nih.gov/gene/?term=10376	K-ALPHA-1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000961	103784	Wdr92	http://www.ncbi.nlm.nih.gov/gene/?term=103784	"AI553587, HZGJ "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000962	10379	IRF9	http://www.ncbi.nlm.nih.gov/gene/?term=10379	"IRF-9, ISGF3, ISGF3G, p48 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000963	10380	BPNT1	http://www.ncbi.nlm.nih.gov/gene/?term=10380	"HEL20, PIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000964	10380	BPNT1	http://www.ncbi.nlm.nih.gov/gene/?term=10380	"HEL20, PIP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000965	10380	BPNT1	http://www.ncbi.nlm.nih.gov/gene/?term=10380	"HEL20, PIP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000966	103836	Zfp692	http://www.ncbi.nlm.nih.gov/gene/?term=103836	"AI746306, AI839920-ps, Znf692, Zfp692 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000967	10383	TUBB4B	http://www.ncbi.nlm.nih.gov/gene/?term=10383	"Beta2, TUBB2, TUBB2C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000968	10383	TUBB4B	http://www.ncbi.nlm.nih.gov/gene/?term=10383	"Beta2, TUBB2, TUBB2C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000969	10384	BTN3A3	http://www.ncbi.nlm.nih.gov/gene/?term=10384	"BTF3, BTN3.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000970	103850	Nt5m	http://www.ncbi.nlm.nih.gov/gene/?term=103850	"2010013E09Rik, AI846937, dNT-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000971	10385	BTN2A2	http://www.ncbi.nlm.nih.gov/gene/?term=10385	"BT2.2, BTF2, BTN2.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000972	10389	SCML2	http://www.ncbi.nlm.nih.gov/gene/?term=10389		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000973	10389	SCML2	http://www.ncbi.nlm.nih.gov/gene/?term=10389		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00000974	10390	CEPT1	http://www.ncbi.nlm.nih.gov/gene/?term=10390		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000975	10390	CEPT1	http://www.ncbi.nlm.nih.gov/gene/?term=10390		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000976	103910	MYL12B	http://www.ncbi.nlm.nih.gov/gene/?term=103910	"MLC-B, MRLC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000977	103910	MYL12B	http://www.ncbi.nlm.nih.gov/gene/?term=103910	"MLC-B, MRLC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000978	10393	ANAPC10	http://www.ncbi.nlm.nih.gov/gene/?term=10393	"APC10, DOC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000979	10395	DLC1	http://www.ncbi.nlm.nih.gov/gene/?term=10395	"ARHGAP7, HP, STARD12, p122-RhoGAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000980	10395	DLC1	http://www.ncbi.nlm.nih.gov/gene/?term=10395	"ARHGAP7, HP, STARD12, p122-RhoGAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000981	103963	Rpn1	http://www.ncbi.nlm.nih.gov/gene/?term=103963	"AU018702, D6Wsu137e, Rpn-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000982	10396	ATP8A1	http://www.ncbi.nlm.nih.gov/gene/?term=10396	"ATPASEII, ATPIA, ATPP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000983	10397	NDRG1	http://www.ncbi.nlm.nih.gov/gene/?term=10397	"CAP43, CMT4D, DRG-1, DRG1, GC4, HMSNL, NDR1, NMSL, PROXY1, RIT42, RTP, TARG1, TDD5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000984	10397	NDRG1	http://www.ncbi.nlm.nih.gov/gene/?term=10397	"CAP43, CMT4D, DRG-1, DRG1, GC4, HMSNL, NDR1, NMSL, PROXY1, RIT42, RTP, TARG1, TDD5 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00000985	10398	MYL9	http://www.ncbi.nlm.nih.gov/gene/?term=10398	"LC20, MLC-2C, MLC2, MRLC1, MYRL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000986	10399	RACK1	http://www.ncbi.nlm.nih.gov/gene/?term=10399	"GNB2L1, Gnb2-rs1, H12.3, HLC-7, PIG21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000987	10399	RACK1	http://www.ncbi.nlm.nih.gov/gene/?term=10399	"GNB2L1, Gnb2-rs1, H12.3, HLC-7, PIG21 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000988	10399	RACK1	http://www.ncbi.nlm.nih.gov/gene/?term=10399	"GNB2L1, Gnb2-rs1, H12.3, HLC-7, PIG21 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000989	1039	CDR2	http://www.ncbi.nlm.nih.gov/gene/?term=1039	"CDR62, Yo "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000990	1039	CDR2	http://www.ncbi.nlm.nih.gov/gene/?term=1039	"CDR62, Yo "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000991	1039	CDR2	http://www.ncbi.nlm.nih.gov/gene/?term=1039	"CDR62, Yo "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000992	103	ADAR	http://www.ncbi.nlm.nih.gov/gene/?term=103	"ADAR1, AGS6, DRADA, DSH, DSRAD, G1P1, IFI-4, IFI4, K88DSRBP, P136 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000993	103	ADAR	http://www.ncbi.nlm.nih.gov/gene/?term=103	"ADAR1, AGS6, DRADA, DSH, DSRAD, G1P1, IFI-4, IFI4, K88DSRBP, P136 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000994	103	ADAR	http://www.ncbi.nlm.nih.gov/gene/?term=103	"ADAR1, AGS6, DRADA, DSH, DSRAD, G1P1, IFI-4, IFI4, K88DSRBP, P136 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00000995	10400	PEMT	http://www.ncbi.nlm.nih.gov/gene/?term=10400	"PEAMT, PEMPT, PEMT2, PNMT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00000996	10400	PEMT	http://www.ncbi.nlm.nih.gov/gene/?term=10400	"PEAMT, PEMPT2, PNMT, PEMT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00000997	104010	Cdh22	http://www.ncbi.nlm.nih.gov/gene/?term=104010		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00000998	104015	Synj1	http://www.ncbi.nlm.nih.gov/gene/?term=104015	"A930006D20Rik, AA675315, mKIAA0910 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00000999	10402	ST3GAL6	http://www.ncbi.nlm.nih.gov/gene/?term=10402	"SIAT10, ST3GALVI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001000	10403	NDC80	http://www.ncbi.nlm.nih.gov/gene/?term=10403	"HEC, HEC1, HsHec1, KNTC2, TID3, hsNDC80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001001	10404	CPQ	http://www.ncbi.nlm.nih.gov/gene/?term=10404	"LDP, PGCP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001002	10406	WFDC2	http://www.ncbi.nlm.nih.gov/gene/?term=10406	"EDDM4, HE4, WAP5, dJ461P17.6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001003	1040	CDS1	http://www.ncbi.nlm.nih.gov/gene/?term=1040	CDS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001004	1040	CDS1	http://www.ncbi.nlm.nih.gov/gene/?term=1040	CDS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001005	1040	CDS1	http://www.ncbi.nlm.nih.gov/gene/?term=1040	CDS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001006	104103	Airn	http://www.ncbi.nlm.nih.gov/gene/?term=104103	"2810051F02Rik, 2810434M15Rik, AI256653, AI597500, AW049873, Air, B930018I07Rik, D17Ertd663e, IGF2RAS "	lncRNA	Mus musculus	16874305	Cytoplasm	Fibroblast	qRT-PCR|Northern blot	All Air splice variants are also exported with a similar efficiency as Igf2r (Figure 6D). This indicates that spliced Air in contrast to the majority of unspliced Air can be exported to the cytoplasm.
RLID00001007	104103	Airn	http://www.ncbi.nlm.nih.gov/gene/?term=104103	"2810051F02Rik, 2810434M15Rik, AI256653, AI597500, AW049873, Air, B930018I07Rik, D17Ertd663e, IGF2RAS "	lncRNA	Mus musculus	16874305	Nucleus	Fibroblast	qRT-PCR|Northern blot	"We show that Air is transcribed from a DNA methylation-sensitive promoter by RNA polymerase II (RNAPII). However, although it is capped and polyadenylated similar to other RNAPII transcripts, the majority of Air transcripts evade cotranscriptional splicing resulting in a mature 108 kb ncRNA. As a consequence, the mature unspliced Air is nuclear localized and highly unstable. "
RLID00001008	104103	Airn	http://www.ncbi.nlm.nih.gov/gene/?term=104103	"2810051F02Rik, 2810434M15Rik, AI256653, AI597500, AW049873, Air, B930018I07Rik, D17Ertd663e, IGF2RAS "	lncRNA	Mus musculus	18988810	Nucleus	Placenta	In situ hybridization	Air is largely unspliced and is retained in the nucleus. Air RNA FISH signals are considerably larger than primary transcript signals for protein-coding genes (Fig. 1A and fig. S2).
RLID00001009	104103	Airn	http://www.ncbi.nlm.nih.gov/gene/?term=104103	"2810051F02Rik, 2810434M15Rik, AI256653, AI597500, AW049873, Air, B930018I07Rik, D17Ertd663e, IGF2RAS "	lncRNA	Mus musculus	23239737	Nucleus	Placenta	In situ hybridization	"The nuclear size of the Airn lncRNA product correlates with silencing Slc22a3 in the placenta(9). We used RNA FISH to test whether Airn nuclear size or its subnuclear localization correlates with Igf2r silencing in embryonic cells. Both parameters showed no difference between T51, which silences Igf2r, and T16, which does not (Fig. 3A and fig. S7). "
RLID00001010	104103	Airn	http://www.ncbi.nlm.nih.gov/gene/?term=104103	"2810051F02Rik, 2810434M15Rik, AI256653, AI597500, AW049873, Air, B930018I07Rik, D17Ertd663e, IGF2RAS "	lncRNA	Mus musculus	23209567	Nucleus	Spleen	Next-generation sequencing|qRT-PCR	"Furthermore, we found the Air long non-coding RNA almost exclusively in the nuclear fraction in agreement with the finding that Air RNA is retained in the nucleus. "
RLID00001011	104103	Airn	http://www.ncbi.nlm.nih.gov/gene/?term=104103	"2810051F02Rik, 2810434M15Rik, AI256653, AI597500, AW049873, Air, B930018I07Rik, D17Ertd663e, IGF2RAS "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001012	10410	IFITM3	http://www.ncbi.nlm.nih.gov/gene/?term=10410	"1-8U, DSPA2b, IP15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001013	10412	NSA2	http://www.ncbi.nlm.nih.gov/gene/?term=10412	"CDK105, HCL-G1, HCLG1, HUSSY-29, HUSSY29, TINP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001014	10412	NSA2	http://www.ncbi.nlm.nih.gov/gene/?term=10412	"CDK105, HCL-G1, HCLG1, HUSSY-29, HUSSY29, TINP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001015	10413	YAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10413	"COB1, YAP, YAP2, YAP65, YKI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001016	104175	Sbk1	http://www.ncbi.nlm.nih.gov/gene/?term=104175	Sbk	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001017	104184	Blmh	http://www.ncbi.nlm.nih.gov/gene/?term=104184	"AI035728, Bh, Bmh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001018	10419	PRMT5	http://www.ncbi.nlm.nih.gov/gene/?term=10419	"HRMT1L5, IBP72, JBP1, SKB1, SKB1Hs "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001019	10419	PRMT5	http://www.ncbi.nlm.nih.gov/gene/?term=10419	"HRMT1L5, IBP72, JBP1, SKB1, SKB1Hs "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001020	10421	CD2BP2	http://www.ncbi.nlm.nih.gov/gene/?term=10421	"FWP010, LIN1, PPP1R59, Snu40, U5-52K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001021	10423	CDIPT	http://www.ncbi.nlm.nih.gov/gene/?term=10423	"PIS, PIS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001022	10423	CDIPT	http://www.ncbi.nlm.nih.gov/gene/?term=10423	"PIS, PIS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001023	10423	CDIPT	http://www.ncbi.nlm.nih.gov/gene/?term=10423	"PIS, PIS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001024	10424	PGRMC2	http://www.ncbi.nlm.nih.gov/gene/?term=10424	"DG6, PMBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001025	104252	Cdc42ep2	http://www.ncbi.nlm.nih.gov/gene/?term=104252	"1110008C05Rik, Borg1, Cep2, D19Bwg1013e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001026	10425	ARIH2	http://www.ncbi.nlm.nih.gov/gene/?term=10425	"ARI2, TRIAD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001027	10425	ARIH2	http://www.ncbi.nlm.nih.gov/gene/?term=10425	"ARI2, TRIAD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001028	104263	Kdm3a	http://www.ncbi.nlm.nih.gov/gene/?term=104263	"1700105C21Rik, C230043E16Rik, JHDM2a, Jmjd1, Jmjd1a, KDM2A, TGSA, Tsga "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001029	10426	TUBGCP3	http://www.ncbi.nlm.nih.gov/gene/?term=10426	"104p, GCP3, Grip104, SPBC98, Spc98, Spc98p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001030	10426	TUBGCP3	http://www.ncbi.nlm.nih.gov/gene/?term=10426	"104p, GCP3, Grip104, SPBC98, Spc98, Spc98p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001031	10426	TUBGCP3	http://www.ncbi.nlm.nih.gov/gene/?term=10426	"104p, GCP3, Grip104, SPBC98, Spc98, Spc98p "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001032	10426	TUBGCP3	http://www.ncbi.nlm.nih.gov/gene/?term=10426	"104p, GCP3, Grip104, SPBC98, Spc98, Spc98p "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001033	10426	TUBGCP3	http://www.ncbi.nlm.nih.gov/gene/?term=10426	"104p, GCP3, Grip104, SPBC98, Spc98, Spc98p "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001034	10427	SEC24B	http://www.ncbi.nlm.nih.gov/gene/?term=10427	SEC24	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001035	10428	CFDP1	http://www.ncbi.nlm.nih.gov/gene/?term=10428	"BCNT, BUCENTAUR, CENP-29, CP27, SWC5, Yeti, p97 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001036	10428	CFDP1	http://www.ncbi.nlm.nih.gov/gene/?term=10428	"BCNT, BUCENTAUR, CENP-29, CP27, SWC5, Yeti, p97 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001037	10430	TMEM147	http://www.ncbi.nlm.nih.gov/gene/?term=10430	NIFIE14	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001038	10430	TMEM147	http://www.ncbi.nlm.nih.gov/gene/?term=10430	NIFIE14	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001039	10432	RBM14	http://www.ncbi.nlm.nih.gov/gene/?term=10432	"COAA, PSP2, SIP, SYTIP1, TMEM137 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001040	10432	RBM14	http://www.ncbi.nlm.nih.gov/gene/?term=10432	"COAA, PSP2, SIP, SYTIP1, TMEM137 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001041	10432	RBM14	http://www.ncbi.nlm.nih.gov/gene/?term=10432	"COAA, PSP2, SIP, SYTIP1, TMEM137 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001042	104355148	CYP4A22-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=104355148	ncRNA-a3	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/cyp4a22-as1/
RLID00001043	104355148	CYP4A22-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=104355148	ncRNA-a3	lncRNA	Homo sapiens	22955988	Nucleus	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00001044	10435	CDC42EP2	http://www.ncbi.nlm.nih.gov/gene/?term=10435	"BORG1, CEP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001045	104362	Meig1	http://www.ncbi.nlm.nih.gov/gene/?term=104362	"MLZ-278, Meg1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001046	10436	EMG1	http://www.ncbi.nlm.nih.gov/gene/?term=10436	"C2F, Grcc2f, NEP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001047	10437	IFI30	http://www.ncbi.nlm.nih.gov/gene/?term=10437	"GILT, IFI-30, IP-30, IP30 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001048	104382	Barhl2	http://www.ncbi.nlm.nih.gov/gene/?term=104382	"E130309B19Rik, MBH1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001049	10438	C1D	http://www.ncbi.nlm.nih.gov/gene/?term=10438	"LRP1, Rrp47, SUN-CoR, SUNCOR, hC1D "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001050	10439	OLFM1	http://www.ncbi.nlm.nih.gov/gene/?term=10439	"AMY, NOE1, NOELIN1, OlfA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001051	10440	TIMM17A	http://www.ncbi.nlm.nih.gov/gene/?term=10440	"TIM17, TIM17A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001052	10440	TIMM17A	http://www.ncbi.nlm.nih.gov/gene/?term=10440	"TIM17, TIM17A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001053	10443	N4BP2L2	http://www.ncbi.nlm.nih.gov/gene/?term=10443	"92M18.3, CG005, PFAAP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001054	10443	N4BP2L2	http://www.ncbi.nlm.nih.gov/gene/?term=10443	"92M18.3, CG005, CG016, PFAAP5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001055	104445	Cdc42ep1	http://www.ncbi.nlm.nih.gov/gene/?term=104445	"1810058K22Rik, AA980734, Borg5, CEP1, MSE55 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001056	10444	ZER1	http://www.ncbi.nlm.nih.gov/gene/?term=10444	"C9orf60, ZYG, ZYG11BL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001057	10444	ZER1	http://www.ncbi.nlm.nih.gov/gene/?term=10444	"C9orf60, ZYG, ZYG11BL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001058	104457	0610010K14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=104457	"1110020A23Rik, AL033328, AU045833, Bap18 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001059	104458	Rars	http://www.ncbi.nlm.nih.gov/gene/?term=104458	"2610011N19Rik, 2610037E21Rik, AL033339, AW985894 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001060	10445	MCRS1	http://www.ncbi.nlm.nih.gov/gene/?term=10445	"ICP22BP, INO80Q, MCRS2, MSP58, P78 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001061	10445	MCRS1	http://www.ncbi.nlm.nih.gov/gene/?term=10445	"ICP22BP, INO80Q, MCRS2, MSP58, P78 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001062	10445	MCRS1	http://www.ncbi.nlm.nih.gov/gene/?term=10445	"ICP22BP, INO80Q, MCRS2, MSP58, P78 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001063	104472717	LINC01224	http://www.ncbi.nlm.nih.gov/gene/?term=104472717		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001064	104479	Ccdc117	http://www.ncbi.nlm.nih.gov/gene/?term=104479	"1110004K02Rik, 1700026O03Rik, AU018638, AU042822, AV173073, BC018601 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001065	10447	FAM3C	http://www.ncbi.nlm.nih.gov/gene/?term=10447	"GS3786, ILEI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001066	10447	FAM3C	http://www.ncbi.nlm.nih.gov/gene/?term=10447	"GS3786, ILEI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001067	10449	ACAA2	http://www.ncbi.nlm.nih.gov/gene/?term=10449	DSAEC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001068	1044	CDX1	http://www.ncbi.nlm.nih.gov/gene/?term=1044		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001069	10450	PPIE	http://www.ncbi.nlm.nih.gov/gene/?term=10450	"CYP-33, CYP33 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001070	10451	VAV3	http://www.ncbi.nlm.nih.gov/gene/?term=10451		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001071	10452	TOMM40	http://www.ncbi.nlm.nih.gov/gene/?term=10452	"C19orf1, D19S1177E, PER-EC1, PEREC1, TOM40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001072	10452	TOMM40	http://www.ncbi.nlm.nih.gov/gene/?term=10452	"C19orf1, D19S1177E, PER-EC1, PEREC1, TOM40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001073	10454	TAB1	http://www.ncbi.nlm.nih.gov/gene/?term=10454	"3'-Tab1, MAP3K7IP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001074	10454	TAB1	http://www.ncbi.nlm.nih.gov/gene/?term=10454	"3'-Tab1, MAP3K7IP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001075	10455	ECI2	http://www.ncbi.nlm.nih.gov/gene/?term=10455	"ACBD2, DRS-1, DRS1, HCA88, PECI, dJ1013A10.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001076	10456	HAX1	http://www.ncbi.nlm.nih.gov/gene/?term=10456	"HCLSBP1, HS1BP1, SCN3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001077	10456	HAX1	http://www.ncbi.nlm.nih.gov/gene/?term=10456	"HCLSBP1, HS1BP1, SCN3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001078	104570	Smek2	http://www.ncbi.nlm.nih.gov/gene/?term=104570	"AW011752, AW557776, Ppp4r3b, mKIAA1387 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001079	10457	GPNMB	http://www.ncbi.nlm.nih.gov/gene/?term=10457	"HGFIN, NMB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001080	10458	BAIAP2	http://www.ncbi.nlm.nih.gov/gene/?term=10458	"BAP2, FLAF3, IRSP53 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001081	10459	MAD2L2	http://www.ncbi.nlm.nih.gov/gene/?term=10459	"MAD2B, POLZ2, REV7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001082	1045	CDX2	http://www.ncbi.nlm.nih.gov/gene/?term=1045	"CDX-3, CDX2/AS, CDX3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001083	1045	CDX2	http://www.ncbi.nlm.nih.gov/gene/?term=1045	"CDX-3/AS, CDX3, CDX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001084	10460	TACC3	http://www.ncbi.nlm.nih.gov/gene/?term=10460	"ERIC-1, ERIC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001085	10460	TACC3	http://www.ncbi.nlm.nih.gov/gene/?term=10460	"ERIC-1, ERIC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001086	10460	TACC3	http://www.ncbi.nlm.nih.gov/gene/?term=10460	"ERIC-1, ERIC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001087	10461	MERTK	http://www.ncbi.nlm.nih.gov/gene/?term=10461	"MER, RP38, Tyro12, c-Eyk, c-mer "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001088	10461	MERTK	http://www.ncbi.nlm.nih.gov/gene/?term=10461	"MER, RP38, Tyro12, c-Eyk, c-mer "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001089	104625	Cnot6	http://www.ncbi.nlm.nih.gov/gene/?term=104625	CCR4	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001090	10463	SLC30A9	http://www.ncbi.nlm.nih.gov/gene/?term=10463	"C4orf1, GAC63, HUEL, ZNT9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001091	10463	SLC30A9	http://www.ncbi.nlm.nih.gov/gene/?term=10463	"C4orf1, GAC63, HUEL, ZNT9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001092	10465	PPIH	http://www.ncbi.nlm.nih.gov/gene/?term=10465	"CYP-20, CYPH, SnuCyp-20, USA-CYP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001093	10465	PPIH	http://www.ncbi.nlm.nih.gov/gene/?term=10465	"CYP-20, CYPH, SnuCyp-20, USA-CYP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001094	10465	PPIH	http://www.ncbi.nlm.nih.gov/gene/?term=10465	"CYP-20, CYPH, SnuCyp-20, USA-CYP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001095	104662	Tsr1	http://www.ncbi.nlm.nih.gov/gene/?term=104662	"AU040765, AW550801, mKIAA1401 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001096	10467	ZNHIT1	http://www.ncbi.nlm.nih.gov/gene/?term=10467	"CG1I, ZNFN4A1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001097	10467	ZNHIT1	http://www.ncbi.nlm.nih.gov/gene/?term=10467	"CG1I, ZNFN4A1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001098	104681	Slc16a6	http://www.ncbi.nlm.nih.gov/gene/?term=104681	"AW743111, ESTM12, MCT 6, MCT 7, MCT6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001099	10469	TIMM44	http://www.ncbi.nlm.nih.gov/gene/?term=10469	TIM44	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001100	10471	PFDN6	http://www.ncbi.nlm.nih.gov/gene/?term=10471	"H2-KE2, HKE2, KE-2, PFD6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001101	10471	PFDN6	http://www.ncbi.nlm.nih.gov/gene/?term=10471	"H2-KE2, HKE2, KE-2, PFD6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001102	104721	Ddx1	http://www.ncbi.nlm.nih.gov/gene/?term=104721	"AA409185, DBP-RB "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001103	10472	ZBTB18	http://www.ncbi.nlm.nih.gov/gene/?term=10472	"C2H2-171, MRD22, RP58, TAZ-1, ZNF238 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001104	10473	HMGN4	http://www.ncbi.nlm.nih.gov/gene/?term=10473	"HMG17L3, NHC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001105	10473	HMGN4	http://www.ncbi.nlm.nih.gov/gene/?term=10473	"HMG17L3, NHC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001106	10474	TADA3	http://www.ncbi.nlm.nih.gov/gene/?term=10474	"ADA3, NGG1, STAF54, TADA3L, hADA3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001107	10474	TADA3	http://www.ncbi.nlm.nih.gov/gene/?term=10474	"ADA3, NGG1, STAF54L, hADA3, TADA3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001108	10474	TADA3	http://www.ncbi.nlm.nih.gov/gene/?term=10474	"ADA3, NGG1, STAF54L, hADA3, TADA3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001109	10475	TRIM38	http://www.ncbi.nlm.nih.gov/gene/?term=10475	"RNF15, RORET "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001110	10476	ATP5H	http://www.ncbi.nlm.nih.gov/gene/?term=10476	ATPQ	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001111	104771	Jkamp	http://www.ncbi.nlm.nih.gov/gene/?term=104771	"1200003C05Rik, 2310047L11Rik, Jamp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001112	104771	Jkamp	http://www.ncbi.nlm.nih.gov/gene/?term=104771	"1200003C05Rik, 2310047L11Rik, Jamp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001113	104776	Aldh6a1	http://www.ncbi.nlm.nih.gov/gene/?term=104776	"1110038I05Rik, Mmsdh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001114	10477	UBE2E3	http://www.ncbi.nlm.nih.gov/gene/?term=10477	"UBCH9, UbcM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001115	10477	UBE2E3	http://www.ncbi.nlm.nih.gov/gene/?term=10477	"UBCH9, UbcM2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001116	10477	UBE2E3	http://www.ncbi.nlm.nih.gov/gene/?term=10477	"UBCH9, UbcM2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001117	10478	SLC25A17	http://www.ncbi.nlm.nih.gov/gene/?term=10478	PMP34	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001118	10478	SLC25A17	http://www.ncbi.nlm.nih.gov/gene/?term=10478	PMP34	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001119	104799	Vipas39	http://www.ncbi.nlm.nih.gov/gene/?term=104799	"6720456H09Rik, 9330175H22Rik, AI413782, SPE-39, Spe39, Vipar, hSPE-39 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001120	10479	SLC9A6	http://www.ncbi.nlm.nih.gov/gene/?term=10479	"MRSA, NHE6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001121	10479	SLC9A6	http://www.ncbi.nlm.nih.gov/gene/?term=10479	"MRSA, NHE6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001122	10479	SLC9A6	http://www.ncbi.nlm.nih.gov/gene/?term=10479	"MRSA, NHE6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001123	1047	CLGN	http://www.ncbi.nlm.nih.gov/gene/?term=1047		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001124	1047	CLGN	http://www.ncbi.nlm.nih.gov/gene/?term=1047		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001125	104806	Fancm	http://www.ncbi.nlm.nih.gov/gene/?term=104806	"AI427100, C730036B14Rik, D12Ertd364e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001126	10480	EIF3M	http://www.ncbi.nlm.nih.gov/gene/?term=10480	"B5, GA17, PCID1, TANGO7, hfl-B5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001127	10480	EIF3M	http://www.ncbi.nlm.nih.gov/gene/?term=10480	"B5, GA17, PCID1, TANGO7, hfl-B5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001128	10480	EIF3M	http://www.ncbi.nlm.nih.gov/gene/?term=10480	"B5, GA17, PCID1, TANGO7, hfl-B5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001129	10481	HOXB13	http://www.ncbi.nlm.nih.gov/gene/?term=10481	PSGD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001130	10482	NXF1	http://www.ncbi.nlm.nih.gov/gene/?term=10482	"MEX67, TAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001131	10482	NXF1	http://www.ncbi.nlm.nih.gov/gene/?term=10482	"MEX67, TAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001132	104836	Cbll1	http://www.ncbi.nlm.nih.gov/gene/?term=104836	"AI467391, Hakai, c-Cbl-like "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001133	10483	SEC23B	http://www.ncbi.nlm.nih.gov/gene/?term=10483	"CDA-II, CDAII, CDAN2, HEMPAS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001134	10483	SEC23B	http://www.ncbi.nlm.nih.gov/gene/?term=10483	"CDA-II, CDAII, CDAN2, CWS7, HEMPAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001135	10484	SEC23A	http://www.ncbi.nlm.nih.gov/gene/?term=10484	CLSD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001136	10484	SEC23A	http://www.ncbi.nlm.nih.gov/gene/?term=10484	CLSD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001137	10485	C1orf61	http://www.ncbi.nlm.nih.gov/gene/?term=10485	CROC4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001138	10487	CAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10487	"CAP-PEN, CAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001139	104885	Tmem179	http://www.ncbi.nlm.nih.gov/gene/?term=104885	AI839735	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001140	104886	Rab15	http://www.ncbi.nlm.nih.gov/gene/?term=104886	"2310012G06Rik, AI840042 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001141	10488	CREB3	http://www.ncbi.nlm.nih.gov/gene/?term=10488	"LUMAN, LZIP, sLZIP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001142	10488	CREB3	http://www.ncbi.nlm.nih.gov/gene/?term=10488	"LUMAN, LZIP, sLZIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001143	10488	CREB3	http://www.ncbi.nlm.nih.gov/gene/?term=10488	"LUMAN, LZIP, sLZIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001144	10489	LRRC41	http://www.ncbi.nlm.nih.gov/gene/?term=10489	"MUF1, PP7759 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001145	10489	LRRC41	http://www.ncbi.nlm.nih.gov/gene/?term=10489	"MUF1, PP7759 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001146	1048	CEACAM5	http://www.ncbi.nlm.nih.gov/gene/?term=1048	"CD66e, CEA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001147	10490	VTI1B	http://www.ncbi.nlm.nih.gov/gene/?term=10490	"VTI1, VTI1-LIKE, VTI1L, VTI2, v-SNARE, vti1-rp1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001148	10491	CRTAP	http://www.ncbi.nlm.nih.gov/gene/?term=10491	"CASP, LEPREL3, OI7, P3H5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001149	10491	CRTAP	http://www.ncbi.nlm.nih.gov/gene/?term=10491	"CASP, LEPREL3, OI7, P3H5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001150	10491	CRTAP	http://www.ncbi.nlm.nih.gov/gene/?term=10491	"CASP, LEPREL3, OI7, P3H5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001151	10492	SYNCRIP	http://www.ncbi.nlm.nih.gov/gene/?term=10492	"GRY-RBP, GRYRBP, HNRNPQ, HNRPQ1, NSAP1, PP68, hnRNP-Q "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001152	10492	SYNCRIP	http://www.ncbi.nlm.nih.gov/gene/?term=10492	"GRY-RBP, GRYRBP, HNRNPQ, HNRPQ1, NSAP1, PP68, hnRNP-Q "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001153	10492	SYNCRIP	http://www.ncbi.nlm.nih.gov/gene/?term=10492	"GRY-RBP, GRYRBP, HNRNPQ, HNRPQ1, NSAP1, PP68, hnRNP-Q "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001154	10493	VAT1	http://www.ncbi.nlm.nih.gov/gene/?term=10493	VATI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001155	10493	VAT1	http://www.ncbi.nlm.nih.gov/gene/?term=10493	VATI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001156	10495	ENOX2	http://www.ncbi.nlm.nih.gov/gene/?term=10495	"APK1, COVA1, tNOX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001157	10495	ENOX2	http://www.ncbi.nlm.nih.gov/gene/?term=10495	"APK1, COVA1, tNOX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001158	10497	UNC13B	http://www.ncbi.nlm.nih.gov/gene/?term=10497	"MUNC13, UNC13, Unc13h2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001159	10497	UNC13B	http://www.ncbi.nlm.nih.gov/gene/?term=10497	"MUNC13, UNC13, Unc13h2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001160	10497	UNC13B	http://www.ncbi.nlm.nih.gov/gene/?term=10497	"MUNC13, UNC13, Unc13h2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001161	10498	CARM1	http://www.ncbi.nlm.nih.gov/gene/?term=10498	PRMT4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001162	10499	NCOA2	http://www.ncbi.nlm.nih.gov/gene/?term=10499	"GRIP1, KAT13C, NCoA-2, SRC2, TIF2, bHLHe75 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001163	104	ADARB1	http://www.ncbi.nlm.nih.gov/gene/?term=104	"ADAR2, DRABA2, DRADA2, RED1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001164	104	ADARB1	http://www.ncbi.nlm.nih.gov/gene/?term=104	"ADAR2, DRABA2, DRADA2, RED1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001165	105000	Dnal1	http://www.ncbi.nlm.nih.gov/gene/?term=105000	"1700010H15Rik, AW121714, Dnalc1, E330027P08Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001166	10500	SEMA6C	http://www.ncbi.nlm.nih.gov/gene/?term=10500	"SEMAY, m-SemaY, m-SemaY2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001167	10507	SEMA4D	http://www.ncbi.nlm.nih.gov/gene/?term=10507	"C9orf164, CD100, M-sema-G, SEMAJ, coll-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001168	10512	SEMA3C	http://www.ncbi.nlm.nih.gov/gene/?term=10512	"SEMAE, SemE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001169	10513	APPBP2	http://www.ncbi.nlm.nih.gov/gene/?term=10513	"APP-BP2, HS.84084, PAT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001170	10513	APPBP2	http://www.ncbi.nlm.nih.gov/gene/?term=10513	"APP-BP2, HS.84084, PAT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001171	10513	APPBP2	http://www.ncbi.nlm.nih.gov/gene/?term=10513	"APP-BP2, HS.84084, PAT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001172	10514	MYBBP1A	http://www.ncbi.nlm.nih.gov/gene/?term=10514	"P160, PAP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001173	10517	FBXW10	http://www.ncbi.nlm.nih.gov/gene/?term=10517	"Fbw10, HREP, SM25H2, SM2SH2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001174	10517	FBXW10	http://www.ncbi.nlm.nih.gov/gene/?term=10517	"Fbw10, HREP, SM25H2, SM2SH2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001175	10518	CIB2	http://www.ncbi.nlm.nih.gov/gene/?term=10518	"DFNB48, KIP2, USH1J "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001176	105193	Nhlrc1	http://www.ncbi.nlm.nih.gov/gene/?term=105193	"AI505271, B230309E09Rik, EPM2B "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001177	10519	CIB1	http://www.ncbi.nlm.nih.gov/gene/?term=10519	"CIB, CIBP, KIP1, PRKDCIP, SIP2-28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001178	10519	CIB1	http://www.ncbi.nlm.nih.gov/gene/?term=10519	"CIB, CIBP, KIP1, PRKDCIP, SIP2-28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001179	10519	CIB1	http://www.ncbi.nlm.nih.gov/gene/?term=10519	"CIB, CIBP, KIP1, PRKDCIP, SIP2-28 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001180	1051	CEBPB	http://www.ncbi.nlm.nih.gov/gene/?term=1051	"C/EBP-beta, IL6DBP, NF-IL6, TCF5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001181	105203	Fam208b	http://www.ncbi.nlm.nih.gov/gene/?term=105203	"AI645998, Pap20, mKIAA2006 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001182	10521	DDX17	http://www.ncbi.nlm.nih.gov/gene/?term=10521	"P72, RH70 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001183	10521	DDX17	http://www.ncbi.nlm.nih.gov/gene/?term=10521	"P72, RH70 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001184	10522	DEAF1	http://www.ncbi.nlm.nih.gov/gene/?term=10522	"MRD24, NUDR, SPN, ZMYND5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001185	10522	DEAF1	http://www.ncbi.nlm.nih.gov/gene/?term=10522	"MRD24, NUDR, SPN, ZMYND5 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001186	10523	CHERP	http://www.ncbi.nlm.nih.gov/gene/?term=10523	"DAN16, SCAF6, SRA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001187	105243045	Gm15774	http://www.ncbi.nlm.nih.gov/gene/?term=105243045	OTTMUSG00000026125	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001188	105243395	Gm39329	http://www.ncbi.nlm.nih.gov/gene/?term=105243395		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001189	105243704	Gm39526	http://www.ncbi.nlm.nih.gov/gene/?term=105243704		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001190	105243929	Gm39644	http://www.ncbi.nlm.nih.gov/gene/?term=105243929		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001191	105245179	Gm20513	http://www.ncbi.nlm.nih.gov/gene/?term=105245179		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001192	105245	Txndc5	http://www.ncbi.nlm.nih.gov/gene/?term=105245	"AL022641, ERp46, PC-TRP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001193	105246095	Gm26562	http://www.ncbi.nlm.nih.gov/gene/?term=105246095		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001194	105246278	B230354K17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=105246278		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001195	10524	KAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10524	"ESA1, HTATIP, HTATIP1, PLIP, TIP, TIP60, ZC2HC5, cPLA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001196	10524	KAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10524	"ESA1, HTATIP, HTATIP1, PLIP, TIP, TIP60, ZC2HC5, cPLA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001197	10525	HYOU1	http://www.ncbi.nlm.nih.gov/gene/?term=10525	"GRP-170, Grp170, HSP12A, ORP-150, ORP150 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001198	10526	IPO8	http://www.ncbi.nlm.nih.gov/gene/?term=10526	RANBP8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001199	10526	IPO8	http://www.ncbi.nlm.nih.gov/gene/?term=10526	RANBP8	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001200	10526	IPO8	http://www.ncbi.nlm.nih.gov/gene/?term=10526	RANBP8	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001201	105278	Cdk20	http://www.ncbi.nlm.nih.gov/gene/?term=105278	"4932702G04Rik, AU019450, AW558027, CDCH, Ccrk, PNQLARE, p42 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001202	10527	IPO7	http://www.ncbi.nlm.nih.gov/gene/?term=10527	"Imp7, RANBP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001203	10527	IPO7	http://www.ncbi.nlm.nih.gov/gene/?term=10527	"Imp7, RANBP7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001204	10527	IPO7	http://www.ncbi.nlm.nih.gov/gene/?term=10527	"Imp7, RANBP7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001205	10528	NOP56	http://www.ncbi.nlm.nih.gov/gene/?term=10528	"NOL5A, SCA36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001206	10528	NOP56	http://www.ncbi.nlm.nih.gov/gene/?term=10528	"NOL5A, SCA36 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001207	10529	NEBL	http://www.ncbi.nlm.nih.gov/gene/?term=10529	"LASP2, LNEBL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001208	1052	CEBPD	http://www.ncbi.nlm.nih.gov/gene/?term=1052	"C/EBP-delta, CELF, CRP3, NF-IL6-beta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001209	10531	PITRM1	http://www.ncbi.nlm.nih.gov/gene/?term=10531	"MP1, PreP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001210	10531	PITRM1	http://www.ncbi.nlm.nih.gov/gene/?term=10531	"MP1, PreP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001211	10533	ATG7	http://www.ncbi.nlm.nih.gov/gene/?term=10533	"APG7-LIKE, APG7L, GSA7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001212	105348	Golm1	http://www.ncbi.nlm.nih.gov/gene/?term=105348	"2310001L02Rik, AW125446, D030064E01Rik, GP73, Golph2, PSEC0257 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001213	10534	SSSCA1	http://www.ncbi.nlm.nih.gov/gene/?term=10534	p27	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001214	10534	SSSCA1	http://www.ncbi.nlm.nih.gov/gene/?term=10534	p27	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001215	105351	AW209491	http://www.ncbi.nlm.nih.gov/gene/?term=105351		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001216	10535	RNASEH2A	http://www.ncbi.nlm.nih.gov/gene/?term=10535	"AGS4, JUNB, RNASEHI, RNHIA, RNHL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001217	105370541	LOC105370541	http://www.ncbi.nlm.nih.gov/gene/?term=105370541		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00001218	105377	Slf1	http://www.ncbi.nlm.nih.gov/gene/?term=105377	"2700017A04Rik, AW545819, Ankrd32, Brctd1, Brctx, C730024G01Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001219	10539	GLRX3	http://www.ncbi.nlm.nih.gov/gene/?term=10539	"GLRX4, GRX3, GRX4, PICOT, TXNL2, TXNL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001220	10539	GLRX3	http://www.ncbi.nlm.nih.gov/gene/?term=10539	"GLRX4, GRX3, GRX4, PICOT, TXNL2, TXNL3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001221	10539	GLRX3	http://www.ncbi.nlm.nih.gov/gene/?term=10539	"GLRX4, GRX3, GRX4, PICOT, TXNL2, TXNL3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001222	10540	DCTN2	http://www.ncbi.nlm.nih.gov/gene/?term=10540	"DCTN50, DYNAMITIN, HEL-S-77, RBP50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001223	10540	DCTN2	http://www.ncbi.nlm.nih.gov/gene/?term=10540	"DCTN50, DYNAMITIN, HEL-S-77, RBP50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001224	10540	DCTN2	http://www.ncbi.nlm.nih.gov/gene/?term=10540	"DCTN50, DYNAMITIN, HEL-S-77, RBP50 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001225	10541	ANP32B	http://www.ncbi.nlm.nih.gov/gene/?term=10541	"APRIL, PHAPI2, SSP29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001226	10541	ANP32B	http://www.ncbi.nlm.nih.gov/gene/?term=10541	"APRIL, PHAPI2, SSP29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001227	10542	LAMTOR5	http://www.ncbi.nlm.nih.gov/gene/?term=10542	"HBXIP, XIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001228	105440	Kctd9	http://www.ncbi.nlm.nih.gov/gene/?term=105440		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001229	105445	Dock9	http://www.ncbi.nlm.nih.gov/gene/?term=105445	"AA959601, AW538057, B230309H04Rik, D14Wsu89e, Zizimin1, mKIAA1058 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001230	10544	PROCR	http://www.ncbi.nlm.nih.gov/gene/?term=10544	"CCCA, CCD41, EPCR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001231	10544	PROCR	http://www.ncbi.nlm.nih.gov/gene/?term=10544	"CCCA, CCD41, EPCR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001232	105463124	Borg	http://www.ncbi.nlm.nih.gov/gene/?term=105463124		lncRNA	Mus musculus	24732794	Nucleus	Breast cancer cell	RT-PCR|In situ hybridization	"As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei.  "
RLID00001233	10548	TM9SF1	http://www.ncbi.nlm.nih.gov/gene/?term=10548	"HMP70, MP70 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001234	10549	PRDX4	http://www.ncbi.nlm.nih.gov/gene/?term=10549	"AOE37-2, AOE372, HEL-S-97n, PRX-4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001235	10549	PRDX4	http://www.ncbi.nlm.nih.gov/gene/?term=10549	"AOE37-2, AOE372, HEL-S-97n, PRX-4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001236	10549	PRDX4	http://www.ncbi.nlm.nih.gov/gene/?term=10549	"AOE37-2, AOE372, HEL-S-97n, PRX-4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001237	1054	CEBPG	http://www.ncbi.nlm.nih.gov/gene/?term=1054	"GPE1BP, IG/EBP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001238	105501	Abhd4	http://www.ncbi.nlm.nih.gov/gene/?term=105501	"1110035H23Rik, AI429574, Abh4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001239	105504	Exoc5	http://www.ncbi.nlm.nih.gov/gene/?term=105504	"AI447711, AI448003, Gm76, PRO1912, SEC10, Sec10l1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001240	10550	ARL6IP5	http://www.ncbi.nlm.nih.gov/gene/?term=10550	"DERP11, GTRAP3-18, HSPC127, JWA, PRAF3, Yip6b, addicsin, hp22, jmx "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001241	10550	ARL6IP5	http://www.ncbi.nlm.nih.gov/gene/?term=10550	"DERP11, GTRAP3-18, HSPC127, JWA, PRAF3, Yip6b, addicsin, hp22, jmx "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001242	10551	AGR2	http://www.ncbi.nlm.nih.gov/gene/?term=10551	"AG2, GOB-4, HAG-2, HEL-S-116, PDIA17, XAG-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001243	10551	AGR2	http://www.ncbi.nlm.nih.gov/gene/?term=10551	"AG2, GOB-4, HAG-2, HEL-S-116, PDIA17, XAG-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001244	105522	Ankrd28	http://www.ncbi.nlm.nih.gov/gene/?term=105522	"AI465466, AI604979, E430019N21Rik, mKIAA0379 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001245	10552	ARPC1A	http://www.ncbi.nlm.nih.gov/gene/?term=10552	"Arc40, HEL-68, HEL-S-307, SOP2Hs, SOP2L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001246	10552	ARPC1A	http://www.ncbi.nlm.nih.gov/gene/?term=10552	"Arc40, HEL-68, HEL-S-307, SOP2Hs, SOP2L "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001247	10552	ARPC1A	http://www.ncbi.nlm.nih.gov/gene/?term=10552	"Arc40, HEL-68, HEL-S-307, SOP2Hs, SOP2L "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001248	10553	HTATIP2	http://www.ncbi.nlm.nih.gov/gene/?term=10553	"CC3, SDR44U1, TIP30 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001249	10554	AGPAT1	http://www.ncbi.nlm.nih.gov/gene/?term=10554	"1-AGPAT1, G15, LPAAT-alpha, LPAATA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001250	10554	AGPAT1	http://www.ncbi.nlm.nih.gov/gene/?term=10554	"1-AGPAT1, G15, LPAAT-alpha, LPAATA "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001251	105559	Mbnl2	http://www.ncbi.nlm.nih.gov/gene/?term=105559	"1110002M11Rik, AI047808, AI837313, AI849185, AL118326, MBLL, R75232, mKIAA4072 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001252	10555	AGPAT2	http://www.ncbi.nlm.nih.gov/gene/?term=10555	"1-AGPAT2, BSCL, BSCL1, LPAAB, LPAAT-beta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001253	10556	RPP30	http://www.ncbi.nlm.nih.gov/gene/?term=10556	TSG15	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001254	10556	RPP30	http://www.ncbi.nlm.nih.gov/gene/?term=10556	TSG15	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001255	10556	RPP30	http://www.ncbi.nlm.nih.gov/gene/?term=10556	TSG15	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001256	10556	RPP30	http://www.ncbi.nlm.nih.gov/gene/?term=10556	TSG15	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001257	10558	SPTLC1	http://www.ncbi.nlm.nih.gov/gene/?term=10558	"HSAN1, HSN1, LBC1, LCB1, SPT1, SPTI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001258	10558	SPTLC1	http://www.ncbi.nlm.nih.gov/gene/?term=10558	"HSAN1, HSN1, LBC1, LCB1, SPT1, SPTI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001259	10558	SPTLC1	http://www.ncbi.nlm.nih.gov/gene/?term=10558	"HSAN1, HSN1, LBC1, LCB1, SPT1, SPTI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001260	10559	SLC35A1	http://www.ncbi.nlm.nih.gov/gene/?term=10559	"CDG2F, CMPST, CST, hCST "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001261	10559	SLC35A1	http://www.ncbi.nlm.nih.gov/gene/?term=10559	"CDG2F, CMPST, CST, hCST "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001262	10560	SLC19A2	http://www.ncbi.nlm.nih.gov/gene/?term=10560	"TC1, THMD1, THT1, THTR1, TRMA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001263	10564	ARFGEF2	http://www.ncbi.nlm.nih.gov/gene/?term=10564	"BIG2, PVNH2, dJ1164I10.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001264	10564	ARFGEF2	http://www.ncbi.nlm.nih.gov/gene/?term=10564	"BIG2, PVNH2, dJ1164I10.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001265	105653	Phyhip	http://www.ncbi.nlm.nih.gov/gene/?term=105653	"AW049870, C630010D02Rik, Lnap1ip, PAHX-AP#1, PAHX-AP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001266	10565	ARFGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=10565	"ARFGEP1, BIG1, P200 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001267	10565	ARFGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=10565	"ARFGEP1, BIG1, P200 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001268	10566	AKAP3	http://www.ncbi.nlm.nih.gov/gene/?term=10566	"AKAP 110, AKAP110, CT82, FSP95, HEL159, PRKA3, SOB1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001269	10566	AKAP3	http://www.ncbi.nlm.nih.gov/gene/?term=10566	"AKAP 110, AKAP110, CT82, FSP95, HEL159, PRKA3, SOB1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001270	10567	RABAC1	http://www.ncbi.nlm.nih.gov/gene/?term=10567	"PRA1, PRAF1, YIP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001271	105689	Mycbp2	http://www.ncbi.nlm.nih.gov/gene/?term=105689	"AU023734, AW107953, AW546647, C130061D10Rik, Pam, Phr1, R75243 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001272	105689	Mycbp2	http://www.ncbi.nlm.nih.gov/gene/?term=105689	"AU023734, AW107953, AW546647, C130061D10Rik, Pam, Phr1, R75243 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001273	10569	SLU7	http://www.ncbi.nlm.nih.gov/gene/?term=10569	"9G8, hSlu7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001274	10569	SLU7	http://www.ncbi.nlm.nih.gov/gene/?term=10569	"9G8, hSlu7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001275	10570	DPYSL4	http://www.ncbi.nlm.nih.gov/gene/?term=10570	"CRMP3, DRP-4, ULIP4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001276	105722	Ano6	http://www.ncbi.nlm.nih.gov/gene/?term=105722	"2900059G15Rik, AA407480, AW554778, F730003B03Rik, Tmem16f "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001277	105727	Slc38a1	http://www.ncbi.nlm.nih.gov/gene/?term=105727	"AA408026, AA409865, AL022800, AU015942, NAT2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001278	105727	Slc38a1	http://www.ncbi.nlm.nih.gov/gene/?term=105727	"AA408026, AA409865, AL022800, AU015942, NAT2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001279	10572	SIVA1	http://www.ncbi.nlm.nih.gov/gene/?term=10572	"CD27BP, SIVA, Siva-1, Siva-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001280	10572	SIVA1	http://www.ncbi.nlm.nih.gov/gene/?term=10572	"CD27BP, SIVA, Siva-1, Siva-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001281	10572	SIVA1	http://www.ncbi.nlm.nih.gov/gene/?term=10572	"CD27BP, SIVA, Siva-1, Siva-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001282	10573	MRPL28	http://www.ncbi.nlm.nih.gov/gene/?term=10573	"MAAT1, p15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001283	10574	CCT7	http://www.ncbi.nlm.nih.gov/gene/?term=10574	"CCTETA, CCTH, NIP7-1, TCP1ETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001284	10574	CCT7	http://www.ncbi.nlm.nih.gov/gene/?term=10574	"CCTETA, CCTH, NIP7-1, TCP1ETA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001285	10574	CCT7	http://www.ncbi.nlm.nih.gov/gene/?term=10574	"CCTETA, CCTH, NIP7-1, TCP1ETA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001286	10575	CCT4	http://www.ncbi.nlm.nih.gov/gene/?term=10575	"CCT-DELTA, Cctd, SRB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001287	10575	CCT4	http://www.ncbi.nlm.nih.gov/gene/?term=10575	"CCT-DELTA, Cctd, SRB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001288	10575	CCT4	http://www.ncbi.nlm.nih.gov/gene/?term=10575	"CCT-DELTA, Cctd, SRB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001289	10576	CCT2	http://www.ncbi.nlm.nih.gov/gene/?term=10576	"99D8.1, CCT-beta, CCTB, HEL-S-100n, PRO1633, TCP-1-beta "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001290	10576	CCT2	http://www.ncbi.nlm.nih.gov/gene/?term=10576	"99D8.1, CCT-beta, CCTB, HEL-S-100n, PRO1633, TCP-1-beta "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001291	10577	NPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10577	"EDDM1, HE1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001292	10577	NPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10577	"EDDM1, HE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001293	10577	NPC2	http://www.ncbi.nlm.nih.gov/gene/?term=10577	"EDDM1, HE1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001294	10580	SORBS1	http://www.ncbi.nlm.nih.gov/gene/?term=10580	"CAP, FLAF2, R85FL, SH3D5, SH3P12, SORB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001295	10580	SORBS1	http://www.ncbi.nlm.nih.gov/gene/?term=10580	"CAP, FLAF2, R85FL, SH3D5, SH3P12, SORB1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001296	10580	SORBS1	http://www.ncbi.nlm.nih.gov/gene/?term=10580	"CAP, FLAF2, R85FL, SH3D5, SH3P12, SORB1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001297	10581	IFITM2	http://www.ncbi.nlm.nih.gov/gene/?term=10581	"1-8D, DSPA2c "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001298	10581	IFITM2	http://www.ncbi.nlm.nih.gov/gene/?term=10581	"1-8D, DSPA2c "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001299	105837	Mtbp	http://www.ncbi.nlm.nih.gov/gene/?term=105837	"AI429604, MDM2BP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001300	10585	POMT1	http://www.ncbi.nlm.nih.gov/gene/?term=10585	"LGMD2K, MDDGA1, MDDGB1, MDDGC1, RT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001301	10585	POMT1	http://www.ncbi.nlm.nih.gov/gene/?term=10585	"LGMD2K, MDDGA1, MDDGB1, MDDGC1, RT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001302	10587	TXNRD2	http://www.ncbi.nlm.nih.gov/gene/?term=10587	"SELZ, TR, TR-BETA, TR3, TRXR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001303	10589	DRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10589	NC2-alpha	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001304	10589	DRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10589	NC2-alpha	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001305	1058	CENPA	http://www.ncbi.nlm.nih.gov/gene/?term=1058	"CENP-A, CenH3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001306	10591	DNPH1	http://www.ncbi.nlm.nih.gov/gene/?term=10591	"C6orf108, RCL, dJ330M21.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001307	10591	DNPH1	http://www.ncbi.nlm.nih.gov/gene/?term=10591	"C6orf108, RCL, dJ330M21.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001308	10592	SMC2	http://www.ncbi.nlm.nih.gov/gene/?term=10592	"CAP-E, CAPE, SMC-2, SMC2L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001309	10592	SMC2	http://www.ncbi.nlm.nih.gov/gene/?term=10592	"CAP-E, CAPE, SMC-2L1, SMC2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001310	10592	SMC2	http://www.ncbi.nlm.nih.gov/gene/?term=10592	"CAP-E, CAPE, SMC-2L1, SMC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001311	10594	PRPF8	http://www.ncbi.nlm.nih.gov/gene/?term=10594	"HPRP8, PRP8, PRPC8, RP13, SNRNP220 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001312	10594	PRPF8	http://www.ncbi.nlm.nih.gov/gene/?term=10594	"HPRP8, PRP8, PRPC8, RP13, SNRNP220 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001313	10595	ERN2	http://www.ncbi.nlm.nih.gov/gene/?term=10595	"IRE1-BETA, IRE1b, IRE2p, hIRE2p "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001314	10595	ERN2	http://www.ncbi.nlm.nih.gov/gene/?term=10595	"IRE1-BETA, IRE1b, IRE2p, hIRE2p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001315	105968	AU021063	http://www.ncbi.nlm.nih.gov/gene/?term=105968		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001316	10598	AHSA1	http://www.ncbi.nlm.nih.gov/gene/?term=10598	"AHA1, C14orf3, hAha1, p38 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001317	1059	CENPB	http://www.ncbi.nlm.nih.gov/gene/?term=1059		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001318	1059	CENPB	http://www.ncbi.nlm.nih.gov/gene/?term=1059		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001319	10600	USP16	http://www.ncbi.nlm.nih.gov/gene/?term=10600	"UBP-M, UBPM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001320	10600	USP16	http://www.ncbi.nlm.nih.gov/gene/?term=10600	"UBP-M, UBPM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001321	10600	USP16	http://www.ncbi.nlm.nih.gov/gene/?term=10600	"UBP-M, UBPM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001322	106039	Gga1	http://www.ncbi.nlm.nih.gov/gene/?term=106039	"4930406E12Rik, AU016030, AW209092 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001323	10605	PAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10605		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001324	10605	PAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10605		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001325	106064	AW549877	http://www.ncbi.nlm.nih.gov/gene/?term=106064	AI195826	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001326	10606	PAICS	http://www.ncbi.nlm.nih.gov/gene/?term=10606	"ADE2, ADE2H1, AIRC, PAIS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001327	10606	PAICS	http://www.ncbi.nlm.nih.gov/gene/?term=10606	"ADE2, ADE2H1, AIRC, PAIS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001328	10606	PAICS	http://www.ncbi.nlm.nih.gov/gene/?term=10606	"ADE2, ADE2H1, AIRC, PAIS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001329	10606	PAICS	http://www.ncbi.nlm.nih.gov/gene/?term=10606	"ADE2, ADE2H1, AIRC, PAIS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001330	10607	TBL3	http://www.ncbi.nlm.nih.gov/gene/?term=10607	"SAZD, UTP13 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001331	10608	MXD4	http://www.ncbi.nlm.nih.gov/gene/?term=10608	"MAD4, MST149, MSTP149, bHLHc12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001332	10608	MXD4	http://www.ncbi.nlm.nih.gov/gene/?term=10608	"MAD4, MST149, MSTP149, bHLHc12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001333	10609	P3H4	http://www.ncbi.nlm.nih.gov/gene/?term=10609	"LEPREL4, NO55, NOL55, SC65 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001334	10609	P3H4	http://www.ncbi.nlm.nih.gov/gene/?term=10609	"LEPREL4, NO55, NOL55, SC65 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001335	1060	CENPC	http://www.ncbi.nlm.nih.gov/gene/?term=1060	"CENP-C, CENPC1, MIF2, hcp-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001336	10611	PDLIM5	http://www.ncbi.nlm.nih.gov/gene/?term=10611	"ENH, ENH1, L9, LIM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001337	10611	PDLIM5	http://www.ncbi.nlm.nih.gov/gene/?term=10611	"ENH, ENH1, L9, LIM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001338	10613	ERLIN1	http://www.ncbi.nlm.nih.gov/gene/?term=10613	"C10orf69, Erlin-1, KE04, KEO4, SPFH1, SPG62 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001339	106143	Cggbp1	http://www.ncbi.nlm.nih.gov/gene/?term=106143	"AA960172, AL023996, AW045841 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001340	106143	Cggbp1	http://www.ncbi.nlm.nih.gov/gene/?term=106143	"AA960172, AL023996, AW045841 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001341	10614	HEXIM1	http://www.ncbi.nlm.nih.gov/gene/?term=10614	"CLP1, EDG1, HIS1, MAQ1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001342	10614	HEXIM1	http://www.ncbi.nlm.nih.gov/gene/?term=10614	"CLP1, EDG1, HIS1, MAQ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001343	10615	SPAG5	http://www.ncbi.nlm.nih.gov/gene/?term=10615	"DEEPEST, MAP126, hMAP126 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001344	10616	RBCK1	http://www.ncbi.nlm.nih.gov/gene/?term=10616	"C20orf18, HOIL-1, HOIL1, PBMEI, PGBM1, RBCK2, RNF54, UBCE7IP3, XAP3, XAP4, ZRANB4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001345	10616	RBCK1	http://www.ncbi.nlm.nih.gov/gene/?term=10616	"C20orf18, HOIL-1, HOIL1, PBMEI, PGBM1, RBCK2, RNF54, UBCE7IP3, XAP3, XAP4, ZRANB4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001346	10617	STAMBP	http://www.ncbi.nlm.nih.gov/gene/?term=10617	"AMSH, MICCAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001347	10617	STAMBP	http://www.ncbi.nlm.nih.gov/gene/?term=10617	"AMSH, MICCAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001348	10618	TGOLN2	http://www.ncbi.nlm.nih.gov/gene/?term=10618	"TGN38, TGN46, TGN48, TGN51, TTGN2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001349	10618	TGOLN2	http://www.ncbi.nlm.nih.gov/gene/?term=10618	"TGN38, TGN46, TGN48, TGN51, TTGN2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001350	10618	TGOLN2	http://www.ncbi.nlm.nih.gov/gene/?term=10618	"TGN38, TGN46, TGN48, TGN51, TTGN2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001351	106205	Zc3h7a	http://www.ncbi.nlm.nih.gov/gene/?term=106205	"A430104C18Rik, AI447294, AW556219, HSPC055, Zc3h7, Zc3hdc7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001352	10621	POLR3F	http://www.ncbi.nlm.nih.gov/gene/?term=10621	"RPC39, RPC6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001353	10622	POLR3G	http://www.ncbi.nlm.nih.gov/gene/?term=10622	"RPC32, RPC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001354	10622	POLR3G	http://www.ncbi.nlm.nih.gov/gene/?term=10622	"RPC32, RPC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001355	10623	POLR3C	http://www.ncbi.nlm.nih.gov/gene/?term=10623	"RPC3, RPC62 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001356	10625	IVNS1ABP	http://www.ncbi.nlm.nih.gov/gene/?term=10625	"FLARA3, HSPC068, KLHL39, ND1, NS-1, NS1-BP, NS1BP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001357	10625	IVNS1ABP	http://www.ncbi.nlm.nih.gov/gene/?term=10625	"FLARA3, HSPC068, KLHL39, ND1, NS-1, NS1-BP, NS1BP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001358	10627	MYL12A	http://www.ncbi.nlm.nih.gov/gene/?term=10627	"HEL-S-24, MLC-2B, MLCB, MRCL3, MRLC3, MYL2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001359	10628	TXNIP	http://www.ncbi.nlm.nih.gov/gene/?term=10628	"EST01027, HHCPA78, THIF, VDUP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001360	10628	TXNIP	http://www.ncbi.nlm.nih.gov/gene/?term=10628	"EST01027, HHCPA78, THIF, VDUP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001361	10629	TAF6L	http://www.ncbi.nlm.nih.gov/gene/?term=10629	PAF65A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001362	1062	CENPE	http://www.ncbi.nlm.nih.gov/gene/?term=1062	"CENP-E, KIF10, MCPH13, PPP1R61 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001363	1062	CENPE	http://www.ncbi.nlm.nih.gov/gene/?term=1062	"CENP-E, KIF10, MCPH13, PPP1R61 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001364	1062	CENPE	http://www.ncbi.nlm.nih.gov/gene/?term=1062	"CENP-E, KIF10, MCPH13, PPP1R61 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001365	10630	PDPN	http://www.ncbi.nlm.nih.gov/gene/?term=10630	"AGGRUS, GP36, GP40, Gp38, HT1A-1, OTS8, PA2.26, T1A, T1A-2, T1A2, TI1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001366	10630	PDPN	http://www.ncbi.nlm.nih.gov/gene/?term=10630	"AGGRUS, GP36, GP40, Gp38, HT1A-1, OTS8, PA2.26, T1A, T1A-2, T1A2, TI1A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001367	10630	PDPN	http://www.ncbi.nlm.nih.gov/gene/?term=10630	"AGGRUS, GP36, GP40, Gp38, HT1A-1, OTS8, PA2.26, T1A, T1A-2, T1A2, TI1A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001368	10632	ATP5L	http://www.ncbi.nlm.nih.gov/gene/?term=10632	ATP5JG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001369	10634	GAS2L1	http://www.ncbi.nlm.nih.gov/gene/?term=10634	GAR22	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001370	10635	RAD51AP1	http://www.ncbi.nlm.nih.gov/gene/?term=10635	PIR51	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001371	1063	CENPF	http://www.ncbi.nlm.nih.gov/gene/?term=1063	"CENF, CILD31, PRO1779, STROMS, hcp-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001372	1063	CENPF	http://www.ncbi.nlm.nih.gov/gene/?term=1063	"CENF, CILD31, PRO1779, hcp-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001373	10640	EXOC5	http://www.ncbi.nlm.nih.gov/gene/?term=10640	"HSEC10, PRO1912, SEC10, SEC10L1, SEC10P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001374	10640	EXOC5	http://www.ncbi.nlm.nih.gov/gene/?term=10640	"HSEC10, PRO1912, SEC10, SEC10L1, SEC10P "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001375	10640	EXOC5	http://www.ncbi.nlm.nih.gov/gene/?term=10640	"HSEC10, PRO1912, SEC10, SEC10L1, SEC10P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001376	10642	IGF2BP1	http://www.ncbi.nlm.nih.gov/gene/?term=10642	"CRD-BP, CRDBP, IMP-1, IMP1, VICKZ1, ZBP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001377	10642	IGF2BP1	http://www.ncbi.nlm.nih.gov/gene/?term=10642	"CRD-BP, CRDBP, IMP-1, IMP1, VICKZ1, ZBP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001378	10645	CAMKK2	http://www.ncbi.nlm.nih.gov/gene/?term=10645	"CAMKK, CAMKKB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001379	10645	CAMKK2	http://www.ncbi.nlm.nih.gov/gene/?term=10645	"CAMKK, CAMKKB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001380	106504	Stk38	http://www.ncbi.nlm.nih.gov/gene/?term=106504	"5830476G13Rik, 9530097A09Rik, AA617404, Ndr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001381	10651	MTX2	http://www.ncbi.nlm.nih.gov/gene/?term=10651		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001382	10651	MTX2	http://www.ncbi.nlm.nih.gov/gene/?term=10651		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001383	10651	MTX2	http://www.ncbi.nlm.nih.gov/gene/?term=10651		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001384	10652	YKT6	http://www.ncbi.nlm.nih.gov/gene/?term=10652		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001385	10652	YKT6	http://www.ncbi.nlm.nih.gov/gene/?term=10652		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001386	10653	SPINT2	http://www.ncbi.nlm.nih.gov/gene/?term=10653	"DIAR3, HAI-2, HAI2, Kop, PB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001387	10653	SPINT2	http://www.ncbi.nlm.nih.gov/gene/?term=10653	"DIAR3, HAI-2, HAI2, Kop, PB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001388	10654	PMVK	http://www.ncbi.nlm.nih.gov/gene/?term=10654	"HUMPMKI, PMK, PMKA, PMKASE, POROK1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001389	10654	PMVK	http://www.ncbi.nlm.nih.gov/gene/?term=10654	"HUMPMKI, PMK, PMKA, PMKASE, POROK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001390	10655	DMRT2	http://www.ncbi.nlm.nih.gov/gene/?term=10655		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001391	10657	KHDRBS1	http://www.ncbi.nlm.nih.gov/gene/?term=10657	"Sam68, p62, p68 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001392	106585	Ankrd12	http://www.ncbi.nlm.nih.gov/gene/?term=106585	"2900001A12Rik, AI447928, ANCO-2, AV347965, GAC-1, mKIAA0874 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001393	10658	CELF1	http://www.ncbi.nlm.nih.gov/gene/?term=10658	"BRUNOL2, CUG-BP, CUGBP, CUGBP1, EDEN-BP, NAB50, NAPOR, hNab50 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001394	10658	CELF1	http://www.ncbi.nlm.nih.gov/gene/?term=10658	"BRUNOL2, CUG-BP, CUGBP, CUGBP1, EDEN-BP, NAB50, NAPOR, hNab50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001395	10659	CELF2	http://www.ncbi.nlm.nih.gov/gene/?term=10659	"BRUNOL3, CUGBP2, ETR-3, ETR3, NAPOR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001396	10661	KLF1	http://www.ncbi.nlm.nih.gov/gene/?term=10661	"CDAN4, EKLF, HBFQTL6, INLU "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001397	106631781	RNA18S4	http://www.ncbi.nlm.nih.gov/gene/?term=106631781		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001398	106631781	RNA18S4	http://www.ncbi.nlm.nih.gov/gene/?term=106631781		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001399	106631781	RNA18S4	http://www.ncbi.nlm.nih.gov/gene/?term=106631781		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001400	106631781	RNA18S4	http://www.ncbi.nlm.nih.gov/gene/?term=106631781		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001401	106631782	RNA18S3	http://www.ncbi.nlm.nih.gov/gene/?term=106631782		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001402	106631782	RNA18S3	http://www.ncbi.nlm.nih.gov/gene/?term=106631782		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001403	106631782	RNA18S3	http://www.ncbi.nlm.nih.gov/gene/?term=106631782		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001404	106631782	RNA18S3	http://www.ncbi.nlm.nih.gov/gene/?term=106631782		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001405	106632258	RNA18S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632258		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001406	106632258	RNA18S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632258		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001407	106632258	RNA18S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632258		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001408	106632258	RNA18S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632258		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001409	106632259	RNA18S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632259		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001410	106632259	RNA18S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632259		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001411	106632259	RNA18S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632259		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001412	106632259	RNA18S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632259		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001413	106632260	RNA5-8S4	http://www.ncbi.nlm.nih.gov/gene/?term=106632260		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001414	106632260	RNA5-8S4	http://www.ncbi.nlm.nih.gov/gene/?term=106632260		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001415	106632261	RNA5-8S3	http://www.ncbi.nlm.nih.gov/gene/?term=106632261		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001416	106632261	RNA5-8S3	http://www.ncbi.nlm.nih.gov/gene/?term=106632261		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001417	106632262	RNA5-8S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632262		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001418	106632262	RNA5-8S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632262		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001419	106632263	RNA5-8S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632263		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001420	106632263	RNA5-8S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632263		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001421	106632264	RNA28S4	http://www.ncbi.nlm.nih.gov/gene/?term=106632264		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001422	106632264	RNA28S4	http://www.ncbi.nlm.nih.gov/gene/?term=106632264		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001423	106632264	RNA28S4	http://www.ncbi.nlm.nih.gov/gene/?term=106632264		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001424	106632264	RNA28S4	http://www.ncbi.nlm.nih.gov/gene/?term=106632264		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001425	106632265	RNA28S3	http://www.ncbi.nlm.nih.gov/gene/?term=106632265		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001426	106632265	RNA28S3	http://www.ncbi.nlm.nih.gov/gene/?term=106632265		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001427	106632265	RNA28S3	http://www.ncbi.nlm.nih.gov/gene/?term=106632265		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001428	106632265	RNA28S3	http://www.ncbi.nlm.nih.gov/gene/?term=106632265		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001429	106632266	RNA28S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632266		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001430	106632266	RNA28S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632266		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001431	106632266	RNA28S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632266		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001432	106632266	RNA28S2	http://www.ncbi.nlm.nih.gov/gene/?term=106632266		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001433	106632267	RNA28S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632267		rRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001434	106632267	RNA28S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632267		rRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001435	106632267	RNA28S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632267		rRNA	Homo sapiens	25753659	Cytoplasm	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001436	106632267	RNA28S1	http://www.ncbi.nlm.nih.gov/gene/?term=106632267		rRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00001437	106633806	SNORD142	http://www.ncbi.nlm.nih.gov/gene/?term=106633806	"SNORA85, SNORD174, ZL68 "	snoRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00001438	106633806	SNORD142	http://www.ncbi.nlm.nih.gov/gene/?term=106633806	"SNORA85, SNORD174, ZL68 "	snoRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00001439	10664	CTCF	http://www.ncbi.nlm.nih.gov/gene/?term=10664	MRD21	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001440	10664	CTCF	http://www.ncbi.nlm.nih.gov/gene/?term=10664	MRD21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001441	10667	FARS2	http://www.ncbi.nlm.nih.gov/gene/?term=10667	"COXPD14, FARS1, HSPC320, PheRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001442	10667	FARS2	http://www.ncbi.nlm.nih.gov/gene/?term=10667	"COXPD14, FARS1, HSPC320, PheRS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001443	10667	FARS2	http://www.ncbi.nlm.nih.gov/gene/?term=10667	"COXPD14, FARS1, HSPC320, PheRS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001444	10668	CGRRF1	http://www.ncbi.nlm.nih.gov/gene/?term=10668	"CGR19, RNF197 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001445	10669	CGREF1	http://www.ncbi.nlm.nih.gov/gene/?term=10669	CGR11	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001446	1066	CES1	http://www.ncbi.nlm.nih.gov/gene/?term=1066	"ACAT, CE-1, CEH, CES2, HMSE, HMSE1, PCE-1, REH, SES1, TGH, hCE-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001447	106707	Rpusd1	http://www.ncbi.nlm.nih.gov/gene/?term=106707	"2310051D06Rik, AU019540, Rlucl "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001448	10670	RRAGA	http://www.ncbi.nlm.nih.gov/gene/?term=10670	"FIP-1, FIP1, RAGA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001449	10671	DCTN6	http://www.ncbi.nlm.nih.gov/gene/?term=10671	"WS-3, WS3, p27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001450	10672	GNA13	http://www.ncbi.nlm.nih.gov/gene/?term=10672	G13	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001451	10673	TNFSF13B	http://www.ncbi.nlm.nih.gov/gene/?term=10673	"BAFF, BLYS, CD257, DTL, TALL-1, TALL1, THANK, TNFSF20, TNLG7A, ZTNF4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001452	10675	CSPG5	http://www.ncbi.nlm.nih.gov/gene/?term=10675	NGC	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001453	10678	B3GNT2	http://www.ncbi.nlm.nih.gov/gene/?term=10678	"3-Gn-T1, 3-Gn-T2, B3GN-T2, B3GNT, B3GNT-2, B3GNT1, BETA3GNT, BGNT2, BGnT-2, beta-1, beta3Gn-T1, beta3Gn-T2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001454	10678	B3GNT2	http://www.ncbi.nlm.nih.gov/gene/?term=10678	"3-Gn-T1, 3-Gn-T2, B3GN-T2, B3GNT, B3GNT-2, B3GNT1, BETA3GNT, BGNT2, BGnT-2, beta-1, beta3Gn-T1, beta3Gn-T2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001455	10678	B3GNT2	http://www.ncbi.nlm.nih.gov/gene/?term=10678	"3-Gn-T1, 3-Gn-T2, B3GN-T2, B3GNT, B3GNT-2, B3GNT1, BETA3GNT, BGNT2, BGnT-2, beta-1, beta3Gn-T1, beta3Gn-T2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001456	106794	Dhx57	http://www.ncbi.nlm.nih.gov/gene/?term=106794	AW494914	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001457	10682	EBP	http://www.ncbi.nlm.nih.gov/gene/?term=10682	"CDPX2, CHO2, CPX, CPXD, MEND "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001458	10682	EBP	http://www.ncbi.nlm.nih.gov/gene/?term=10682	"CDPX2, CHO2, CPX, CPXD, MEND "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001459	10682	EBP	http://www.ncbi.nlm.nih.gov/gene/?term=10682	"CDPX2, CHO2, CPX, CPXD, MEND "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001460	10687	PNMA2	http://www.ncbi.nlm.nih.gov/gene/?term=10687	"MA2, MM2, RGAG2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001461	10687	PNMA2	http://www.ncbi.nlm.nih.gov/gene/?term=10687	"MA2, MM2, RGAG2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001462	106885	AI314760	http://www.ncbi.nlm.nih.gov/gene/?term=106885		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001463	106885	AI314760	http://www.ncbi.nlm.nih.gov/gene/?term=106885		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001464	106885	AI314760	http://www.ncbi.nlm.nih.gov/gene/?term=106885		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001465	10691	GMEB1	http://www.ncbi.nlm.nih.gov/gene/?term=10691	"P96PIF, PIF96 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001466	10694	CCT8	http://www.ncbi.nlm.nih.gov/gene/?term=10694	"C21orf112, Cctq, D21S246, PRED71 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001467	10694	CCT8	http://www.ncbi.nlm.nih.gov/gene/?term=10694	"C21orf112, Cctq, D21S246, PRED71 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001468	10694	CCT8	http://www.ncbi.nlm.nih.gov/gene/?term=10694	"C21orf112, Cctq, D21S246, PRED71 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001469	106957	Slc39a6	http://www.ncbi.nlm.nih.gov/gene/?term=106957	Ermelin	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001470	10695	CNPY3	http://www.ncbi.nlm.nih.gov/gene/?term=10695	"CAG4A, ERDA5, PRAT4A, TNRC5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001471	10695	CNPY3	http://www.ncbi.nlm.nih.gov/gene/?term=10695	"CAG4A, ERDA5, PRAT4A, TNRC5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001472	10695	CNPY3	http://www.ncbi.nlm.nih.gov/gene/?term=10695	"CAG4A, ERDA5, PRAT4A, TNRC5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001473	10699	CORIN	http://www.ncbi.nlm.nih.gov/gene/?term=10699	"ATC2, CRN, Lrp4, PEE5, TMPRSS10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001474	1069	CETN2	http://www.ncbi.nlm.nih.gov/gene/?term=1069	"CALT, CEN2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001475	1069	CETN2	http://www.ncbi.nlm.nih.gov/gene/?term=1069	"CALT, CEN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001476	107029	Me2	http://www.ncbi.nlm.nih.gov/gene/?term=107029	"AW120568, D030040L20Rik, NAD-ME "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001477	107045	Lars	http://www.ncbi.nlm.nih.gov/gene/?term=107045	"2310045K21Rik, 3110009L02Rik, AW536573, mKIAA1352 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001478	1070	CETN3	http://www.ncbi.nlm.nih.gov/gene/?term=1070	"CDC31, CEN3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001479	107105261	RNU1-5P	http://www.ncbi.nlm.nih.gov/gene/?term=107105261	RNU1-5	lncRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00001480	10712	FAM189B	http://www.ncbi.nlm.nih.gov/gene/?term=10712	"C1orf2, COTE1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001481	10712	FAM189B	http://www.ncbi.nlm.nih.gov/gene/?term=10712	"C1orf2, COTE1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001482	10713	USP39	http://www.ncbi.nlm.nih.gov/gene/?term=10713	"65K, CGI-21, HSPC332, SAD1, SNRNP65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001483	10714	POLD3	http://www.ncbi.nlm.nih.gov/gene/?term=10714	"P66, P68, PPP1R128 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001484	10714	POLD3	http://www.ncbi.nlm.nih.gov/gene/?term=10714	"P66, P68, PPP1R128 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001485	10715	CERS1	http://www.ncbi.nlm.nih.gov/gene/?term=10715	"EPM8, LAG1, LASS1, UOG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001486	107173	Gpr137	http://www.ncbi.nlm.nih.gov/gene/?term=107173	AI428855	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001487	107182	Btaf1	http://www.ncbi.nlm.nih.gov/gene/?term=107182	"AI414500, AI447930, E430027O22Rik, TAF170 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001488	107227	Macrod1	http://www.ncbi.nlm.nih.gov/gene/?term=107227	"AI604841, AW743046, D930010J01Rik, Lrp16 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001489	10723	SLC12A7	http://www.ncbi.nlm.nih.gov/gene/?term=10723	KCC4	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001490	10723	SLC12A7	http://www.ncbi.nlm.nih.gov/gene/?term=10723	KCC4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001491	107242	AI837181	http://www.ncbi.nlm.nih.gov/gene/?term=107242	"Bles03, N28173 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001492	10724	MGEA5	http://www.ncbi.nlm.nih.gov/gene/?term=10724	"MEA5, NCOAT, OGA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001493	10724	MGEA5	http://www.ncbi.nlm.nih.gov/gene/?term=10724	"MEA5, NCOAT, OGA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001494	10724	MGEA5	http://www.ncbi.nlm.nih.gov/gene/?term=10724	"MEA5, NCOAT, OGA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001495	10725	NFAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10725	"NF-AT5, NFATL1, NFATZ, OREBP, TONEBP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001496	10725	NFAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10725	"NF-AT5, NFATL1, NFATZ, OREBP, TONEBP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001497	10725	NFAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10725	"NF-AT5, NFATL1, NFATZ, OREBP, TONEBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001498	107260	Otub1	http://www.ncbi.nlm.nih.gov/gene/?term=107260	AI850305	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001499	10726	NUDC	http://www.ncbi.nlm.nih.gov/gene/?term=10726	"HNUDC, MNUDC, NPD011 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001500	10726	NUDC	http://www.ncbi.nlm.nih.gov/gene/?term=10726	"HNUDC, MNUDC, NPD011 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001501	10726	NUDC	http://www.ncbi.nlm.nih.gov/gene/?term=10726	"HNUDC, MNUDC, NPD011 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001502	10728	PTGES3	http://www.ncbi.nlm.nih.gov/gene/?term=10728	"P23, TEBP, cPGES "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001503	10728	PTGES3	http://www.ncbi.nlm.nih.gov/gene/?term=10728	"P23, TEBP, cPGES "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001504	10728	PTGES3	http://www.ncbi.nlm.nih.gov/gene/?term=10728	"P23, TEBP, cPGES "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001505	1072	CFL1	http://www.ncbi.nlm.nih.gov/gene/?term=1072	"CFL, HEL-S-15, cofilin "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001506	1072	CFL1	http://www.ncbi.nlm.nih.gov/gene/?term=1072	"CFL, HEL-S-15, cofilin "	mRNA	Homo sapiens	25908858	Cell leading edge	Lung cancer cell	In situ hybridization	Localization of cofilin mRNA to the leading edge of migrating cells promotes directed cell migration.
RLID00001507	1072	CFL1	http://www.ncbi.nlm.nih.gov/gene/?term=1072	"CFL, HEL-S-15, cofilin "	mRNA	Homo sapiens	25908858	Cell leading edge	Lung carcinoma cell	In situ hybridization	We have found that cofilin-1 mRNA is rapidly localized to the leading edge of human lung carcinoma cells and that VICKZ family RNA-binding proteins help mediate this localization through specific interactions with the 3'UTR of cofilin mRNA.
RLID00001508	1072	CFL1	http://www.ncbi.nlm.nih.gov/gene/?term=1072	"CFL, HEL-S-15, cofilin "	mRNA	Homo sapiens	25908858	Lamellipodium	Lung cancer cell	In situ hybridization	Cofilin mRNA is rapidly localized to lamellipodia in motile cells
RLID00001509	10730	YME1L1	http://www.ncbi.nlm.nih.gov/gene/?term=10730	"FTSH, MEG4, PAMP, YME1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001510	10730	YME1L1	http://www.ncbi.nlm.nih.gov/gene/?term=10730	"FTSH, MEG4, PAMP, YME1L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001511	107328	Trpt1	http://www.ncbi.nlm.nih.gov/gene/?term=107328	"AU079016, AW045591, Tpt1, Tpt1h "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001512	10733	PLK4	http://www.ncbi.nlm.nih.gov/gene/?term=10733	"MCCRP2, SAK, STK18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001513	107358	Tm9sf3	http://www.ncbi.nlm.nih.gov/gene/?term=107358	"1810073M23Rik, 2810031D16Rik, AI115521, AI413748, AW146116, AW549777, Smbp, mKIAA4036 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001514	10735	STAG2	http://www.ncbi.nlm.nih.gov/gene/?term=10735	"SA-2, SA2, SCC3B, bA517O1.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001515	10735	STAG2	http://www.ncbi.nlm.nih.gov/gene/?term=10735	"SA-2, SA2, SCC3B, bA517O1.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001516	107373	Fam111a	http://www.ncbi.nlm.nih.gov/gene/?term=107373	"4632417K18Rik, AW413625 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001517	107392	Brms1	http://www.ncbi.nlm.nih.gov/gene/?term=107392	"AV003220, AW554636 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001518	107392	Brms1	http://www.ncbi.nlm.nih.gov/gene/?term=107392	"AV003220, AW554636 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001519	1073	CFL2	http://www.ncbi.nlm.nih.gov/gene/?term=1073	NEM7	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001520	1073	CFL2	http://www.ncbi.nlm.nih.gov/gene/?term=1073	NEM7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001521	10741	RBBP9	http://www.ncbi.nlm.nih.gov/gene/?term=10741	"BOG, RBBP10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001522	10741	RBBP9	http://www.ncbi.nlm.nih.gov/gene/?term=10741	"BOG, RBBP10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001523	10741	RBBP9	http://www.ncbi.nlm.nih.gov/gene/?term=10741	"BOG, RBBP10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001524	107435	Hat1	http://www.ncbi.nlm.nih.gov/gene/?term=107435	"2410071B14Rik, AA536933, Hat-1, KAT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001525	107449	Unc5b	http://www.ncbi.nlm.nih.gov/gene/?term=107449	"6330415E02Rik, A630020F16, D10Bwg0792e, Unc5h2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001526	10746	MAP3K2	http://www.ncbi.nlm.nih.gov/gene/?term=10746	"MEKK2, MEKK2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001527	10746	MAP3K2	http://www.ncbi.nlm.nih.gov/gene/?term=10746	"MEKK2, MEKK2B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001528	10746	MAP3K2	http://www.ncbi.nlm.nih.gov/gene/?term=10746	"MEKK2, MEKK2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001529	10749	KIF1C	http://www.ncbi.nlm.nih.gov/gene/?term=10749	"LTXS1, SATX2, SAX2, SPAX2, SPG58 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001530	10749	KIF1C	http://www.ncbi.nlm.nih.gov/gene/?term=10749	"LTXS1, SATX2, SAX2, SPAX2, SPG58 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001531	107503	Atf5	http://www.ncbi.nlm.nih.gov/gene/?term=107503	"AFTA, Atf7, Atfx, ODA-10 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001532	107503	Atf5	http://www.ncbi.nlm.nih.gov/gene/?term=107503	"AFTA, Atf7, Atfx, ODA-10 "	mRNA	Mus musculus	18195013	Ribosome	S/S MEF cell	RT-PCR	"In the non-stressed condition, when protein synthesis is plentiful, the ATF5 mRNA was associated with fewer ribosomes, as compared with the large polysomes associated with actin mRNA. In response to ER stress, ATF5 mRNA was readily detected in the larger polysome fractions, consistent with the idea that ATF5 mRNA was bound to multiple ribosomes and was more efficiently translated. "
RLID00001533	107508	Eprs	http://www.ncbi.nlm.nih.gov/gene/?term=107508	"2410081F06Rik, 3010002K18Rik, C79379, Qprs "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001534	107513	Ssr1	http://www.ncbi.nlm.nih.gov/gene/?term=107513	"2510001K09Rik, 6330400D04, AI159733, AI452176, SSR, TRAPA "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001535	107513	Ssr1	http://www.ncbi.nlm.nih.gov/gene/?term=107513	"2510001K09Rik, 6330400D04, AI159733, AI452176, SSR, TRAPA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001536	107522	Ece2	http://www.ncbi.nlm.nih.gov/gene/?term=107522	"1810009K13Rik, 6330509A19Rik, 9630025D12Rik, BB127715, Ece-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001537	107528	Magee1	http://www.ncbi.nlm.nih.gov/gene/?term=107528	"AI847422, DAMAGE, mMage-e1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001538	10752	CHL1	http://www.ncbi.nlm.nih.gov/gene/?term=10752	"CALL, L1CAM2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001539	10755	GIPC1	http://www.ncbi.nlm.nih.gov/gene/?term=10755	"C19orf3, GIPC, GLUT1CBP, Hs.6454, IIP-1, NIP, RGS19IP1, SEMCAP, SYNECTIIN, SYNECTIN, TIP-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001540	10755	GIPC1	http://www.ncbi.nlm.nih.gov/gene/?term=10755	"C19orf3, GIPC, GLUT1CBP, Hs.6454, IIP-1, NIP, RGS19IP1, SEMCAP, SYNECTIIN, SYNECTIN, TIP-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001541	10758	TRAF3IP2	http://www.ncbi.nlm.nih.gov/gene/?term=10758	"ACT1, C6orf2, C6orf4, C6orf5, C6orf6, CANDF8, CIKS, PSORS13 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001542	10758	TRAF3IP2	http://www.ncbi.nlm.nih.gov/gene/?term=10758	"ACT1, C6orf2, C6orf4, C6orf5, C6orf6, CANDF8, CIKS, PSORS13 "	mRNA	Homo sapiens	26222413	Nucleus	Neuron	In situ hybridization|qRT-PCR	"Interestingly, the subcellular distribution of TRAF3IP2 protein-coding transcript (from the strand opposite TRAF3IP2-AS1) was quite distinct from that of TRAF3IP2-AS1 transcript, being found throughout the nucleus, cytoplasm, and processes of DA neurons (Fig. 2i and j). "
RLID00001543	10758	TRAF3IP2	http://www.ncbi.nlm.nih.gov/gene/?term=10758	"ACT1, C6orf2, C6orf4, C6orf5, C6orf6, CANDF8, CIKS, PSORS13 "	mRNA	Homo sapiens	26222413	Cytoplasm	Neuron	In situ hybridization|qRT-PCR	"Interestingly, the subcellular distribution of TRAF3IP2 protein-coding transcript (from the strand opposite TRAF3IP2-AS1) was quite distinct from that of TRAF3IP2-AS1 transcript, being found throughout the nucleus, cytoplasm, and processes of DA neurons (Fig. 2i and j). "
RLID00001544	1075	CTSC	http://www.ncbi.nlm.nih.gov/gene/?term=1075	"CPPI, DPP-I, DPP1, DPPI, HMS, JP, JPD, PALS, PDON1, PLS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001545	1075	CTSC	http://www.ncbi.nlm.nih.gov/gene/?term=1075	"CPPI, DPP-I, DPP1, DPPI, HMS, JP, JPD, PALS, PDON1, PLS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001546	1075	CTSC	http://www.ncbi.nlm.nih.gov/gene/?term=1075	"CPPI, DPP-I, DPP1, DPPI, HMS, JP, JPD, PALS, PDON1, PLS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001547	10761	PLAC1	http://www.ncbi.nlm.nih.gov/gene/?term=10761	"CT92, OOSP2L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001548	10762	NUP50	http://www.ncbi.nlm.nih.gov/gene/?term=10762	"NPAP60, NPAP60L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001549	10762	NUP50	http://www.ncbi.nlm.nih.gov/gene/?term=10762	"NPAP60, NPAP60L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001550	107650	Pi4kb	http://www.ncbi.nlm.nih.gov/gene/?term=107650	"ESTM41, PI4K-beta, PI4Kbeta, Pik4cb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001551	10765	KDM5B	http://www.ncbi.nlm.nih.gov/gene/?term=10765	"CT31, JARID1B, PLU-1, PLU1, PPP1R98, PUT1, RBBP2H1A, RBP2-H1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001552	10766	TOB2	http://www.ncbi.nlm.nih.gov/gene/?term=10766	"TOB4, TOBL, TROB2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001553	10766	TOB2	http://www.ncbi.nlm.nih.gov/gene/?term=10766	"TOB4, TOBL, TROB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001554	10767	HBS1L	http://www.ncbi.nlm.nih.gov/gene/?term=10767	"EF-1a, ERFS, HBS1, HSPC276, eRF3c "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001555	10767	HBS1L	http://www.ncbi.nlm.nih.gov/gene/?term=10767	"EF-1a, ERFS, HBS1, HSPC276, eRF3c "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001556	10767	HBS1L	http://www.ncbi.nlm.nih.gov/gene/?term=10767	"EF-1a, ERFS, HBS1, HSPC276, eRF3c "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001557	10768	AHCYL1	http://www.ncbi.nlm.nih.gov/gene/?term=10768	"DCAL, IRBIT, PPP1R78, PRO0233, XPVKONA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001558	10768	AHCYL1	http://www.ncbi.nlm.nih.gov/gene/?term=10768	"DCAL, IRBIT, PPP1R78, PRO0233, XPVKONA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001559	10769	PLK2	http://www.ncbi.nlm.nih.gov/gene/?term=10769	"SNK, hPlk2, hSNK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001560	107701	Sf3b4	http://www.ncbi.nlm.nih.gov/gene/?term=107701	"SF3b49, SF3b50, Sap49 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001561	107701	Sf3b4	http://www.ncbi.nlm.nih.gov/gene/?term=107701	"SF3b49, SF3b50, Sap49 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001562	107702	Rnh1	http://www.ncbi.nlm.nih.gov/gene/?term=107702	"AW546468, C80305, RNH "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001563	10771	ZMYND11	http://www.ncbi.nlm.nih.gov/gene/?term=10771	"BRAM1, BS69, MRD30 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001564	10772	SRSF10	http://www.ncbi.nlm.nih.gov/gene/?term=10772	"FUSIP1, FUSIP2, NSSR, PPP1R149, SFRS13, SFRS13A, SRp38, SRrp40, TASR, TASR1, TASR2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001565	10772	SRSF10	http://www.ncbi.nlm.nih.gov/gene/?term=10772	"FUSIP1, FUSIP2, NSSR, PPP1R149, SFRS13, SFRS13A, SRp38, SRrp40, TASR, TASR1, TASR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001566	10775	POP4	http://www.ncbi.nlm.nih.gov/gene/?term=10775	RPP29	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001567	10775	POP4	http://www.ncbi.nlm.nih.gov/gene/?term=10775	RPP29	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001568	107767	Scamp1	http://www.ncbi.nlm.nih.gov/gene/?term=107767	"4930505M11Rik, AI415563, AW122395 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001569	10776	ARPP19	http://www.ncbi.nlm.nih.gov/gene/?term=10776	"ARPP-16, ARPP-19, ARPP16, ENSAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001570	10776	ARPP19	http://www.ncbi.nlm.nih.gov/gene/?term=10776	"ARPP-16, ARPP-19, ARPP16, ENSAL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001571	10776	ARPP19	http://www.ncbi.nlm.nih.gov/gene/?term=10776	"ARPP-16, ARPP-19, ARPP16, ENSAL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001572	10776	ARPP19	http://www.ncbi.nlm.nih.gov/gene/?term=10776	"ARPP-16, ARPP-19, ARPP16, ENSAL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001573	107770	Tm6sf2	http://www.ncbi.nlm.nih.gov/gene/?term=107770		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001574	107771	Bmyc	http://www.ncbi.nlm.nih.gov/gene/?term=107771	"2900002K07Rik, AW060705, Mycb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001575	107815	Scml2	http://www.ncbi.nlm.nih.gov/gene/?term=107815	4932420G07Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001576	10781	ZNF266	http://www.ncbi.nlm.nih.gov/gene/?term=10781	HZF1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001577	107823	Whsc1	http://www.ncbi.nlm.nih.gov/gene/?term=107823	"5830445G22Rik, 9430010A17Rik, AW555663, C130020C13Rik, D030027O06Rik, D930023B08Rik, MMSET, NSD2l, mKIAA1090, Whsc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001578	10783	NEK6	http://www.ncbi.nlm.nih.gov/gene/?term=10783	SID6-1512	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001579	10787	NCKAP1	http://www.ncbi.nlm.nih.gov/gene/?term=10787	"HEM2, NAP1, NAP125, p125Nap1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001580	10788	IQGAP2	http://www.ncbi.nlm.nih.gov/gene/?term=10788		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001581	107932	Chd4	http://www.ncbi.nlm.nih.gov/gene/?term=107932	"9530019N15Rik, AA617397, BC005710, D6Ertd380e, Mi-2beta, mKIAA4075 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001582	10793	ZNF273	http://www.ncbi.nlm.nih.gov/gene/?term=10793	HZF9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001583	10794	ZNF460	http://www.ncbi.nlm.nih.gov/gene/?term=10794	"HZF8, ZNF272 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001584	107971	Frs3	http://www.ncbi.nlm.nih.gov/gene/?term=107971	"4930417B13Rik, AI449674, Frs2beta, Snt2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001585	107975	Pacs1	http://www.ncbi.nlm.nih.gov/gene/?term=107975	AI325977	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001586	107976	Bre	http://www.ncbi.nlm.nih.gov/gene/?term=107976	"6030405P19Rik, AI429776, B830038C02Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001587	10797	MTHFD2	http://www.ncbi.nlm.nih.gov/gene/?term=10797	NMDMC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001588	10797	MTHFD2	http://www.ncbi.nlm.nih.gov/gene/?term=10797	NMDMC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001589	107986	Ddb2	http://www.ncbi.nlm.nih.gov/gene/?term=107986	2610043A19Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001590	107993	Bfsp2	http://www.ncbi.nlm.nih.gov/gene/?term=107993	"AI448593, CP49 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001591	10799	RPP40	http://www.ncbi.nlm.nih.gov/gene/?term=10799	"RNASEP1, bA428J1.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001592	108013	Celf4	http://www.ncbi.nlm.nih.gov/gene/?term=108013	"A230070D14Rik, BRUNOL-4, Brul4, Brunol4, C130060B05Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001593	10801	SEPT9	http://www.ncbi.nlm.nih.gov/gene/?term=10801	"AF17q25, MSF, MSF1, NAPB, PNUTL4, SINT1, SeptD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001594	10802	SEC24A	http://www.ncbi.nlm.nih.gov/gene/?term=10802		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001595	10802	SEC24A	http://www.ncbi.nlm.nih.gov/gene/?term=10802		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001596	108030	Lin7a	http://www.ncbi.nlm.nih.gov/gene/?term=108030	"AI848705, LIN-7A, MALS-1, TIP-33, Veli, Veli1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001597	10807	SDCCAG3	http://www.ncbi.nlm.nih.gov/gene/?term=10807	NY-CO-3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001598	10807	SDCCAG3	http://www.ncbi.nlm.nih.gov/gene/?term=10807	NY-CO-3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001599	10807	SDCCAG3	http://www.ncbi.nlm.nih.gov/gene/?term=10807	NY-CO-3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001600	108086	Rnf216	http://www.ncbi.nlm.nih.gov/gene/?term=108086	"2810055G22Rik, AI647468, AU019462, C86502, F830018F18Rik, TRIAD3, UIP83, Ubce7ip1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001601	108089	Rnf144a	http://www.ncbi.nlm.nih.gov/gene/?term=108089	"Rnf144, UIP4, Ubce7ip4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001602	10808	HSPH1	http://www.ncbi.nlm.nih.gov/gene/?term=10808	"HSP105, HSP105A, HSP105B, NY-CO-25 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001603	10808	HSPH1	http://www.ncbi.nlm.nih.gov/gene/?term=10808	"HSP105, HSP105A, HSP105B, NY-CO-25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001604	10809	STARD10	http://www.ncbi.nlm.nih.gov/gene/?term=10809	"CGI-52, NY-CO-28, PCTP2, SDCCAG28 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001605	10809	STARD10	http://www.ncbi.nlm.nih.gov/gene/?term=10809	"CGI-52, NY-CO-28, PCTP2, SDCCAG28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001606	108112	Eif4ebp3	http://www.ncbi.nlm.nih.gov/gene/?term=108112	4e-bp3	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001607	108116	Slco3a1	http://www.ncbi.nlm.nih.gov/gene/?term=108116	"5830414C08Rik, Anr1, MJAM, OATP-D, R75096, Slc21a11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001608	108121	U2af1	http://www.ncbi.nlm.nih.gov/gene/?term=108121	"2010107D16Rik, 35kDa "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001609	108123	Napg	http://www.ncbi.nlm.nih.gov/gene/?term=108123	"2400003O04Rik, SNARE "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001610	108138	Xrcc4	http://www.ncbi.nlm.nih.gov/gene/?term=108138	"2310057B22Rik, AW413319, AW545101 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001611	10813	UTP14A	http://www.ncbi.nlm.nih.gov/gene/?term=10813	"NYCO16, SDCCAG16, dJ537K23.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001612	108150	Galnt7	http://www.ncbi.nlm.nih.gov/gene/?term=108150	AI225872	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001613	108154	Adamts6	http://www.ncbi.nlm.nih.gov/gene/?term=108154	"5031426K13, A930019D11Rik, ADAM-TS6, b2b1879.1Clo, b2b2029Clo, b2b2182Clo, b2b2187.1Clo, b2b2228Clo "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001614	10815	CPLX1	http://www.ncbi.nlm.nih.gov/gene/?term=10815	"CPX-I, CPX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001615	10826	FAXDC2	http://www.ncbi.nlm.nih.gov/gene/?term=10826	C5orf4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001616	10827	FAM114A2	http://www.ncbi.nlm.nih.gov/gene/?term=10827	"133K02, C5orf3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001617	10838	ZNF275	http://www.ncbi.nlm.nih.gov/gene/?term=10838		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001618	10838	ZNF275	http://www.ncbi.nlm.nih.gov/gene/?term=10838		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001619	10844	TUBGCP2	http://www.ncbi.nlm.nih.gov/gene/?term=10844	"GCP-2, GCP2, Grip103, SPBC97, Spc97p, h103p, hGCP2, hSpc97 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001620	10845	CLPX	http://www.ncbi.nlm.nih.gov/gene/?term=10845		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001621	10847	SRCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10847	"DOMO1, EAF1, FLHS, SWR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001622	10847	SRCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10847	"DOMO1, EAF1, FLHS, SWR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001623	10849	CD3EAP	http://www.ncbi.nlm.nih.gov/gene/?term=10849	"ASE-1, ASE1, CAST, PAF49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001624	10849	CD3EAP	http://www.ncbi.nlm.nih.gov/gene/?term=10849	"ASE-1, ASE1, CAST, PAF49 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001625	10849	CD3EAP	http://www.ncbi.nlm.nih.gov/gene/?term=10849	"ASE-1, ASE1, CAST, PAF49 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001626	10857	PGRMC1	http://www.ncbi.nlm.nih.gov/gene/?term=10857	"HPR6.6, MPR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001627	10857	PGRMC1	http://www.ncbi.nlm.nih.gov/gene/?term=10857	"HPR6.6, MPR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001628	10857	PGRMC1	http://www.ncbi.nlm.nih.gov/gene/?term=10857	"HPR6.6, MPR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001629	108645	Mat2b	http://www.ncbi.nlm.nih.gov/gene/?term=108645	"1110064C04Rik, 2410018D16Rik, AI182287, AU022853, MAT-II, MATIIbeta, TGR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001630	108652	Slc35b3	http://www.ncbi.nlm.nih.gov/gene/?term=108652	"4921526O06Rik, AI428480, CGI-19, PABST2, PAPST2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001631	108655	Foxp1	http://www.ncbi.nlm.nih.gov/gene/?term=108655	"3110052D19Rik, 4932443N09Rik, AI461938, AW494214 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001632	10865	ARID5A	http://www.ncbi.nlm.nih.gov/gene/?term=10865	"MRF-1, MRF1, RP11-363D14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001633	108664	Atp6v1h	http://www.ncbi.nlm.nih.gov/gene/?term=108664	"0710001F19Rik, AU022349, CGI-11, SFD, SFDalpha, SFDbeta, VMA13 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001634	108672	Zdhhc15	http://www.ncbi.nlm.nih.gov/gene/?term=108672	6030457O13Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001635	108686	Ccdc88a	http://www.ncbi.nlm.nih.gov/gene/?term=108686	"A430106J12Rik, AI848406, Ape, C130096N06Rik, C330012F17Rik, D130005J21Rik, Girdin, Giv, Grdn, Hkrp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001636	108699	Chn1	http://www.ncbi.nlm.nih.gov/gene/?term=108699	"0610007I19Rik, 0710001E19Rik, 1700112L09Rik, 2900046J01Rik, AI413815, ARHGAP2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001637	10869	USP19	http://www.ncbi.nlm.nih.gov/gene/?term=10869	ZMYND9	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001638	108707	Fam207a	http://www.ncbi.nlm.nih.gov/gene/?term=108707	"1810008A18Rik, AI303072 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001639	10871	CD300C	http://www.ncbi.nlm.nih.gov/gene/?term=10871	"CLM-6, CMRF-35, CMRF-35A, CMRF35, CMRF35-A1, CMRF35A, CMRF35A1, IGSF16, LIR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001640	10873	ME3	http://www.ncbi.nlm.nih.gov/gene/?term=10873	NADP-ME	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001641	10874	NMU	http://www.ncbi.nlm.nih.gov/gene/?term=10874		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001642	10874	NMU	http://www.ncbi.nlm.nih.gov/gene/?term=10874		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001643	108755	Lyrm2	http://www.ncbi.nlm.nih.gov/gene/?term=108755	2610208E05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001644	10878	CFHR3	http://www.ncbi.nlm.nih.gov/gene/?term=10878	"CFHL3, DOWN16, FHR-3, FHR3, HLF4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001645	1087	CEACAM7	http://www.ncbi.nlm.nih.gov/gene/?term=1087	CGM2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001646	108803	4933402P03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=108803		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001647	108829	Jmjd1c	http://www.ncbi.nlm.nih.gov/gene/?term=108829	"5430433L24Rik, D630035I23Rik, Jmjdic, TRIP8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001648	10884	MRPS30	http://www.ncbi.nlm.nih.gov/gene/?term=10884	"MRP-S30, PAP, PDCD9, S30mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001649	108853	Mtrf1l	http://www.ncbi.nlm.nih.gov/gene/?term=108853	9130004K12Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001650	108857	Ankhd1	http://www.ncbi.nlm.nih.gov/gene/?term=108857	"1110004O12Rik, 4933432B13Rik, 9130019P20Rik, A530027J04Rik, A630021B20Rik, AA571404, Mask, mFLJ00246, mKIAA1085 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001651	10885	WDR3	http://www.ncbi.nlm.nih.gov/gene/?term=10885	"DIP2, UTP12 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001652	10888	GPR83	http://www.ncbi.nlm.nih.gov/gene/?term=10888	"GIR, GPR72 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001653	10888	GPR83	http://www.ncbi.nlm.nih.gov/gene/?term=10888	"GIR, GPR72 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001654	10888	GPR83	http://www.ncbi.nlm.nih.gov/gene/?term=10888	"GIR, GPR72 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001655	108897	Aif1l	http://www.ncbi.nlm.nih.gov/gene/?term=108897	"2810003C17Rik, AI043124, C87647, Iba2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001656	1088	CEACAM8	http://www.ncbi.nlm.nih.gov/gene/?term=1088	"CD66b, CD67, CGM6, NCA-95 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001657	1088	CEACAM8	http://www.ncbi.nlm.nih.gov/gene/?term=1088	"CD66b, CD67, CGM6, NCA-95 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001658	10890	RAB10	http://www.ncbi.nlm.nih.gov/gene/?term=10890		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001659	108927	Lhfp	http://www.ncbi.nlm.nih.gov/gene/?term=108927	"2810489O06Rik, AI194968 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001660	108934	Smim13	http://www.ncbi.nlm.nih.gov/gene/?term=108934	2900036K02Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001661	10893	MMP24	http://www.ncbi.nlm.nih.gov/gene/?term=10893	"MMP-24, MMP25, MT-MMP 5, MT-MMP5, MT5-MMP, MT5MMP, MTMMP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001662	108943	Trmt10a	http://www.ncbi.nlm.nih.gov/gene/?term=108943	"3110023L08Rik, AA794508, Rg9mtd2, Rnmtd2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001663	108954	Ppp1r15b	http://www.ncbi.nlm.nih.gov/gene/?term=108954	"1810033K10Rik, AI606441, C530022L24Rik, CReP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001664	10897	YIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=10897	"54TM, FinGER7, YIF1, YIF1P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001665	10897	YIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=10897	"54TM, FinGER7, YIF1, YIF1P "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001666	10897	YIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=10897	"54TM, FinGER7, YIF1, YIF1P "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001667	108989	Tpr	http://www.ncbi.nlm.nih.gov/gene/?term=108989	"2610029M07Rik, C77892 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001668	10899	JTB	http://www.ncbi.nlm.nih.gov/gene/?term=10899	"HJTB, HSPC222, PAR, hJT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001669	10899	JTB	http://www.ncbi.nlm.nih.gov/gene/?term=10899	"HJTB, HSPC222, PAR, hJT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001670	109006	Ciapin1	http://www.ncbi.nlm.nih.gov/gene/?term=109006	"2810413N20Rik, AA617265, AU021794, anamorsin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001671	10900	RUNDC3A	http://www.ncbi.nlm.nih.gov/gene/?term=10900	"RAP2IP, RPIP-8, RPIP8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001672	109011	1700020M10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=109011		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001673	109019	Nabp1	http://www.ncbi.nlm.nih.gov/gene/?term=109019	"4930434H03Rik, 4930442A21Rik, 4930488J04Rik, 4933440J18Rik, 5830411E10Rik, AI852561, Nbp1, Obfc2a, Ssb2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001674	10901	DHRS4	http://www.ncbi.nlm.nih.gov/gene/?term=10901	"CR, NRDR, PHCR, PSCD, SCAD-SRL, SDR-SRL, SDR25C1, SDR25C2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001675	10901	DHRS4	http://www.ncbi.nlm.nih.gov/gene/?term=10901	"CR, NRDR, PHCR, PSCD, SCAD-SRL, SDR-SRL, SDR25C1, SDR25C2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001676	10902	BRD8	http://www.ncbi.nlm.nih.gov/gene/?term=10902	"SMAP, SMAP2, p120 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001677	10902	BRD8	http://www.ncbi.nlm.nih.gov/gene/?term=10902	"SMAP, SMAP2, p120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001678	10904	BLCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10904	BC10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001679	10905	MAN1A2	http://www.ncbi.nlm.nih.gov/gene/?term=10905	MAN1B	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001680	10905	MAN1A2	http://www.ncbi.nlm.nih.gov/gene/?term=10905	MAN1B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001681	10906	TRAFD1	http://www.ncbi.nlm.nih.gov/gene/?term=10906	FLN29	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001682	109075	Exosc4	http://www.ncbi.nlm.nih.gov/gene/?term=109075	"1110039I09Rik, 1500001N04Rik, Rrp41 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001683	109077	Ints5	http://www.ncbi.nlm.nih.gov/gene/?term=109077	"1110055N21Rik, mKIAA1698 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001684	109077	Ints5	http://www.ncbi.nlm.nih.gov/gene/?term=109077	"1110055N21Rik, mKIAA1698 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001685	10907	TXNL4A	http://www.ncbi.nlm.nih.gov/gene/?term=10907	"BMKS, DIB1, DIM1, SNRNP15, TXNL4, U5-15kD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001686	10908	PNPLA6	http://www.ncbi.nlm.nih.gov/gene/?term=10908	"BNHS, LNMS, NTE, NTEMND, OMCS, SPG39, iPLA2delta, sws "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001687	10908	PNPLA6	http://www.ncbi.nlm.nih.gov/gene/?term=10908	"BNHS, LNMS, NTE, NTEMND, OMCS, SPG39, iPLA2delta, sws "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001688	109095	Rbm15b	http://www.ncbi.nlm.nih.gov/gene/?term=109095	1810017N16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001689	109108	Slc30a9	http://www.ncbi.nlm.nih.gov/gene/?term=109108	"2310024J23Rik, AL024256, GAC63, HUEL, znT-9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001690	10910	SUGT1	http://www.ncbi.nlm.nih.gov/gene/?term=10910	SGT1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001691	10910	SUGT1	http://www.ncbi.nlm.nih.gov/gene/?term=10910	SGT1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001692	10910	SUGT1	http://www.ncbi.nlm.nih.gov/gene/?term=10910	SGT1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001693	109113	Uhrf2	http://www.ncbi.nlm.nih.gov/gene/?term=109113	"2310065A22Rik, AI426270, AW214556, D130071B19Rik, Nirf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001694	109115	Supt3	http://www.ncbi.nlm.nih.gov/gene/?term=109115	"2310066G22Rik, AI315192, SPT3, SPT3Lh, Supt3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001695	10911	UTS2	http://www.ncbi.nlm.nih.gov/gene/?term=10911	"PRO1068, U-II, UCN2, UII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001696	109135	Plekha5	http://www.ncbi.nlm.nih.gov/gene/?term=109135	"2810431N21Rik, AI428202, AK129423, AMH-Cre, Ayu21-9, Gt(pU21)9Imeg, Pepp2, Tg(AMH-cre)1Flor "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001697	10914	PAPOLA	http://www.ncbi.nlm.nih.gov/gene/?term=10914	PAP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001698	10914	PAPOLA	http://www.ncbi.nlm.nih.gov/gene/?term=10914	PAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001699	10915	TCERG1	http://www.ncbi.nlm.nih.gov/gene/?term=10915	"CA150, TAF2S, Urn1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001700	10915	TCERG1	http://www.ncbi.nlm.nih.gov/gene/?term=10915	"CA150, TAF2S, Urn1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001701	109163	3010003L21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=109163		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001702	109181	Trip11	http://www.ncbi.nlm.nih.gov/gene/?term=109181	"2610511G22Rik, 3110031G15Rik, 6030460N08Rik, AI450776, GMAP-210, TRIP230 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001703	10919	EHMT2	http://www.ncbi.nlm.nih.gov/gene/?term=10919	"BAT8, C6orf30, G9A, GAT8, KMT1C, NG36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001704	109202	A930024E05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=109202		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001705	10920	COPS8	http://www.ncbi.nlm.nih.gov/gene/?term=10920	"COP9, CSN8, SGN8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001706	10920	COPS8	http://www.ncbi.nlm.nih.gov/gene/?term=10920	"COP9, CSN8, SGN8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001707	10920	COPS8	http://www.ncbi.nlm.nih.gov/gene/?term=10920	"COP9, CSN8, SGN8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001708	10921	RNPS1	http://www.ncbi.nlm.nih.gov/gene/?term=10921	E5.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001709	10921	RNPS1	http://www.ncbi.nlm.nih.gov/gene/?term=10921	E5.1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001710	10921	RNPS1	http://www.ncbi.nlm.nih.gov/gene/?term=10921	E5.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001711	10922	FASTK	http://www.ncbi.nlm.nih.gov/gene/?term=10922	FAST	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001712	10922	FASTK	http://www.ncbi.nlm.nih.gov/gene/?term=10922	FAST	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001713	109232	Sccpdh	http://www.ncbi.nlm.nih.gov/gene/?term=109232	"AW214504, C330023F11Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001714	109232	Sccpdh	http://www.ncbi.nlm.nih.gov/gene/?term=109232	"AW214504, C330023F11Rik "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00001715	10923	SUB1	http://www.ncbi.nlm.nih.gov/gene/?term=10923	"P15, PC4, p14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001716	10923	SUB1	http://www.ncbi.nlm.nih.gov/gene/?term=10923	"P15, PC4, p14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001717	109242	Kif24	http://www.ncbi.nlm.nih.gov/gene/?term=109242	"4933425J19Rik, 9430029L23Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001718	10924	SMPDL3A	http://www.ncbi.nlm.nih.gov/gene/?term=10924	"ASM3A, ASML3a, yR36GH4.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001719	10924	SMPDL3A	http://www.ncbi.nlm.nih.gov/gene/?term=10924	"ASM3A, ASML3a, yR36GH4.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001720	109270	Prr5	http://www.ncbi.nlm.nih.gov/gene/?term=109270	"AU043908, Arhgap8, C030017C09Rik, C78947, Protor-1, Protor1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001721	10927	SPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=10927	"SPIN, TDRD24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001722	109284	R3hdm4	http://www.ncbi.nlm.nih.gov/gene/?term=109284	"AI503502, C030046I01Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001723	10928	RALBP1	http://www.ncbi.nlm.nih.gov/gene/?term=10928	"RIP1, RLIP1, RLIP76 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001724	10928	RALBP1	http://www.ncbi.nlm.nih.gov/gene/?term=10928	"RIP1, RLIP1, RLIP76 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001725	10929	SRSF8	http://www.ncbi.nlm.nih.gov/gene/?term=10929	"DSM-1, SFRS2B, SRP46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001726	109332	Cdcp1	http://www.ncbi.nlm.nih.gov/gene/?term=109332	"9030022E12Rik, AA409659, E030027H19Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001727	109333	Pkn2	http://www.ncbi.nlm.nih.gov/gene/?term=109333	"6030436C20Rik, AI507382, PRK2, Prkcl2, Stk7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001728	109346	Ankrd39	http://www.ncbi.nlm.nih.gov/gene/?term=109346	"9130416N05Rik, C030004B10Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001729	109359	Fam175b	http://www.ncbi.nlm.nih.gov/gene/?term=109359	"AA589499, AI853413, Abro1, C430003P19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001730	10935	PRDX3	http://www.ncbi.nlm.nih.gov/gene/?term=10935	"AOP-1, AOP1, HBC189, MER5, PRO1748, SP-22, prx-III "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001731	10935	PRDX3	http://www.ncbi.nlm.nih.gov/gene/?term=10935	"AOP-1, AOP1, HBC189, MER5, PRO1748, SP-22, prx-III "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001732	10935	PRDX3	http://www.ncbi.nlm.nih.gov/gene/?term=10935	"AOP-1, AOP1, HBC189, MER5, PRO1748, SP-22, prx-III "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001733	10938	EHD1	http://www.ncbi.nlm.nih.gov/gene/?term=10938	"H-PAST, HPAST1, PAST, PAST1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001734	10939	AFG3L2	http://www.ncbi.nlm.nih.gov/gene/?term=10939	"SCA28, SPAX5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001735	10940	POP1	http://www.ncbi.nlm.nih.gov/gene/?term=10940		mRNA	Homo sapiens	21854988	Mitochondrion	-	Next-generation sequencing	"Firstly, to validate the two-phase sequencing approach, we considered three noncoding RNAs (ncRNAs), 5S rRNA, MRP and RNase P, that have been previously shown to be present in the mitochondrial matrix (Wang et al., 2010), finding all transcripts, though lowly expressed, enriched in mitoplasts (Figure S2D). "
RLID00001736	10943	MSL3	http://www.ncbi.nlm.nih.gov/gene/?term=10943	MSL3L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001737	10944	C11orf58	http://www.ncbi.nlm.nih.gov/gene/?term=10944	"IMAGE145052, SMAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001738	10944	C11orf58	http://www.ncbi.nlm.nih.gov/gene/?term=10944	"IMAGE145052, SMAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001739	10945	KDELR1	http://www.ncbi.nlm.nih.gov/gene/?term=10945	"ERD2, ERD2.1, HDEL, PM23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001740	10945	KDELR1	http://www.ncbi.nlm.nih.gov/gene/?term=10945	"ERD2, ERD2.1, HDEL, PM23 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001741	10945	KDELR1	http://www.ncbi.nlm.nih.gov/gene/?term=10945	"ERD2, ERD2.1, HDEL, PM23 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001742	10946	SF3A3	http://www.ncbi.nlm.nih.gov/gene/?term=10946	"PRP9, PRPF9, SAP61, SF3a60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001743	10946	SF3A3	http://www.ncbi.nlm.nih.gov/gene/?term=10946	"PRP9, PRPF9, SAP61, SF3a60 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001744	10947	AP3M2	http://www.ncbi.nlm.nih.gov/gene/?term=10947	"AP47B, CLA20, P47B "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001745	10947	AP3M2	http://www.ncbi.nlm.nih.gov/gene/?term=10947	"AP47B, CLA20, P47B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001746	10948	STARD3	http://www.ncbi.nlm.nih.gov/gene/?term=10948	"CAB1, MLN64, es64 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001747	10949	HNRNPA0	http://www.ncbi.nlm.nih.gov/gene/?term=10949	HNRPA0	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001748	10950	BTG3	http://www.ncbi.nlm.nih.gov/gene/?term=10950	"ANA, TOB5, TOB55, TOFA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001749	10950	BTG3	http://www.ncbi.nlm.nih.gov/gene/?term=10950	"ANA, TOB5, TOB55, TOFA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001750	10950	BTG3	http://www.ncbi.nlm.nih.gov/gene/?term=10950	"ANA, TOB5, TOB55, TOFA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001751	10951	CBX1	http://www.ncbi.nlm.nih.gov/gene/?term=10951	"CBX, HP1-BETA, HP1Hs-beta, HP1Hsbeta, M31, MOD1, p25beta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001752	10951	CBX1	http://www.ncbi.nlm.nih.gov/gene/?term=10951	"CBX, HP1-BETA, HP1Hs-beta, HP1Hsbeta, M31, MOD1, p25beta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001753	10952	SEC61B	http://www.ncbi.nlm.nih.gov/gene/?term=10952		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001754	10952	SEC61B	http://www.ncbi.nlm.nih.gov/gene/?term=10952		mRNA	Homo sapiens	26272916	Endoplasmic reticulum	U2OS cell	Fluorescence in situ hybridization	"Next, we monitored the localization of nesprin-2 (SYNE2) mRNA, which encodes a giant tail-anchored protein (796 kDa) that is present on the outer nuclear envelope and is involved in nuclear positioning (Luxton et al., 2010). After extraction, about two thirds of the foci remained, indicating that some of this mRNA was anchored to the ER (Fig. 1A,B). To ensure that the FISH signal was specific, we also probed cells that were depleted of the endogenous nesprin-2 mRNA using RNA interference (RNAi). Indeed, small hairpin RNA (shRNA)-treated cells lost 90% of their signal (supplementary material Fig. S1), indicating that our nesprin-2 probes detected the intended target. Like Sec61b, nesprin-2 mRNA largely remained associated with the ER in cells treated with HHT, or puromycin and EDTA. Thus nesprin-2, like Sec61b, can associate with the ER membrane, and this activity is mostly independent of translation. "
RLID00001755	10952	SEC61B	http://www.ncbi.nlm.nih.gov/gene/?term=10952		mRNA	Homo sapiens	26272916	Nucleus	U2OS cell	Fluorescence in situ hybridization	"Fig. 5.The initial targeting of Sec61b mRNA to the ER is partially dependent on ribosomes and translation. (B) Quantification of the fluorescence intensities of mRNAs in the ER and nucleus of extracted cell. Sec61b mRNA can occur to a certain extent in the absence of translation, it is clearly enhanced in the presence of translating ribosomes. "
RLID00001756	10952	SEC61B	http://www.ncbi.nlm.nih.gov/gene/?term=10952		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001757	10952	SEC61B	http://www.ncbi.nlm.nih.gov/gene/?term=10952		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001758	10953	TOMM34	http://www.ncbi.nlm.nih.gov/gene/?term=10953	"HTOM34P, TOM34, URCC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001759	10953	TOMM34	http://www.ncbi.nlm.nih.gov/gene/?term=10953	"HTOM34P, TOM34, URCC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001760	10953	TOMM34	http://www.ncbi.nlm.nih.gov/gene/?term=10953	"HTOM34P, TOM34, URCC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001761	10954	PDIA5	http://www.ncbi.nlm.nih.gov/gene/?term=10954	PDIR	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001762	10955	SERINC3	http://www.ncbi.nlm.nih.gov/gene/?term=10955	"AIGP1, DIFF33, SBBI99, TDE, TDE1, TMS-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001763	10955	SERINC3	http://www.ncbi.nlm.nih.gov/gene/?term=10955	"AIGP1, DIFF33, SBBI99, TDE, TDE1, TMS-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001764	10956	OS9	http://www.ncbi.nlm.nih.gov/gene/?term=10956	"ERLEC2, OS-9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001765	10956	OS9	http://www.ncbi.nlm.nih.gov/gene/?term=10956	"ERLEC2, OS-9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001766	10957	PNRC1	http://www.ncbi.nlm.nih.gov/gene/?term=10957	"B4-2, PNAS-145, PROL2, PRR2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001767	10957	PNRC1	http://www.ncbi.nlm.nih.gov/gene/?term=10957	"B4-2, PNAS-145, PROL2, PRR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001768	109594	Lmo1	http://www.ncbi.nlm.nih.gov/gene/?term=109594	"Rbtn-1, Rbtn1, Ttg1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001769	10959	TMED2	http://www.ncbi.nlm.nih.gov/gene/?term=10959	"P24A, RNP24, p24, p24b1, p24beta1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001770	10959	TMED2	http://www.ncbi.nlm.nih.gov/gene/?term=10959	"P24A, RNP24, p24, p24b1, p24beta1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001771	10959	TMED2	http://www.ncbi.nlm.nih.gov/gene/?term=10959	"P24A, RNP24, p24, p24b1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001772	10960	LMAN2	http://www.ncbi.nlm.nih.gov/gene/?term=10960	"C5orf8, GP36B, VIP36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001773	10961	ERP29	http://www.ncbi.nlm.nih.gov/gene/?term=10961	"C12orf8, ERp28, ERp31, HEL-S-107, PDI-DB, PDIA9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001774	10961	ERP29	http://www.ncbi.nlm.nih.gov/gene/?term=10961	"C12orf8, ERp28, ERp31, HEL-S-107, PDI-DB, PDIA9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001775	109624	Cald1	http://www.ncbi.nlm.nih.gov/gene/?term=109624	"4833423D12Rik, AI195384, AV071549, AW536160, C920027I18Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001776	10962	MLLT11	http://www.ncbi.nlm.nih.gov/gene/?term=10962	AF1Q	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001777	10963	STIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10963	"HEL-S-94n, HOP, IEF-SSP-3521, P60, STI1, STI1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001778	10963	STIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10963	"HEL-S-94n, HOP, IEF-SSP-3521, P60, STI1, STI1L "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001779	10963	STIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10963	"HEL-S-94n, HOP, IEF-SSP-3521, P60, STI1, STI1L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001780	109652	Acy1	http://www.ncbi.nlm.nih.gov/gene/?term=109652	"1110014J22Rik, Acy-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001781	10966	RAB40B	http://www.ncbi.nlm.nih.gov/gene/?term=10966	"RAR, SEC4L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001782	10966	RAB40B	http://www.ncbi.nlm.nih.gov/gene/?term=10966	"RAR, SEC4L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001783	109676	Ank2	http://www.ncbi.nlm.nih.gov/gene/?term=109676	"AI835472, AW491075, Ank-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001784	10969	EBNA1BP2	http://www.ncbi.nlm.nih.gov/gene/?term=10969	"EBP2, NOBP, P40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001785	10969	EBNA1BP2	http://www.ncbi.nlm.nih.gov/gene/?term=10969	"EBP2, NOBP, P40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001786	109700	Itga1	http://www.ncbi.nlm.nih.gov/gene/?term=109700	"CD49A, E130012M19Rik, Vla1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001787	10970	CKAP4	http://www.ncbi.nlm.nih.gov/gene/?term=10970	"CLIMP-63, ERGIC-63, p63 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001788	10970	CKAP4	http://www.ncbi.nlm.nih.gov/gene/?term=10970	"CLIMP-63, ERGIC-63, p63 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001789	109711	Actn1	http://www.ncbi.nlm.nih.gov/gene/?term=109711	"3110023F10Rika, Actn1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001790	10971	YWHAQ	http://www.ncbi.nlm.nih.gov/gene/?term=10971	"14-3-3, 1C5, HS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001791	10971	YWHAQ	http://www.ncbi.nlm.nih.gov/gene/?term=10971	"14-3-3, 1C5, HS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001792	10971	YWHAQ	http://www.ncbi.nlm.nih.gov/gene/?term=10971	"14-3-3, 1C5, HS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001793	10972	TMED10	http://www.ncbi.nlm.nih.gov/gene/?term=10972	"P24(DELTA), S31I125, S31III125, TMP21, Tmp-21-I, p23, p24d1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001794	10972	TMED10	http://www.ncbi.nlm.nih.gov/gene/?term=10972	"P24(DELTA), S31I125, S31III125, TMP21, Tmp-21-I, p23, p24d1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001795	10972	TMED10	http://www.ncbi.nlm.nih.gov/gene/?term=10972	"P24(DELTA), S31I125, S31III125, TMP21, Tmp-21-I, p23, p24d1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001796	10973	ASCC3	http://www.ncbi.nlm.nih.gov/gene/?term=10973	"ASC1p200, HELIC1, RNAH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001797	10974	ADIRF	http://www.ncbi.nlm.nih.gov/gene/?term=10974	"AFRO, APM2, C10orf116, apM-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001798	10974	ADIRF	http://www.ncbi.nlm.nih.gov/gene/?term=10974	"AFRO, APM2, C10orf116, apM-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001799	109754	Cyb5r3	http://www.ncbi.nlm.nih.gov/gene/?term=109754	"0610016L08Rik, 2500002N19Rik, C85115, Dia-1, Dia1, WU:AL591952.1-001, WU:AL591952.1-002, WU:AL591952.1-003, WU:Cyb5r3 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00001800	10975	UQCR11	http://www.ncbi.nlm.nih.gov/gene/?term=10975	"0710008D09Rik, QCR10, UQCR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001801	109785	Pgm3	http://www.ncbi.nlm.nih.gov/gene/?term=109785	"2810473H05Rik, Agm1, BB187688, C77933, PAGM, Pgm-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001802	10978	CLP1	http://www.ncbi.nlm.nih.gov/gene/?term=10978	"HEAB, hClp1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001803	10979	FERMT2	http://www.ncbi.nlm.nih.gov/gene/?term=10979	"KIND2, MIG2, PLEKHC1, UNC112, UNC112B, mig-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001804	10979	FERMT2	http://www.ncbi.nlm.nih.gov/gene/?term=10979	"KIND2, MIG2, PLEKHC1, UNC112, UNC112B, mig-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001805	10980	COPS6	http://www.ncbi.nlm.nih.gov/gene/?term=10980	"CSN6, MOV34-34KD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001806	10981	RAB32	http://www.ncbi.nlm.nih.gov/gene/?term=10981		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001807	10981	RAB32	http://www.ncbi.nlm.nih.gov/gene/?term=10981		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001808	10982	MAPRE2	http://www.ncbi.nlm.nih.gov/gene/?term=10982	"CSCSC2, EB1, EB2, RP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001809	10982	MAPRE2	http://www.ncbi.nlm.nih.gov/gene/?term=10982	"CSCSC2, EB1, EB2, RP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001810	10984	KCNQ1OT1	http://www.ncbi.nlm.nih.gov/gene/?term=10984	"KCNQ1-AS2, KCNQ10T1, Kncq1, KvDMR1, KvLQT1-AS, LIT1, NCRNA00012 "	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00001811	10984	KCNQ1OT1	http://www.ncbi.nlm.nih.gov/gene/?term=10984	"KCNQ1-AS2, KCNQ10T1, Kncq1, KvDMR1, KvLQT1-AS, LIT1, NCRNA00012 "	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00001812	109857	Cbr3	http://www.ncbi.nlm.nih.gov/gene/?term=109857	"1110001J05Rik, C81353 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001813	10985	GCN1	http://www.ncbi.nlm.nih.gov/gene/?term=10985	"GCN1LL1, PRIC295, GCN1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001814	10985	GCN1	http://www.ncbi.nlm.nih.gov/gene/?term=10985	"GCN1LL1, PRIC295, GCN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001815	10985	GCN1	http://www.ncbi.nlm.nih.gov/gene/?term=10985	"GCN1L, GCN1L1, PRIC295 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001816	10987	COPS5	http://www.ncbi.nlm.nih.gov/gene/?term=10987	"CSN5, JAB1, MOV-34, SGN5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001817	10987	COPS5	http://www.ncbi.nlm.nih.gov/gene/?term=10987	"CSN5, JAB1, MOV-34, SGN5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001818	10987	COPS5	http://www.ncbi.nlm.nih.gov/gene/?term=10987	"CSN5, JAB1, MOV-34, SGN5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001819	109880	Braf	http://www.ncbi.nlm.nih.gov/gene/?term=109880	"9930012E13Rik, AA120551, AA387315, AA473386, B-raf-2, Braf2, C230098H17, C87398, D6Ertd631e, Braf "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001820	10988	METAP2	http://www.ncbi.nlm.nih.gov/gene/?term=10988	"MAP2, MNPEP, p67eIF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001821	10988	METAP2	http://www.ncbi.nlm.nih.gov/gene/?term=10988	"MAP2, MNPEP, p67eIF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001822	10988	METAP2	http://www.ncbi.nlm.nih.gov/gene/?term=10988	"MAP2, MNPEP, p67eIF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001823	10989	IMMT	http://www.ncbi.nlm.nih.gov/gene/?term=10989	"HMP, MINOS2, Mic60, P87, P87/89, P89, PIG4, PIG52 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001824	10989	IMMT	http://www.ncbi.nlm.nih.gov/gene/?term=10989	"HMP, MINOS2, Mic60, P87, P87/89, P89, PIG4, PIG52 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001825	109900	Asl	http://www.ncbi.nlm.nih.gov/gene/?term=109900	2510006M18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001826	109910	Zfp91	http://www.ncbi.nlm.nih.gov/gene/?term=109910	"9130014I08Rik, A530054C17Rik, AL024263, AW545902, Pzf, Zfp-91 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001827	10992	SF3B2	http://www.ncbi.nlm.nih.gov/gene/?term=10992	"Cus1, SAP145, SF3B145, SF3b1, SF3b150 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001828	10992	SF3B2	http://www.ncbi.nlm.nih.gov/gene/?term=10992	"Cus1, SAP145, SF3B145, SF3b1, SF3b150 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001829	10994	ILVBL	http://www.ncbi.nlm.nih.gov/gene/?term=10994	"209L8, AHAS, ILV2H "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001830	10994	ILVBL	http://www.ncbi.nlm.nih.gov/gene/?term=10994	"209L8, AHAS, ILV2H "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001831	10998	SLC27A5	http://www.ncbi.nlm.nih.gov/gene/?term=10998	"ACSB, ACSVL6, BACS, BAL, FACVL3, FATP-5, FATP5, VLACSR, VLCS-H2, VLCSH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001832	10998	SLC27A5	http://www.ncbi.nlm.nih.gov/gene/?term=10998	"ACSB, ACSVL6, BACS, BAL, FACVL3, FATP-5, FATP5, VLACSR, VLCS-H2, VLCSH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001833	10999	SLC27A4	http://www.ncbi.nlm.nih.gov/gene/?term=10999	"ACSVL4, FATP4, IPS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001834	109	ADCY3	http://www.ncbi.nlm.nih.gov/gene/?term=109	"AC-III, AC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001835	109	ADCY3	http://www.ncbi.nlm.nih.gov/gene/?term=109	"AC-III, AC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001836	11001	SLC27A2	http://www.ncbi.nlm.nih.gov/gene/?term=11001	"ACSVL1, FACVL1, FATP2, HsT17226, VLACS, VLCS, hFACVL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001837	11004	KIF2C	http://www.ncbi.nlm.nih.gov/gene/?term=11004	"CT139, KNSL6, MCAK "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001838	11004	KIF2C	http://www.ncbi.nlm.nih.gov/gene/?term=11004	"CT139, KNSL6, MCAK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001839	11004	KIF2C	http://www.ncbi.nlm.nih.gov/gene/?term=11004	"CT139, KNSL6, MCAK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001840	11005	SPINK5	http://www.ncbi.nlm.nih.gov/gene/?term=11005	"LEKTI, LETKI, NETS, NS, VAKTI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001841	11007	CCDC85B	http://www.ncbi.nlm.nih.gov/gene/?term=11007	DIPA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001842	11007	CCDC85B	http://www.ncbi.nlm.nih.gov/gene/?term=11007	DIPA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001843	11009	IL24	http://www.ncbi.nlm.nih.gov/gene/?term=11009	"C49A, FISP, IL10B, MDA7, MOB5, ST16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001844	11010	GLIPR1	http://www.ncbi.nlm.nih.gov/gene/?term=11010	"CRISP7, GLIPR, RTVP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001845	11011	TLK2	http://www.ncbi.nlm.nih.gov/gene/?term=11011	"HsHPK, PKU-ALPHA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001846	110135	Fgb	http://www.ncbi.nlm.nih.gov/gene/?term=110135	2510049G14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001847	11014	KDELR2	http://www.ncbi.nlm.nih.gov/gene/?term=11014	"ELP-1, ERD2.2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001848	11014	KDELR2	http://www.ncbi.nlm.nih.gov/gene/?term=11014	"ELP-1, ERD2.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001849	110157	Raf1	http://www.ncbi.nlm.nih.gov/gene/?term=110157	"6430402F14Rik, AA990557, BB129353, Craf1, D830050J10Rik, Raf-1, c-Raf, v-Raf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001850	11015	KDELR3	http://www.ncbi.nlm.nih.gov/gene/?term=11015	ERD2L3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001851	11015	KDELR3	http://www.ncbi.nlm.nih.gov/gene/?term=11015	ERD2L3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001852	11016	ATF7	http://www.ncbi.nlm.nih.gov/gene/?term=11016	ATFA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001853	110175	Ggct	http://www.ncbi.nlm.nih.gov/gene/?term=110175	"A030007L17Rik, AA673177, Gctg, Ggc "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001854	11017	SNRNP27	http://www.ncbi.nlm.nih.gov/gene/?term=11017	"27K, RY1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001855	11017	SNRNP27	http://www.ncbi.nlm.nih.gov/gene/?term=11017	"27K, RY1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001856	11018	TMED1	http://www.ncbi.nlm.nih.gov/gene/?term=11018	"IL1RL1LG, Il1rl1l, Tp24, p24g1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001857	110198	Akr7a5	http://www.ncbi.nlm.nih.gov/gene/?term=110198	"0610025K21Rik, Afar, Afar1, Akr7a2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001858	11019	LIAS	http://www.ncbi.nlm.nih.gov/gene/?term=11019	"HGCLAS, HUSSY-01, LAS, LIP1, LS, PDHLD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001859	11019	LIAS	http://www.ncbi.nlm.nih.gov/gene/?term=11019	"HUSSY-01, LAS, LIP1, LS, PDHLD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001860	11020	IFT27	http://www.ncbi.nlm.nih.gov/gene/?term=11020	"BBS19, RABL4, RAYL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001861	11021	RAB35	http://www.ncbi.nlm.nih.gov/gene/?term=11021	"H-ray, RAB1C, RAY "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001862	11021	RAB35	http://www.ncbi.nlm.nih.gov/gene/?term=11021	"H-ray, RAB1C, RAY "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001863	11025	LILRB3	http://www.ncbi.nlm.nih.gov/gene/?term=11025	"CD85A, HL9, ILT-5, ILT5, LILRA6, LIR-3, LIR3, PIR-B, PIRB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001864	11025	LILRB3	http://www.ncbi.nlm.nih.gov/gene/?term=11025	"CD85A, HL9, ILT-5, ILT5, LILRA6, LIR-3, LIR3, PIR-B, PIRB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001865	11025	LILRB3	http://www.ncbi.nlm.nih.gov/gene/?term=11025	"CD85A, HL9, ILT-5, ILT5, LILRA6, LIR-3, LIR3, PIRB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001866	11027	LILRA2	http://www.ncbi.nlm.nih.gov/gene/?term=11027	"CD85H, ILT1, LIR-7, LIR7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001867	1102	RCBTB2	http://www.ncbi.nlm.nih.gov/gene/?term=1102	"CHC1L, RLG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001868	11031	RAB31	http://www.ncbi.nlm.nih.gov/gene/?term=11031	Rab22B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001869	110326	Tas1r1	http://www.ncbi.nlm.nih.gov/gene/?term=110326	"Gpr70, T1r1, TR1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001870	110333	Rmst	http://www.ncbi.nlm.nih.gov/gene/?term=110333	"AI853140, C230053E11Rik, D930049J19Rik, Dmt2, M2, Ncrms "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001871	110333	Rmst	http://www.ncbi.nlm.nih.gov/gene/?term=110333	"AI853140, C230053E11Rik, D930049J19Rik, Dmt2, M2, Ncrms "	lncRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"We then analyzed the abundance of several lncRNAs, namely Malat1, Meg3, Rmst, Xist and Miat. All of these lncRNAs were present in the axonal compartment.  "
RLID00001872	11033	ADAP1	http://www.ncbi.nlm.nih.gov/gene/?term=11033	"CENTA1, GCS1L, p42IP4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001873	11034	DSTN	http://www.ncbi.nlm.nih.gov/gene/?term=11034	"ACTDP, ADF, HEL32, bA462D18.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001874	110350	Dync2h1	http://www.ncbi.nlm.nih.gov/gene/?term=110350	"4432416O06Rik, AI448217, D030010H02Rik, D330044F14Rik, DHC1b, DHC2, Dnchc2, b2b414Clo, mKIAA1997 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001875	11037	STON1	http://www.ncbi.nlm.nih.gov/gene/?term=11037	"SALF, SBLF, STN1, STNB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001876	11039	SMA4	http://www.ncbi.nlm.nih.gov/gene/?term=11039	"SMA3, b55C20.2 "	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001877	11040	PIM2	http://www.ncbi.nlm.nih.gov/gene/?term=11040		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001878	11040	PIM2	http://www.ncbi.nlm.nih.gov/gene/?term=11040		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001879	11040	PIM2	http://www.ncbi.nlm.nih.gov/gene/?term=11040		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001880	11044	PAPD7	http://www.ncbi.nlm.nih.gov/gene/?term=11044	"LAK-1, LAK1, POLK, POLS, TRF4, TRF4-1, TRF41, TUTASE5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001881	11046	SLC35D2	http://www.ncbi.nlm.nih.gov/gene/?term=11046	"HFRC1, SQV7L, UGTrel8, hfrc "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001882	11046	SLC35D2	http://www.ncbi.nlm.nih.gov/gene/?term=11046	"HFRC1, SQV7L, UGTrel8, hfrc "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001883	11047	ADRM1	http://www.ncbi.nlm.nih.gov/gene/?term=11047	"ARM-1, ARM1, GP110 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001884	11047	ADRM1	http://www.ncbi.nlm.nih.gov/gene/?term=11047	"ARM-1, ARM1, GP110 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001885	11047	ADRM1	http://www.ncbi.nlm.nih.gov/gene/?term=11047	"ARM-1, ARM1, GP110 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001886	11049	NUS1P3	http://www.ncbi.nlm.nih.gov/gene/?term=11049	YDD19	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001887	1104	RCC1	http://www.ncbi.nlm.nih.gov/gene/?term=1104	"CHC1-I, SNHG3-RCC1, RCC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001888	1104	RCC1	http://www.ncbi.nlm.nih.gov/gene/?term=1104	"CHC1-I, SNHG3-RCC1, RCC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001889	1104	RCC1	http://www.ncbi.nlm.nih.gov/gene/?term=1104	"CHC1, RCC1-I, SNHG3-RCC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001890	11051	NUDT21	http://www.ncbi.nlm.nih.gov/gene/?term=11051	"CFIM25, CPSF5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001891	11051	NUDT21	http://www.ncbi.nlm.nih.gov/gene/?term=11051	"CFIM25, CPSF5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001892	110524	Dgkq	http://www.ncbi.nlm.nih.gov/gene/?term=110524	"110kDa, DAGK, DAGK7, Dagk4, Dgkd "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001893	11052	CPSF6	http://www.ncbi.nlm.nih.gov/gene/?term=11052	"CFIM, CFIM68, HPBRII-4, HPBRII-7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001894	11052	CPSF6	http://www.ncbi.nlm.nih.gov/gene/?term=11052	"CFIM, CFIM68, HPBRII-4, HPBRII-7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001895	110532	Adarb1	http://www.ncbi.nlm.nih.gov/gene/?term=110532	"1700057H01Rik, AW124433, AW558573, Adar2, BB220382, D10Bwg0447e, Red1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001896	110542	Amhr2	http://www.ncbi.nlm.nih.gov/gene/?term=110542	"Misiir, Misrii, Mrii "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001897	11054	OGFR	http://www.ncbi.nlm.nih.gov/gene/?term=11054		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001898	11056	DDX52	http://www.ncbi.nlm.nih.gov/gene/?term=11056	"HUSSY19, ROK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001899	11057	ABHD2	http://www.ncbi.nlm.nih.gov/gene/?term=11057	"HS1-2, LABH2, PHPS1-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001900	11057	ABHD2	http://www.ncbi.nlm.nih.gov/gene/?term=11057	"HS1-2, LABH2, PHPS1-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001901	11059	WWP1	http://www.ncbi.nlm.nih.gov/gene/?term=11059	"AIP5, Tiul1, hSDRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001902	1105	CHD1	http://www.ncbi.nlm.nih.gov/gene/?term=1105		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001903	1105	CHD1	http://www.ncbi.nlm.nih.gov/gene/?term=1105		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001904	11060	WWP2	http://www.ncbi.nlm.nih.gov/gene/?term=11060	"AIP2, WWp2-like "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001905	11060	WWP2	http://www.ncbi.nlm.nih.gov/gene/?term=11060	"AIP2, WWp2-like "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001906	110611	Hdlbp	http://www.ncbi.nlm.nih.gov/gene/?term=110611	"1110005P14Rik, AA960365, AI118566, D1Ertd101e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001907	110616	Atxn3	http://www.ncbi.nlm.nih.gov/gene/?term=110616	"2210008M02Rik, AI463012, AI647473, ATX3, MJD1, Mjd, Sca3, ataxin-3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001908	11062	DUS4L	http://www.ncbi.nlm.nih.gov/gene/?term=11062	"DUS4, PP35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001909	11063	SOX30	http://www.ncbi.nlm.nih.gov/gene/?term=11063		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001910	110651	Rps6ka3	http://www.ncbi.nlm.nih.gov/gene/?term=110651	"MAPKAPK-1b, MPK-9, Rsk2, S6K-alpha3, p90RSK3, pp90RSK2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001911	11066	SNRNP35	http://www.ncbi.nlm.nih.gov/gene/?term=11066	"HM-1, U1SNRNPBP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001912	11066	SNRNP35	http://www.ncbi.nlm.nih.gov/gene/?term=11066	"HM-1, U1SNRNPBP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001913	11067	C10orf10	http://www.ncbi.nlm.nih.gov/gene/?term=11067	"DEPP, FIG, Fseg "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001914	11067	C10orf10	http://www.ncbi.nlm.nih.gov/gene/?term=11067	"DEPP, FIG, Fseg "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001915	11068	CYB561D2	http://www.ncbi.nlm.nih.gov/gene/?term=11068	"101F6, TSP10, XXcos-LUCA11.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001916	11068	CYB561D2	http://www.ncbi.nlm.nih.gov/gene/?term=11068	"101F6, TSP10, XXcos-LUCA11.4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001917	1106	CHD2	http://www.ncbi.nlm.nih.gov/gene/?term=1106	EEOC	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001918	1106	CHD2	http://www.ncbi.nlm.nih.gov/gene/?term=1106	EEOC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001919	11070	TMEM115	http://www.ncbi.nlm.nih.gov/gene/?term=11070	PL6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001920	11070	TMEM115	http://www.ncbi.nlm.nih.gov/gene/?term=11070	PL6	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001921	11072	DUSP14	http://www.ncbi.nlm.nih.gov/gene/?term=11072	"MKP-L, MKP6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001922	11073	TOPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=11073	TOP2BP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001923	11074	TRIM31	http://www.ncbi.nlm.nih.gov/gene/?term=11074	"C6orf13, HCG1, HCGI, RNF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001924	110750	Cse1l	http://www.ncbi.nlm.nih.gov/gene/?term=110750	"2610100P18Rik, AA407533, Capts, Cas, Xpo2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001925	11076	TPPP	http://www.ncbi.nlm.nih.gov/gene/?term=11076	"TPPP/p25, TPPP1, p24, p25, p25alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001926	11078	TRIOBP	http://www.ncbi.nlm.nih.gov/gene/?term=11078	"DFNB28, HRIHFB2122, TAP68, TARA, dJ37E16.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001927	11078	TRIOBP	http://www.ncbi.nlm.nih.gov/gene/?term=11078	"DFNB28, HRIHFB2122, TAP68, TARA, dJ37E16.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001928	11079	RER1	http://www.ncbi.nlm.nih.gov/gene/?term=11079		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001929	11079	RER1	http://www.ncbi.nlm.nih.gov/gene/?term=11079		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001930	11079	RER1	http://www.ncbi.nlm.nih.gov/gene/?term=11079		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001931	1107	CHD3	http://www.ncbi.nlm.nih.gov/gene/?term=1107	"Mi-2a, Mi2-ALPHA, ZFH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001932	110809	Srsf1	http://www.ncbi.nlm.nih.gov/gene/?term=110809	"1110054N12Rik, 5730507C05Rik, 6330415C05Rik, AI482334, AW491331, Asf, Sf2, Sfrs1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001933	110834	Chrna3	http://www.ncbi.nlm.nih.gov/gene/?term=110834	"(a)3, A730007P14Rik, Acra-3, Acra3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001934	11083	DIDO1	http://www.ncbi.nlm.nih.gov/gene/?term=11083	"BYE1, C20orf158, DATF-1, DATF1, DIDO2, DIDO3, DIO-1, DIO1, dJ885L7.8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001935	11083	DIDO1	http://www.ncbi.nlm.nih.gov/gene/?term=11083	"BYE1, C20orf158, DATF-1, DATF1, DIDO2, DIDO3, DIO-1, DIO1, dJ885L7.8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001936	110842	Etfa	http://www.ncbi.nlm.nih.gov/gene/?term=110842	"2010200I21Rik, D9Ertd394e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001937	110876	Scn2a1	http://www.ncbi.nlm.nih.gov/gene/?term=110876	"6430408L10, A230052E19Rik, Nav1.2, Scn2a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001938	110877	Slc18a1	http://www.ncbi.nlm.nih.gov/gene/?term=110877	"4832416I10Rik, Vat1, Vmat1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001939	110886	Gabra5	http://www.ncbi.nlm.nih.gov/gene/?term=110886	A230018I05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001940	110893	Slc8a3	http://www.ncbi.nlm.nih.gov/gene/?term=110893	"AW742262, Ncx3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001941	1108	CHD4	http://www.ncbi.nlm.nih.gov/gene/?term=1108	"CHD-4, Mi-2b, Mi2-BETA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001942	1108	CHD4	http://www.ncbi.nlm.nih.gov/gene/?term=1108	"CHD-4, Mi-2b, Mi2-BETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001943	11091	WDR5	http://www.ncbi.nlm.nih.gov/gene/?term=11091	"BIG-3, CFAP89, SWD3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001944	110920	Hspa13	http://www.ncbi.nlm.nih.gov/gene/?term=110920	"1600002I10Rik, AV006182, B230217N24Rik, Stch "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001945	110924	Tmevp3	http://www.ncbi.nlm.nih.gov/gene/?term=110924	NeST	lncRNA	Mus musculus	23415224	Nucleus	T cell	RT-PCR	"We hypothesized that, like several lncRNAs, NeST RNA affects IFN-γ accumulation at the transcriptional level by interacting with chromatin modification complexes. Consistent with this idea, most of the NeST RNA in either congenic or transgenic mice was found in the nuclear fraction of CD8+ T cells, co-fractionating with unspliced, but not spliced, actin mRNA (Fig. 6A). "
RLID00001946	11094	CACFD1	http://www.ncbi.nlm.nih.gov/gene/?term=11094	"C9orf7, D9S2135, FLOWER "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001947	110954	Rpl10	http://www.ncbi.nlm.nih.gov/gene/?term=110954	"D0HXS648, DXHXS648, DXHXS648E, QM, QM16 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00001948	110956	D17H6S56E-5	http://www.ncbi.nlm.nih.gov/gene/?term=110956	G7e	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001949	110960	Tars	http://www.ncbi.nlm.nih.gov/gene/?term=110960	"D15Wsu59e, ThrRS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001950	11096	ADAMTS5	http://www.ncbi.nlm.nih.gov/gene/?term=11096	"ADAM-TS 11, ADAM-TS 5, ADAM-TS5, ADAMTS-11, ADAMTS-5, ADAMTS11, ADMP-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001951	11097	NUPL2	http://www.ncbi.nlm.nih.gov/gene/?term=11097	"CG1, NLP-1, NLP_1, hCG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001952	110989	Rnu1-ps1	http://www.ncbi.nlm.nih.gov/gene/110989	Rnu1-1	snRNA	Mus musculus	26195734	Nucleus	Fibroblast	Sticky-Flare Synthesis	"Furthermore, we investigate the application of Sticky-flares for tracking transcripts that undergo more extensive compartmentalization by fluorophore-labeling U1 small nuclear RNA and observing its distribution in the nucleus of live cells. "
RLID00001953	11098	PRSS23	http://www.ncbi.nlm.nih.gov/gene/?term=11098	"SIG13, SPUVE, ZSIG13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001954	11098	PRSS23	http://www.ncbi.nlm.nih.gov/gene/?term=11098	"SIG13, SPUVE, ZSIG13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001955	11098	PRSS23	http://www.ncbi.nlm.nih.gov/gene/?term=11098	"SIG13, SPUVE, ZSIG13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001956	11100	HNRNPUL1	http://www.ncbi.nlm.nih.gov/gene/?term=11100	"E1B-AP5, E1BAP5, HNRPUL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001957	11101	ATE1	http://www.ncbi.nlm.nih.gov/gene/?term=11101		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001958	11102	RPP14	http://www.ncbi.nlm.nih.gov/gene/?term=11102	P14	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001959	11103	KRR1	http://www.ncbi.nlm.nih.gov/gene/?term=11103	"HRB2, RIP-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001960	11103	KRR1	http://www.ncbi.nlm.nih.gov/gene/?term=11103	"HRB2, RIP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001961	11104	KATNA1	http://www.ncbi.nlm.nih.gov/gene/?term=11104		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001962	11104	KATNA1	http://www.ncbi.nlm.nih.gov/gene/?term=11104		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001963	11112	HIBADH	http://www.ncbi.nlm.nih.gov/gene/?term=11112	NS5ATP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001964	11112	HIBADH	http://www.ncbi.nlm.nih.gov/gene/?term=11112	NS5ATP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001965	11113	CIT	http://www.ncbi.nlm.nih.gov/gene/?term=11113	"CRIK, STK21 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001966	11113	CIT	http://www.ncbi.nlm.nih.gov/gene/?term=11113	"CRIK, STK21 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001967	11116	FGFR1OP	http://www.ncbi.nlm.nih.gov/gene/?term=11116	FOP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001968	111173	Erc1	http://www.ncbi.nlm.nih.gov/gene/?term=111173	"4930404L01Rik, 5033405M01Rik, 9630025C19Rik, B430107L16Rik, CAST2, ELKS, Elks1, RAB6IP2A, RAB6IP2B, Rab6ip2, mKIAA1081 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00001969	11117	EMILIN1	http://www.ncbi.nlm.nih.gov/gene/?term=11117	"EMI, EMILIN, gp115 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001970	11118	BTN3A2	http://www.ncbi.nlm.nih.gov/gene/?term=11118	"BT3.2, BTF4, BTN3.2, CD277 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001971	11119	BTN3A1	http://www.ncbi.nlm.nih.gov/gene/?term=11119	"BT3.1, BTF5, BTN3.1, CD277 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001972	11119	BTN3A1	http://www.ncbi.nlm.nih.gov/gene/?term=11119	"BT3.1, BTF5, BTN3.1, CD277 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001973	11119	BTN3A1	http://www.ncbi.nlm.nih.gov/gene/?term=11119	"BT3.1, BTF5, BTN3.1, CD277 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001974	1111	CHEK1	http://www.ncbi.nlm.nih.gov/gene/?term=1111	CHK1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001975	1111	CHEK1	http://www.ncbi.nlm.nih.gov/gene/?term=1111	CHK1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001976	11120	BTN2A1	http://www.ncbi.nlm.nih.gov/gene/?term=11120	"BK14H9.1, BT2.1, BTF1, BTN2.1, DJ3E1.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001977	11124	FAF1	http://www.ncbi.nlm.nih.gov/gene/?term=11124	"CGI-03, HFAF1s, UBXD12, UBXN3A, hFAF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001978	11124	FAF1	http://www.ncbi.nlm.nih.gov/gene/?term=11124	"CGI-03, HFAF1s, UBXD12, UBXN3A, hFAF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001979	11127	KIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=11127	"FLA10, KLP-20 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001980	11127	KIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=11127	"FLA10, KLP-20 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001981	11127	KIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=11127	"FLA10, KLP-20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001982	11128	POLR3A	http://www.ncbi.nlm.nih.gov/gene/?term=11128	"ADDH, HLD7, RPC1, RPC155, hRPC155 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001983	1112	FOXN3	http://www.ncbi.nlm.nih.gov/gene/?term=1112	"C14orf116, CHES1, PRO1635 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001984	11130	ZWINT	http://www.ncbi.nlm.nih.gov/gene/?term=11130	"HZwint-1, KNTC2AP, SIP301, ZWINT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001985	11130	ZWINT	http://www.ncbi.nlm.nih.gov/gene/?term=11130	"HZwint-1, KNTC2AP, SIP30, ZWINT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001986	111357	Rsp6	http://www.ncbi.nlm.nih.gov/gene/?term=111357	Rsp-6	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00001987	11135	CDC42EP1	http://www.ncbi.nlm.nih.gov/gene/?term=11135	"BORG5, CEP1, MSE55 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001988	11135	CDC42EP1	http://www.ncbi.nlm.nih.gov/gene/?term=11135	"BORG5, CEP1, MSE55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001989	11137	PWP1	http://www.ncbi.nlm.nih.gov/gene/?term=11137	IEF-SSP-9502	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001990	11137	PWP1	http://www.ncbi.nlm.nih.gov/gene/?term=11137	IEF-SSP-9502	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001991	11138	TBC1D8	http://www.ncbi.nlm.nih.gov/gene/?term=11138	"AD3, GRAMD8, HBLP1A, VRP, TBC1D8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001992	11140	CDC37	http://www.ncbi.nlm.nih.gov/gene/?term=11140	P50CDC37	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001993	11140	CDC37	http://www.ncbi.nlm.nih.gov/gene/?term=11140	P50CDC37	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00001994	11140	CDC37	http://www.ncbi.nlm.nih.gov/gene/?term=11140	P50CDC37	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001995	11142	PKIG	http://www.ncbi.nlm.nih.gov/gene/?term=11142	PKI-gamma	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00001996	11143	KAT7	http://www.ncbi.nlm.nih.gov/gene/?term=11143	"HBO1, HBOA, MYST2, ZC2HC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001997	11145	PLA2G16	http://www.ncbi.nlm.nih.gov/gene/?term=11145	"AdPLA, H-REV107-1, HRASLS3, HREV107, HREV107-1, HREV107-3, HRSL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00001998	11149	BVES	http://www.ncbi.nlm.nih.gov/gene/?term=11149	"HBVES, LGMD2X, POP1, POPDC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00001999	11149	BVES	http://www.ncbi.nlm.nih.gov/gene/?term=11149	"HBVES, LGMD2X, POP1, POPDC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002000	11151	CORO1A	http://www.ncbi.nlm.nih.gov/gene/?term=11151	"CLABP, CLIPINA, HCORO1, IMD8, TACO, p57 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002001	11152	WDR45	http://www.ncbi.nlm.nih.gov/gene/?term=11152	"JM5, NBIA4, NBIA5, WDRX1, WIPI-4, WIPI4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002002	11152	WDR45	http://www.ncbi.nlm.nih.gov/gene/?term=11152	"JM5, NBIA4, NBIA5, WDRX1, WIPI-4, WIPI4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002003	11154	AP4S1	http://www.ncbi.nlm.nih.gov/gene/?term=11154	"AP47B, CLA20, CLAPS4, CPSQ6, SPG52 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002004	11156	PTP4A3	http://www.ncbi.nlm.nih.gov/gene/?term=11156	"PRL-3, PRL-R, PRL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002005	11157	LSM6	http://www.ncbi.nlm.nih.gov/gene/?term=11157	YDR378C	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002006	11158	RABL2B	http://www.ncbi.nlm.nih.gov/gene/?term=11158		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002007	11158	RABL2B	http://www.ncbi.nlm.nih.gov/gene/?term=11158		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002008	11158	RABL2B	http://www.ncbi.nlm.nih.gov/gene/?term=11158		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002009	11159	RABL2A	http://www.ncbi.nlm.nih.gov/gene/?term=11159		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002010	11159	RABL2A	http://www.ncbi.nlm.nih.gov/gene/?term=11159		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002011	11160	ERLIN2	http://www.ncbi.nlm.nih.gov/gene/?term=11160	"C8orf2, Erlin-2, NET32, SPFH2, SPG18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002012	11160	ERLIN2	http://www.ncbi.nlm.nih.gov/gene/?term=11160	"C8orf2, Erlin-2, NET32, SPFH2, SPG18 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002013	11161	C14orf1	http://www.ncbi.nlm.nih.gov/gene/?term=11161	"ERG28, NET51 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002014	11162	NUDT6	http://www.ncbi.nlm.nih.gov/gene/?term=11162	"ASFGF2, FGF-AS, FGF2AS, GFG-1, GFG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002015	11162	NUDT6	http://www.ncbi.nlm.nih.gov/gene/?term=11162	"ASFGF2, FGF-AS, FGF2AS, GFG-1, GFG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002016	11163	NUDT4	http://www.ncbi.nlm.nih.gov/gene/?term=11163	"DIPP2, DIPP2alpha, DIPP2beta, HDCMB47P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002017	11164	NUDT5	http://www.ncbi.nlm.nih.gov/gene/?term=11164	"YSA1, YSA1H, YSAH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002018	11165	NUDT3	http://www.ncbi.nlm.nih.gov/gene/?term=11165	"DIPP, DIPP-1, DIPP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002019	11165	NUDT3	http://www.ncbi.nlm.nih.gov/gene/?term=11165	"DIPP, DIPP-1, DIPP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002020	11167	FSTL1	http://www.ncbi.nlm.nih.gov/gene/?term=11167	"FRP, FSL1, MIR198 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002021	11168	PSIP1	http://www.ncbi.nlm.nih.gov/gene/?term=11168	"DFS70, LEDGF, PAIP, PSIP2, p52, p75 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002022	1116	CHI3L1	http://www.ncbi.nlm.nih.gov/gene/?term=1116	"ASRT7, CGP-39, GP-39, GP39, HC-gp39, HCGP-3P, YKL-40, YKL40, YYL-40, hCGP-39 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002023	11171	STRAP	http://www.ncbi.nlm.nih.gov/gene/?term=11171	"MAWD, PT-WD, UNRIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002024	11174	ADAMTS6	http://www.ncbi.nlm.nih.gov/gene/?term=11174	"ADAM-TS 6, ADAM-TS6, ADAMTS-6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002025	11177	BAZ1A	http://www.ncbi.nlm.nih.gov/gene/?term=11177	"ACF1, WALp1, WCRF180, hACF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002026	11178	LZTS1	http://www.ncbi.nlm.nih.gov/gene/?term=11178	"F37, FEZ1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002027	11178	LZTS1	http://www.ncbi.nlm.nih.gov/gene/?term=11178	"F37, FEZ1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002028	11178	LZTS1	http://www.ncbi.nlm.nih.gov/gene/?term=11178	"F37, FEZ1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002029	11180	WDR6	http://www.ncbi.nlm.nih.gov/gene/?term=11180		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002030	11180	WDR6	http://www.ncbi.nlm.nih.gov/gene/?term=11180		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002031	11180	WDR6	http://www.ncbi.nlm.nih.gov/gene/?term=11180		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002032	11181	TREH	http://www.ncbi.nlm.nih.gov/gene/?term=11181	"TRE, TREA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002033	11182	SLC2A6	http://www.ncbi.nlm.nih.gov/gene/?term=11182	"GLUT6, GLUT9, HSA011372 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002034	11184	MAP4K1	http://www.ncbi.nlm.nih.gov/gene/?term=11184	HPK1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002035	11184	MAP4K1	http://www.ncbi.nlm.nih.gov/gene/?term=11184	HPK1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002036	11185	INMT	http://www.ncbi.nlm.nih.gov/gene/?term=11185	TEMT	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002037	11185	INMT	http://www.ncbi.nlm.nih.gov/gene/?term=11185	TEMT	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002038	11186	RASSF1	http://www.ncbi.nlm.nih.gov/gene/?term=11186	"123F2, NORE2AA, RDA32, REH3P21, RASSF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002039	11187	PKP3	http://www.ncbi.nlm.nih.gov/gene/?term=11187		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002040	11188	NISCH	http://www.ncbi.nlm.nih.gov/gene/?term=11188	"I-1, IR1, IRAS, hIRAS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002041	11190	CEP250	http://www.ncbi.nlm.nih.gov/gene/?term=11190	"C-NAP1, CEP2, CNAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002042	11191	PTENP1	http://www.ncbi.nlm.nih.gov/gene/?term=11191	"PTEN-rs, PTEN2, PTENpg1, PTH2, psiPTEN "	lncRNA	Homo sapiens	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/PTENP1/
RLID00002043	11193	WBP4	http://www.ncbi.nlm.nih.gov/gene/?term=11193	FBP21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002044	11194	ABCB8	http://www.ncbi.nlm.nih.gov/gene/?term=11194	"EST328128, M-ABC1, MABC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002045	11194	ABCB8	http://www.ncbi.nlm.nih.gov/gene/?term=11194	"EST328128, M-ABC1, MABC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002046	11196	SEC23IP	http://www.ncbi.nlm.nih.gov/gene/?term=11196	"MSTP053, P125, P125A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002047	11196	SEC23IP	http://www.ncbi.nlm.nih.gov/gene/?term=11196	"MSTP053, P125, P125A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002048	111975	Igf2os	http://www.ncbi.nlm.nih.gov/gene/?term=111975	"Igf2as, Peg8 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002049	11198	SUPT16H	http://www.ncbi.nlm.nih.gov/gene/?term=11198	"CDC68, FACTP140, SPT16, SPT16/CDC68 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002050	11198	SUPT16H	http://www.ncbi.nlm.nih.gov/gene/?term=11198	"CDC68, FACTP140, SPT16, SPT16/CDC68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002051	1119	CHKA	http://www.ncbi.nlm.nih.gov/gene/?term=1119	"CHK, CK, CKI, EK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002052	1119	CHKA	http://www.ncbi.nlm.nih.gov/gene/?term=1119	"CHK, CK, CKI, EK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002053	1119	CHKA	http://www.ncbi.nlm.nih.gov/gene/?term=1119	"CHK, CK, CKI, EK "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002054	1119	CHKA	http://www.ncbi.nlm.nih.gov/gene/?term=1119	"CHK, CK, CKI, EK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002055	11200	CHEK2	http://www.ncbi.nlm.nih.gov/gene/?term=11200	"CDS1, CHK2, HuCds1, LFS2, PP1425, RAD53, hCds1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002056	11201	POLI	http://www.ncbi.nlm.nih.gov/gene/?term=11201	"RAD30B, RAD3OB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002057	11201	POLI	http://www.ncbi.nlm.nih.gov/gene/?term=11201	"RAD30B, RAD3OB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002058	1120	CHKB	http://www.ncbi.nlm.nih.gov/gene/?term=1120	"CHETK, CHKL, CK, CKB, CKEKB, EK, EKB, MDCMC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002059	11212	PROSC	http://www.ncbi.nlm.nih.gov/gene/?term=11212		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002060	11212	PROSC	http://www.ncbi.nlm.nih.gov/gene/?term=11212		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002061	11214	AKAP13	http://www.ncbi.nlm.nih.gov/gene/?term=11214	"AKAP-13, AKAP-Lbc, ARHGEF13, BRX, HA-3, Ht31, LBC, PRKA13, PROTO-LB, PROTO-LBC, c-lbc, p47 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002062	11214	AKAP13	http://www.ncbi.nlm.nih.gov/gene/?term=11214	"AKAP-13, AKAP-Lbc, ARHGEF13, BRX, HA-3, Ht31, LBC, PRKA13, PROTO-LB, PROTO-LBC, c-lbc, p47 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002063	11214	AKAP13	http://www.ncbi.nlm.nih.gov/gene/?term=11214	"AKAP-13, AKAP-Lbc, ARHGEF13, BRX, HA-3, Ht31, LBC, PRKA13, PROTO-LB, PROTO-LBC, c-lbc, p47 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002064	11214	AKAP13	http://www.ncbi.nlm.nih.gov/gene/?term=11214	"AKAP-13, AKAP-Lbc, ARHGEF13, BRX, HA-3, Ht31, LBC, PRKA13, PROTO-LB, PROTO-LBC, c-lbc, p47 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002065	11215	AKAP11	http://www.ncbi.nlm.nih.gov/gene/?term=11215	"AKAP-11, AKAP220, PPP1R44, PRKA11 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002066	11215	AKAP11	http://www.ncbi.nlm.nih.gov/gene/?term=11215	"AKAP-11, AKAP220, PPP1R44, PRKA11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002067	11215	AKAP11	http://www.ncbi.nlm.nih.gov/gene/?term=11215	"AKAP-11, AKAP220, PPP1R44, PRKA11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002068	11217	AKAP2	http://www.ncbi.nlm.nih.gov/gene/?term=11217	"AKAP-2, AKAPKL, PRKA2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002069	11218	DDX20	http://www.ncbi.nlm.nih.gov/gene/?term=11218	"DP103, GEMIN3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002070	11218	DDX20	http://www.ncbi.nlm.nih.gov/gene/?term=11218	"DP103, GEMIN3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002071	1121	CHM	http://www.ncbi.nlm.nih.gov/gene/?term=1121	"DXS540, GGTA, HSD-32, REP-1, TCD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002072	11221	DUSP10	http://www.ncbi.nlm.nih.gov/gene/?term=11221	"MKP-5, MKP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002073	11222	MRPL3	http://www.ncbi.nlm.nih.gov/gene/?term=11222	"COXPD9, MRL3, RPML3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002074	11224	RPL35	http://www.ncbi.nlm.nih.gov/gene/?term=11224	L35	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002075	11224	RPL35	http://www.ncbi.nlm.nih.gov/gene/?term=11224	L35	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002076	11224	RPL35	http://www.ncbi.nlm.nih.gov/gene/?term=11224	L35	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002077	11226	GALNT6	http://www.ncbi.nlm.nih.gov/gene/?term=11226	"GALNAC-T6, GalNAcT6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002078	11227	GALNT5	http://www.ncbi.nlm.nih.gov/gene/?term=11227	"GALNAC-T5, GALNACT5 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00002079	11227	GALNT5	http://www.ncbi.nlm.nih.gov/gene/?term=11227	"GALNAC-T5, GALNACT5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002080	11227	GALNT5	http://www.ncbi.nlm.nih.gov/gene/?term=11227	"GALNAC-T5, GALNACT5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002081	1122	CHML	http://www.ncbi.nlm.nih.gov/gene/?term=1122	REP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002082	1122	CHML	http://www.ncbi.nlm.nih.gov/gene/?term=1122	REP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002083	11231	SEC63	http://www.ncbi.nlm.nih.gov/gene/?term=11231	"DNAJC23, ERdj2, PRO2507L, SEC63 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002084	11231	SEC63	http://www.ncbi.nlm.nih.gov/gene/?term=11231	"DNAJC23, ERdj2, PRO2507, SEC63L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002085	11234	HPS5	http://www.ncbi.nlm.nih.gov/gene/?term=11234	"AIBP63, BLOC2S2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002086	11234	HPS5	http://www.ncbi.nlm.nih.gov/gene/?term=11234	"AIBP63, BLOC2S2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002087	11235	PDCD10	http://www.ncbi.nlm.nih.gov/gene/?term=11235	"CCM3, TFAR15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002088	11235	PDCD10	http://www.ncbi.nlm.nih.gov/gene/?term=11235	"CCM3, TFAR15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002089	11236	RNF139	http://www.ncbi.nlm.nih.gov/gene/?term=11236	"HRCA1, RCA1, TRC8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002090	11236	RNF139	http://www.ncbi.nlm.nih.gov/gene/?term=11236	"HRCA1, RCA1, TRC8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002091	11237	RNF24	http://www.ncbi.nlm.nih.gov/gene/?term=11237	G1L	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002092	11238	CA5B	http://www.ncbi.nlm.nih.gov/gene/?term=11238	CA-VB	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002093	11238	CA5B	http://www.ncbi.nlm.nih.gov/gene/?term=11238	CA-VB	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002094	112399	EGLN3	http://www.ncbi.nlm.nih.gov/gene/?term=112399	"HIFP4H3, HIFPH3, PHD3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002095	112399	EGLN3	http://www.ncbi.nlm.nih.gov/gene/?term=112399	"HIFP4H3, HIFPH3, PHD3 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00002096	1123	CHN1	http://www.ncbi.nlm.nih.gov/gene/?term=1123	"ARHGAP2, CHN, DURS2, NC, RHOGAP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002097	112405	Egln1	http://www.ncbi.nlm.nih.gov/gene/?term=112405	"AI503754, C1orf12, HIF-PH2, HPH-2, Hif-p4h-2, ORF13, Phd2, SM-20 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002098	112406	Egln2	http://www.ncbi.nlm.nih.gov/gene/?term=112406	"0610011A13Rik, C85656, Hif-p4h-1, Ier4, Phd1, SM-20 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002099	11243	PMF1	http://www.ncbi.nlm.nih.gov/gene/?term=11243		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002100	11243	PMF1	http://www.ncbi.nlm.nih.gov/gene/?term=11243		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002101	11244	ZHX1	http://www.ncbi.nlm.nih.gov/gene/?term=11244		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002102	11245	GPR176	http://www.ncbi.nlm.nih.gov/gene/?term=11245	HB-954	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002103	112483	SAT2	http://www.ncbi.nlm.nih.gov/gene/?term=112483	SSAT2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002104	112487	DTD2	http://www.ncbi.nlm.nih.gov/gene/?term=112487	C14orf126	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002105	112487	DTD2	http://www.ncbi.nlm.nih.gov/gene/?term=112487	C14orf126	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002106	112487	DTD2	http://www.ncbi.nlm.nih.gov/gene/?term=112487	C14orf126	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002107	112487	DTD2	http://www.ncbi.nlm.nih.gov/gene/?term=112487	C14orf126	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002108	11248	NXPH3	http://www.ncbi.nlm.nih.gov/gene/?term=11248	NPH3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002109	112495	GTF3C6	http://www.ncbi.nlm.nih.gov/gene/?term=112495	"C6orf51, TFIIIC35, bA397G5.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002110	112495	GTF3C6	http://www.ncbi.nlm.nih.gov/gene/?term=112495	"C6orf51, TFIIIC35, bA397G5.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002111	11252	PACSIN2	http://www.ncbi.nlm.nih.gov/gene/?term=11252	SDPII	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002112	11252	PACSIN2	http://www.ncbi.nlm.nih.gov/gene/?term=11252	SDPII	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002113	11252	PACSIN2	http://www.ncbi.nlm.nih.gov/gene/?term=11252	SDPII	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002114	11253	MAN1B1	http://www.ncbi.nlm.nih.gov/gene/?term=11253	"ERMAN1, ERManI, MANA-ER, MRT15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002115	11253	MAN1B1	http://www.ncbi.nlm.nih.gov/gene/?term=11253	"ERMAN1, ERManI, MANA-ER, MRT15 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002116	11257	TP53TG1	http://www.ncbi.nlm.nih.gov/gene/?term=11257	"LINC00096, NCRNA00096, P53TG1, P53TG1-D, TP53AP1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002117	11258	DCTN3	http://www.ncbi.nlm.nih.gov/gene/?term=11258	"DCTN-22, DCTN22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002118	112597	LINC00152	http://www.ncbi.nlm.nih.gov/gene/?term=112597	"C2orf59, NCRNA00152 "	lncRNA	Homo sapiens	25391424	Exosome	Plasma	qRT-PCR	"All these results suggested that LINC00152 can be detected in plasma, and one of the possible mechanisms of its stable existence in blood was protected by exosomes. "
RLID00002119	112597	LINC00152	http://www.ncbi.nlm.nih.gov/gene/?term=112597	"C2orf59, NCRNA00152 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002120	112609	MRAP2	http://www.ncbi.nlm.nih.gov/gene/?term=112609	"BMIQ18, C6orf117, bA51G5.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002121	11260	XPOT	http://www.ncbi.nlm.nih.gov/gene/?term=11260	XPO3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002122	11260	XPOT	http://www.ncbi.nlm.nih.gov/gene/?term=11260	XPO3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002123	112611	RWDD2A	http://www.ncbi.nlm.nih.gov/gene/?term=112611	"RWDD2, dJ747H23.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002124	112616	CMTM7	http://www.ncbi.nlm.nih.gov/gene/?term=112616	CKLFSF7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002125	112616	CMTM7	http://www.ncbi.nlm.nih.gov/gene/?term=112616	CKLFSF7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002126	11261	CHP1	http://www.ncbi.nlm.nih.gov/gene/?term=11261	"CHP, SLC9A1BP, Sid470p, p22, p24 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002127	11261	CHP1	http://www.ncbi.nlm.nih.gov/gene/?term=11261	"CHP, SLC9A1BP, Sid470p, p22, p24 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002128	11261	CHP1	http://www.ncbi.nlm.nih.gov/gene/?term=11261	"CHP, SLC9A1BP, Sid470p, p22, p24 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002129	11264	PXMP4	http://www.ncbi.nlm.nih.gov/gene/?term=11264	PMP24	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002130	11264	PXMP4	http://www.ncbi.nlm.nih.gov/gene/?term=11264	PMP24	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002131	11264	PXMP4	http://www.ncbi.nlm.nih.gov/gene/?term=11264	PMP24	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002132	11264	PXMP4	http://www.ncbi.nlm.nih.gov/gene/?term=11264	PMP24	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002133	11266	DUSP12	http://www.ncbi.nlm.nih.gov/gene/?term=11266	"DUSP1, YVH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002134	11266	DUSP12	http://www.ncbi.nlm.nih.gov/gene/?term=11266	"DUSP1, YVH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002135	11267	SNF8	http://www.ncbi.nlm.nih.gov/gene/?term=11267	"Dot3, EAP30, VPS22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002136	11270	NRM	http://www.ncbi.nlm.nih.gov/gene/?term=11270	NRM29	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002137	112724	RDH13	http://www.ncbi.nlm.nih.gov/gene/?term=112724	SDR7C3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002138	112724	RDH13	http://www.ncbi.nlm.nih.gov/gene/?term=112724	SDR7C3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002139	112724	RDH13	http://www.ncbi.nlm.nih.gov/gene/?term=112724	SDR7C3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002140	11272	PRR4	http://www.ncbi.nlm.nih.gov/gene/?term=11272	"LPRP, PROL4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002141	11273	ATXN2L	http://www.ncbi.nlm.nih.gov/gene/?term=11273	"A2D, A2LG, A2LP, A2RP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002142	11274	USP18	http://www.ncbi.nlm.nih.gov/gene/?term=11274	"ISG43, UBP43 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002143	112752	IFT43	http://www.ncbi.nlm.nih.gov/gene/?term=112752	"C14orf179, CED3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002144	112755	STX1B	http://www.ncbi.nlm.nih.gov/gene/?term=112755	"GEFSP9, STX1B1, STX1B2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002145	11276	SYNRG	http://www.ncbi.nlm.nih.gov/gene/?term=11276	"AP1GBP1, SYNG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002146	11277	TREX1	http://www.ncbi.nlm.nih.gov/gene/?term=11277	"AGS1, CRV, DRN3, HERNS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002147	11279	KLF8	http://www.ncbi.nlm.nih.gov/gene/?term=11279	"BKLF3, ZNF741 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002148	11282	MGAT4B	http://www.ncbi.nlm.nih.gov/gene/?term=11282	"GNT-IV, GNT-IVB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002149	112840	WDR89	http://www.ncbi.nlm.nih.gov/gene/?term=112840	"C14orf150, MSTP050 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002150	112840	WDR89	http://www.ncbi.nlm.nih.gov/gene/?term=112840	"C14orf150, MSTP050 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002151	11284	PNKP	http://www.ncbi.nlm.nih.gov/gene/?term=11284	"AOA4, EIEE10, MCSZ, PNK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002152	112858	TP53RK	http://www.ncbi.nlm.nih.gov/gene/?term=112858	"BUD32, C20orf64, Nori-2, Nori-2p, PRPK, dJ101A2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002153	112858	TP53RK	http://www.ncbi.nlm.nih.gov/gene/?term=112858	"BUD32, C20orf64, Nori-2, Nori-2p, PRPK, dJ101A2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002154	11285	B4GALT7	http://www.ncbi.nlm.nih.gov/gene/?term=11285	"EDSP1, XGALT1, XGPT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002155	112936	VPS26B	http://www.ncbi.nlm.nih.gov/gene/?term=112936	Pep8b	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002156	112936	VPS26B	http://www.ncbi.nlm.nih.gov/gene/?term=112936	Pep8b	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002157	112936	VPS26B	http://www.ncbi.nlm.nih.gov/gene/?term=112936	Pep8b	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002158	112937	GLB1L3	http://www.ncbi.nlm.nih.gov/gene/?term=112937		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002159	112937	GLB1L3	http://www.ncbi.nlm.nih.gov/gene/?term=112937		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002160	112939	NACC1	http://www.ncbi.nlm.nih.gov/gene/?term=112939	"BEND8, BTBD14B, BTBD30, NAC-1, NAC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002161	112942	CFAP36	http://www.ncbi.nlm.nih.gov/gene/?term=112942	CCDC104	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002162	112942	CFAP36	http://www.ncbi.nlm.nih.gov/gene/?term=112942	CCDC104	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002163	112950	MED8	http://www.ncbi.nlm.nih.gov/gene/?term=112950	ARC32	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002164	112970	KTI12	http://www.ncbi.nlm.nih.gov/gene/?term=112970	"SBBI81, TOT4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002165	112	ADCY6	http://www.ncbi.nlm.nih.gov/gene/?term=112	"AC6, LCCS8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002166	112	ADCY6	http://www.ncbi.nlm.nih.gov/gene/?term=112	"AC6, LCCS8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002167	112	ADCY6	http://www.ncbi.nlm.nih.gov/gene/?term=112	"AC6, LCCS8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002168	112	ADCY6	http://www.ncbi.nlm.nih.gov/gene/?term=112	"AC6, LCCS8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002169	113000	RPUSD1	http://www.ncbi.nlm.nih.gov/gene/?term=113000	"C16orf40, RLUCL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002170	113000	RPUSD1	http://www.ncbi.nlm.nih.gov/gene/?term=113000	"C16orf40, RLUCL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002171	113026	PLCD3	http://www.ncbi.nlm.nih.gov/gene/?term=113026	PLC-delta-3	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002172	113026	PLCD3	http://www.ncbi.nlm.nih.gov/gene/?term=113026	PLC-delta-3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002173	113026	PLCD3	http://www.ncbi.nlm.nih.gov/gene/?term=113026	PLC-delta-3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002174	11304	Abca4	http://www.ncbi.nlm.nih.gov/gene/?term=11304	"AW050280, Abc10, Abcr, D430003I15Rik, RmP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002175	1130	LYST	http://www.ncbi.nlm.nih.gov/gene/?term=1130	"CHS, CHS1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002176	113130	CDCA5	http://www.ncbi.nlm.nih.gov/gene/?term=113130	SORORIN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002177	113130	CDCA5	http://www.ncbi.nlm.nih.gov/gene/?term=113130	SORORIN	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002178	113130	CDCA5	http://www.ncbi.nlm.nih.gov/gene/?term=113130	SORORIN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002179	11313	LYPLA2	http://www.ncbi.nlm.nih.gov/gene/?term=11313	"APT-2, APT2, DJ886K2.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002180	11314	CD300A	http://www.ncbi.nlm.nih.gov/gene/?term=11314	"CLM-8, CMRF-35-H9, CMRF-35H, CMRF35-H, CMRF35-H9, CMRF35H, CMRF35H9, IGSF12, IRC1, IRC1/IRC2, IRC2, IRp60 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002181	11315	PARK7	http://www.ncbi.nlm.nih.gov/gene/?term=11315	"DJ-1, DJ1, HEL-S-67p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002182	11316	COPE	http://www.ncbi.nlm.nih.gov/gene/?term=11316	epsilon-COP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002183	11316	COPE	http://www.ncbi.nlm.nih.gov/gene/?term=11316	epsilon-COP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002184	113174	SAAL1	http://www.ncbi.nlm.nih.gov/gene/?term=113174	SPACIA1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002185	113174	SAAL1	http://www.ncbi.nlm.nih.gov/gene/?term=113174	SPACIA1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002186	113177	IZUMO4	http://www.ncbi.nlm.nih.gov/gene/?term=113177	"C19orf36, IMAGE:4215339 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002187	113178	SCAMP4	http://www.ncbi.nlm.nih.gov/gene/?term=113178	SCAMP-4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002188	113178	SCAMP4	http://www.ncbi.nlm.nih.gov/gene/?term=113178	SCAMP-4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002189	113178	SCAMP4	http://www.ncbi.nlm.nih.gov/gene/?term=113178	SCAMP-4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002190	113178	SCAMP4	http://www.ncbi.nlm.nih.gov/gene/?term=113178	SCAMP-4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002191	113201	CASC4	http://www.ncbi.nlm.nih.gov/gene/?term=113201	H63	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002192	113201	CASC4	http://www.ncbi.nlm.nih.gov/gene/?term=113201	H63	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002193	11320	MGAT4A	http://www.ncbi.nlm.nih.gov/gene/?term=11320	"GNT-IV, GNT-IVA, GnT-4a "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002194	11320	MGAT4A	http://www.ncbi.nlm.nih.gov/gene/?term=11320	"GNT-IV, GNT-IVA, GnT-4a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002195	11320	MGAT4A	http://www.ncbi.nlm.nih.gov/gene/?term=11320	"GNT-IV, GNT-IVA, GnT-4a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002196	11320	MGAT4A	http://www.ncbi.nlm.nih.gov/gene/?term=11320	"GNT-IV, GNT-IVA, GnT-4a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002197	11321	GPN1	http://www.ncbi.nlm.nih.gov/gene/?term=11321	"ATPBD1A, MBDIN, NTPBP, RPAP4, XAB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002198	11322	TMC6	http://www.ncbi.nlm.nih.gov/gene/?term=11322	"EV1, EVER1, EVIN1, LAK-4P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002199	113235	SLC46A1	http://www.ncbi.nlm.nih.gov/gene/?term=113235	"G21, HCP1, PCFT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002200	113235	SLC46A1	http://www.ncbi.nlm.nih.gov/gene/?term=113235	"G21, HCP1, PCFT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002201	113246	C12orf57	http://www.ncbi.nlm.nih.gov/gene/?term=113246	"C10, GRCC10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002202	113251	LARP4	http://www.ncbi.nlm.nih.gov/gene/?term=113251	PP13296	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002203	113251	LARP4	http://www.ncbi.nlm.nih.gov/gene/?term=113251	PP13296	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002204	113263	GLCCI1	http://www.ncbi.nlm.nih.gov/gene/?term=113263	"FAM117C, GCTR, GIG18, TSSN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002205	113263	GLCCI1	http://www.ncbi.nlm.nih.gov/gene/?term=113263	"FAM117C, GCTR, GIG18, TSSN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002206	11326	VSIG4	http://www.ncbi.nlm.nih.gov/gene/?term=11326	"CRIg, Z39IG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002207	11328	FKBP9	http://www.ncbi.nlm.nih.gov/gene/?term=11328	"FKBP60, FKBP63, PPIase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002208	11328	FKBP9	http://www.ncbi.nlm.nih.gov/gene/?term=11328	"FKBP60, FKBP63, PPIase "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002209	11328	FKBP9	http://www.ncbi.nlm.nih.gov/gene/?term=11328	"FKBP60, FKBP63, PPIase "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002210	11331	PHB2	http://www.ncbi.nlm.nih.gov/gene/?term=11331	"BAP, BCAP37, Bap37, PNAS-141, REA, hBAP, p22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002211	11332	ACOT7	http://www.ncbi.nlm.nih.gov/gene/?term=11332	"ACH1, ACT, BACH, CTE-II, LACH, LACH1, hBACH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002212	11332	ACOT7	http://www.ncbi.nlm.nih.gov/gene/?term=11332	"ACH1, ACT, BACH, CTE-II, LACH, LACH1, hBACH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002213	11332	ACOT7	http://www.ncbi.nlm.nih.gov/gene/?term=11332	"ACH1, ACT, BACH, CTE-II, LACH, LACH1, hBACH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002214	11333	PDAP1	http://www.ncbi.nlm.nih.gov/gene/?term=11333	"HASPP28, PAP, PAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002215	11333	PDAP1	http://www.ncbi.nlm.nih.gov/gene/?term=11333	"HASPP28, PAP, PAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002216	11334	TUSC2	http://www.ncbi.nlm.nih.gov/gene/?term=11334	"C3orf11, FUS1, PAP, PDAP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002217	11334	TUSC2	http://www.ncbi.nlm.nih.gov/gene/?term=11334	"C3orf11, FUS1, PAP, PDAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002218	11335	CBX3	http://www.ncbi.nlm.nih.gov/gene/?term=11335	"HECH, HP1-GAMMA, HP1Hs-gamma "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002219	11335	CBX3	http://www.ncbi.nlm.nih.gov/gene/?term=11335	"HECH, HP1-GAMMA, HP1Hs-gamma "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002220	11336	EXOC3	http://www.ncbi.nlm.nih.gov/gene/?term=11336	"SEC6, SEC6L1, Sec6p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002221	11337	GABARAP	http://www.ncbi.nlm.nih.gov/gene/?term=11337	"ATG8A-a, MM46, GABARAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002222	11337	GABARAP	http://www.ncbi.nlm.nih.gov/gene/?term=11337	"ATG8A-a, MM46, GABARAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002223	11337	GABARAP	http://www.ncbi.nlm.nih.gov/gene/?term=11337	"ATG8A, GABARAP-a, MM46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002224	11338	U2AF2	http://www.ncbi.nlm.nih.gov/gene/?term=11338	U2AF65	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002225	11338	U2AF2	http://www.ncbi.nlm.nih.gov/gene/?term=11338	U2AF65	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002226	11339	OIP5	http://www.ncbi.nlm.nih.gov/gene/?term=11339	"5730547N13Rik, CT86, LINT-25, MIS18B, MIS18beta, hMIS18beta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002227	113402	SFT2D1	http://www.ncbi.nlm.nih.gov/gene/?term=113402	"C6orf83, pRGR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002228	113402	SFT2D1	http://www.ncbi.nlm.nih.gov/gene/?term=113402	"C6orf83, pRGR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002229	11340	EXOSC8	http://www.ncbi.nlm.nih.gov/gene/?term=11340	"CIP3, EAP2, OIP2, PCH1C, RRP43, Rrp43p, bA421P11.3, p9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002230	11340	EXOSC8	http://www.ncbi.nlm.nih.gov/gene/?term=11340	"CIP3, EAP2, OIP2, PCH1C, RRP43, Rrp43p, bA421P11.3, p9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002231	11340	EXOSC8	http://www.ncbi.nlm.nih.gov/gene/?term=11340	"CIP3, EAP2, OIP2, PCH1C, RRP43, Rrp43p, bA421P11.3, p9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002232	113419	TEX261	http://www.ncbi.nlm.nih.gov/gene/?term=113419	TEG-261	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002233	11342	RNF13	http://www.ncbi.nlm.nih.gov/gene/?term=11342	RZF	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002234	113444	SMIM12	http://www.ncbi.nlm.nih.gov/gene/?term=113444	C1orf212	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002235	113444	SMIM12	http://www.ncbi.nlm.nih.gov/gene/?term=113444	C1orf212	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002236	113444	SMIM12	http://www.ncbi.nlm.nih.gov/gene/?term=113444	C1orf212	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002237	113444	SMIM12	http://www.ncbi.nlm.nih.gov/gene/?term=113444	C1orf212	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002238	11344	TWF2	http://www.ncbi.nlm.nih.gov/gene/?term=11344	"A6RP, A6r, MSTP011, PTK9L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002239	113452	TMEM54	http://www.ncbi.nlm.nih.gov/gene/?term=113452	"BCLP, CAC-1, CAC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002240	113452	TMEM54	http://www.ncbi.nlm.nih.gov/gene/?term=113452	"BCLP, CAC-1, CAC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002241	113457	TUBA3D	http://www.ncbi.nlm.nih.gov/gene/?term=113457	H2-ALPHA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002242	11345	GABARAPL2	http://www.ncbi.nlm.nih.gov/gene/?term=11345	"ATG8, ATG8C, GATE-16, GATE16, GEF-2, GEF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002243	11345	GABARAPL2	http://www.ncbi.nlm.nih.gov/gene/?term=11345	"ATG8, ATG8C, GATE-16, GATE16, GEF-2, GEF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002244	11346	SYNPO	http://www.ncbi.nlm.nih.gov/gene/?term=11346		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002245	11350	Abl1	http://www.ncbi.nlm.nih.gov/gene/?term=11350	"AI325092, Abl, E430008G22Rik, c-Abl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002246	11354	Scgb1b27	http://www.ncbi.nlm.nih.gov/gene/?term=11354	"Abp, Abpa, Abpa27, Sal-1, Tcp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002247	113612	CYP2U1	http://www.ncbi.nlm.nih.gov/gene/?term=113612	"P450TEC, SPG49, SPG56 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002248	113612	CYP2U1	http://www.ncbi.nlm.nih.gov/gene/?term=113612	"P450TEC, SPG49, SPG56 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002249	113622	ADPRHL1	http://www.ncbi.nlm.nih.gov/gene/?term=113622	ARH2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002250	113655	MFSD3	http://www.ncbi.nlm.nih.gov/gene/?term=113655		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002251	113675	SDSL	http://www.ncbi.nlm.nih.gov/gene/?term=113675	"SDH 2, SDS-RS1, TDH, cSDH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002252	113675	SDSL	http://www.ncbi.nlm.nih.gov/gene/?term=113675	"SDH 2, SDS-RS1, TDH, cSDH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002253	113791	PIK3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=113791	"HGFL, hHGFL(S) "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002254	113828	FAM83F	http://www.ncbi.nlm.nih.gov/gene/?term=113828		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002255	113829	SLC35A4	http://www.ncbi.nlm.nih.gov/gene/?term=113829		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002256	113878	DTX2	http://www.ncbi.nlm.nih.gov/gene/?term=113878	RNF58	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002257	113892	Nat8f3	http://www.ncbi.nlm.nih.gov/gene/?term=113892		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002258	1139	CHRNA7	http://www.ncbi.nlm.nih.gov/gene/?term=1139	"CHRNA7-2, NACHRA7 "	mRNA	Homo sapiens	26206074	Nucleus	Neocortex	In situ hybridization	"CHRNA7 and CHRFAM7A mRNAs were expressed in the same neuronal nuclei of the human neocortex.  We demonstrated that CHRNA7 and CHRFAM7A mRNAs are colocalized in a subset of putative neuronal nuclei (large DAPI-stained nuclei), both in the dorsolateral prefrontal cortex and anterior cingulate cortex (Figure 3). "
RLID00002259	113	ADCY7	http://www.ncbi.nlm.nih.gov/gene/?term=113	AC7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002260	114034	TOE1	http://www.ncbi.nlm.nih.gov/gene/?term=114034	hCaf1z	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002261	114043	TSPEAR-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=114043	C21orf90	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002262	114049	WBSCR22	http://www.ncbi.nlm.nih.gov/gene/?term=114049	"HASJ4442, HUSSY-3, MERM1, PP3381, WBMT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002263	114049	WBSCR22	http://www.ncbi.nlm.nih.gov/gene/?term=114049	"HASJ4442, HUSSY-3, MERM1, PP3381, WBMT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002264	11409	Acads	http://www.ncbi.nlm.nih.gov/gene/?term=11409	"AI196007, Bcd-1, Bcd1, Hdlq8, SCAD "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002265	11416	Slc33a1	http://www.ncbi.nlm.nih.gov/gene/?term=11416	"AI315656, AI788741, Acatn, D630022N01Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002266	114255	Dok4	http://www.ncbi.nlm.nih.gov/gene/?term=114255		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002267	11426	Macf1	http://www.ncbi.nlm.nih.gov/gene/?term=11426	"ABP620, Acf7, Aclp7, MACF, R74989, mKIAA0465 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002268	114294	LACTB	http://www.ncbi.nlm.nih.gov/gene/?term=114294	"G24, MRPL56 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002269	11431	Acp1	http://www.ncbi.nlm.nih.gov/gene/?term=11431	"4632432E04Rik, AI427468, Acp-1, LMW-PTP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002270	114327	EFHC1	http://www.ncbi.nlm.nih.gov/gene/?term=114327	"EJM1, dJ304B14.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002271	11434	Acr	http://www.ncbi.nlm.nih.gov/gene/?term=11434		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002272	11440	Chrna6	http://www.ncbi.nlm.nih.gov/gene/?term=11440	"Acra6, Nica6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002273	114548	NLRP3	http://www.ncbi.nlm.nih.gov/gene/?term=114548	"AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1, FCAS, FCAS1, FCU, MWS, NALP3, PYPAF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002274	114548	NLRP3	http://www.ncbi.nlm.nih.gov/gene/?term=114548	"AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1, FCAS, FCAS1, FCU, MWS, NALP3, PYPAF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002275	114564	Csprs	http://www.ncbi.nlm.nih.gov/gene/?term=114564	"D1Lub1, HSR "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002276	114569	MAL2	http://www.ncbi.nlm.nih.gov/gene/?term=114569		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002277	114599	SNORD15B	http://www.ncbi.nlm.nih.gov/gene/?term=114599	"RNU15B, U15B "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002278	114599	SNORD15B	http://www.ncbi.nlm.nih.gov/gene/?term=114599	"RNU15B, U15B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002279	114599	SNORD15B	http://www.ncbi.nlm.nih.gov/gene/?term=114599	"RNU15B, U15B "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002280	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	22817891	Cytoplasm	Bone marrow Macrophage	Next-generation sequencing	"Cluster 11, by contrast, contains abundant cytoplasmic transcripts, with fewer transcripts in the chromatin and nucleoplasm. This cluster includes genes that are likely to encode highly stable mRNAs, such as Actb (beta-actin) and Tuba (alpha-tubulin). "
RLID00002281	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002282	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	14623865	Growth cone	Motoneuron	In situ hybridization	"Overexpression of Smn or its binding partner, heterogeneous nuclear ribonucleoprotein (hnRNP) R, promotes neurite growth in differentiating PC12 cells. Reduced axon growth in Smn-deficient motoneurons correlates with reduced β-actin protein and mRNA staining in distal axons and growth cones.Overexpression of Smn or its binding partner, heterogeneous nuclear ribonucleoprotein (hnRNP) R, promotes neurite growth in differentiating PC12 cells. Reduced axon growth in Smn-deficient motoneurons correlates with reduced β-actin protein and mRNA staining in distal axons and growth cones. "
RLID00002283	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	15972000	Endoplasmic reticulum	MIN6 cell	Northern blot	"As expected, the actin mRNA was mainly found in the cytosolic fraction (Figure 2a). However, glucose stimulated the recruitment of a small fraction of the actin mRNA to the ER (Figure 2a). "
RLID00002284	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	15972000	Cytosol	MIN6 cell	Northern blot	"As expected, the actin mRNA was mainly found in the cytosolic fraction (Figure 2a). However, glucose stimulated the recruitment of a small fraction of the actin mRNA to the ER (Figure 2a). "
RLID00002285	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	16317045	Dendrite	Hippocampus	In situ hybridization	"Nd1-L transcripts were increased in the dendrites upon mGluR activation and significantly reduced in TLS-null dendrites. Cell in situ hybridization revealed that both Nd1-L and beta-actin mRNAs were increased in dendrites in DHPG-treated neurons by about 4.1-fold and 7.8-fold, respectively compared with those in non-treated WT neurons (Fig. 3A, left, and B).  "
RLID00002286	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	18195013	Ribosome	S/S MEF cell	RT-PCR	"In the non-stressed S/S cells, actin mRNA was bound to large polyribosomes (Fig. 8,fractions 12-14). "
RLID00002287	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	18539120	Dendrite	Neuron	Fluorescence in situ hybridization	"Fig. 1 Fluorescence in situ hybridization (FISH) of hippocampal neurons. (a-d) Neurons from wild-type (WT, right panels) or FMRP-knockout (KO, left panels) were cultured for 10 days and either not stimulated ('unstim', upper panels') or stimulated with 50uM DHPG for 15 minutes ('DHPG' lower panels). Corresponding histograms showing dendritic quantification of FISH experiments are shown to the right. Results for WT (black bars) and KO (white bars) are labeled on the x-axis. Close-up images of dendritic signals are shown to the right (in same order). (a) MAP1b mRNA (n=15-16; *p<0.001 for unstimulated vs. DHPG in WT, P>0.25 for KO). (b)CaMKIIa mRNA (n=15-17; *p<0.01 for WT, p>0.2 for KO). There was no significant difference in CaMKIIa abundance of unstimulated neurons between WT and KO (n=15, p>0.1). (c) Beta-actin mRNA (n=11-13; p>0.2). Scale bars=12um. (d-e) FISH for other mRNA targets of FMRP in both WT (right image panels) and KO (left image panels). Representative images shown for unstimulated (upper panels; 'unstim' and stimulated (lower panels; DHPG, 50uM), and close-up images of dendrites are displayed above the histograms (in same order). Histograms (right) showing dendritic fluorescence quantification are shown for WT (green) and KO (red) using probes to (d) SAPAP4 (n=16-17; p<0.01 for WT, p>25 for KO) and (e) GABA-A receptor delta (n=13-15; *, ***p<0.01 for unstimulated vs. DHPG in WT and for DHPG in WT and KO, **p<0.05 for unstimulated vs. DHPG in KO). (c) Dendritic CaMKIIa mRNA localization in response to DHPG (11DIV). (d) Dendritic SAPAP4 mRNA localization in response to DHPG (11DIV). "
RLID00002288	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	22832165	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 2A shows a representative image of primary CEF cells in which β-actin mRNA is localized to the leading edge (indicated with arrowheads), whereas GAPDH mRNA is more uniformly distributed.  "
RLID00002289	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	24381269	Axon	Soma	qRT-PCR	"As a control, the purity of the axonal RNA samples was tested by qRT-PCR, confirming that axonal samples were enriched in beta-actin mRNA and essentially devoid of beta-actin mRNA, which is present exclusively in the soma. "
RLID00002290	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	26140598	Cell leading edge	MEF cell	Florescence micrograph	"Next,we focused on the interaction in the cytoplasm, more specifically, the leading edge (Figure 2F, circle) and perinuclear regions (Figure 2F, square). In immortalized MEFs (Figures 2H and 2I), we found that ZBP1 bound b-actin mRNAs almost equally in both compartments (p > 0.1) (Figure 2J). It has been shown that b-actin mRNA localizes to the leading edge of primary fibroblasts. "
RLID00002291	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	26140598	Perinuclear	MEF cell	Florescence micrograph	"Next,we focused on the interaction in the cytoplasm, more specifically, the leading edge (Figure 2F, circle) and perinuclear regions (Figure 2F, square). In immortalized MEFs (Figures 2H and 2I), we found that ZBP1 bound b-actin mRNAs almost equally in both compartments (p > 0.1) (Figure 2J). These results provide a quantitative corroboration that ZBP1 binds b-actin mRNAs in the nuclear periphery and that phosphorylation of Y396F on ZBP1 leads to the release of the mRNA at the leading edge. "
RLID00002292	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"As a positive control, Actb, which has previously been detected in motor axons (8), was also abundant in the somatodendritic and axonal compartments. "
RLID00002293	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	26464439	Somatodendritic compartment	Motoneuron	In situ hybridization|qRT-PCR	"As a positive control, Actb, which has previously been detected in motor axons (8), was also abundant in the somatodendritic and axonal compartments. "
RLID00002294	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	18451862	Lamellipodium	Migrating cell	qRT-PCR	"These RNAs do not include beta-actin mRNA and the mRNAs for subunits of the arp2/3 complex, which have been previously observed at lamellipodial regions, possibly because in some cell types beta-actin mRNA accumulates at the leading edge in only a small percentage of cells. "
RLID00002295	11461	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=11461	"Actx, E430023M04Rik, beta-actin "	mRNA	Mus musculus	18451862	Cell leading edge	Migrating cell	qRT-PCR	"These RNAs do not include beta-actin mRNA and the mRNAs for subunits of the arp2/3 complex, which have been previously observed at lamellipodial regions, possibly because in some cell types beta-actin mRNA accumulates at the leading edge in only a small percentage of cells. "
RLID00002296	114641	Rpl31	http://www.ncbi.nlm.nih.gov/gene/?term=114641	Dts	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002297	114641	Rpl31	http://www.ncbi.nlm.nih.gov/gene/?term=114641	Dts	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002298	114670	4930573O21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=114670		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002299	114671	4930444G20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=114671		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002300	114675	4932431P20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=114675		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002301	114713	Rasa2	http://www.ncbi.nlm.nih.gov/gene/?term=114713	"5430433H21Rik, AA517451, AU023900, GAP1m "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002302	114715	Spred1	http://www.ncbi.nlm.nih.gov/gene/?term=114715	"5730461F13Rik, AL024345, AW047647 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002303	114716	Spred2	http://www.ncbi.nlm.nih.gov/gene/?term=114716	C79158	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002304	11472	Actn2	http://www.ncbi.nlm.nih.gov/gene/?term=11472	1110008F24Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002305	114741	Supt16	http://www.ncbi.nlm.nih.gov/gene/?term=114741	"Cdc68, Fact140, Spt16h, Supt16 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002306	114757	CYGB	http://www.ncbi.nlm.nih.gov/gene/?term=114757	"HGB, STAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002307	11477	Acvr1	http://www.ncbi.nlm.nih.gov/gene/?term=11477	"ALK2, ActR-I, ActRIA, Acvr, Acvrlk2, Alk-2, Alk8, D330013D15Rik, SKR1, Tsk7L "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002308	11477	Acvr1	http://www.ncbi.nlm.nih.gov/gene/?term=11477	"ALK2, ActR-I, ActRIA, Acvr, Acvrlk2, Alk-2, Alk8, D330013D15Rik, SKR1, Tsk7L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002309	114781	BTBD9	http://www.ncbi.nlm.nih.gov/gene/?term=114781	dJ322I12.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002310	114789	SLC25A25	http://www.ncbi.nlm.nih.gov/gene/?term=114789	"MCSC, PCSCL, SCAMC-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002311	114789	SLC25A25	http://www.ncbi.nlm.nih.gov/gene/?term=114789	"MCSC, PCSCL, SCAMC-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002312	114793	FMNL2	http://www.ncbi.nlm.nih.gov/gene/?term=114793	FHOD2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002313	114793	FMNL2	http://www.ncbi.nlm.nih.gov/gene/?term=114793	FHOD2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002314	1147	CHUK	http://www.ncbi.nlm.nih.gov/gene/?term=1147	"IKBKA, IKK-alpha, IKK1, IKKA, NFKBIKA, TCF16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002315	114804	RNF157	http://www.ncbi.nlm.nih.gov/gene/?term=114804		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002316	114804	RNF157	http://www.ncbi.nlm.nih.gov/gene/?term=114804		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002317	114804	RNF157	http://www.ncbi.nlm.nih.gov/gene/?term=114804		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002318	11481	Acvr2b	http://www.ncbi.nlm.nih.gov/gene/?term=11481	"4930516B21Rik, ActRIIB "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002319	114822	RHPN1	http://www.ncbi.nlm.nih.gov/gene/?term=114822	"ODF5, RHOPHILIN, RHPN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002320	114822	RHPN1	http://www.ncbi.nlm.nih.gov/gene/?term=114822	"ODF5, RHOPHILIN, RHPN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002321	114825	PWWP2A	http://www.ncbi.nlm.nih.gov/gene/?term=114825	MST101	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002322	114825	PWWP2A	http://www.ncbi.nlm.nih.gov/gene/?term=114825	MST101	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002323	11486	Ada	http://www.ncbi.nlm.nih.gov/gene/?term=11486		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002324	114871	Psg28	http://www.ncbi.nlm.nih.gov/gene/?term=114871	cea16	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002325	114874	Ddhd1	http://www.ncbi.nlm.nih.gov/gene/?term=114874	"Mir5131, PA-PLA1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002326	114879	OSBPL5	http://www.ncbi.nlm.nih.gov/gene/?term=114879	"OBPH1, ORP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002327	114879	OSBPL5	http://www.ncbi.nlm.nih.gov/gene/?term=114879	"OBPH1, ORP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002328	11487	Adam10	http://www.ncbi.nlm.nih.gov/gene/?term=11487	"1700031C13Rik, MADM, kuz, kuzbanian "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002329	114880	OSBPL6	http://www.ncbi.nlm.nih.gov/gene/?term=114880	ORP6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002330	114882	OSBPL8	http://www.ncbi.nlm.nih.gov/gene/?term=114882	"MST120, MSTP120, ORP8, OSBP10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002331	114882	OSBPL8	http://www.ncbi.nlm.nih.gov/gene/?term=114882	"MST120, MSTP120, ORP8, OSBP10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002332	114884	OSBPL10	http://www.ncbi.nlm.nih.gov/gene/?term=114884	"ORP10, OSBP9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002333	114884	OSBPL10	http://www.ncbi.nlm.nih.gov/gene/?term=114884	"ORP10, OSBP9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002334	114885	OSBPL11	http://www.ncbi.nlm.nih.gov/gene/?term=114885	"ORP-11, ORP11, OSBP12, TCCCIA00292 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002335	114893	Dcun1d1	http://www.ncbi.nlm.nih.gov/gene/?term=114893	"Rp42, SCCRO, Tes3, pTes3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002336	114899	C1QTNF3	http://www.ncbi.nlm.nih.gov/gene/?term=114899	"C1ATNF3, CORCS, CORS, CORS-26, CORS26, CTRP3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002337	114899	C1QTNF3	http://www.ncbi.nlm.nih.gov/gene/?term=114899	"C1ATNF3, CORCS, CORS, CORS-26, CORS26, CTRP3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002338	114904	C1QTNF6	http://www.ncbi.nlm.nih.gov/gene/?term=114904	"CTFP6, CTRP6, ZACRP6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002339	114915	EPB41L4A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=114915	"C5orf26, NCRNA00219, TIGA1 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002340	114915	EPB41L4A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=114915	"C5orf26, NCRNA00219, TIGA1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002341	11491	Adam17	http://www.ncbi.nlm.nih.gov/gene/?term=11491	"CD156b, Tace "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002342	114926	SMIM19	http://www.ncbi.nlm.nih.gov/gene/?term=114926	C8orf40	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002343	114926	SMIM19	http://www.ncbi.nlm.nih.gov/gene/?term=114926	C8orf40	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002344	114932	MRFAP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=114932	PP784	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002345	114971	PTPMT1	http://www.ncbi.nlm.nih.gov/gene/?term=114971	"DUSP23, MOSP, PLIP, PNAS-129 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002346	114971	PTPMT1	http://www.ncbi.nlm.nih.gov/gene/?term=114971	"DUSP23, MOSP, PLIP, PNAS-129 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002347	114984	FLYWCH2	http://www.ncbi.nlm.nih.gov/gene/?term=114984		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002348	114984	FLYWCH2	http://www.ncbi.nlm.nih.gov/gene/?term=114984		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002349	114987	WDR31	http://www.ncbi.nlm.nih.gov/gene/?term=114987		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002350	114991	ZNF618	http://www.ncbi.nlm.nih.gov/gene/?term=114991	"FP13169, NEDD10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002351	11500	Adam7	http://www.ncbi.nlm.nih.gov/gene/?term=11500	"ADAM 7, EAP1, EAPI "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002352	115024	NT5C3B	http://www.ncbi.nlm.nih.gov/gene/?term=115024	"NT5C3L, cN-IIIB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002353	115024	NT5C3B	http://www.ncbi.nlm.nih.gov/gene/?term=115024	NT5C3L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002354	11502	Adam9	http://www.ncbi.nlm.nih.gov/gene/?term=11502	"AU020942, MDC9, Mltng, mKIAA0021 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002355	115098	CCDC124	http://www.ncbi.nlm.nih.gov/gene/?term=115098		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002356	115098	CCDC124	http://www.ncbi.nlm.nih.gov/gene/?term=115098		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002357	115106	HAUS1	http://www.ncbi.nlm.nih.gov/gene/?term=115106	"CCDC5, HEI-C, HEIC, HsT1461 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002358	115123	MARCH3	http://www.ncbi.nlm.nih.gov/gene/?term=115123	"MARCH-III, RNF173 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002359	11515	Adcy9	http://www.ncbi.nlm.nih.gov/gene/?term=11515	"AC9, ACtp10, AW125421, D16Wsu65e, mKIAA0520 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002360	11517	Adcyap1r1	http://www.ncbi.nlm.nih.gov/gene/?term=11517	"2900024I10Rik, AI846590, PAC1, PAC1R, PACAP1-R "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002361	115196	ZNF554	http://www.ncbi.nlm.nih.gov/gene/?term=115196		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002362	115196	ZNF554	http://www.ncbi.nlm.nih.gov/gene/?term=115196		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002363	115201	ATG4A	http://www.ncbi.nlm.nih.gov/gene/?term=115201	"APG4A, AUTL2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002364	115201	ATG4A	http://www.ncbi.nlm.nih.gov/gene/?term=115201	"APG4A, AUTL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002365	115209	OMA1	http://www.ncbi.nlm.nih.gov/gene/?term=115209	"2010001O09Rik, DAB1, MPRP-1, YKR087C, ZMPOMA1, peptidase "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002366	115209	OMA1	http://www.ncbi.nlm.nih.gov/gene/?term=115209	"2010001O09Rik, DAB1, MPRP-1, YKR087C, ZMPOMA1, peptidase "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002367	11520	Plin2	http://www.ncbi.nlm.nih.gov/gene/?term=11520	"AA407157, ADPH, Adfp, Adrp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002368	115286	SLC25A26	http://www.ncbi.nlm.nih.gov/gene/?term=115286	"COXPD28, SAMC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002369	1152	CKB	http://www.ncbi.nlm.nih.gov/gene/?term=1152	"B-CK, BCKB, HEL-211, HEL-S-29, CKB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002370	1152	CKB	http://www.ncbi.nlm.nih.gov/gene/?term=1152	"B-CK, BCKB, HEL-211, HEL-S-29, CKB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002371	1152	CKB	http://www.ncbi.nlm.nih.gov/gene/?term=1152	"B-CK, BCK, CKBB, HEL-211, HEL-S-29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002372	115330	GPR146	http://www.ncbi.nlm.nih.gov/gene/?term=115330	PGR8	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002373	115350	FCRL1	http://www.ncbi.nlm.nih.gov/gene/?term=115350	"CD307a, FCRH1, IFGP1, IRTA5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002374	115350	FCRL1	http://www.ncbi.nlm.nih.gov/gene/?term=115350	"CD307a, FCRH1, IFGP1, IRTA5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002375	115353	LRRC42	http://www.ncbi.nlm.nih.gov/gene/?term=115353	dJ167A19.4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002376	115353	LRRC42	http://www.ncbi.nlm.nih.gov/gene/?term=115353	dJ167A19.4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002377	115361	GBP4	http://www.ncbi.nlm.nih.gov/gene/?term=115361	Mpa2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002378	115361	GBP4	http://www.ncbi.nlm.nih.gov/gene/?term=115361	Mpa2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002379	115399	LRRC56	http://www.ncbi.nlm.nih.gov/gene/?term=115399		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002380	115399	LRRC56	http://www.ncbi.nlm.nih.gov/gene/?term=115399		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002381	115399	LRRC56	http://www.ncbi.nlm.nih.gov/gene/?term=115399		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002382	11539	Adora1	http://www.ncbi.nlm.nih.gov/gene/?term=11539	"A1-AR, A1AR, A1R, AA1R, AI848715, BB176431, Ri "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002383	1153	CIRBP	http://www.ncbi.nlm.nih.gov/gene/?term=1153	CIRP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002384	1153	CIRBP	http://www.ncbi.nlm.nih.gov/gene/?term=1153	CIRP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002385	1153	CIRBP	http://www.ncbi.nlm.nih.gov/gene/?term=1153	CIRP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002386	11540	Adora2a	http://www.ncbi.nlm.nih.gov/gene/?term=11540	"A2AAR, A2aR, AA2AR "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002387	115416	MALSU1	http://www.ncbi.nlm.nih.gov/gene/?term=115416	"C7orf30, mtRsfA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002388	115416	MALSU1	http://www.ncbi.nlm.nih.gov/gene/?term=115416	"C7orf30, mtRsfA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002389	115426	UHRF2	http://www.ncbi.nlm.nih.gov/gene/?term=115426	"NIRF, RNF107, TDRD23, URF2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002390	11545	Parp1	http://www.ncbi.nlm.nih.gov/gene/?term=11545	"5830444G22Rik, AI893648, ARTD1, Adprp, Adprt1, C80510, PARP, PPOL, parp-1, sPARP-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002391	11546	Parp2	http://www.ncbi.nlm.nih.gov/gene/?term=11546	"ARTD2, Adprt2, Adprtl2, Aspartl2, C78626, PARP-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002392	1154	CISH	http://www.ncbi.nlm.nih.gov/gene/?term=1154	"BACTS2, CIS, CIS-1, G18, SOCS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002393	11554	Adrb1	http://www.ncbi.nlm.nih.gov/gene/?term=11554	"Adrb-1, beta-AR "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002394	115560	ZNF501	http://www.ncbi.nlm.nih.gov/gene/?term=115560	"ZNF, ZNF52 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002395	115560	ZNF501	http://www.ncbi.nlm.nih.gov/gene/?term=115560	"ZNF, ZNF52 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002396	115560	ZNF501	http://www.ncbi.nlm.nih.gov/gene/?term=115560	"ZNF, ZNF52 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002397	1155	TBCB	http://www.ncbi.nlm.nih.gov/gene/?term=1155	"CG22, CKAP1, CKAPI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002398	1155	TBCB	http://www.ncbi.nlm.nih.gov/gene/?term=1155	"CG22, CKAP1, CKAPI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002399	1155	TBCB	http://www.ncbi.nlm.nih.gov/gene/?term=1155	"CG22, CKAP1, CKAPI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002400	11566	Adss	http://www.ncbi.nlm.nih.gov/gene/?term=11566	"AI314886, AS2, Adss "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002401	11568	Aebp1	http://www.ncbi.nlm.nih.gov/gene/?term=11568	ACLP	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002402	11569	Aebp2	http://www.ncbi.nlm.nih.gov/gene/?term=11569	"AU023766, B230313N05Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002403	11569	Aebp2	http://www.ncbi.nlm.nih.gov/gene/?term=11569	"AU023766, B230313N05Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002404	115704	EVI5L	http://www.ncbi.nlm.nih.gov/gene/?term=115704		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002405	115708	TRMT61A	http://www.ncbi.nlm.nih.gov/gene/?term=115708	"C14orf172, GCD14, Gcd14p, TRM61, hTRM61 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002406	115727	RASGRP4	http://www.ncbi.nlm.nih.gov/gene/?term=115727		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002407	115749	C12orf56	http://www.ncbi.nlm.nih.gov/gene/?term=115749		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002408	115761	ARL11	http://www.ncbi.nlm.nih.gov/gene/?term=115761	ARLTS1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002409	115761	ARL11	http://www.ncbi.nlm.nih.gov/gene/?term=115761	ARLTS1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002410	115817	DHRS1	http://www.ncbi.nlm.nih.gov/gene/?term=115817	SDR19C1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002411	115825	WDFY2	http://www.ncbi.nlm.nih.gov/gene/?term=115825	"PROF, WDF2, ZFYVE22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002412	115827	RAB3C	http://www.ncbi.nlm.nih.gov/gene/?term=115827		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002413	115939	TSR3	http://www.ncbi.nlm.nih.gov/gene/?term=115939	C16orf42	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002414	115948	CCDC151	http://www.ncbi.nlm.nih.gov/gene/?term=115948	CILD30	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00002415	11595	Acan	http://www.ncbi.nlm.nih.gov/gene/?term=11595	"Agc, Agc1, Cspg1, b2b183Clo, cmd "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002416	115992	RNF166	http://www.ncbi.nlm.nih.gov/gene/?term=115992		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002417	1159	CKMT1B	http://www.ncbi.nlm.nih.gov/gene/?term=1159	"CKMT, CKMT1, UMTCK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002418	116028	RMI2	http://www.ncbi.nlm.nih.gov/gene/?term=116028	"BLAP18, C16orf75 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002419	11603	Agrn	http://www.ncbi.nlm.nih.gov/gene/?term=11603	"Agrin, nmf380 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002420	116064	LRRC58	http://www.ncbi.nlm.nih.gov/gene/?term=116064		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002421	116064	LRRC58	http://www.ncbi.nlm.nih.gov/gene/?term=116064		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002422	116064	LRRC58	http://www.ncbi.nlm.nih.gov/gene/?term=116064		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002423	116064	LRRC58	http://www.ncbi.nlm.nih.gov/gene/?term=116064		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002424	1160	CKMT2	http://www.ncbi.nlm.nih.gov/gene/?term=1160	SMTCK	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002425	116113	FOXP4	http://www.ncbi.nlm.nih.gov/gene/?term=116113	hFKHLA	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002426	116113	FOXP4	http://www.ncbi.nlm.nih.gov/gene/?term=116113	hFKHLA	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002427	116115	ZNF526	http://www.ncbi.nlm.nih.gov/gene/?term=116115		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002428	116115	ZNF526	http://www.ncbi.nlm.nih.gov/gene/?term=116115		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002429	116115	ZNF526	http://www.ncbi.nlm.nih.gov/gene/?term=116115		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002430	116115	ZNF526	http://www.ncbi.nlm.nih.gov/gene/?term=116115		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002431	116138	KLHDC3	http://www.ncbi.nlm.nih.gov/gene/?term=116138	"PEAS, dJ20C7.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002432	116143	WDR92	http://www.ncbi.nlm.nih.gov/gene/?term=116143		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002433	116143	WDR92	http://www.ncbi.nlm.nih.gov/gene/?term=116143		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002434	116150	NUS1	http://www.ncbi.nlm.nih.gov/gene/?term=116150	"C6orf68, MGC:7199, NgBR, TANGO14 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002435	116151	FAM210B	http://www.ncbi.nlm.nih.gov/gene/?term=116151	"5A3, C20orf108, dJ1167H4.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002436	116159	CYYR1	http://www.ncbi.nlm.nih.gov/gene/?term=116159	C21orf95	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002437	1161	ERCC8	http://www.ncbi.nlm.nih.gov/gene/?term=1161	"CKN1, CSA, UVSS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002438	1161	ERCC8	http://www.ncbi.nlm.nih.gov/gene/?term=1161	"CKN1, CSA, UVSS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002439	116225	ZMYND19	http://www.ncbi.nlm.nih.gov/gene/?term=116225	MIZIP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002440	116228	COX20	http://www.ncbi.nlm.nih.gov/gene/?term=116228	FAM36A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002441	116228	COX20	http://www.ncbi.nlm.nih.gov/gene/?term=116228	FAM36A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002442	11622	Ahr	http://www.ncbi.nlm.nih.gov/gene/?term=11622	"Ah, Ahhe, In, bHLHe76, Ahr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002443	116236	ABHD15	http://www.ncbi.nlm.nih.gov/gene/?term=116236		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002444	116236	ABHD15	http://www.ncbi.nlm.nih.gov/gene/?term=116236		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002445	116238	TLCD1	http://www.ncbi.nlm.nih.gov/gene/?term=116238		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002446	11632	Aip	http://www.ncbi.nlm.nih.gov/gene/?term=11632	"AA408703, AW476050, Ara9, D19Bwg1412e, Fkbp16, Xap2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002447	116349	EXOC3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=116349	C5orf55	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002448	116349	EXOC3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=116349	C5orf55	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002449	11634	Aire	http://www.ncbi.nlm.nih.gov/gene/?term=11634		mRNA	Mus musculus	18322189	Dendrite	Embryotem cell	qRT-PCR	"Although in agreement with previous studies, low levels of Aire mRNA was detected in all dendritic cell subtypes however lacZ staining, immunohistochemistry and flow cytometry failed to detect Aire protein.  "
RLID00002450	116362	RBP7	http://www.ncbi.nlm.nih.gov/gene/?term=116362	"CRBP4, CRBPIV "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002451	116369	SLC26A8	http://www.ncbi.nlm.nih.gov/gene/?term=116369	"SPGF3, TAT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002452	11636	Ak1	http://www.ncbi.nlm.nih.gov/gene/?term=11636	"Ak-1, B430205N08Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002453	1163	CKS1B	http://www.ncbi.nlm.nih.gov/gene/?term=1163	"CKS1, PNAS-16, PNAS-18, ckshs1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002454	1163	CKS1B	http://www.ncbi.nlm.nih.gov/gene/?term=1163	"CKS1, PNAS-16, PNAS-18, ckshs1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002455	116461	TSEN15	http://www.ncbi.nlm.nih.gov/gene/?term=116461	"C1orf19, sen15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002456	116461	TSEN15	http://www.ncbi.nlm.nih.gov/gene/?term=116461	"C1orf19, sen15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002457	116496	FAM129A	http://www.ncbi.nlm.nih.gov/gene/?term=116496	"C1orf24, GIG39, NIBAN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002458	116496	FAM129A	http://www.ncbi.nlm.nih.gov/gene/?term=116496	"C1orf24, GIG39, NIBAN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002459	116496	FAM129A	http://www.ncbi.nlm.nih.gov/gene/?term=116496	"C1orf24, GIG39, NIBAN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002460	116496	FAM129A	http://www.ncbi.nlm.nih.gov/gene/?term=116496	"C1orf24, GIG39, NIBAN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002461	1164	CKS2	http://www.ncbi.nlm.nih.gov/gene/?term=1164	CKSHS2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002462	1164	CKS2	http://www.ncbi.nlm.nih.gov/gene/?term=1164	CKSHS2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002463	1164	CKS2	http://www.ncbi.nlm.nih.gov/gene/?term=1164	CKSHS2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002464	116541	MRPL54	http://www.ncbi.nlm.nih.gov/gene/?term=116541	"L54mt, MRP-L54 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002465	11657	Alb	http://www.ncbi.nlm.nih.gov/gene/?term=11657	"Alb-11, BCL002, Alb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002466	116636	Eif4ebp1	http://www.ncbi.nlm.nih.gov/gene/?term=116636	PHAS-I	mRNA	Rattus norvegicus	23091324	Dendrite	Hippocampus	Fluorescence in situ hybridization	"In situ hybridization (ISH) and Fluorescence ISH (FISH) revealed that 4EBP1 mRNA was present in dendrites.  In the present report we provide evidence that eIF4E-binding protein 1 (4EBP1) and its mRNA are also localized to dendrites in unstimulated rat hippocampal neurons, and that KCl treatment upregulates the mRNA in dendrites. The FISH signals for 4EBP1 mRNA are distributed in clusters along dendrites (Fig. 2B, AS-4EBP1).  "
RLID00002467	11666	Abcd1	http://www.ncbi.nlm.nih.gov/gene/?term=11666	"ALDP, Ald, Aldgh "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002468	11670	Aldh3a1	http://www.ncbi.nlm.nih.gov/gene/?term=11670	"Ahd-4, Ahd4, Aldh, Aldh3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002469	11674	Aldoa	http://www.ncbi.nlm.nih.gov/gene/?term=11674	"Aldo-1, Aldo1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002470	11674	Aldoa	http://www.ncbi.nlm.nih.gov/gene/?term=11674	"Aldo-1, Aldo1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002471	11677	Akr1b3	http://www.ncbi.nlm.nih.gov/gene/?term=11677	"ALR2, AR, Ahr-1, Ahr1, Akr1b1, Aldor1, Aldr1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002472	116832	RPL39L	http://www.ncbi.nlm.nih.gov/gene/?term=116832	RPL39L1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002473	116838	Rims2	http://www.ncbi.nlm.nih.gov/gene/?term=116838	"2810036I15Rik, AW048769, RIM2, Rab3ip2, Rim2(+40A), Rim2(+44A), Rim2(+4A), Serg2, Syt3-rs, mKIAA0751 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002474	116840	CNTROB	http://www.ncbi.nlm.nih.gov/gene/?term=116840	"LIP8, PP1221 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002475	116840	CNTROB	http://www.ncbi.nlm.nih.gov/gene/?term=116840	"LIP8, PP1221 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002476	116841	SNAP47	http://www.ncbi.nlm.nih.gov/gene/?term=116841	"C1orf142, ESFI5812, HEL-S-290, HEL170, SNAP-47, SVAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002477	116843	SLC18B1	http://www.ncbi.nlm.nih.gov/gene/?term=116843	"C6orf192, dJ55C23.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002478	116843	SLC18B1	http://www.ncbi.nlm.nih.gov/gene/?term=116843	"C6orf192, dJ55C23.6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002479	116850	A430106F20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=116850		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002480	116871	Mta3	http://www.ncbi.nlm.nih.gov/gene/?term=116871	"1110002J22Rik, mKIAA1266 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002481	116905	Dph1	http://www.ncbi.nlm.nih.gov/gene/?term=116905	"2310011M22Rik, 4930488F09Rik, AW551873, Dph2l1, Ovca1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002482	116914	Slc19a2	http://www.ncbi.nlm.nih.gov/gene/?term=116914	"AV276020, AW322295, DDA1, THTR1, TRMA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002483	116937	SNORD83A	http://www.ncbi.nlm.nih.gov/gene/?term=116937	"RNU83A, U83A "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00002484	116937	SNORD83A	http://www.ncbi.nlm.nih.gov/gene/?term=116937	"RNU83A, U83A "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002485	116937	SNORD83A	http://www.ncbi.nlm.nih.gov/gene/?term=116937	"RNU83A, U83A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00002486	116937	SNORD83A	http://www.ncbi.nlm.nih.gov/gene/?term=116937	"RNU83A, U83A "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002487	116938	SNORD83B	http://www.ncbi.nlm.nih.gov/gene/?term=116938	"RNU83B, U83B "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00002488	116938	SNORD83B	http://www.ncbi.nlm.nih.gov/gene/?term=116938	"RNU83B, U83B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002489	116938	SNORD83B	http://www.ncbi.nlm.nih.gov/gene/?term=116938	"RNU83B, U83B "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002490	116983	ACAP3	http://www.ncbi.nlm.nih.gov/gene/?term=116983	CENTB5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002491	116984	ARAP2	http://www.ncbi.nlm.nih.gov/gene/?term=116984	"CENTD1, PARX "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002492	116988	AGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=116988	"AGAP-3, CENTG3, CRAG, MRIP-1, cnt-g3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002493	11702	Amd1	http://www.ncbi.nlm.nih.gov/gene/?term=11702	"AdoMetDC, Amd-1, SAMDC, SAMDC 1, adoMetDC1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002494	117030	Erp29	http://www.ncbi.nlm.nih.gov/gene/?term=117030		mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00002495	117030	Erp29	http://www.ncbi.nlm.nih.gov/gene/?term=117030		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00002496	117143	TADA1	http://www.ncbi.nlm.nih.gov/gene/?term=117143	"ADA1, HFI1, STAF42L, hADA1, TADA1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002497	117143	TADA1	http://www.ncbi.nlm.nih.gov/gene/?term=117143	"ADA1, HFI1, STAF42, TADA1L, hADA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002498	117145	THEM4	http://www.ncbi.nlm.nih.gov/gene/?term=117145	CTMP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002499	117177	RAB3IP	http://www.ncbi.nlm.nih.gov/gene/?term=117177	"RABIN3, RABIN8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002500	117178	SSX2IP	http://www.ncbi.nlm.nih.gov/gene/?term=117178	ADIP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002501	117178	SSX2IP	http://www.ncbi.nlm.nih.gov/gene/?term=117178	ADIP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002502	117178	SSX2IP	http://www.ncbi.nlm.nih.gov/gene/?term=117178	ADIP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002503	117178	SSX2IP	http://www.ncbi.nlm.nih.gov/gene/?term=117178	ADIP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002504	117198	Ivns1abp	http://www.ncbi.nlm.nih.gov/gene/?term=117198	"1190004M08Rik, 1700126I16Rik, AA960440, HSPC068, ND1, NS-1, NS1-BP, Nd1-L, Nd1-S, mKIAA0850 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002505	117198	Ivns1abp	http://www.ncbi.nlm.nih.gov/gene/?term=117198	"1190004M08Rik, 1700126I16Rik, AA960440, HSPC068, ND1, NS-1, NS1-BP, Nd1-L, Nd1-S, mKIAA0850 "	mRNA	Mus musculus	16317045	Dendrite	Hippocampus	In situ hybridization	"Nd1-L transcripts were increased in the dendrites upon mGluR activation and significantly reduced in TLS-null dendrites. Cell in situ hybridization revealed that both Nd1-L and beta-actin mRNAs were increased in dendrites in DHPG-treated neurons by about 4.1-fold and 7.8-fold, respectively compared with those in non-treated WT neurons (Fig. 3A, left, and B).  "
RLID00002506	11720	Mat1a	http://www.ncbi.nlm.nih.gov/gene/?term=11720	"AI046368, AdoMet, Ams, MAT, MATA1, SAMS, SAMS1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002507	117246	FTSJ3	http://www.ncbi.nlm.nih.gov/gene/?term=117246	"EPCS3, SPB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002508	117254	Prdx1	http://www.ncbi.nlm.nih.gov/gene/?term=117254	Hbp23	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00002509	117273	Rhoa	http://www.ncbi.nlm.nih.gov/gene/?term=117273	"Arha, Arha2 "	mRNA	Rattus norvegicus	16723529	Growth cone	Embryo	In situ hybridization	"RhoA mRNA is localized to axons and growth cones, and intra-axonal translation of RhoA is required for growth cone collapse elicited by Semaphorin 3A (Sema3A), an axonal guidance cue. Selective knock-down of axonal RhoA mRNA abolishes Sema3A-dependent growth cone collapse "
RLID00002510	117273	Rhoa	http://www.ncbi.nlm.nih.gov/gene/?term=117273	"Arha, Arha2 "	mRNA	Rattus norvegicus	16723529	Axon	Embryo	In situ hybridization	"RhoA mRNA is localized to axons and growth cones, and intra-axonal translation of RhoA is required for growth cone collapse elicited by Semaphorin 3A (Sema3A), an axonal guidance cue. Selective knock-down of axonal RhoA mRNA abolishes Sema3A-dependent growth cone collapse "
RLID00002511	11727	Ang	http://www.ncbi.nlm.nih.gov/gene/?term=11727	"AI3855861, Rnase5, Rnase5a, Ang "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002512	117287	Park7	http://www.ncbi.nlm.nih.gov/gene/?term=117287	"CAP1, DJ-1, Dj1, SP22 "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00002513	117287	Park7	http://www.ncbi.nlm.nih.gov/gene/?term=117287	"CAP1, DJ-1, Dj1, SP22 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00002514	117294	Dsp1	http://www.ncbi.nlm.nih.gov/gene/?term=117294	"Dmel_CG12223, CG12223, DSP1, Dmel\CG12223, Hmg14B, Hmg14D, Ssrp2, dsp1, hmg, ssrp2 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00002515	117294	Dsp1	http://www.ncbi.nlm.nih.gov/gene/?term=117294	"Dmel_CG12223, CG12223, DSP1, Dmel\CG12223, Hmg14B, Hmg14D, Ssrp2, dsp1, hmg, ssrp2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00002516	11735	Ank3	http://www.ncbi.nlm.nih.gov/gene/?term=11735	"2900054D09Rik, AI314020, Ank-3, AnkG, Ankyrin-3, Ankyrin-G "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002517	11735	Ank3	http://www.ncbi.nlm.nih.gov/gene/?term=11735	"2900054D09Rik, AI314020, Ank-3, AnkG, Ankyrin-3, Ankyrin-G "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002518	117369	Desat1	http://www.ncbi.nlm.nih.gov/gene/?term=117369	"Dmel_CG5887, BEST:SD05462, CG5887, Dmel\CG5887, Fad, anon-WO0118547.726, anon-WO0118547.730, desat, desat1, ds1, fad, l(3)S028813 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00002519	117369	Desat1	http://www.ncbi.nlm.nih.gov/gene/?term=117369	"Dmel_CG5887, BEST:SD05462, CG5887, Dmel\CG5887, Fad, anon-WO0118547.726, anon-WO0118547.730, desat, desat1, ds1, fad, l(3)S028813 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00002520	117369	Desat1	http://www.ncbi.nlm.nih.gov/gene/?term=117369	"Dmel_CG5887, BEST:SD05462, CG5887, Dmel\CG5887, Fad, anon-WO0118547.726, anon-WO0118547.730, desat, desat1, ds1, fad, l(3)S028813 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00002521	117369	Desat1	http://www.ncbi.nlm.nih.gov/gene/?term=117369	"Dmel_CG5887, BEST:SD05462, CG5887, Dmel\CG5887, Fad, anon-WO0118547.726, anon-WO0118547.730, desat, desat1, ds1, fad, l(3)S028813 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00002522	11736	Ankfy1	http://www.ncbi.nlm.nih.gov/gene/?term=11736	"Ankhzn, ZFYVE14, mKIAA1255 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002523	11737	Anp32a	http://www.ncbi.nlm.nih.gov/gene/?term=11737	"Anp32, I1PP2A, LANP, PHAP1, W91701, pp32 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002524	1173	AP2M1	http://www.ncbi.nlm.nih.gov/gene/?term=1173	"AP50, CLAPM1, mu2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002525	11740	Slc25a5	http://www.ncbi.nlm.nih.gov/gene/?term=11740	Ant2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002526	11745	Anxa3	http://www.ncbi.nlm.nih.gov/gene/?term=11745	Anx3	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00002527	1174	AP1S1	http://www.ncbi.nlm.nih.gov/gene/?term=1174	"AP19, CLAPS1, EKV3, MEDNIK, SIGMA1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002528	1174	AP1S1	http://www.ncbi.nlm.nih.gov/gene/?term=1174	"AP19, CLAPS1, EKV3, MEDNIK, SIGMA1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002529	117531	TMC1	http://www.ncbi.nlm.nih.gov/gene/?term=117531	"DFNA36, DFNB11, DFNB7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002530	117531	TMC1	http://www.ncbi.nlm.nih.gov/gene/?term=117531	"DFNA36, DFNB11, DFNB7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002531	117557	Tpm3	http://www.ncbi.nlm.nih.gov/gene/?term=117557	"TM30nm, Tpm5 "	mRNA	Rattus norvegicus	15673657	Cell body	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00002532	117557	Tpm3	http://www.ncbi.nlm.nih.gov/gene/?term=117557	"TM30nm, Tpm5 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00002533	117584	RFFL	http://www.ncbi.nlm.nih.gov/gene/?term=117584	"CARP-2, CARP2, FRING, RIFIFYLIN, RNF189, RNF34L "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002534	117584	RFFL	http://www.ncbi.nlm.nih.gov/gene/?term=117584	"CARP-2, CARP2, FRING, RIFIFYLIN, RNF189, RNF34L "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002535	117584	RFFL	http://www.ncbi.nlm.nih.gov/gene/?term=117584	"CARP-2, CARP2, FRING, RIFIFYLIN, RNF189, RNF34L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002536	117584	RFFL	http://www.ncbi.nlm.nih.gov/gene/?term=117584	"CARP-2, CARP2, FRING, RIFIFYLIN, RNF189, RNF34L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002537	117584	RFFL	http://www.ncbi.nlm.nih.gov/gene/?term=117584	"CARP-2, CARP2, FRING, RIFIFYLIN, RNF189, RNF34L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002538	117599	Helb	http://www.ncbi.nlm.nih.gov/gene/?term=117599	"AI447783, D10Ertd664e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002539	1175	AP2S1	http://www.ncbi.nlm.nih.gov/gene/?term=1175	"AP17, CLAPS2, FBH3, FBHOk, HHC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002540	1175	AP2S1	http://www.ncbi.nlm.nih.gov/gene/?term=1175	"AP17, CLAPS2, FBH3, FBHOk, HHC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002541	11761	Aox1	http://www.ncbi.nlm.nih.gov/gene/?term=11761	"AI196512, AI255253, Ao, Aox-1, Aox-2, Aox2, Moro, Ro "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002542	11765	Ap1g1	http://www.ncbi.nlm.nih.gov/gene/?term=11765	"AA409002, AU041323, AW551707, Adtg, D8Ertd374e "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002543	1176	AP3S1	http://www.ncbi.nlm.nih.gov/gene/?term=1176	"CLAPS3, Sigma3A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002544	1176	AP3S1	http://www.ncbi.nlm.nih.gov/gene/?term=1176	"CLAPS3, Sigma3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002545	11774	Ap3b1	http://www.ncbi.nlm.nih.gov/gene/?term=11774	"AP-3, AU015684, C78395, Hps2, beta3A, pe, pearl, rim2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002546	117852	TRIM78P	http://www.ncbi.nlm.nih.gov/gene/?term=117852	TRIMP1	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002547	117854	TRIM6	http://www.ncbi.nlm.nih.gov/gene/?term=117854	RNF89	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002548	117854	TRIM6	http://www.ncbi.nlm.nih.gov/gene/?term=117854	RNF89	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002549	11787	Apbb2	http://www.ncbi.nlm.nih.gov/gene/?term=11787	"2310007D03Rik, FE65L1, Rirl1, TR2L, Zfra "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002550	11789	Apc	http://www.ncbi.nlm.nih.gov/gene/?term=11789	"AI047805, AU020952, AW124434, CC1, Min, mAPC "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00002551	11797	Birc2	http://www.ncbi.nlm.nih.gov/gene/?term=11797	"AW146227, Api1, Api2, Birc3, C330006D17Rik, HIAP1, HIAP2, IAP1, IAP2, MIAP1, MIAP2, MIHB, MIHC, RNF48, cIAP1, cIAP2, mcIAP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002552	11800	Api5	http://www.ncbi.nlm.nih.gov/gene/?term=11800	"AAC-11, AI196452, API-5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002553	11801	Cd5l	http://www.ncbi.nlm.nih.gov/gene/?term=11801	"1/6, AAC-11, AI047839, Api6, CT2, Pdp, Sp-alpha, mAIM "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002554	11804	Aplp2	http://www.ncbi.nlm.nih.gov/gene/?term=11804	"AI790698, APLP-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002555	11804	Aplp2	http://www.ncbi.nlm.nih.gov/gene/?term=11804	"AI790698, APLP-2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002556	11816	Apoe	http://www.ncbi.nlm.nih.gov/gene/?term=11816	"AI255918, Apo-E "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002557	11819	Nr2f2	http://www.ncbi.nlm.nih.gov/gene/?term=11819	"2700033K02Rik, 9430015G03Rik, ARP-1, Aporp1, COUP-TF2, COUP-TFII, COUPTFB, EAR3, SVP40, Tcfcoup2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002558	11820	App	http://www.ncbi.nlm.nih.gov/gene/?term=11820	"Abeta, Abpp, Adap, Ag, Cvap, E030013M08Rik, betaApp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002559	11820	App	http://www.ncbi.nlm.nih.gov/gene/?term=11820	"Abeta, Abpp, Adap, Ag, Cvap, E030013M08Rik, betaApp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002560	1182	CLCN3	http://www.ncbi.nlm.nih.gov/gene/?term=1182	"CLC3, ClC-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002561	1182	CLCN3	http://www.ncbi.nlm.nih.gov/gene/?term=1182	"CLC3, ClC-3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002562	1182	CLCN3	http://www.ncbi.nlm.nih.gov/gene/?term=1182	"CLC3, ClC-3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002563	11837	Rplp0	http://www.ncbi.nlm.nih.gov/gene/?term=11837	"36B4, Arbp, L10E "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002564	11838	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=11838	"Arc3.1, C86064, arg3.1, mArc "	mRNA	Mus musculus	22945799	Synapse	Brain	RT-PCR|Immunoprecipitation	"Fig. 5 a Detection of KIF1Bb in purified mouse synaptoneurosomes. KIF1Bb is detected in total lysates from the cortex (T; 5 lg total protein) and is enriched in a sample of synaptoneurosomes purified from the cortex (S; 5 lg). The analysis, by RT-PCR, revealed the presence of Arc (activity regulated cytoskeleton-associated protein) mRNA (Fig. 8c), a well-known, dendritically localized mRNA [43-45]. Interestingly, Calmodulin mRNA was also part of this complex. Both were specifically found in the KIF1Bb-immunoprecipitated complex, but not in the negative control reaction (Fig. 8c, compare lanes 2 and 3). The specific association of Arc and Calmodulin mRNAs with the KIF1Bb-containing complex is further supported by the absence of non-synaptically or other synaptically localized mRNAs such as eEIF1a and aCaMKII (Fig. 8c). These observations would suggest the participation of KIF1Bb in RNP particles in association with at least two dendritically targeted mRNAs, Arc and CaM. "
RLID00002565	1183	CLCN4	http://www.ncbi.nlm.nih.gov/gene/?term=1183	"CLC4, ClC-4, ClC-4A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002566	11840	Arf1	http://www.ncbi.nlm.nih.gov/gene/?term=11840		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002567	118424	UBE2J2	http://www.ncbi.nlm.nih.gov/gene/?term=118424	"NCUBE-2, NCUBE2, PRO2121 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002568	118424	UBE2J2	http://www.ncbi.nlm.nih.gov/gene/?term=118424	"NCUBE-2, NCUBE2, PRO2121 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002569	118429	ANTXR2	http://www.ncbi.nlm.nih.gov/gene/?term=118429	"CMG-2, CMG2, HFS, ISH, JHF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002570	118429	ANTXR2	http://www.ncbi.nlm.nih.gov/gene/?term=118429	"CMG-2, CMG2, HFS, ISH, JHF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002571	118433	RPL23AP7	http://www.ncbi.nlm.nih.gov/gene/?term=118433	"RPL23AL1, RPL23A_6_267, bA395L14.9 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002572	118445	Klf16	http://www.ncbi.nlm.nih.gov/gene/?term=118445	"AI843742, BTEB4, DRRF "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002573	11844	Arf5	http://www.ncbi.nlm.nih.gov/gene/?term=11844		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002574	11845	Arf6	http://www.ncbi.nlm.nih.gov/gene/?term=11845	"AI788669, AW496366 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002575	11845	Arf6	http://www.ncbi.nlm.nih.gov/gene/?term=11845	"AI788669, AW496366 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002576	118460	EXOSC6	http://www.ncbi.nlm.nih.gov/gene/?term=118460	"EAP4, MTR3, Mtr3p, hMtr3p, p11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002577	11846	Arg1	http://www.ncbi.nlm.nih.gov/gene/?term=11846	"AI, AI256583, Arg-1, PGIF "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002578	118472	ZNF511	http://www.ncbi.nlm.nih.gov/gene/?term=118472		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002579	11847	Arg2	http://www.ncbi.nlm.nih.gov/gene/?term=11847	"AII, AU022422 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002580	118487	CHCHD1	http://www.ncbi.nlm.nih.gov/gene/?term=118487	"C10orf34, C2360, MRP-S37 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002581	11848	Rhoa	http://www.ncbi.nlm.nih.gov/gene/?term=11848	"Arha, Arha1, Arha2 "	mRNA	Mus musculus	20035871	Dendrite	Brain	RT-PCR	"Using this preparation, we have found that RhoA mRNA is dendritically localized and its local translation is enhanced by BDNF stimulation. "
RLID00002582	1184	CLCN5	http://www.ncbi.nlm.nih.gov/gene/?term=1184	"CLC5, CLCK2, ClC-5, DENTS, NPHL1, NPHL2, XLRH, XRN, hCIC-K2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002583	1184	CLCN5	http://www.ncbi.nlm.nih.gov/gene/?term=1184	"CLC5, CLCK2, ClC-5, DENTS, NPHL1, NPHL2, XLRH, XRN, hCIC-K2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002584	1184	CLCN5	http://www.ncbi.nlm.nih.gov/gene/?term=1184	"CLC5, CLCK2, ClC-5, DENTS, NPHL1, NPHL2, XLRH, XRN, hCIC-K2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002585	11852	Rhob	http://www.ncbi.nlm.nih.gov/gene/?term=11852	"AA017882, Arh6, Arhb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002586	11857	Arhgdib	http://www.ncbi.nlm.nih.gov/gene/?term=11857	"D4, Gdid4, Ly-GDI "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002587	11859	Phox2a	http://www.ncbi.nlm.nih.gov/gene/?term=11859	"Arix, Phox2, Pmx2, Pmx2a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002588	1185	CLCN6	http://www.ncbi.nlm.nih.gov/gene/?term=1185	CLC-6	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002589	11864	Arnt2	http://www.ncbi.nlm.nih.gov/gene/?term=11864	"Hif-2b, bHLHe1, mKIAA0307 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002590	1186	CLCN7	http://www.ncbi.nlm.nih.gov/gene/?term=1186	"CLC-7, CLC7, OPTA2, OPTB4, PPP1R63 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002591	11877	Arvcf	http://www.ncbi.nlm.nih.gov/gene/?term=11877		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002592	118788	PIK3AP1	http://www.ncbi.nlm.nih.gov/gene/?term=118788	BCAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002593	1187	CLCNKA	http://www.ncbi.nlm.nih.gov/gene/?term=1187	"CLCK1, ClC-K1, hClC-Ka "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002594	118812	MORN4	http://www.ncbi.nlm.nih.gov/gene/?term=118812	"C10orf83, bA548K23.4, rtp "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002595	118812	MORN4	http://www.ncbi.nlm.nih.gov/gene/?term=118812	"C10orf83, bA548K23.4, rtp "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002596	118812	MORN4	http://www.ncbi.nlm.nih.gov/gene/?term=118812	"C10orf83, bA548K23.4, rtp "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002597	118813	ZFYVE27	http://www.ncbi.nlm.nih.gov/gene/?term=118813	"PROTRUDIN, SPG33 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002598	11886	Asah1	http://www.ncbi.nlm.nih.gov/gene/?term=11886	"2310081N20Rik, AC, Asah "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002599	118881	COMTD1	http://www.ncbi.nlm.nih.gov/gene/?term=118881		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002600	118924	FRA10AC1	http://www.ncbi.nlm.nih.gov/gene/?term=118924	"C10orf4, F26C11.1-like, FRA10A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002601	118980	SFXN2	http://www.ncbi.nlm.nih.gov/gene/?term=118980		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002602	118980	SFXN2	http://www.ncbi.nlm.nih.gov/gene/?term=118980		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002603	118980	SFXN2	http://www.ncbi.nlm.nih.gov/gene/?term=118980		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002604	118980	SFXN2	http://www.ncbi.nlm.nih.gov/gene/?term=118980		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002605	118987	PDZD8	http://www.ncbi.nlm.nih.gov/gene/?term=118987	PDZK8	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002606	11898	Ass1	http://www.ncbi.nlm.nih.gov/gene/?term=11898	"AA408052, ASS, Ass-1, fold "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002607	118	ADD1	http://www.ncbi.nlm.nih.gov/gene/?term=118	ADDA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002608	118	ADD1	http://www.ncbi.nlm.nih.gov/gene/?term=118	ADDA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002609	119032	BORCS7	http://www.ncbi.nlm.nih.gov/gene/?term=119032	C10orf32	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002610	119032	BORCS7	http://www.ncbi.nlm.nih.gov/gene/?term=119032	C10orf32	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002611	11906	Zfhx3	http://www.ncbi.nlm.nih.gov/gene/?term=11906	"A230102L03Rik, Atbf1, Sci, WBP9, mKIAA4228 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002612	11906	Zfhx3	http://www.ncbi.nlm.nih.gov/gene/?term=11906	"A230102L03Rik, Atbf1, Sci, WBP9, mKIAA4228 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002613	11907	Ate1	http://www.ncbi.nlm.nih.gov/gene/?term=11907	"AI225793, AW547406 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002614	11909	Atf2	http://www.ncbi.nlm.nih.gov/gene/?term=11909	"Atf-2, CRE-BP, Creb2, D130078H02Rik, D18875, Tg(Gzma-Klra1)7Wum, mXBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002615	11911	Atf4	http://www.ncbi.nlm.nih.gov/gene/?term=11911	"Atf-4, C/ATF, CREB2, TAXREB67 "	mRNA	Mus musculus	18195013	Ribosome	S/S MEF cell	RT-PCR	"The resulting lowered eIF2-GTP levels leads to reduced polysomes and accumulation of free ribosomal subunits in the polysome profile (Fig. 8,top panels). This stress arrangement led to a shift in the ATF4 mRNA to the larger polysome fractions (Fig. 8,fractions 7-11). "
RLID00002616	11911	Atf4	http://www.ncbi.nlm.nih.gov/gene/?term=11911	"Atf-4, C/ATF, CREB2, TAXREB67 "	mRNA	Mus musculus	26131922	Axon	Brain	In situ hybridization	"Finally, Atf4 mRNA is found in adult axons of mice and human brains in the context of Abeta-induced neurodegeneration. "
RLID00002617	1191	CLU	http://www.ncbi.nlm.nih.gov/gene/?term=1191	"AAG4, APO-J, APOJ, CLI1, CLU2, KUB1, NA1/NA2, SGP-2, SGP2, SP-40, TRPM-2, TRPM2, CLU "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002618	1191	CLU	http://www.ncbi.nlm.nih.gov/gene/?term=1191	"AAG4, APO-J, APOJ, CLI1, CLU2, KUB1, NA1/NA2, SGP-2, SGP2, SP-40, TRPM-2, TRPM2, CLU "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002619	1191	CLU	http://www.ncbi.nlm.nih.gov/gene/?term=1191	"AAG4, APO-J, APOJ, CLI, CLU1, CLU2, KUB1, NA1/NA2, SGP-2, SGP2, SP-40, TRPM-2, TRPM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002620	11920	Atm	http://www.ncbi.nlm.nih.gov/gene/?term=11920	"AI256621, C030026E19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002621	11921	Atoh1	http://www.ncbi.nlm.nih.gov/gene/?term=11921	"Hath1, MATH-1, Math1, bHLHa14 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002622	11922	Neurod6	http://www.ncbi.nlm.nih.gov/gene/?term=11922	"Atoh2, Math-2, Math2, Nex, Nex1m, bHLHa2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002623	11927	Atox1	http://www.ncbi.nlm.nih.gov/gene/?term=11927	"AI256639, Atx1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002624	1192	CLIC1	http://www.ncbi.nlm.nih.gov/gene/?term=1192	"G6, NCC27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002625	1192	CLIC1	http://www.ncbi.nlm.nih.gov/gene/?term=1192	"G6, NCC27 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002626	1192	CLIC1	http://www.ncbi.nlm.nih.gov/gene/?term=1192	"G6, NCC27 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002627	11933	Atp1b3	http://www.ncbi.nlm.nih.gov/gene/?term=11933	"AA409958, AI664000, AW212096 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002628	119391	GSTO2	http://www.ncbi.nlm.nih.gov/gene/?term=119391	"GSTO 2-2, bA127L20.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002629	1193	CLIC2	http://www.ncbi.nlm.nih.gov/gene/?term=1193	"CLIC2b, MRXS32, XAP121 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002630	119467	CLRN3	http://www.ncbi.nlm.nih.gov/gene/?term=119467	"TMEM12, USH3AL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002631	119504	ANAPC16	http://www.ncbi.nlm.nih.gov/gene/?term=119504	"APC16, C10orf104, CENP-27, MSAG, bA570G20.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002632	119504	ANAPC16	http://www.ncbi.nlm.nih.gov/gene/?term=119504	"APC16, C10orf104, CENP-27, MSAG, bA570G20.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002633	11950	Atp5f1	http://www.ncbi.nlm.nih.gov/gene/?term=11950	C76477	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002634	119587	CPXM2	http://www.ncbi.nlm.nih.gov/gene/?term=119587	"CPX2, UNQ676 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002635	119587	CPXM2	http://www.ncbi.nlm.nih.gov/gene/?term=119587	"CPX2, UNQ676 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002636	1195	CLK1	http://www.ncbi.nlm.nih.gov/gene/?term=1195	"CLK, CLK/STY, STY "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002637	11964	Atp6v1a	http://www.ncbi.nlm.nih.gov/gene/?term=11964	"AI647066, Atp6a1, Atp6a21, VA68, VPP2, Atp6v1a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002638	11966	Atp6v1b2	http://www.ncbi.nlm.nih.gov/gene/?term=11966	"AI194269, AI790362, Atp6b2, HO57, R74844 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002639	1196	CLK2	http://www.ncbi.nlm.nih.gov/gene/?term=1196		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002640	11977	Atp7a	http://www.ncbi.nlm.nih.gov/gene/?term=11977	MNK	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002641	11980	Atp8a1	http://www.ncbi.nlm.nih.gov/gene/?term=11980	"AI481521, AI853962, APLT, AW743152, AW822227, Atp3a2, B230107D19Rik, ClassI "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002642	11983	Atpif1	http://www.ncbi.nlm.nih.gov/gene/?term=11983	"Atpi, IF(1), If1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002643	11984	Atp6v0c	http://www.ncbi.nlm.nih.gov/gene/?term=11984	"Atp6c, Atp6c2, Atp6l, Atpl, Atpl-rs1, PL16, VATL, Vma3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002644	11987	Slc7a1	http://www.ncbi.nlm.nih.gov/gene/?term=11987	"4831426K01Rik, AI447493, Atrc-1, Atrc1, Cat1, Rec-1, Rev-1, mCAT-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002645	11988	Slc7a2	http://www.ncbi.nlm.nih.gov/gene/?term=11988	"20.5, AI158848, Atrc2, CAT-2, Cat2, Tea "	mRNA	Mus musculus	16239143	Nucleus	NIH 3T3 cell	Fluorescence in situ hybridization	"We have identified CTN-RNA, a mouse tissue-specific approximately 8 kb nuclear-retained poly(A)+ RNA that regulates the level of its protein-coding partner. CTN-RNA is transcribed from the protein-coding mouse cationic amino acid transporter 2 (mCAT2) gene through alternative promoter and poly(A) site usage. CTN-RNA is diffusely distributed in nuclei and is also localized to paraspeckles. "
RLID00002646	1198	CLK3	http://www.ncbi.nlm.nih.gov/gene/?term=1198	"PHCLK3, PHCLK3/152 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002647	1198	CLK3	http://www.ncbi.nlm.nih.gov/gene/?term=1198	"PHCLK3, PHCLK3/152 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002648	11990	Atrn	http://www.ncbi.nlm.nih.gov/gene/?term=11990	"AW558010, Mgca, mKIAA0548, mahogany, mg "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002649	11997	Akr1b7	http://www.ncbi.nlm.nih.gov/gene/?term=11997	"AR, Avdp, MVDP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002650	119	ADD2	http://www.ncbi.nlm.nih.gov/gene/?term=119	ADDB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002651	120071	GYLTL1B	http://www.ncbi.nlm.nih.gov/gene/?term=120071	"LARGE2, PP5656 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002652	1200	TPP1	http://www.ncbi.nlm.nih.gov/gene/?term=1200	"CLN2, GIG1, LPIC, SCAR7, TPP-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002653	1200	TPP1	http://www.ncbi.nlm.nih.gov/gene/?term=1200	"CLN2, GIG1, LPIC, SCAR7, TPP-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002654	120103	SLC36A4	http://www.ncbi.nlm.nih.gov/gene/?term=120103	PAT4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002655	12010	B2m	http://www.ncbi.nlm.nih.gov/gene/?term=12010	"Ly-m11, beta2-m, beta2m "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002656	12013	Bach1	http://www.ncbi.nlm.nih.gov/gene/?term=12013	"6230421P05Rik, AI323795 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002657	12014	Bach2	http://www.ncbi.nlm.nih.gov/gene/?term=12014	E030004N02Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002658	12015	Bad	http://www.ncbi.nlm.nih.gov/gene/?term=12015	"AI325008, Bbc2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002659	12018	Bak1	http://www.ncbi.nlm.nih.gov/gene/?term=12018	"Bak, N-BAK1, N-Bak "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002660	1201	CLN3	http://www.ncbi.nlm.nih.gov/gene/?term=1201	"BTS, JNCL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002661	120224	TMEM45B	http://www.ncbi.nlm.nih.gov/gene/?term=120224		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002662	120227	CYP2R1	http://www.ncbi.nlm.nih.gov/gene/?term=120227		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002663	120227	CYP2R1	http://www.ncbi.nlm.nih.gov/gene/?term=120227		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002664	12033	Bcap29	http://www.ncbi.nlm.nih.gov/gene/?term=12033	"AW208404, Bap29 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002665	12036	Bcat2	http://www.ncbi.nlm.nih.gov/gene/?term=12036	"Bcat-2, Eca40 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002666	12039	Bckdha	http://www.ncbi.nlm.nih.gov/gene/?term=12039		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002667	1203	CLN5	http://www.ncbi.nlm.nih.gov/gene/?term=1203	NCL	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002668	12041	Bckdk	http://www.ncbi.nlm.nih.gov/gene/?term=12041	AI327402	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002669	120425	JAML	http://www.ncbi.nlm.nih.gov/gene/?term=120425	"AMICA, AMICA1, CREA7-1, CREA7-4, Gm638 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002670	12043	Bcl2	http://www.ncbi.nlm.nih.gov/gene/?term=12043	"AW986256, Bcl-2, C430015F12Rik, D630044D05Rik, D830018M01Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002671	120526	DNAJC24	http://www.ncbi.nlm.nih.gov/gene/?term=120526	"DPH4, JJJ3, ZCSL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002672	12064	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=12064		mRNA	Mus musculus	18614020	Dendrite	Neuron	In situ hybridization	"In a mouse mutant where the long 3' UTR is truncated, dendritic targeting of BDNF mRNAs is impaired. "
RLID00002673	12064	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=12064		mRNA	Mus musculus	25692578	Dendrite	Hippocampus	Fluorescence in situ hybridization	"We demonstrate that the neuronal ELAV family of RNA binding proteins associates in vivo with several Bdnf mRNA isoforms present in the adult brain in an activity-dependent manner, and that one member, HuD, interacts directly with sequences in the long Bdnf 3' untranslated region (3'UTR) and co-localizes with Bdnf mRNA in dendrites of hippocampal neurons. "
RLID00002674	1207	CLNS1A	http://www.ncbi.nlm.nih.gov/gene/?term=1207	"CLCI, CLNS1B, ICln "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002675	1207	CLNS1A	http://www.ncbi.nlm.nih.gov/gene/?term=1207	"CLCI, CLNS1B, ICln "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002676	1207	CLNS1A	http://www.ncbi.nlm.nih.gov/gene/?term=1207	"CLCI, CLNS1B, ICln "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002677	1209	CLPTM1	http://www.ncbi.nlm.nih.gov/gene/?term=1209		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002678	1209	CLPTM1	http://www.ncbi.nlm.nih.gov/gene/?term=1209		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002679	1209	CLPTM1	http://www.ncbi.nlm.nih.gov/gene/?term=1209		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002680	120	ADD3	http://www.ncbi.nlm.nih.gov/gene/?term=120	ADDL	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002681	120	ADD3	http://www.ncbi.nlm.nih.gov/gene/?term=120	ADDL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002682	121053	C12orf45	http://www.ncbi.nlm.nih.gov/gene/?term=121053		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002683	121053	C12orf45	http://www.ncbi.nlm.nih.gov/gene/?term=121053		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002684	12116	Bhmt	http://www.ncbi.nlm.nih.gov/gene/?term=12116		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002685	1211	CLTA	http://www.ncbi.nlm.nih.gov/gene/?term=1211	LCA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002686	1211	CLTA	http://www.ncbi.nlm.nih.gov/gene/?term=1211	LCA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002687	12121	Bicd1	http://www.ncbi.nlm.nih.gov/gene/?term=12121	B830009D06Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002688	12123	Hrk	http://www.ncbi.nlm.nih.gov/gene/?term=12123	"AI838259, Bid3, DP5, harakiri "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002689	12124	Bik	http://www.ncbi.nlm.nih.gov/gene/?term=12124	"Biklk, Blk, Nbk "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002690	121260	SLC15A4	http://www.ncbi.nlm.nih.gov/gene/?term=121260	"FP12591, PHT1, PTR4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002691	121274	ZNF641	http://www.ncbi.nlm.nih.gov/gene/?term=121274		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002692	1212	CLTB	http://www.ncbi.nlm.nih.gov/gene/?term=1212	LCB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002693	1212	CLTB	http://www.ncbi.nlm.nih.gov/gene/?term=1212	LCB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002694	1213	CLTC	http://www.ncbi.nlm.nih.gov/gene/?term=1213	"CHC, CHC17, CLH-17L2, Hc, CLTC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002695	1213	CLTC	http://www.ncbi.nlm.nih.gov/gene/?term=1213	"CHC, CHC17, CLH-17, CLTCL2, Hc "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002696	12142	Prdm1	http://www.ncbi.nlm.nih.gov/gene/?term=12142	"Blimp-1, Blimp1, PRDI-BF1, ZNFPR1A1, b2b1765Clo "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002697	121441	NEDD1	http://www.ncbi.nlm.nih.gov/gene/?term=121441	"GCP-WD, TUBGCP7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002698	12144	Blm	http://www.ncbi.nlm.nih.gov/gene/?term=12144		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002699	121457	IKBIP	http://www.ncbi.nlm.nih.gov/gene/?term=121457	IKIP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002700	121457	IKBIP	http://www.ncbi.nlm.nih.gov/gene/?term=121457	IKIP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002701	121504	HIST4H4	http://www.ncbi.nlm.nih.gov/gene/?term=121504	H4/p	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002702	121506	ERP27	http://www.ncbi.nlm.nih.gov/gene/?term=121506	"C12orf46, PDIA8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002703	121506	ERP27	http://www.ncbi.nlm.nih.gov/gene/?term=121506	"C12orf46, PDIA8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002704	12151	Bmi1	http://www.ncbi.nlm.nih.gov/gene/?term=12151	"AW546694, Bmi-1, Pcgf4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002705	12153	Bmp1	http://www.ncbi.nlm.nih.gov/gene/?term=12153	"Pcp, Tld "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002706	12161	Bmp6	http://www.ncbi.nlm.nih.gov/gene/?term=12161	"D13Wsu115e, Vgr1 "	mRNA	Mus musculus	9856831	Cell leading edge	Skin	-	"Protein was confined to outermost suprabasal epidermal layers, whereas BMP-6-specific RNA was distributed throughout all epidermal layers including basal keratinocytes and the leading edge of the migrating keratinocytes. "
RLID00002707	121642	ALKBH2	http://www.ncbi.nlm.nih.gov/gene/?term=121642	ABH2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002708	121665	SPPL3	http://www.ncbi.nlm.nih.gov/gene/?term=121665	"IMP2, MDHV1887, PRO4332, PSH1, PSL4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002709	12166	Bmpr1a	http://www.ncbi.nlm.nih.gov/gene/?term=12166	"1110037I22Rik, ALK3, AU045487, BMPR-IA, Bmpr "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002710	12168	Bmpr2	http://www.ncbi.nlm.nih.gov/gene/?term=12168	"2610024H22Rik, AL117858, AW546137, BB189135, BMP-2, BMPR-2, BMPR-II, BMPRII, BRK-3, Gm20272 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002711	12168	Bmpr2	http://www.ncbi.nlm.nih.gov/gene/?term=12168	"2610024H22Rik, AL117858, AW546137, BB189135, BMP-2, BMPR-2, BMPR-II, BMPRII, BRK-3, Gm20272 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002712	12176	Bnip3	http://www.ncbi.nlm.nih.gov/gene/?term=12176	Nip3	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00002713	12177	Bnip3l	http://www.ncbi.nlm.nih.gov/gene/?term=12177	"C86132, D14Ertd719e, Nip3L, Nix "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002714	12180	Smyd1	http://www.ncbi.nlm.nih.gov/gene/?term=12180	"4632404M21Rik, Bop, C78565, Zmynd18 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002715	12189	Brca1	http://www.ncbi.nlm.nih.gov/gene/?term=12189		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002716	12193	Zfp36l2	http://www.ncbi.nlm.nih.gov/gene/?term=12193	"Brf2, ERF2, Tis11d "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002717	12211	Birc6	http://www.ncbi.nlm.nih.gov/gene/?term=12211	"A430032G04Rik, A430040A19Rik, AA501170, Bruce, D630005A10Rik, mKIAA1289 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002718	12211	Birc6	http://www.ncbi.nlm.nih.gov/gene/?term=12211	"A430032G04Rik, A430040A19Rik, AA501170, Bruce, D630005A10Rik, mKIAA1289 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002719	12223	Btc	http://www.ncbi.nlm.nih.gov/gene/?term=12223	Bcn	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002720	12238	Commd3	http://www.ncbi.nlm.nih.gov/gene/?term=12238	"AW550818, Bup, D2Ertd542e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002721	122416	ANKRD9	http://www.ncbi.nlm.nih.gov/gene/?term=122416		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002722	122509	IFI27L1	http://www.ncbi.nlm.nih.gov/gene/?term=122509	"FAM14B, ISG12C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002723	122509	IFI27L1	http://www.ncbi.nlm.nih.gov/gene/?term=122509	"FAM14B, ISG12C "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002724	122553	TRAPPC6B	http://www.ncbi.nlm.nih.gov/gene/?term=122553	TPC6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002725	12257	Tspo	http://www.ncbi.nlm.nih.gov/gene/?term=12257	"Bzrp, IBP, PBR1, Tspo "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002726	122622	ADSSL1	http://www.ncbi.nlm.nih.gov/gene/?term=122622		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002727	12265	Ciita	http://www.ncbi.nlm.nih.gov/gene/?term=12265	"C2ta, EG669998, Gm9475, Mhc2ta "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002728	122704	MRPL52	http://www.ncbi.nlm.nih.gov/gene/?term=122704		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002729	122769	LRR1	http://www.ncbi.nlm.nih.gov/gene/?term=122769	"4-1BBLRR, LRR-1, PPIL5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002730	122809	SOCS4	http://www.ncbi.nlm.nih.gov/gene/?term=122809	SOCS7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002731	122830	NAA30	http://www.ncbi.nlm.nih.gov/gene/?term=122830	"C14orf35, MAK3, Mak3p, NAT12, NAT12P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002732	122830	NAA30	http://www.ncbi.nlm.nih.gov/gene/?term=122830	"C14orf35, MAK3, Mak3p, NAT12, NAT12P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002733	12283	Cab39	http://www.ncbi.nlm.nih.gov/gene/?term=12283	"AA408805, AA960512, C78372, MO25, MO25alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002734	12290	Cacna1e	http://www.ncbi.nlm.nih.gov/gene/?term=12290	"A430040I15, BII, Cach6, Cacnl1a6, Cav2.3, Cchra1, alpha1E "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002735	12293	Cacna2d1	http://www.ncbi.nlm.nih.gov/gene/?term=12293	"Ca(v)alpha2delta1, Cacna2, Cchl2a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002736	122953	JDP2	http://www.ncbi.nlm.nih.gov/gene/?term=122953	JUNDM2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002737	122953	JDP2	http://www.ncbi.nlm.nih.gov/gene/?term=122953	JUNDM2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002738	12295	Cacnb1	http://www.ncbi.nlm.nih.gov/gene/?term=12295	"CAB1, Cchb1, Cchlb1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002739	122961	ISCA2	http://www.ncbi.nlm.nih.gov/gene/?term=122961	"HBLD1, ISA2, MMDS4, c14_5557 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002740	122961	ISCA2	http://www.ncbi.nlm.nih.gov/gene/?term=122961	"HBLD1, ISA2, MMDS4, c14_5557 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002741	12300	Cacng2	http://www.ncbi.nlm.nih.gov/gene/?term=12300	"AW060990, B230105C07Rik, B930041E13Rik, stargazer, stargazin, stg, wag, waggler "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002742	123036	TC2N	http://www.ncbi.nlm.nih.gov/gene/?term=123036	"C14orf47, C2CD1, MTAC2D1, Tac2-N "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002743	12304	Pdia4	http://www.ncbi.nlm.nih.gov/gene/?term=12304	"AI987846, Cai, ERp-72, Erp72 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002744	12306	Anxa2	http://www.ncbi.nlm.nih.gov/gene/?term=12306	"AW215814, Cal1h "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	RT-PCR	Two mRNAs (Anxa2 and Cox4i2) colocalize with the SMN protein in axons from differentiated NSC-34 cells and that their axonal localization is dramatically reduced in SMN-deficient cells
RLID00002745	12306	Anxa2	http://www.ncbi.nlm.nih.gov/gene/?term=12306	"AW215814, Cal1h "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00002746	12307	Calb1	http://www.ncbi.nlm.nih.gov/gene/?term=12307	"Brain-2, CB, Calb, Calb-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002747	12307	Calb1	http://www.ncbi.nlm.nih.gov/gene/?term=12307	"Brain-2, CB, Calb, Calb-1 "	mRNA	Mus musculus	9387927	Cell body	Purkinje cell	In situ hybridizationq|Immunocytochemistry	"Whereas calbindin mRNA was found to be in the cell body only, L7 transcripts could be detected within the molecular layer, corresponding to Purkinje cell dendrites. "
RLID00002748	12308	Calb2	http://www.ncbi.nlm.nih.gov/gene/?term=12308	CR	mRNA	Mus musculus	9387927	Cell body	Purkinje cell	In situ hybridizationq|Immunocytochemistry	"Whereas calbindin mRNA was found to be in the cell body only, L7 transcripts could be detected within the molecular layer, corresponding to Purkinje cell dendrites. "
RLID00002749	123096	SLC25A29	http://www.ncbi.nlm.nih.gov/gene/?term=123096	"C14orf69, CACL, ORNT3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002750	123096	SLC25A29	http://www.ncbi.nlm.nih.gov/gene/?term=123096	"C14orf69, CACL, ORNT3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002751	123099	DEGS2	http://www.ncbi.nlm.nih.gov/gene/?term=123099	"C14orf66, DES2, FADS8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002752	12313	Calm1	http://www.ncbi.nlm.nih.gov/gene/?term=12313	"AI256814, AI327027, AI461935, AL024000, CaM, Calm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002753	12313	Calm1	http://www.ncbi.nlm.nih.gov/gene/?term=12313	"AI256814, AI327027, AI461935, AL024000, CaM, Calm "	mRNA	Mus musculus	22945799	Synapse	Brain	RT-PCR|Immunoprecipitation	"Fig. 5 a Detection of KIF1Bb in purified mouse synaptoneurosomes. KIF1Bb is detected in total lysates from the cortex (T; 5 lg total protein) and is enriched in a sample of synaptoneurosomes purified from the cortex (S; 5 lg). The analysis, by RT-PCR, revealed the presence of Arc (activity regulated cytoskeleton-associated protein) mRNA (Fig. 8c), a well-known, dendritically localized mRNA [43-45]. Interestingly, Calmodulin mRNA was also part of this complex. Both were specifically found in the KIF1Bb-immunoprecipitated complex, but not in the negative control reaction (Fig. 8c, compare lanes 2 and 3). The specific association of Arc and Calmodulin mRNAs with the KIF1Bb-containing complex is further supported by the absence of non-synaptically or other synaptically localized mRNAs such as eEIF1a and aCaMKII (Fig. 8c). These observations would suggest the participation of KIF1Bb in RNP particles in association with at least two dendritically targeted mRNAs, Arc and CaM. "
RLID00002754	12315	Calm3	http://www.ncbi.nlm.nih.gov/gene/?term=12315	"CaMA, R75142 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002755	123169	LEO1	http://www.ncbi.nlm.nih.gov/gene/?term=123169	RDL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002756	12316	Aspm	http://www.ncbi.nlm.nih.gov/gene/?term=12316	"Calmbp1, D330028K02Rik, MCPH5, Sha1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002757	12317	Calr	http://www.ncbi.nlm.nih.gov/gene/?term=12317	"CRTegulin, Calr "	mRNA	Mus musculus	12923260	Endoplasmic reticulum	B cell	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00002758	12317	Calr	http://www.ncbi.nlm.nih.gov/gene/?term=12317	"CRTegulin, Calr "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. mRNAs for resident proteins of the ER lumen, including BiP, calreticulin, and GRP94, were also highly enriched on membrane-bound polysomes. "
RLID00002759	12317	Calr	http://www.ncbi.nlm.nih.gov/gene/?term=12317	"CRT, Calregulin "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00002760	123207	C15orf40	http://www.ncbi.nlm.nih.gov/gene/?term=123207		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002761	12321	Calu	http://www.ncbi.nlm.nih.gov/gene/?term=12321	9530075H20Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002762	123228	SENP8	http://www.ncbi.nlm.nih.gov/gene/?term=123228	"DEN1, NEDP1, PRSC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002763	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	18539120	Dendrite	Neuron	Fluorescence in situ hybridization	Figure 5c: Dendritic CaMKIIa mRNA localization in response to DHPG (11DIV).
RLID00002764	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	18539120	Synapse	Brain	qRT-PCR	"The mRNA targets reduced in Kif5 association included genes involved in actin remodeling at synapses (cofilin phosphatase (PP2Ac); p116-RIP), synapse-associated signaling (DAG1;RGS5) and synapse structure (SAPAP4; CaMKIIa; MAP1b). Not all mRNAs were significantly reduced in Kif5 IPs, as OCRL1 mRNA was similar in KO brain (P>0.05, n=8). "
RLID00002765	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	20713728	Dendrite	Hippocampus	Fluorescence in situ hybridization	"Moreover, in WT neurons, CaMKIIα mRNA can be delivered and translated in dendritic spines within 10 min in response to group I mGluR stimulation, whereas KO neurons fail to show this response. CaMKIIα mRNAs and protein synthesis were more enriched at dendritic spines in WT but not fmr1 KO neurons.  "
RLID00002766	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	22768241	Dendrite	Granule cell	qRT-PCR|Fluorescence in situ hybridization	"Through in situ hybridization and synaptosome preparation, we show that CaMKIIα mRNA is transported in GC dendrites, synaptically localized and might be locally translated at GC synapses. "
RLID00002767	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	22768241	Synapse	Granule cell	qRT-PCR|Fluorescence in situ hybridization	"Taken together, these results strongly suggest that CaMKIIα mRNA is dendritically and synaptically localized in GCs. Through in situ hybridization and synaptosome preparation, we show that CaMKIIα mRNA is transported in GC dendrites, synaptically localized and might be locally translated at GC synapses. "
RLID00002768	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	22945799	Synapse	Brain	RT-PCR|Immunoprecipitation	"Fig. 5 a Detection of KIF1Bb in purified mouse synaptoneurosomes. KIF1Bb is detected in total lysates from the cortex (T; 5 lg total protein) and is enriched in a sample of synaptoneurosomes purified from the cortex (S; 5 lg). The analysis, by RT-PCR, revealed the presence of Arc (activity regulated cytoskeleton-associated protein) mRNA (Fig. 8c), a well-known, dendritically localized mRNA [43-45]. Interestingly, Calmodulin mRNA was also part of this complex. Both were specifically found in the KIF1Bb-immunoprecipitated complex, but not in the negative control reaction (Fig. 8c, compare lanes 2 and 3). The specific association of Arc and Calmodulin mRNAs with the KIF1Bb-containing complex is further supported by the absence of non-synaptically or other synaptically localized mRNAs such as eEIF1a and aCaMKII (Fig. 8c). These observations would suggest the participation of KIF1Bb in RNP particles in association with at least two dendritically targeted mRNAs, Arc and CaM. "
RLID00002769	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	24671994	Synapse	-	Fluorescence in situ hybridization	"However, aCaMKII mRNA does localize to activated synapses, indicating that there is mRNA transport to activated synapses but that the mRNA degradation mechanism is selective for Arc. "
RLID00002770	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	26512708	Axon	ForeBrain	Immunoprecipitation|RIP-Chip	"HuD has also been implicated in axonal localization of other neuronal mRNAs including Tau, Neuritin/CPG15, Kv.1.1 and CaMKIIα mRNAs "
RLID00002771	12322	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=12322	"CaMKII, R74975, mKIAA0968 "	mRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR	"We noted that levels of all RNAs measured, including ribosomal 18S RNA, U6, CAMK2a and BC1, as well as mature microRNAs and their precursors, were lower in synaptosomes relative to that observed in synaptoneurosomes. "
RLID00002772	123263	MTFMT	http://www.ncbi.nlm.nih.gov/gene/?term=123263	"COXPD15, FMT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002773	123263	MTFMT	http://www.ncbi.nlm.nih.gov/gene/?term=123263	"COXPD15, FMT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002774	123263	MTFMT	http://www.ncbi.nlm.nih.gov/gene/?term=123263	"COXPD15, FMT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002775	123264	SLC51B	http://www.ncbi.nlm.nih.gov/gene/?term=123264	"OSTB, OSTBETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002776	12330	Canx	http://www.ncbi.nlm.nih.gov/gene/?term=12330	"1110069N15Rik, AI988026, Cnx, D11Ertd153e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002777	12330	Canx	http://www.ncbi.nlm.nih.gov/gene/?term=12330	"1110069N15Rik, AI988026, Cnx, D11Ertd153e "	mRNA	Mus musculus	12923260	Endoplasmic reticulum	B cell	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00002778	12330	Canx	http://www.ncbi.nlm.nih.gov/gene/?term=12330	"1110069N15Rik, AI988026, Cnx, D11Ertd153e "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. As depicted in Figure 4, Sec61a and calnexin were highly enriched in the membrane-bound fraction, as may be predicted for those mRNAs encoding signal sequences. "
RLID00002779	12330	Canx	http://www.ncbi.nlm.nih.gov/gene/?term=12330	"Cnx, AI988026, D11Ertd153e, 1110069N15Rik "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00002780	123355	LRRC28	http://www.ncbi.nlm.nih.gov/gene/?term=123355		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002781	123355	LRRC28	http://www.ncbi.nlm.nih.gov/gene/?term=123355		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002782	12338	Capn6	http://www.ncbi.nlm.nih.gov/gene/?term=12338		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002783	12339	Capn7	http://www.ncbi.nlm.nih.gov/gene/?term=12339	"AU022319, PalBH "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002784	12343	Capza2	http://www.ncbi.nlm.nih.gov/gene/?term=12343	"1110053K06Rik, AW208808, Cappa2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002785	12349	Car2	http://www.ncbi.nlm.nih.gov/gene/?term=12349	"AI131712, CAII, Ca2, Car-2, Ltw-5, Lvtw-5 "	mRNA	Mus musculus	20820888	Cytosol	Gland tissue	qRT-PCR	"In the present study, we examined the mRNA expression of all 13 enzymatically active CA isozymes by qRT-PCR in the mouse harderian gland. As shown in Fig. 1, nine of the 13 isozymes were detected in the harderian gland tissue at the mRNA level. Four isoforms were cytosolic (Car2, Car3, Car7, and Car13), three were membrane-associated (Car4, Car12, and Car15), one was mitochondrial (Car5b), and one was secreted (Car6). "
RLID00002786	12350	Car3	http://www.ncbi.nlm.nih.gov/gene/?term=12350	"BB219044, Ca3, Car-3 "	mRNA	Mus musculus	20820888	Cytosol	Gland tissue	qRT-PCR	"In the present study, we examined the mRNA expression of all 13 enzymatically active CA isozymes by qRT-PCR in the mouse harderian gland. As shown in Fig. 1, nine of the 13 isozymes were detected in the harderian gland tissue at the mRNA level. Four isoforms were cytosolic (Car2, Car3, Car7, and Car13), three were membrane-associated (Car4, Car12, and Car15), one was mitochondrial (Car5b), and one was secreted (Car6). "
RLID00002787	12354	Car7	http://www.ncbi.nlm.nih.gov/gene/?term=12354	"AV343731, Ca7 "	mRNA	Mus musculus	20820888	Cytosol	Gland tissue	qRT-PCR	"In the present study, we examined the mRNA expression of all 13 enzymatically active CA isozymes by qRT-PCR in the mouse harderian gland. As shown in Fig. 1, nine of the 13 isozymes were detected in the harderian gland tissue at the mRNA level. Four isoforms were cytosolic (Car2, Car3, Car7, and Car13), three were membrane-associated (Car4, Car12, and Car15), one was mitochondrial (Car5b), and one was secreted (Car6). "
RLID00002788	12361	Cask	http://www.ncbi.nlm.nih.gov/gene/?term=12361	"DXPri1, DXRib1, LIN-2, Pals3, mLin-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002789	12364	Casp12	http://www.ncbi.nlm.nih.gov/gene/?term=12364		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002790	12367	Casp3	http://www.ncbi.nlm.nih.gov/gene/?term=12367	"A830040C14Rik, AC-3, CASP-3, CC3, CPP-32, CPP32, Lice, SCA-1, Yama, mldy "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002791	12370	Casp8	http://www.ncbi.nlm.nih.gov/gene/?term=12370	"CASP-8, FLICE, MACH, Mch5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002792	123720	WHAMM	http://www.ncbi.nlm.nih.gov/gene/?term=123720	"WHAMM1, WHDC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002793	123720	WHAMM	http://www.ncbi.nlm.nih.gov/gene/?term=123720	"WHAMM1, WHDC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002794	123803	NTAN1	http://www.ncbi.nlm.nih.gov/gene/?term=123803	"PNAA, PNAD "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002795	123811	FOPNL	http://www.ncbi.nlm.nih.gov/gene/?term=123811	"C16orf63, FOR20, PHSECRG2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002796	123811	FOPNL	http://www.ncbi.nlm.nih.gov/gene/?term=123811	"C16orf63, FOR20, PHSECRG2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002797	123811	FOPNL	http://www.ncbi.nlm.nih.gov/gene/?term=123811	"C16orf63, FOR20, PHSECRG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002798	12385	Ctnna1	http://www.ncbi.nlm.nih.gov/gene/?term=12385	"2010010M04Rik, AA517462, AI988031, Catna1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002799	123872	DNAAF1	http://www.ncbi.nlm.nih.gov/gene/?term=123872	"CILD13, LRRC50, ODA7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002800	12387	Ctnnb1	http://www.ncbi.nlm.nih.gov/gene/?term=12387	"Bfc, Catnb, Mesc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002801	1238	ACKR2	http://www.ncbi.nlm.nih.gov/gene/?term=1238	"CCBP2, CCR10, CCR9, CMKBR9, D6, hD6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002802	1238	ACKR2	http://www.ncbi.nlm.nih.gov/gene/?term=1238	"CCBP2, CCR10, CCR9, CMKBR9, D6, hD6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002803	12391	Cav3	http://www.ncbi.nlm.nih.gov/gene/?term=12391	"AI385751, Cav-3, M-cav "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002804	123920	CMTM3	http://www.ncbi.nlm.nih.gov/gene/?term=123920	"BNAS2, CKLFSF3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002805	12394	Runx1	http://www.ncbi.nlm.nih.gov/gene/?term=12394	"AML1, CBF-alpha-2, Cbfa2, Pebp2a2, Pebpa2b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002806	12395	Runx1t1	http://www.ncbi.nlm.nih.gov/gene/?term=12395	"Cbfa2t1h, ETO, MTG8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002807	12398	Cbfa2t3	http://www.ncbi.nlm.nih.gov/gene/?term=12398	"A630044F12Rik, AI465270, AW229127h, ETO-2, Eto2, MTGR2, Cbfa2t3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002808	123	PLIN2	http://www.ncbi.nlm.nih.gov/gene/?term=123	"ADFP, ADRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002809	124044	SPATA2L	http://www.ncbi.nlm.nih.gov/gene/?term=124044	"C16orf76, tamo "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002810	124044	SPATA2L	http://www.ncbi.nlm.nih.gov/gene/?term=124044	"C16orf76, tamo "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002811	124045	SPATA33	http://www.ncbi.nlm.nih.gov/gene/?term=124045	C16orf55	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002812	124056	NOXO1	http://www.ncbi.nlm.nih.gov/gene/?term=124056	"P41NOX, P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002813	12405	Cbln2	http://www.ncbi.nlm.nih.gov/gene/?term=12405	"6330593N19Rik, A730004O05 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002814	12411	Cbs	http://www.ncbi.nlm.nih.gov/gene/?term=12411	"AI047524, AI303044, HIP4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002815	12412	Cbx1	http://www.ncbi.nlm.nih.gov/gene/?term=12412	"Cbx, Cbx-rs2, E430007M08Rik, HP1B, Hp1beta, M31, MOD1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002816	12417	Cbx3	http://www.ncbi.nlm.nih.gov/gene/?term=12417	"HP1g, M32 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002817	12419	Cbx5	http://www.ncbi.nlm.nih.gov/gene/?term=12419	"2610029O15Rik, C75991, HP1, Hp1a, Hp1alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002818	1241	LTB4R	http://www.ncbi.nlm.nih.gov/gene/?term=1241	"BLT1, BLTR, CMKRL1, GPR161, LTBR1, P2RY7, P2Y7, LTB4R "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002819	1241	LTB4R	http://www.ncbi.nlm.nih.gov/gene/?term=1241	"BLT1, BLTR, CMKRL1, GPR161, LTBR1, P2RY7, P2Y7, LTB4R "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002820	124222	PAQR4	http://www.ncbi.nlm.nih.gov/gene/?term=124222		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002821	124323	Rps23	http://www.ncbi.nlm.nih.gov/gene/?term=124323		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00002822	124402	UBALD1	http://www.ncbi.nlm.nih.gov/gene/?term=124402	"FAM100A, PP11303 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002823	124411	ZNF720	http://www.ncbi.nlm.nih.gov/gene/?term=124411		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002824	124446	TMEM219	http://www.ncbi.nlm.nih.gov/gene/?term=124446	IGFBP-3R	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002825	124446	TMEM219	http://www.ncbi.nlm.nih.gov/gene/?term=124446	IGFBP-3R	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002826	12444	Ccnd2	http://www.ncbi.nlm.nih.gov/gene/?term=12444	"2600016F06Rik, AI256817, BF642806, C86853, Vin-1, Vin1, cD2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002827	12444	Ccnd2	http://www.ncbi.nlm.nih.gov/gene/?term=12444	"2600016F06Rik, AI256817, BF642806, C86853, Vin-1, Vin1, cD2 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00002828	124454	EARS2	http://www.ncbi.nlm.nih.gov/gene/?term=124454	"COXPD12, MSE1, gluRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002829	124454	EARS2	http://www.ncbi.nlm.nih.gov/gene/?term=124454	"COXPD12, MSE1, gluRS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002830	124454	EARS2	http://www.ncbi.nlm.nih.gov/gene/?term=124454	"COXPD12, MSE1, gluRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002831	12445	Ccnd3	http://www.ncbi.nlm.nih.gov/gene/?term=12445	"9230106B05Rik, AA682053, AL024085, AW146355, C78795 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002832	12445	Ccnd3	http://www.ncbi.nlm.nih.gov/gene/?term=12445	"9230106B05Rik, AA682053, AL024085, AW146355, C78795 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002833	124460	SNX20	http://www.ncbi.nlm.nih.gov/gene/?term=124460	SLIC1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002834	124491	TMEM170A	http://www.ncbi.nlm.nih.gov/gene/?term=124491	TMEM170	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002835	1244	ABCC2	http://www.ncbi.nlm.nih.gov/gene/?term=1244	"ABC30, CMOAT, DJS, MRP2, cMRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002836	12450	Ccng1	http://www.ncbi.nlm.nih.gov/gene/?term=12450	AI314029	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002837	12450	Ccng1	http://www.ncbi.nlm.nih.gov/gene/?term=12450	AI314029	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002838	124512	METTL23	http://www.ncbi.nlm.nih.gov/gene/?term=124512	"C17orf95, MRT44 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002839	12452	Ccng2	http://www.ncbi.nlm.nih.gov/gene/?term=12452		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002840	12453	Ccni	http://www.ncbi.nlm.nih.gov/gene/?term=12453		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002841	12455	Ccnt1	http://www.ncbi.nlm.nih.gov/gene/?term=12455	"2810478G24Rik, AI115585, CycT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002842	124565	SLC38A10	http://www.ncbi.nlm.nih.gov/gene/?term=124565	PP1744	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002843	124565	SLC38A10	http://www.ncbi.nlm.nih.gov/gene/?term=124565	PP1744	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002844	12457	Noct	http://www.ncbi.nlm.nih.gov/gene/?term=12457	"AU043840, Ccr4, Ccrn4l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002845	12457	Noct	http://www.ncbi.nlm.nih.gov/gene/?term=12457	"AU043840, Ccr4, Ccrn4l "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002846	124583	CANT1	http://www.ncbi.nlm.nih.gov/gene/?term=124583	"DBQD, DBQD1, SCAN-1, SCAN1, SHAPY "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002847	124583	CANT1	http://www.ncbi.nlm.nih.gov/gene/?term=124583	"DBQD, DBQD1, SCAN-1, SCAN1, SHAPY "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002848	124583	CANT1	http://www.ncbi.nlm.nih.gov/gene/?term=124583	"DBQD, DBQD1, SCAN-1, SCAN1, SHAPY "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002849	12460	Ccs	http://www.ncbi.nlm.nih.gov/gene/?term=12460	Ccsd	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002850	12462	Cct3	http://www.ncbi.nlm.nih.gov/gene/?term=12462	"AL024092, Cctg, Tcp1-rs3, TriC-P5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002851	124637	CYB5D1	http://www.ncbi.nlm.nih.gov/gene/?term=124637		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002852	124637	CYB5D1	http://www.ncbi.nlm.nih.gov/gene/?term=124637		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002853	12464	Cct4	http://www.ncbi.nlm.nih.gov/gene/?term=12464	"2610204B21Rik, A45, C78323, Cctd "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002854	12469	Cct8	http://www.ncbi.nlm.nih.gov/gene/?term=12469	"AI132397, Cctq, Tcpq "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002855	124801	LSM12	http://www.ncbi.nlm.nih.gov/gene/?term=124801	PNAS-135	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002856	124808	CCDC43	http://www.ncbi.nlm.nih.gov/gene/?term=124808		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002857	124808	CCDC43	http://www.ncbi.nlm.nih.gov/gene/?term=124808		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002858	124817	CNTD1	http://www.ncbi.nlm.nih.gov/gene/?term=124817	CNTD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002859	12484	Cd24a	http://www.ncbi.nlm.nih.gov/gene/?term=12484	"Cd24, HSA, Ly-52, nectadrin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002860	12491	Cd36	http://www.ncbi.nlm.nih.gov/gene/?term=12491	"FAT, GPIV, Scarb3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002861	124925	SEZ6	http://www.ncbi.nlm.nih.gov/gene/?term=124925	BSRPC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002862	12492	Scarb2	http://www.ncbi.nlm.nih.gov/gene/?term=12492	"9330185J12Rik, Cd36l2, LGP85, LIMP II, LIMP-2, MLGP85 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002863	124935	SLC43A2	http://www.ncbi.nlm.nih.gov/gene/?term=124935	LAT4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002864	124936	CYB5D2	http://www.ncbi.nlm.nih.gov/gene/?term=124936		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002865	124975	GGT6	http://www.ncbi.nlm.nih.gov/gene/?term=124975		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002866	124976	SPNS2	http://www.ncbi.nlm.nih.gov/gene/?term=124976		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002867	124976	SPNS2	http://www.ncbi.nlm.nih.gov/gene/?term=124976		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002868	124995	MRPL10	http://www.ncbi.nlm.nih.gov/gene/?term=124995	"L10MT, MRP-L10, MRP-L8, MRPL8, RPML8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002869	124997	WDR81	http://www.ncbi.nlm.nih.gov/gene/?term=124997	"CAMRQ2, PPP1R166 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002870	125050	RN7SK	http://www.ncbi.nlm.nih.gov/gene/?term=125050	7SK	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002871	125050	RN7SK	http://www.ncbi.nlm.nih.gov/gene/?term=125050	7SK	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/7SK/
RLID00002872	125050	RN7SK	http://www.ncbi.nlm.nih.gov/gene/?term=125050	7SK	lncRNA	Homo sapiens	22855529	Nucleus	Hela cell	In situ hybridization	"Nuclear speckle-associated RNAs include uridine-rich small nuclear RNAs (UsnRNAs), 7SK RNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long ncRNA (lncRNA), and a population of uncharacterized poly(A)+ RNAs (Spector and Lamond, 2011 blue right-pointing triangle). "
RLID00002873	125050	RN7SK	http://www.ncbi.nlm.nih.gov/gene/?term=125050	7SK	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00002874	125050	RN7SK	http://www.ncbi.nlm.nih.gov/gene/?term=125050	7SK	snRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00002875	125058	TBC1D16	http://www.ncbi.nlm.nih.gov/gene/?term=125058		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002876	125061	AFMID	http://www.ncbi.nlm.nih.gov/gene/?term=125061	"FKF, KF, KFA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002877	125061	AFMID	http://www.ncbi.nlm.nih.gov/gene/?term=125061	"FKF, KF, KFA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002878	12509	Cd59a	http://www.ncbi.nlm.nih.gov/gene/?term=12509	"AA987121, Cd59, protectin "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002879	125144	LRRC75A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=125144	"C17orf45, C17orf76-AS1, FAM211A-AS1, NCRNA00188, TSAP19 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002880	125144	LRRC75A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=125144	"C17orf45, C17orf76-AS1, FAM211A-AS1, NCRNA00188, TSAP19 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002881	125144	LRRC75A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=125144	"C17orf45, C17orf76-AS1, FAM211A-AS1, NCRNA00188, TSAP19 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002882	125144	LRRC75A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=125144	"C17orf45, C17orf76-AS1, FAM211A-AS1, NCRNA00188, TSAP19 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002883	125170	MIEF2	http://www.ncbi.nlm.nih.gov/gene/?term=125170	"MID49, SMCR7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002884	12519	Cd80	http://www.ncbi.nlm.nih.gov/gene/?term=12519	"B71, Cd28l, Ly-53, Ly53, MIC17, TSA1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002885	125228	FAM210A	http://www.ncbi.nlm.nih.gov/gene/?term=125228	"C18orf19, HsT2329 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002886	125228	FAM210A	http://www.ncbi.nlm.nih.gov/gene/?term=125228	"C18orf19, HsT2329 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002887	125228	FAM210A	http://www.ncbi.nlm.nih.gov/gene/?term=125228	"C18orf19, HsT2329 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002888	12527	Cd9	http://www.ncbi.nlm.nih.gov/gene/?term=12527	Tspan29	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002889	12537	Cdk11b	http://www.ncbi.nlm.nih.gov/gene/?term=12537	"AA989746, CDK11-p110, CDK11-p46, CDK11-p58, Cdc11b, Cdc2l1, Cdc2l2, Cdk11, p58 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002890	12545	Cdc7	http://www.ncbi.nlm.nih.gov/gene/?term=12545	"AI597260l1, muCdc7, Cdc7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002891	12554	Cdh13	http://www.ncbi.nlm.nih.gov/gene/?term=12554	"4932416G01Rik, Cdht, Tcad "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002892	12558	Cdh2	http://www.ncbi.nlm.nih.gov/gene/?term=12558	"CDHN, N-CAD, Ncad "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002893	12569	Cdk5r1	http://www.ncbi.nlm.nih.gov/gene/?term=12569	"Cdk5r, D11Bwg0379e, p25, p35 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002894	12572	Cdk7	http://www.ncbi.nlm.nih.gov/gene/?term=12572	"AI323415, AI528512, C230069N13, Cdkn7, Crk4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002895	12578	Cdkn2a	http://www.ncbi.nlm.nih.gov/gene/?term=12578	"ARF-INK4a, Arf, INK4a-ARF, Ink4a/Arf, MTS1, Pctr1, p16, p16(INK4a), p16INK4a, p19<ARF>, p19ARF "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002896	12589	Ift81	http://www.ncbi.nlm.nih.gov/gene/?term=12589	"AW060663, Cdv-1, Cdv-1r, Cdv1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002897	125919	ZNF543	http://www.ncbi.nlm.nih.gov/gene/?term=125919		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002898	125919	ZNF543	http://www.ncbi.nlm.nih.gov/gene/?term=125919		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002899	125950	RAVER1	http://www.ncbi.nlm.nih.gov/gene/?term=125950		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002900	125950	RAVER1	http://www.ncbi.nlm.nih.gov/gene/?term=125950		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002901	125962	OR7G1	http://www.ncbi.nlm.nih.gov/gene/?term=125962	"OR19-15, OR19-8P, OR7G1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002902	125962	OR7G1	http://www.ncbi.nlm.nih.gov/gene/?term=125962	"OR19-15, OR19-8P, OR7G1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002903	125965	COX6B2	http://www.ncbi.nlm.nih.gov/gene/?term=125965	"COXVIB2, CT59 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002904	125965	COX6B2	http://www.ncbi.nlm.nih.gov/gene/?term=125965	"COXVIB2, CT59 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002905	125988	C19orf70	http://www.ncbi.nlm.nih.gov/gene/?term=125988	"MIC13, P117, QIL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002906	125988	C19orf70	http://www.ncbi.nlm.nih.gov/gene/?term=125988	"MIC13, P117, QIL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002907	1259	CNGA1	http://www.ncbi.nlm.nih.gov/gene/?term=1259	"CNCG, CNCG1, CNG-1, CNG1, RCNC1, RCNCa, RCNCalpha, RP49 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002908	125	ADH1B	http://www.ncbi.nlm.nih.gov/gene/?term=125	"ADH2, HEL-S-117 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002909	126070	ZNF440	http://www.ncbi.nlm.nih.gov/gene/?term=126070		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002910	126070	ZNF440	http://www.ncbi.nlm.nih.gov/gene/?term=126070		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002911	126070	ZNF440	http://www.ncbi.nlm.nih.gov/gene/?term=126070		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002912	12608	Cebpb	http://www.ncbi.nlm.nih.gov/gene/?term=12608	"C/EBPbeta, CRP2, IL-6DBP, LAP, LIP, NF-IL6, NF-M, Nfil6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002913	12608	Cebpb	http://www.ncbi.nlm.nih.gov/gene/?term=12608	"C/EBPbeta, CRP2, IL-6DBP, LAP, LIP, NF-IL6, NF-M, Nfil6 "	mRNA	Mus musculus	18678862	Nucleus	betawt|betad/s cell	RT-PCR	"To investigate the influence of HuR on nuclear processing of the C/EBPb mRNA, we examined nuclear polyadenylation of the C/EBPb transcripts from the betawt and betad/s cell lines. To accumulate the data presented in Fig. 7, RNA was isolated from the nuclear fraction and subjected to reverse transcription using an oligo(dT) primer/adapter followed by PCR using a forward primer located 298 nucleotides upstream of the site of poly(A) addition of the C/EBPb mRNA in conjunction with the n32P-labeled oligo(dT) primer/adapter. The data suggest that in the absence of HuR binding, the C/EBPb mRNA is more extensively polyadenylated, leading to translocation to the cytosol. However, in betawt, which binds HuR, polyadenylation appears to occur to a lesser extent, with approximately one-third of the RNA (relative to betad/s) reaching the cytosol.  "
RLID00002914	12608	Cebpb	http://www.ncbi.nlm.nih.gov/gene/?term=12608	"C/EBPbeta, CRP2, IL-6DBP, LAP, LIP, NF-IL6, NF-M, Nfil6 "	mRNA	Mus musculus	18678862	Cytosol	MEF-3T3 cell	RT-PCR	"The real-time PCR data shown in Fig. 5B indicate that at all time points betad/s mRNA accumulated in the cytosol to a greater degree than the betawt message. Thus, the loss of the ability to bind HuR at the canonical ARE (present in βwt, but absent in betad/s) did not hinder the movement of the C/EBPb mRNA into the cytosol. "
RLID00002915	126119	JOSD2	http://www.ncbi.nlm.nih.gov/gene/?term=126119	SBBI54	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002916	12611	Cebpg	http://www.ncbi.nlm.nih.gov/gene/?term=12611	"C/EBP[g], C/EBPgamma, GPE1-BP, Gpe1bp, Ig/EBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002917	126133	ALDH16A1	http://www.ncbi.nlm.nih.gov/gene/?term=126133		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002918	12616	Cenpb	http://www.ncbi.nlm.nih.gov/gene/?term=12616	CENP-B	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002919	12616	Cenpb	http://www.ncbi.nlm.nih.gov/gene/?term=12616	CENP-B	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00002920	126208	ZNF787	http://www.ncbi.nlm.nih.gov/gene/?term=126208	TIP20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002921	126231	ZNF573	http://www.ncbi.nlm.nih.gov/gene/?term=126231		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002922	126231	ZNF573	http://www.ncbi.nlm.nih.gov/gene/?term=126231		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002923	126282	TNFAIP8L1	http://www.ncbi.nlm.nih.gov/gene/?term=126282	TIPE1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002924	126298	IRGQ	http://www.ncbi.nlm.nih.gov/gene/?term=126298	"FKSG271, IRGQ "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002925	126298	IRGQ	http://www.ncbi.nlm.nih.gov/gene/?term=126298	"FKSG271, IRGQ "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002926	126299	ZNF428	http://www.ncbi.nlm.nih.gov/gene/?term=126299	"C19orf37, Zfp428 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002927	126308	MOB3A	http://www.ncbi.nlm.nih.gov/gene/?term=126308	"MOB1C, MOBKL2A, moblak "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002928	126308	MOB3A	http://www.ncbi.nlm.nih.gov/gene/?term=126308	"MOB1C, MOBKL2A, moblak "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002929	126321	MFSD12	http://www.ncbi.nlm.nih.gov/gene/?term=126321	"C19orf28, PP3501 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002930	126321	MFSD12	http://www.ncbi.nlm.nih.gov/gene/?term=126321	"C19orf28, PP3501 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002931	126328	NDUFA11	http://www.ncbi.nlm.nih.gov/gene/?term=126328	"B14.7, CI-B14.7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002932	126328	NDUFA11	http://www.ncbi.nlm.nih.gov/gene/?term=126328	"B14.7, CI-B14.7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002933	126364	LRRC25	http://www.ncbi.nlm.nih.gov/gene/?term=126364	MAPA	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002934	126364	LRRC25	http://www.ncbi.nlm.nih.gov/gene/?term=126364	MAPA	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002935	126382	NR2C2AP	http://www.ncbi.nlm.nih.gov/gene/?term=126382	TRA16	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002936	1263	PLK3	http://www.ncbi.nlm.nih.gov/gene/?term=1263	"CNK, FNK, PLK-3, PRK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002937	126432	RINL	http://www.ncbi.nlm.nih.gov/gene/?term=126432		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002938	126432	RINL	http://www.ncbi.nlm.nih.gov/gene/?term=126432		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002939	12648	Chd1	http://www.ncbi.nlm.nih.gov/gene/?term=12648	"4930525N21Rik, AI851787, AW555109 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002940	1264	CNN1	http://www.ncbi.nlm.nih.gov/gene/?term=1264	"HEL-S-14, SMCC, Sm-Calp "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002941	12651	Chkb	http://www.ncbi.nlm.nih.gov/gene/?term=12651	"Chetk, Chkl, Ck, Ck/Ek, Ck/Ek-beta, Ckb, Ckekb, Ek "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002942	126526	C19orf47	http://www.ncbi.nlm.nih.gov/gene/?term=126526		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002943	12653	Chgb	http://www.ncbi.nlm.nih.gov/gene/?term=12653	Scg-1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002944	12659	Ovgp1	http://www.ncbi.nlm.nih.gov/gene/?term=12659	"120kDa, AU016433, AU019448, Chit5, MOGP, OGP, muc9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002945	12659	Ovgp1	http://www.ncbi.nlm.nih.gov/gene/?term=12659	"120kDa, AU016433, AU019448, Chit5, MOGP, OGP, muc9 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002946	1265	CNN2	http://www.ncbi.nlm.nih.gov/gene/?term=1265		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002947	1265	CNN2	http://www.ncbi.nlm.nih.gov/gene/?term=1265		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002948	1265	CNN2	http://www.ncbi.nlm.nih.gov/gene/?term=1265		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002949	1265	CNN2	http://www.ncbi.nlm.nih.gov/gene/?term=1265		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002950	12660	Chka	http://www.ncbi.nlm.nih.gov/gene/?term=12660	"CK, CK/EK-alpha, Chetk-alpha, Chk, ChoK, EK, EtnK-alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002951	12662	Chm	http://www.ncbi.nlm.nih.gov/gene/?term=12662	Rep-1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002952	126661	CCDC163P	http://www.ncbi.nlm.nih.gov/gene/?term=126661	C1orf231	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002953	1266	CNN3	http://www.ncbi.nlm.nih.gov/gene/?term=1266		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002954	126731	CCSAP	http://www.ncbi.nlm.nih.gov/gene/?term=126731	"C1orf96, CSAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002955	12675	Chuk	http://www.ncbi.nlm.nih.gov/gene/?term=12675	"AI2566581, Fbx24, Fbxo24, IKBKA, IKK1, Ikka, NFKBIKA, Chuk "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002956	126789	PUSL1	http://www.ncbi.nlm.nih.gov/gene/?term=126789		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002957	126792	B3GALT6	http://www.ncbi.nlm.nih.gov/gene/?term=126792	"EDSP2, SEMDJL1, beta3GalT6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002958	126792	B3GALT6	http://www.ncbi.nlm.nih.gov/gene/?term=126792	"EDSP2, SEMDJL1, beta3GalT6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002959	1267	CNP	http://www.ncbi.nlm.nih.gov/gene/?term=1267	CNP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002960	1267	CNP	http://www.ncbi.nlm.nih.gov/gene/?term=1267	CNP1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00002961	1267	CNP	http://www.ncbi.nlm.nih.gov/gene/?term=1267	CNP1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002962	1267	CNP	http://www.ncbi.nlm.nih.gov/gene/?term=1267	CNP1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002963	1267	CNP	http://www.ncbi.nlm.nih.gov/gene/?term=1267	CNP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002964	1268	CNR1	http://www.ncbi.nlm.nih.gov/gene/?term=1268	"CANN6, CB-R, CB1, CB1A, CB1K5, CB1R, CNR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002965	12695	Inadl	http://www.ncbi.nlm.nih.gov/gene/?term=12695	"Cipp, Patj "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002966	126961	HIST2H3C	http://www.ncbi.nlm.nih.gov/gene/?term=126961	"H3, H3.2, H3/M, H3F2, H3FM, H3FN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002967	126961	HIST2H3C	http://www.ncbi.nlm.nih.gov/gene/?term=126961	"H3, H3.2, H3/M, H3F2, H3FM, H3FN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00002968	127018	LYPLAL1	http://www.ncbi.nlm.nih.gov/gene/?term=127018	Q96AV0	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002969	12704	Cit	http://www.ncbi.nlm.nih.gov/gene/?term=12704	"C030025P15Rik, CRIK, CRIK-SK-k, Cit "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002970	12704	Cit	http://www.ncbi.nlm.nih.gov/gene/?term=12704	"C030025P15Rik, CRIK, CRIK-SK-k, Cit "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002971	1270	CNTF	http://www.ncbi.nlm.nih.gov/gene/?term=1270	HCNTF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002972	12715	Ckm	http://www.ncbi.nlm.nih.gov/gene/?term=12715	"Ckmm, M-CK, MCK "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002973	12721	Coro1a	http://www.ncbi.nlm.nih.gov/gene/?term=12721	"Clabp, Lmb3, TACO, p57 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002974	12722	Clca3a1	http://www.ncbi.nlm.nih.gov/gene/?term=12722	"Cacc, Clca1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002975	12724	Clcn2	http://www.ncbi.nlm.nih.gov/gene/?term=12724	"AL118368, ClC-2, Clc2, nmf240 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002976	12725	Clcn3	http://www.ncbi.nlm.nih.gov/gene/?term=12725	Clc3	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002977	127262	TPRG1L	http://www.ncbi.nlm.nih.gov/gene/?term=127262	"FAM79A, h-mover, mover "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002978	127262	TPRG1L	http://www.ncbi.nlm.nih.gov/gene/?term=127262	"FAM79A, h-mover, mover "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002979	12727	Clcn4	http://www.ncbi.nlm.nih.gov/gene/?term=12727	"Clc4-2-2, Clcn4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002980	127281	FAM213B	http://www.ncbi.nlm.nih.gov/gene/?term=127281	C1orf93	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002981	12728	Clcn5	http://www.ncbi.nlm.nih.gov/gene/?term=12728	"5430408K11Rik, ClC-5, Clc5, D930009B12Rik, DXImx42e, Sfc13, T25545 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002982	127435	PODN	http://www.ncbi.nlm.nih.gov/gene/?term=127435	"PCAN, SLRR5A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002983	12747	Clk1	http://www.ncbi.nlm.nih.gov/gene/?term=12747	STY	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002984	127495	LRRC39	http://www.ncbi.nlm.nih.gov/gene/?term=127495		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002985	12750	Clk4	http://www.ncbi.nlm.nih.gov/gene/?term=12750	"AI987988, C85119 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002986	12751	Tpp1	http://www.ncbi.nlm.nih.gov/gene/?term=12751	"Cln2, LPIC, TPP-1, TPP-I "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002987	12752	Cln3	http://www.ncbi.nlm.nih.gov/gene/?term=12752	AI323623	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002988	12753	Clock	http://www.ncbi.nlm.nih.gov/gene/?term=12753	"5330400M04Rik, KAT13D "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002989	127544	RNF19B	http://www.ncbi.nlm.nih.gov/gene/?term=127544	"IBRDC3, NKLAM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002990	127602	DNAH14	http://www.ncbi.nlm.nih.gov/gene/?term=127602	"C1orf67, Dnahc14, HL-18, HL18 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002991	12764	Cmas	http://www.ncbi.nlm.nih.gov/gene/?term=12764	"AW208911, CMPNeu5Ac, D6Bwg0250e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00002992	127687	C1orf122	http://www.ncbi.nlm.nih.gov/gene/?term=127687	ALAESM	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002993	12769	Ccr9	http://www.ncbi.nlm.nih.gov/gene/?term=12769	"A130091K22Rik, Cmkbr10, GPR-9-6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002994	127703	C1orf216	http://www.ncbi.nlm.nih.gov/gene/?term=127703		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002995	127707	KLHDC7A	http://www.ncbi.nlm.nih.gov/gene/?term=127707		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002996	127733	UBXN10	http://www.ncbi.nlm.nih.gov/gene/?term=127733	UBXD3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00002997	12776	Ccr8	http://www.ncbi.nlm.nih.gov/gene/?term=12776	"C-C, C-C CKR-8, CC-CKR-8, CCR-8, CKR-8, Cmkbr8, mCCR8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00002998	127829	ARL8A	http://www.ncbi.nlm.nih.gov/gene/?term=127829	"ARL10B, GIE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00002999	127829	ARL8A	http://www.ncbi.nlm.nih.gov/gene/?term=127829	"ARL10B, GIE2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003000	127829	ARL8A	http://www.ncbi.nlm.nih.gov/gene/?term=127829	"ARL10B, GIE2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003001	127845	GOLT1A	http://www.ncbi.nlm.nih.gov/gene/?term=127845	"CGI-141, GOT1, HMFN1187, YMR292W "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003002	12785	Cnbp	http://www.ncbi.nlm.nih.gov/gene/?term=12785	"AA4087101, Znf9, Cnbp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003003	1278	COL1A2	http://www.ncbi.nlm.nih.gov/gene/?term=1278	OI4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003004	12793	Cnih1	http://www.ncbi.nlm.nih.gov/gene/?term=12793	"0610007J15, CNIH-1, Cnih "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003005	127943	FCRLB	http://www.ncbi.nlm.nih.gov/gene/?term=127943	"FCRL2, FCRLM2, FCRLY, FREB-2, FcRY "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003006	12795	Plk3	http://www.ncbi.nlm.nih.gov/gene/?term=12795	"Cnk, Fnk, PLK-3, PRK "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003007	12797935	CR32027	http://www.ncbi.nlm.nih.gov/gene/?term=12797935	"Dmel_ BcDNA:RE02231, CG32027, Dmel\CR32027, Dmel_CG32027 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00003008	12799	Cnp	http://www.ncbi.nlm.nih.gov/gene/?term=12799	"CNPase-1, Cnp1, Cnp "	mRNA	Mus musculus	7877439	Cytoplasm	Brain	In situ hybridization	A similar staining pattern was evident in sections hybridized with CNP riboprobe (Fig. 4C) suggesting that the distribution of both CNP and PLP mRNA was primarily perinuclear.
RLID00003009	12801	Cnr1	http://www.ncbi.nlm.nih.gov/gene/?term=12801	"CB-R, CB1, CB1R "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003010	12805	Cntn1	http://www.ncbi.nlm.nih.gov/gene/?term=12805	"AW495098, CNTN, F3cam, usl "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003011	128061	C1orf131	http://www.ncbi.nlm.nih.gov/gene/?term=128061		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003012	12807	Hps3	http://www.ncbi.nlm.nih.gov/gene/?term=12807	coa	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003013	128153	SPATA17	http://www.ncbi.nlm.nih.gov/gene/?term=128153	"IQCH, MSRG-11, MSRG11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003014	12815	Col11a2	http://www.ncbi.nlm.nih.gov/gene/?term=12815		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003015	128178	EDARADD	http://www.ncbi.nlm.nih.gov/gene/?term=128178	"ECTD11A, ECTD11B, ED3, EDA3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003016	128178	EDARADD	http://www.ncbi.nlm.nih.gov/gene/?term=128178	"ECTD11A, ECTD11B, ED3, EDA3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003017	1281	COL3A1	http://www.ncbi.nlm.nih.gov/gene/?term=1281	EDS4A	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003018	128218	TMEM125	http://www.ncbi.nlm.nih.gov/gene/?term=128218		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003019	128239	IQGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=128239		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003020	128240	NAXE	http://www.ncbi.nlm.nih.gov/gene/?term=128240	"AIBP, APOA1BP, YJEFN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003021	128240	NAXE	http://www.ncbi.nlm.nih.gov/gene/?term=128240	"AIBP, APOA1BP, YJEFN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003022	128240	NAXE	http://www.ncbi.nlm.nih.gov/gene/?term=128240	"AIBP, YJEFN1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003023	1282	COL4A1	http://www.ncbi.nlm.nih.gov/gene/?term=1282	"BSVD, RATOR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003024	1282	COL4A1	http://www.ncbi.nlm.nih.gov/gene/?term=1282	"BSVD, RATOR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003025	128308	MRPL55	http://www.ncbi.nlm.nih.gov/gene/?term=128308	"AAVG5835, L55nt, MRP-L55, PRO19675 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003026	128308	MRPL55	http://www.ncbi.nlm.nih.gov/gene/?term=128308	"AAVG5835, L55nt, MRP-L55, PRO19675 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003027	128312	HIST3H2BB	http://www.ncbi.nlm.nih.gov/gene/?term=128312	H2Bb	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003028	12831	Col5a1	http://www.ncbi.nlm.nih.gov/gene/?term=12831	AI413331	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003029	12832	Col5a2	http://www.ncbi.nlm.nih.gov/gene/?term=12832	1110014L14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003030	128338	DRAM2	http://www.ncbi.nlm.nih.gov/gene/?term=128338	"CORD21, PRO180, TMEM77, WWFQ154 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003031	128338	DRAM2	http://www.ncbi.nlm.nih.gov/gene/?term=128338	"CORD21, PRO180, TMEM77, WWFQ154 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003032	128387	TATDN3	http://www.ncbi.nlm.nih.gov/gene/?term=128387		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003033	128387	TATDN3	http://www.ncbi.nlm.nih.gov/gene/?term=128387		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003034	128387	TATDN3	http://www.ncbi.nlm.nih.gov/gene/?term=128387		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003035	128387	TATDN3	http://www.ncbi.nlm.nih.gov/gene/?term=128387		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003036	128439	SNHG11	http://www.ncbi.nlm.nih.gov/gene/?term=128439	"C20orf198, LINC00101, NCRNA00101 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003037	12847	Copa	http://www.ncbi.nlm.nih.gov/gene/?term=12847	"AU040324, xenin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003038	128486	FITM2	http://www.ncbi.nlm.nih.gov/gene/?term=128486	"C20orf142, Fit2, dJ881L22.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003039	12848	Cops2	http://www.ncbi.nlm.nih.gov/gene/?term=12848	"AI315723, C85265, Csn2, Sgn2, TRIP-15, Trip15 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003040	1284	COL4A2	http://www.ncbi.nlm.nih.gov/gene/?term=1284	"ICH, POREN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003041	12856	Cox17	http://www.ncbi.nlm.nih.gov/gene/?term=12856	AI037035	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00003042	12859	Cox5b	http://www.ncbi.nlm.nih.gov/gene/?term=12859		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003043	128637	TBC1D20	http://www.ncbi.nlm.nih.gov/gene/?term=128637	"C20orf140, WARBM4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003044	128637	TBC1D20	http://www.ncbi.nlm.nih.gov/gene/?term=128637	"C20orf140, WARBM4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003045	128637	TBC1D20	http://www.ncbi.nlm.nih.gov/gene/?term=128637	"C20orf140, WARBM4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003046	12865	Cox7a1	http://www.ncbi.nlm.nih.gov/gene/?term=12865	"COX7A, COX7AH, COX7AM "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003047	12866	Cox7a2	http://www.ncbi.nlm.nih.gov/gene/?term=12866	"COX7AL, Cox7a3, CoxVIIa-L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003048	12873	Cpa3	http://www.ncbi.nlm.nih.gov/gene/?term=12873	MC-CPA	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003049	12874	Cpd	http://www.ncbi.nlm.nih.gov/gene/?term=12874	"AA960140, AW322530, D830034L15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003050	12876	Cpe	http://www.ncbi.nlm.nih.gov/gene/?term=12876	"CPH, Cph-1, Cph1, R74677, fat "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003051	12876	Cpe	http://www.ncbi.nlm.nih.gov/gene/?term=12876	"CPH, Cph-1, Cph1, R74677, fat "	mRNA	Mus musculus	15972000	Endoplasmic reticulum	MIN6 cell	Northern blot	"Figure 2: Glucose stimulates the recruitment of mRNAs encoding secretory membrane proteins to the ER: subcellular fractionation using the digitonin method. MIN6 cells were preincubated in KRB containing 2 mM glucose for 1 h followed by incubation in KRB containing 2 or 20 mM glucose for a further period of 1 h. (a) Cells were permeabilized with digitonin and pelleted resulting in a membrane fraction (Mem) and a cytosolic fraction (Cyt). The 10% refers to 10% of total RNA/protein. RNA was isolated from each fraction and run on a 1% agarose formaldehyde gel, transferred on to a nylon membrane and probed for proinsulin (PI), PC2, CPH and actin mRNAs. The intensities of the bands were quantified using ImageJ and the mRNA levels were expressed as a percentage of total mRNA. (b) Protein samples from each fraction were run on SDS/PAGE (20% of membrane fraction and 20% of cytosolic fraction) and subjected to immunoblotting with anti-ERK2, calreticulin and SRP54 antibodies. Detection was by enhanced chemiluminescence. The results presented are representative of three separate experiments. Data are collected from Figure 2. "
RLID00003052	1287	COL4A5	http://www.ncbi.nlm.nih.gov/gene/?term=1287	"ASLN, ATS, CA54 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003053	1287	COL4A5	http://www.ncbi.nlm.nih.gov/gene/?term=1287	"ASLN, ATS, CA54 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003054	128866	CHMP4B	http://www.ncbi.nlm.nih.gov/gene/?term=128866	"C20orf178, CHMP4A, CTPP3, CTRCT31, SNF7, SNF7-2, Shax1, VPS32B, Vps32-2, dJ553F4.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003055	128866	CHMP4B	http://www.ncbi.nlm.nih.gov/gene/?term=128866	"C20orf178, CHMP4A, CTPP3, CTRCT31, SNF7, SNF7-2, Shax1, VPS32B, Vps32-2, dJ553F4.4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003056	128866	CHMP4B	http://www.ncbi.nlm.nih.gov/gene/?term=128866	"C20orf178, CHMP4A, CTPP3, CTRCT31, SNF7, SNF7-2, Shax1, VPS32B, Vps32-2, dJ553F4.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003057	128869	PIGU	http://www.ncbi.nlm.nih.gov/gene/?term=128869	"CDC91L1, GAB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003058	12896	Cpt2	http://www.ncbi.nlm.nih.gov/gene/?term=12896	"AI323697, CPTII "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003059	128977	C22orf39	http://www.ncbi.nlm.nih.gov/gene/?term=128977		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003060	128977	C22orf39	http://www.ncbi.nlm.nih.gov/gene/?term=128977		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003061	128989	TANGO2	http://www.ncbi.nlm.nih.gov/gene/?term=128989	"C22orf25, MECRCN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003062	128989	TANGO2	http://www.ncbi.nlm.nih.gov/gene/?term=128989	"C22orf25, MECRCN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003063	128	ADH5	http://www.ncbi.nlm.nih.gov/gene/?term=128	"ADH-3, ADHX, FALDH, FDH, GSH-FDH, GSNOR, HEL-S-60p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003064	128	ADH5	http://www.ncbi.nlm.nih.gov/gene/?term=128	"ADH-3, ADHX, FALDH, FDH, GSH-FDH, GSNOR, HEL-S-60p "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003065	128	ADH5	http://www.ncbi.nlm.nih.gov/gene/?term=128	"ADH-3, ADHX, FALDH, FDH, GSH-FDH, GSNOR, HEL-S-60p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003066	12903	Crabp1	http://www.ncbi.nlm.nih.gov/gene/?term=12903	"AI326249, CRABP-I, Crabp-1, CrabpI, Rbp-5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003067	12904	Crabp2	http://www.ncbi.nlm.nih.gov/gene/?term=12904	"AI893628, Crabp-2, CrabpII "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003068	12912	Creb1	http://www.ncbi.nlm.nih.gov/gene/?term=12912	"2310001E10Rik, 3526402H21Rik, AV083133, Creb, Creb-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003069	129138	ANKRD54	http://www.ncbi.nlm.nih.gov/gene/?term=129138	LIAR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003070	129285	PPP1R21	http://www.ncbi.nlm.nih.gov/gene/?term=129285	"CCDC128, KLRAQ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003071	1292	COL6A2	http://www.ncbi.nlm.nih.gov/gene/?term=1292	"BTHLM1, PP3610, UCMD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003072	129303	TMEM150A	http://www.ncbi.nlm.nih.gov/gene/?term=129303	"TM6P1, TMEM150 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003073	1293	COL6A3	http://www.ncbi.nlm.nih.gov/gene/?term=1293	"BTHLM1, DYT27, UCMD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003074	12941	Pcdha5	http://www.ncbi.nlm.nih.gov/gene/?term=12941	"Cnr6, Crnr6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003075	1294	COL7A1	http://www.ncbi.nlm.nih.gov/gene/?term=1294	"EBD1, EBDCT, EBR1, NDNC8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003076	12950	Hapln1	http://www.ncbi.nlm.nih.gov/gene/?term=12950	"BB099155, CLP, Crtl1, Crtl1l, LP, LP-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003077	12950	Hapln1	http://www.ncbi.nlm.nih.gov/gene/?term=12950	"BB099155, CLP, Crtl1, Crtl1l, LP, LP-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003078	12955	Cryab	http://www.ncbi.nlm.nih.gov/gene/?term=12955	"Crya-2, Crya2, HspB5, P23 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003079	1295	COL8A1	http://www.ncbi.nlm.nih.gov/gene/?term=1295	C3orf7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003080	129607	CMPK2	http://www.ncbi.nlm.nih.gov/gene/?term=129607	"NDK, TMPK2, TYKi, UMP-CMPK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003081	129607	CMPK2	http://www.ncbi.nlm.nih.gov/gene/?term=129607	"NDK, TMPK2, TYKi, UMP-CMPK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003082	129642	MBOAT2	http://www.ncbi.nlm.nih.gov/gene/?term=129642	"LPCAT4, OACT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003083	129685	TAF8	http://www.ncbi.nlm.nih.gov/gene/?term=129685	"II, TAF, TAFII-43, TAFII43, TBN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003084	129685	TAF8	http://www.ncbi.nlm.nih.gov/gene/?term=129685	"II, TAF, TAFII-43, TAFII43, TBN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003085	12974	Cs	http://www.ncbi.nlm.nih.gov/gene/?term=12974	"2610511A05Rik, 9030605P22Rik, Ahl4, BB234005, Cis "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003086	129787	TMEM18	http://www.ncbi.nlm.nih.gov/gene/?term=129787		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003087	129831	RBM45	http://www.ncbi.nlm.nih.gov/gene/?term=129831	"DRB1, RB-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003088	129831	RBM45	http://www.ncbi.nlm.nih.gov/gene/?term=129831	"DRB1, RB-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003089	12983	Csf2rb	http://www.ncbi.nlm.nih.gov/gene/?term=12983	"AI848964, AIC2B, Bc, CDw1311, Csfgmrb, Il3r, Il3rb, Il3rb1, Il5rb, Csf2rb "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003090	129880	BBS5	http://www.ncbi.nlm.nih.gov/gene/?term=129880		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003091	129880	BBS5	http://www.ncbi.nlm.nih.gov/gene/?term=129880		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003092	1298	COL9A2	http://www.ncbi.nlm.nih.gov/gene/?term=1298	"DJ39G22.4, EDM2, MED, STL5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003093	1299	COL9A3	http://www.ncbi.nlm.nih.gov/gene/?term=1299	"DJ885L7.4.1, EDM3, IDD, MED "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003094	13002	Dnajc5	http://www.ncbi.nlm.nih.gov/gene/?term=13002	"2610314I24Rik, AU018536, Csp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003095	13003	Vcan	http://www.ncbi.nlm.nih.gov/gene/?term=13003	"5430420N07Rik, 9430051N09, Cspg2, DPEAAE, NG2, PG-M, PG-M(V0), PG-M(V1), hdf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003096	13004	Ncan	http://www.ncbi.nlm.nih.gov/gene/?term=13004	"C230035B04, Cspg3, Cspg3-rs, Tgfbit "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003097	130074	FAM168B	http://www.ncbi.nlm.nih.gov/gene/?term=130074	MANI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003098	130074	FAM168B	http://www.ncbi.nlm.nih.gov/gene/?term=130074	MANI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003099	13007	Csrp1	http://www.ncbi.nlm.nih.gov/gene/?term=13007	"AA408841, AA959891, AW545626, CRP1, Csrp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003100	13014	Cstb	http://www.ncbi.nlm.nih.gov/gene/?term=13014	"AA960480, Stfb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003101	13018	Ctcf	http://www.ncbi.nlm.nih.gov/gene/?term=13018	AW108038	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003102	13024	Ctla2a	http://www.ncbi.nlm.nih.gov/gene/?term=13024	Ctla-2a	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003103	130271	PLEKHH2	http://www.ncbi.nlm.nih.gov/gene/?term=130271	PLEKHH1L	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003104	130271	PLEKHH2	http://www.ncbi.nlm.nih.gov/gene/?term=130271	PLEKHH1L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003105	1302	COL11A2	http://www.ncbi.nlm.nih.gov/gene/?term=1302	"DFNA13, DFNB53, FBCG2, HKE5, PARP, STL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003106	13030	Ctsb	http://www.ncbi.nlm.nih.gov/gene/?term=13030	CB	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003107	130340	AP1S3	http://www.ncbi.nlm.nih.gov/gene/?term=130340	PSORS15	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003108	13034	Ctse	http://www.ncbi.nlm.nih.gov/gene/?term=13034	"A430072O03Rik, C920004C08Rik, CE, CatE "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003109	130367	SGPP2	http://www.ncbi.nlm.nih.gov/gene/?term=130367	"SPP2, SPPase2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003110	13039	Ctsl	http://www.ncbi.nlm.nih.gov/gene/?term=13039	"1190035F06Rik, CatL1, MEP, fs, nkt, Ctsl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003111	1303	COL12A1	http://www.ncbi.nlm.nih.gov/gene/?term=1303	"BA209D8.1, BTHLM2L, DJ234P15.1, UCMD2, COL12A1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003112	13043	Cttn	http://www.ncbi.nlm.nih.gov/gene/?term=13043	"1110020L01Rik, Ems1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003113	13047	Cux1	http://www.ncbi.nlm.nih.gov/gene/?term=13047	"CDP, Cutl1, Cux, Cux-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003114	130507	UBR3	http://www.ncbi.nlm.nih.gov/gene/?term=130507	ZNF650	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003115	13052	Cxadr	http://www.ncbi.nlm.nih.gov/gene/?term=13052	"2610206D03Rik, AU016810, AW553441, CAR, MCAR, MCVADR "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003116	130540	ALS2CR12	http://www.ncbi.nlm.nih.gov/gene/?term=130540		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003117	130557	ZNF513	http://www.ncbi.nlm.nih.gov/gene/?term=130557	"HMFT0656, RP58 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003118	130574	LYPD6	http://www.ncbi.nlm.nih.gov/gene/?term=130574		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003119	130589	GALM	http://www.ncbi.nlm.nih.gov/gene/?term=130589	"BLOCK25, GLAT, HEL-S-63p, IBD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003120	130589	GALM	http://www.ncbi.nlm.nih.gov/gene/?term=130589	"BLOCK25, GLAT, HEL-S-63p, IBD1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003121	130589	GALM	http://www.ncbi.nlm.nih.gov/gene/?term=130589	"BLOCK25, GLAT, HEL-S-63p, IBD1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003122	130617	ZFAND2B	http://www.ncbi.nlm.nih.gov/gene/?term=130617	AIRAPL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003123	13063	Cycs	http://www.ncbi.nlm.nih.gov/gene/?term=13063		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003124	1306	COL15A1	http://www.ncbi.nlm.nih.gov/gene/?term=1306		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003125	130813	C2orf50	http://www.ncbi.nlm.nih.gov/gene/?term=130813		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003126	130813	C2orf50	http://www.ncbi.nlm.nih.gov/gene/?term=130813		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003127	130814	PQLC3	http://www.ncbi.nlm.nih.gov/gene/?term=130814	C2orf22	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003128	130872	AHSA2	http://www.ncbi.nlm.nih.gov/gene/?term=130872	Hch1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003129	130872	AHSA2	http://www.ncbi.nlm.nih.gov/gene/?term=130872	Hch1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003130	130872	AHSA2	http://www.ncbi.nlm.nih.gov/gene/?term=130872	Hch1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003131	1308	COL17A1	http://www.ncbi.nlm.nih.gov/gene/?term=1308	"BA16H23.2, BP180, BPA-2, BPAG2, ERED, LAD-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003132	13090	Cyp2b19	http://www.ncbi.nlm.nih.gov/gene/?term=13090	CYPIIB19	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003133	130916	MTERF4	http://www.ncbi.nlm.nih.gov/gene/?term=130916	MTERFD2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003134	13097	Cyp2c38	http://www.ncbi.nlm.nih.gov/gene/?term=13097		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003135	13097	Cyp2c38	http://www.ncbi.nlm.nih.gov/gene/?term=13097		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003136	131034	CPNE4	http://www.ncbi.nlm.nih.gov/gene/?term=131034	"COPN4, CPN4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003137	131076	CCDC58	http://www.ncbi.nlm.nih.gov/gene/?term=131076		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003138	131118	DNAJC19	http://www.ncbi.nlm.nih.gov/gene/?term=131118	"PAM18, TIM14, TIMM14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003139	131118	DNAJC19	http://www.ncbi.nlm.nih.gov/gene/?term=131118	"PAM18, TIM14, TIMM14 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003140	13115	Cyp27b1	http://www.ncbi.nlm.nih.gov/gene/?term=13115	"Cp2b, Cyp1, Cyp27b, Cyp40, P450c1, Pddr, Vdd1, Vddr, VddrI, Vdr "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003141	131177	FAM3D	http://www.ncbi.nlm.nih.gov/gene/?term=131177	"EF7, OIT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003142	13121	Cyp51	http://www.ncbi.nlm.nih.gov/gene/?term=13121	"AI426508, CYPLIa1, Ldm, P450-14DM, P450LI, Cyp51 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003143	1312	COMT	http://www.ncbi.nlm.nih.gov/gene/?term=1312	HEL-S-98n	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003144	1312	COMT	http://www.ncbi.nlm.nih.gov/gene/?term=1312	HEL-S-98n	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003145	13132	Dab2	http://www.ncbi.nlm.nih.gov/gene/?term=13132	"5730435J12Rik, AA960054, AI957090, D15Wsu122e, D630005B22Rik, Doc-2, Doc2, p96 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003146	13139	Dgka	http://www.ncbi.nlm.nih.gov/gene/?term=13139	"80kDa, AW146112, Dagk1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003147	13144	Dapk3	http://www.ncbi.nlm.nih.gov/gene/?term=13144	"ZIPK, dlk "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003148	131474	CHCHD4	http://www.ncbi.nlm.nih.gov/gene/?term=131474	"MIA40, TIMM40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003149	1314	COPA	http://www.ncbi.nlm.nih.gov/gene/?term=1314	"AILJK, HEP-COP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003150	1314	COPA	http://www.ncbi.nlm.nih.gov/gene/?term=1314	"AILJK, HEP-COP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003151	1314	COPA	http://www.ncbi.nlm.nih.gov/gene/?term=1314	"AILJK, HEP-COP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003152	131540	ZDHHC19	http://www.ncbi.nlm.nih.gov/gene/?term=131540	DHHC19	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003153	131544	CRYBG3	http://www.ncbi.nlm.nih.gov/gene/?term=131544	"DKFZp667G2110, vlAKAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003154	131566	DCBLD2	http://www.ncbi.nlm.nih.gov/gene/?term=131566	"CLCP1, ESDN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003155	131566	DCBLD2	http://www.ncbi.nlm.nih.gov/gene/?term=131566	"CLCP1, ESDN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003156	131566	DCBLD2	http://www.ncbi.nlm.nih.gov/gene/?term=131566	"CLCP1, ESDN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003157	1315	COPB1	http://www.ncbi.nlm.nih.gov/gene/?term=1315	COPB	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003158	1315	COPB1	http://www.ncbi.nlm.nih.gov/gene/?term=1315	COPB	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003159	1315	COPB1	http://www.ncbi.nlm.nih.gov/gene/?term=1315	COPB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003160	131601	TPRA1	http://www.ncbi.nlm.nih.gov/gene/?term=131601	"GPR175, TMEM227, TPRA40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003161	13163	Daxx	http://www.ncbi.nlm.nih.gov/gene/?term=13163		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003162	13168	Dbil5	http://www.ncbi.nlm.nih.gov/gene/?term=13168	ELP	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003163	1316	KLF6	http://www.ncbi.nlm.nih.gov/gene/?term=1316	"BCD1, CBA1, COPEB, CPBP, GBF, PAC1, ST12, ZF9 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003164	1316	KLF6	http://www.ncbi.nlm.nih.gov/gene/?term=1316	"BCD1, CBA1, COPEB, CPBP, GBF, PAC1, ST12, ZF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003165	13170	Dbp	http://www.ncbi.nlm.nih.gov/gene/?term=13170		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003166	13171	Dbt	http://www.ncbi.nlm.nih.gov/gene/?term=13171	D3Wsu60e	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003167	13175	Dclk1	http://www.ncbi.nlm.nih.gov/gene/?term=13175	"1700113D08Rik, 2810480F11Rik, AI836758, Click-I, Cpg16, Dcamkl1, Dcl, Dclk, mKIAA0369 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003168	1317	SLC31A1	http://www.ncbi.nlm.nih.gov/gene/?term=1317	"COPT1, CTR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003169	1317	SLC31A1	http://www.ncbi.nlm.nih.gov/gene/?term=1317	"COPT1, CTR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003170	1317	SLC31A1	http://www.ncbi.nlm.nih.gov/gene/?term=1317	"COPT1, CTR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003171	131870	NUDT16	http://www.ncbi.nlm.nih.gov/gene/?term=131870		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003172	131870	NUDT16	http://www.ncbi.nlm.nih.gov/gene/?term=131870		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003173	1318	SLC31A2	http://www.ncbi.nlm.nih.gov/gene/?term=1318	"COPT2, CTR2, hCTR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003174	1318	SLC31A2	http://www.ncbi.nlm.nih.gov/gene/?term=1318	"COPT2, CTR2, hCTR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003175	1318	SLC31A2	http://www.ncbi.nlm.nih.gov/gene/?term=1318	"COPT2, CTR2, hCTR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003176	131965	METTL6	http://www.ncbi.nlm.nih.gov/gene/?term=131965		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003177	131965	METTL6	http://www.ncbi.nlm.nih.gov/gene/?term=131965		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003178	131965	METTL6	http://www.ncbi.nlm.nih.gov/gene/?term=131965		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003179	132001	TAMM41	http://www.ncbi.nlm.nih.gov/gene/?term=132001	"C3orf31, RAM41, TAM41 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003180	13200	Ddost	http://www.ncbi.nlm.nih.gov/gene/?term=13200		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003181	132014	IL17RE	http://www.ncbi.nlm.nih.gov/gene/?term=132014		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003182	13202	Ddt	http://www.ncbi.nlm.nih.gov/gene/?term=13202	C78655	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003183	13207	Ddx5	http://www.ncbi.nlm.nih.gov/gene/?term=13207	"2600009A06Rik, G17P1, HUMP68, Hlr1, p68 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003184	13209	Ddx6	http://www.ncbi.nlm.nih.gov/gene/?term=13209	"1110001P04Rik, E230023J21Rik, HLR2, mRCK/P54, p54, rck "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003185	13209	Ddx6	http://www.ncbi.nlm.nih.gov/gene/?term=13209	"1110001P04Rik, E230023J21Rik, HLR2, mRCK/P54, p54, rck "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003186	13211	Dhx9	http://www.ncbi.nlm.nih.gov/gene/?term=13211	"AI326842, Ddx9, HEL-5, NDHII, RHA, mHEL-5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003187	132299	OCIAD2	http://www.ncbi.nlm.nih.gov/gene/?term=132299		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003188	132320	SCLT1	http://www.ncbi.nlm.nih.gov/gene/?term=132320	"CAP-1A, CAP1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003189	132320	SCLT1	http://www.ncbi.nlm.nih.gov/gene/?term=132320	"CAP-1A, CAP1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003190	1325	CORT	http://www.ncbi.nlm.nih.gov/gene/?term=1325	"CST-14, CST-17, CST-29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003191	132625	ZFP42	http://www.ncbi.nlm.nih.gov/gene/?term=132625	"REX-1, REX1, ZNF754, zfp-42 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003192	132625	ZFP42	http://www.ncbi.nlm.nih.gov/gene/?term=132625	"REX-1, REX1, ZNF754, zfp-42 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003193	1326	MAP3K8	http://www.ncbi.nlm.nih.gov/gene/?term=1326	"AURA2, COT, EST, ESTF, MEKK8, TPL2, Tpl-2, c-COT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003194	132789	GNPDA2	http://www.ncbi.nlm.nih.gov/gene/?term=132789	"GNP2, SB52 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003195	132789	GNPDA2	http://www.ncbi.nlm.nih.gov/gene/?term=132789	"GNP2, SB52 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003196	1327	COX4I1	http://www.ncbi.nlm.nih.gov/gene/?term=1327	"COX IV-1, COX4, COX4-1, COXIV, COXIV-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003197	132864	CPEB2	http://www.ncbi.nlm.nih.gov/gene/?term=132864	"CPE-BP2, CPEB-2, hCPEB-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003198	1329	COX5B	http://www.ncbi.nlm.nih.gov/gene/?term=1329	COXVB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003199	1329	COX5B	http://www.ncbi.nlm.nih.gov/gene/?term=1329	COXVB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003200	132	ADK	http://www.ncbi.nlm.nih.gov/gene/?term=132	AK	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003201	132	ADK	http://www.ncbi.nlm.nih.gov/gene/?term=132	AK	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003202	133015	PACRGL	http://www.ncbi.nlm.nih.gov/gene/?term=133015	C4orf28	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003203	133015	PACRGL	http://www.ncbi.nlm.nih.gov/gene/?term=133015	C4orf28	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003204	133015	PACRGL	http://www.ncbi.nlm.nih.gov/gene/?term=133015	C4orf28	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003205	133015	PACRGL	http://www.ncbi.nlm.nih.gov/gene/?term=133015	C4orf28	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003206	133308	SLC9B2	http://www.ncbi.nlm.nih.gov/gene/?term=133308	"NHA2, NHE10, NHEDC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003207	133383	SETD9	http://www.ncbi.nlm.nih.gov/gene/?term=133383	C5orf35	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003208	13346	Des	http://www.ncbi.nlm.nih.gov/gene/?term=13346		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003209	13353	Dgcr6	http://www.ncbi.nlm.nih.gov/gene/?term=13353		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003210	133558	MROH2B	http://www.ncbi.nlm.nih.gov/gene/?term=133558	HEATR7B2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003211	133584	EGFLAM	http://www.ncbi.nlm.nih.gov/gene/?term=133584	"AGRINL, AGRNL, PIKA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003212	133619	PRRC1	http://www.ncbi.nlm.nih.gov/gene/?term=133619		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003213	133619	PRRC1	http://www.ncbi.nlm.nih.gov/gene/?term=133619		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003214	13363	Dhh	http://www.ncbi.nlm.nih.gov/gene/?term=13363	C78960	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003215	13367	Diaph1	http://www.ncbi.nlm.nih.gov/gene/?term=13367	"D18Wsu154e, Dia1, Diap1, Drf1, p140mDia "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003216	133686	NADK2	http://www.ncbi.nlm.nih.gov/gene/?term=133686	"C5orf33, DECRD, MNADK, NADKD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003217	133686	NADK2	http://www.ncbi.nlm.nih.gov/gene/?term=133686	"C5orf33, DECRD, MNADK, NADKD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003218	133746	JMY	http://www.ncbi.nlm.nih.gov/gene/?term=133746	"WHAMM2, WHDC1L3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003219	1337	COX6A1	http://www.ncbi.nlm.nih.gov/gene/?term=1337	"CMTRID, COX6A, COX6AL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003220	1337	COX6A1	http://www.ncbi.nlm.nih.gov/gene/?term=1337	"CMTRID, COX6A, COX6AL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003221	13382	Dld	http://www.ncbi.nlm.nih.gov/gene/?term=13382		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003222	13385	Dlg4	http://www.ncbi.nlm.nih.gov/gene/?term=13385	"Dlgh4, PSD-95, PSD95, SAP90, SAP90A "	mRNA	Mus musculus	25948262	Dendrite	Hippocampus	Fluorescence in situ hybridization	"However, the local translation of PSD-95 mRNA within dendrites and spines, as well as the roles of FMRP or miR-125a, have not been directly studied. "
RLID00003223	13386	Dlk1	http://www.ncbi.nlm.nih.gov/gene/?term=13386	"AW742678, DLK-1, DlkI, FA1, Ly107, Peg9, SCP1, ZOG, pG2, pref-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003224	13388	Dll1	http://www.ncbi.nlm.nih.gov/gene/?term=13388	Delta1	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003225	13392	Dlx2	http://www.ncbi.nlm.nih.gov/gene/?term=13392	"AW121999, Dlx-2, Tes-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003226	13392	Dlx2	http://www.ncbi.nlm.nih.gov/gene/?term=13392	"AW121999, Dlx-2, Tes-1 "	mRNA	Rattus norvegicus	16705037	Nucleus	Embryonic brain	In situ hybridization|RT-PCR	"The fluorescent pattern of two bright intranuclear Evf-2 spots is consistent with that found in tissue sections vivo (see Fig. ?Fig.1f,1f, panel ii). "
RLID00003227	133957	CCDC127	http://www.ncbi.nlm.nih.gov/gene/?term=133957		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003228	133957	CCDC127	http://www.ncbi.nlm.nih.gov/gene/?term=133957		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003229	133	ADM	http://www.ncbi.nlm.nih.gov/gene/?term=133	"AM, PAMP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003230	133	ADM	http://www.ncbi.nlm.nih.gov/gene/?term=133	"AM, PAMP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003231	13401	Dmwd	http://www.ncbi.nlm.nih.gov/gene/?term=13401	"DMR-N9, Dm9 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003232	13404	Dmc1	http://www.ncbi.nlm.nih.gov/gene/?term=13404	"Dmc1h, Lim15, Mei11, sgdp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003233	1340	COX6B1	http://www.ncbi.nlm.nih.gov/gene/?term=1340	"COX6B, COXG, COXVIb1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003234	1340	COX6B1	http://www.ncbi.nlm.nih.gov/gene/?term=1340	"COX6B, COXG, COXVIb1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003235	134145	FAM173B	http://www.ncbi.nlm.nih.gov/gene/?term=134145	JS-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003236	134145	FAM173B	http://www.ncbi.nlm.nih.gov/gene/?term=134145	JS-2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003237	134147	CMBL	http://www.ncbi.nlm.nih.gov/gene/?term=134147	JS-1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003238	13418	Dnajc1	http://www.ncbi.nlm.nih.gov/gene/?term=13418	"4733401K02Rik, AA960110, D230036H06Rik, Dnajl1, ERdj1, ERj1p, MTJ1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003239	13418	Dnajc1	http://www.ncbi.nlm.nih.gov/gene/?term=13418	"4733401K02Rik, AA960110, D230036H06Rik, Dnajl1, ERdj1, ERj1p, MTJ1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003240	134218	DNAJC21	http://www.ncbi.nlm.nih.gov/gene/?term=134218	"DNAJA5, GS3, JJJ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003241	13424	Dync1h1	http://www.ncbi.nlm.nih.gov/gene/?term=13424	"9930018I23Rik, AI894280, DHC1, DHC1a, DNCL, Dnchc1, Dnec1, Dnecl, Loa, MAP1C, P22, Swl, mKIAA0325 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003242	134266	GRPEL2	http://www.ncbi.nlm.nih.gov/gene/?term=134266	Mt-GrpE#2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003243	13427	Dync1i2	http://www.ncbi.nlm.nih.gov/gene/?term=13427	"3110079H08Rik, AW554389, Dncic2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003244	134285	TMEM171	http://www.ncbi.nlm.nih.gov/gene/?term=134285	PRP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003245	13434	Trdmt1	http://www.ncbi.nlm.nih.gov/gene/?term=13434	"Dnmt2, Rnmt2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003246	134353	LSM11	http://www.ncbi.nlm.nih.gov/gene/?term=134353		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003247	13435	Dnmt3a	http://www.ncbi.nlm.nih.gov/gene/?term=13435	MmuIIIA	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003248	13437	Dnpep	http://www.ncbi.nlm.nih.gov/gene/?term=13437	AA407814	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003249	134429	STARD4	http://www.ncbi.nlm.nih.gov/gene/?term=134429		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003250	134430	WDR36	http://www.ncbi.nlm.nih.gov/gene/?term=134430	"GLC1G, TA-WDRP, TAWDRP, UTP21 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003251	134430	WDR36	http://www.ncbi.nlm.nih.gov/gene/?term=134430	"GLC1G, TA-WDRP, TAWDRP, UTP21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003252	13446	Doc2a	http://www.ncbi.nlm.nih.gov/gene/?term=13446		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003253	13446	Doc2a	http://www.ncbi.nlm.nih.gov/gene/?term=13446		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003254	13448	Dok1	http://www.ncbi.nlm.nih.gov/gene/?term=13448	"AW557123, p62DOK "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003255	134492	NUDCD2	http://www.ncbi.nlm.nih.gov/gene/?term=134492		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003256	134492	NUDCD2	http://www.ncbi.nlm.nih.gov/gene/?term=134492		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003257	134510	UBLCP1	http://www.ncbi.nlm.nih.gov/gene/?term=134510	CPUB1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003258	134549	SHROOM1	http://www.ncbi.nlm.nih.gov/gene/?term=134549	APXL2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003259	134549	SHROOM1	http://www.ncbi.nlm.nih.gov/gene/?term=134549	APXL2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003260	1345	COX6C	http://www.ncbi.nlm.nih.gov/gene/?term=1345		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003261	1345	COX6C	http://www.ncbi.nlm.nih.gov/gene/?term=1345		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003262	1347	COX7A2	http://www.ncbi.nlm.nih.gov/gene/?term=1347	"COX7AL, COX7AL1, COXVIIAL, COXVIIa-L, VIIAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003263	1349	COX7B	http://www.ncbi.nlm.nih.gov/gene/?term=1349	"APLCC, LSDMCA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003264	1349	COX7B	http://www.ncbi.nlm.nih.gov/gene/?term=1349	"APLCC, LSDMCA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003265	13508	Dscam	http://www.ncbi.nlm.nih.gov/gene/?term=13508	4932410A21Rik	mRNA	Mus musculus	20926679	Dendrite	Hippocampus	qRT-PCR	"Here, we provide evidence that DSCAM mRNA is localized to dendrites and associated with CPEB1 in the adult mouse hippocampus, and describe the expression of at least five DSCAM isoforms, bearing different combinations of CPEs at their 3'-UTR. "
RLID00003266	1350	COX7C	http://www.ncbi.nlm.nih.gov/gene/?term=1350		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003267	1350	COX7C	http://www.ncbi.nlm.nih.gov/gene/?term=1350		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003268	135112	NCOA7	http://www.ncbi.nlm.nih.gov/gene/?term=135112	"ERAP140, ESNA1-AS, Nbla00052, Nbla10993, TLDC4, dJ187J11.3, NCOA7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003269	135112	NCOA7	http://www.ncbi.nlm.nih.gov/gene/?term=135112	"ERAP140, ESNA1-AS, Nbla00052, Nbla10993, TLDC4, dJ187J11.3, NCOA7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003270	135114	HINT3	http://www.ncbi.nlm.nih.gov/gene/?term=135114	HINT4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003271	135114	HINT3	http://www.ncbi.nlm.nih.gov/gene/?term=135114	HINT4	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003272	135114	HINT3	http://www.ncbi.nlm.nih.gov/gene/?term=135114	HINT4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003273	135138	PACRG	http://www.ncbi.nlm.nih.gov/gene/?term=135138	"GLUP, HAK005771, PARK2CRG "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003274	135138	PACRG	http://www.ncbi.nlm.nih.gov/gene/?term=135138	"GLUP, HAK005771, PARK2CRG "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003275	135152	B3GAT2	http://www.ncbi.nlm.nih.gov/gene/?term=135152	GLCATS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003276	13518	Dst	http://www.ncbi.nlm.nih.gov/gene/?term=13518	"2310001O04Rik, A830042E19Rik, AW554249, BP230, BPAG1-n, Bpag, Bpag1, Macf2, ah, athetoid, dt, mKIAA0728, nmf203, nmf339 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003277	1351	COX8A	http://www.ncbi.nlm.nih.gov/gene/?term=1351	"COX, COX8, COX8-2, COX8L, VIII, VIII-L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003278	1351	COX8A	http://www.ncbi.nlm.nih.gov/gene/?term=1351	"COX, COX8, COX8-2, COX8L, VIII, VIII-L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003279	13521	Slc26a2	http://www.ncbi.nlm.nih.gov/gene/?term=13521	"Dtd, ST-OB "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003280	135228	CD109	http://www.ncbi.nlm.nih.gov/gene/?term=135228	"CPAMD7, p180, r150 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003281	13527	Dtna	http://www.ncbi.nlm.nih.gov/gene/?term=13527	"2210407P21Rik, DTN-A, Dtn, Gm19389, a-DB-1, adbn "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003282	13528	Dtnb	http://www.ncbi.nlm.nih.gov/gene/?term=13528		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003283	135293	PM20D2	http://www.ncbi.nlm.nih.gov/gene/?term=135293	"ACY1L2, bA63L7.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003284	135293	PM20D2	http://www.ncbi.nlm.nih.gov/gene/?term=135293	"ACY1L2, bA63L7.3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003285	135293	PM20D2	http://www.ncbi.nlm.nih.gov/gene/?term=135293	"ACY1L2, bA63L7.3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003286	1352	COX10	http://www.ncbi.nlm.nih.gov/gene/?term=1352		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003287	1352	COX10	http://www.ncbi.nlm.nih.gov/gene/?term=1352		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003288	13537	Dusp2	http://www.ncbi.nlm.nih.gov/gene/?term=13537	PAC1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003289	1353	COX11	http://www.ncbi.nlm.nih.gov/gene/?term=1353	COX11P	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003290	1353	COX11	http://www.ncbi.nlm.nih.gov/gene/?term=1353	COX11P	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003291	13544	Dvl3	http://www.ncbi.nlm.nih.gov/gene/?term=13544		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003292	135458	HUS1B	http://www.ncbi.nlm.nih.gov/gene/?term=135458		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003293	135458	HUS1B	http://www.ncbi.nlm.nih.gov/gene/?term=135458		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003294	13555	E2f1	http://www.ncbi.nlm.nih.gov/gene/?term=13555	"E2F-1, mKIAA4009 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003295	1355	COX15	http://www.ncbi.nlm.nih.gov/gene/?term=1355	CEMCOX2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003296	1355	COX15	http://www.ncbi.nlm.nih.gov/gene/?term=1355	CEMCOX2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003297	1355	COX15	http://www.ncbi.nlm.nih.gov/gene/?term=1355	CEMCOX2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003298	1355	COX15	http://www.ncbi.nlm.nih.gov/gene/?term=1355	CEMCOX2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003299	1357	CPA1	http://www.ncbi.nlm.nih.gov/gene/?term=1357	CPA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003300	135886	WBSCR28	http://www.ncbi.nlm.nih.gov/gene/?term=135886		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003301	13589	Mapre1	http://www.ncbi.nlm.nih.gov/gene/?term=13589	"5530600P05Rik, AI462499, AI504412, AW260097, BIM1p, D2Ertd459e, Eb1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003302	13592	Ebf2	http://www.ncbi.nlm.nih.gov/gene/?term=13592	"D14Ggc1e, EBF-2, Mmot1, O/E-3, OE-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003303	135932	TMEM139	http://www.ncbi.nlm.nih.gov/gene/?term=135932		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003304	13593	Ebf3	http://www.ncbi.nlm.nih.gov/gene/?term=13593	"3110018A08Rik, O/E-2, mKIAA4201 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003305	13599	Ecel1	http://www.ncbi.nlm.nih.gov/gene/?term=13599	"DINE, xce "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003306	1359	CPA3	http://www.ncbi.nlm.nih.gov/gene/?term=1359	MC-CPA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003307	135	ADORA2A	http://www.ncbi.nlm.nih.gov/gene/?term=135	"A2aR, ADORA2, RDC8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003308	136051	ZNF786	http://www.ncbi.nlm.nih.gov/gene/?term=136051		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003309	136051	ZNF786	http://www.ncbi.nlm.nih.gov/gene/?term=136051		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003310	13614	Edn1	http://www.ncbi.nlm.nih.gov/gene/?term=13614	"ET-1, PPET1, preproET "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003311	13618	Ednrb	http://www.ncbi.nlm.nih.gov/gene/?term=13618	"ET-B, ET-BR, ETR-b, ETb, Sox10m1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003312	13626	Eed	http://www.ncbi.nlm.nih.gov/gene/?term=13626	"ENSMUSG00000039373, l(7)5Rn, l7Rn5, lusk "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003313	13627	Eef1a1	http://www.ncbi.nlm.nih.gov/gene/?term=13627		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003314	13628	Eef1a2	http://www.ncbi.nlm.nih.gov/gene/?term=13628	"Eef1a, S1, wasted, wst "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003315	13629	Eef2	http://www.ncbi.nlm.nih.gov/gene/?term=13629	Ef-2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003316	1362	CPD	http://www.ncbi.nlm.nih.gov/gene/?term=1362	GP180	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003317	1362	CPD	http://www.ncbi.nlm.nih.gov/gene/?term=1362	GP180	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003318	136319	MTPN	http://www.ncbi.nlm.nih.gov/gene/?term=136319	"GCDP, V-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003319	136319	MTPN	http://www.ncbi.nlm.nih.gov/gene/?term=136319	"GCDP, V-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003320	136319	MTPN	http://www.ncbi.nlm.nih.gov/gene/?term=136319	"GCDP, V-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003321	13631	Eef2k	http://www.ncbi.nlm.nih.gov/gene/?term=13631	"C86191, eEF-2K "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00003322	1363	CPE	http://www.ncbi.nlm.nih.gov/gene/?term=1363	CPH	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003323	1363	CPE	http://www.ncbi.nlm.nih.gov/gene/?term=1363	CPH	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003324	13640	Efna5	http://www.ncbi.nlm.nih.gov/gene/?term=13640	"AL-1, AV158822, EFL-5, Ephrin-A5, Epl7, LERK-7, RAGS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003325	13649	Egfr	http://www.ncbi.nlm.nih.gov/gene/?term=13649	"9030024J15Rik, AI552599, Erbb, Errb1, Errp, Wa5, wa-2, wa2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003326	1364	CLDN4	http://www.ncbi.nlm.nih.gov/gene/?term=1364	"CPE-R, CPER, CPETR, CPETR1, WBSCR8, hCPE-R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003327	1364	CLDN4	http://www.ncbi.nlm.nih.gov/gene/?term=1364	"CPE-R, CPER, CPETR, CPETR1, WBSCR8, hCPE-R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003328	136541	PRSS58	http://www.ncbi.nlm.nih.gov/gene/?term=136541	"PRSS1, TRY1, TRYX3, UNQ2540 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003329	13654	Egr2	http://www.ncbi.nlm.nih.gov/gene/?term=13654	"Egr-2, Krox-20, Krox20, NGF1-B, Zfp-25, Zfp-6 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003330	13655	Egr3	http://www.ncbi.nlm.nih.gov/gene/?term=13655	Pilot	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003331	1365	CLDN3	http://www.ncbi.nlm.nih.gov/gene/?term=1365	"C7orf1, CPE-R2, CPETR2, HRVP1, RVP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003332	1365	CLDN3	http://www.ncbi.nlm.nih.gov/gene/?term=1365	"C7orf1, CPE-R2, CPETR2, HRVP1, RVP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003333	136647	MPLKIP	http://www.ncbi.nlm.nih.gov/gene/?term=136647	"ABHS, C7orf11, ORF20, TTD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003334	136647	MPLKIP	http://www.ncbi.nlm.nih.gov/gene/?term=136647	"ABHS, C7orf11, ORF20, TTD4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003335	13664	Eif1a	http://www.ncbi.nlm.nih.gov/gene/?term=13664	"C76390, Ef1a, Eftu, Eif4c, eIF-1A, eIF-4C "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003336	13664	Eif1a	http://www.ncbi.nlm.nih.gov/gene/?term=13664	"C76390, Ef1a, Eftu, Eif4c, eIF-1A, eIF-4C "	mRNA	Mus musculus	22945799	Synapse	Brain	RT-PCR|Immunoprecipitation	"Fig. 5 a Detection of KIF1Bb in purified mouse synaptoneurosomes. KIF1Bb is detected in total lysates from the cortex (T; 5 lg total protein) and is enriched in a sample of synaptoneurosomes purified from the cortex (S; 5 lg). The analysis, by RT-PCR, revealed the presence of Arc (activity regulated cytoskeleton-associated protein) mRNA (Fig. 8c), a well-known, dendritically localized mRNA [43-45]. Interestingly, Calmodulin mRNA was also part of this complex. Both were specifically found in the KIF1Bb-immunoprecipitated complex, but not in the negative control reaction (Fig. 8c, compare lanes 2 and 3). The specific association of Arc and Calmodulin mRNAs with the KIF1Bb-containing complex is further supported by the absence of non-synaptically or other synaptically localized mRNAs such as eEIF1a and aCaMKII (Fig. 8c). These observations would suggest the participation of KIF1Bb in RNP particles in association with at least two dendritically targeted mRNAs, Arc and CaM. "
RLID00003337	13666	Eif2ak3	http://www.ncbi.nlm.nih.gov/gene/?term=13666	"Pek, Perk "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003338	13669	Eif3a	http://www.ncbi.nlm.nih.gov/gene/?term=13669	"A830012B05Rik, Csma, Eif3, Eif3s10, mKIAA0139 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003339	13669	Eif3a	http://www.ncbi.nlm.nih.gov/gene/?term=13669	"A830012B05Rik, Csma, Eif3, Eif3s10, mKIAA0139 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00003340	1366	CLDN7	http://www.ncbi.nlm.nih.gov/gene/?term=1366	"CEPTRL2, CLDN-7, CPETRL2, Hs.84359, claudin-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003341	1366	CLDN7	http://www.ncbi.nlm.nih.gov/gene/?term=1366	"CEPTRL2, CLDN-7, CPETRL2, Hs.84359, claudin-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003342	1368	CPM	http://www.ncbi.nlm.nih.gov/gene/?term=1368		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003343	1368	CPM	http://www.ncbi.nlm.nih.gov/gene/?term=1368		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003344	13690	Eif4g2	http://www.ncbi.nlm.nih.gov/gene/?term=13690	"DAP-5, E130105L11Rik, Nat1, Natm1, p97 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003345	136	ADORA2B	http://www.ncbi.nlm.nih.gov/gene/?term=136	ADORA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003346	136	ADORA2B	http://www.ncbi.nlm.nih.gov/gene/?term=136	ADORA2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003347	136	ADORA2B	http://www.ncbi.nlm.nih.gov/gene/?term=136	ADORA2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003348	137075	CLDN23	http://www.ncbi.nlm.nih.gov/gene/?term=137075	"CLDNL, hCG1646163 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003349	1370	CPN2	http://www.ncbi.nlm.nih.gov/gene/?term=1370	ACBP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003350	13711	Elf5	http://www.ncbi.nlm.nih.gov/gene/?term=13711	"ESE-2, ESE-5, ESE-5. "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003351	13722	Aimp1	http://www.ncbi.nlm.nih.gov/gene/?term=13722	"9830137A06Rik, AIMP1/p43, EMAPII, Emap2, Scye1, p43 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003352	13730	Emp1	http://www.ncbi.nlm.nih.gov/gene/?term=13730	"I-8-09, TMP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003353	137392	FAM92A1	http://www.ncbi.nlm.nih.gov/gene/?term=137392		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003354	1373	CPS1	http://www.ncbi.nlm.nih.gov/gene/?term=1373	"CPSASE1, PHN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003355	1373	CPS1	http://www.ncbi.nlm.nih.gov/gene/?term=1373	"CPSASE1, PHN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003356	1373	CPS1	http://www.ncbi.nlm.nih.gov/gene/?term=1373	"CPSASE1, PHN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003357	1374	CPT1A	http://www.ncbi.nlm.nih.gov/gene/?term=1374	"CPT1, CPT1-L, L-CPT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003358	1374	CPT1A	http://www.ncbi.nlm.nih.gov/gene/?term=1374	"CPT1, CPT1-L, L-CPT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003359	1374	CPT1A	http://www.ncbi.nlm.nih.gov/gene/?term=1374	"CPT1, CPT1-L, L-CPT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003360	137695	TMEM68	http://www.ncbi.nlm.nih.gov/gene/?term=137695		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003361	137695	TMEM68	http://www.ncbi.nlm.nih.gov/gene/?term=137695		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003362	1376	CPT2	http://www.ncbi.nlm.nih.gov/gene/?term=1376	"CPT1, CPTASE, IIAE4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003363	1376	CPT2	http://www.ncbi.nlm.nih.gov/gene/?term=1376	"CPT1, CPTASE, IIAE4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003364	137886	UBXN2B	http://www.ncbi.nlm.nih.gov/gene/?term=137886	p37	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003365	137886	UBXN2B	http://www.ncbi.nlm.nih.gov/gene/?term=137886	p37	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003366	137886	UBXN2B	http://www.ncbi.nlm.nih.gov/gene/?term=137886	p37	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003367	1378	CR1	http://www.ncbi.nlm.nih.gov/gene/?term=1378	"C3BR, C4BR, CD35, KN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003368	1378	CR1	http://www.ncbi.nlm.nih.gov/gene/?term=1378	"C3BR, C4BR, CD35, KN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003369	137964	GPAT4	http://www.ncbi.nlm.nih.gov/gene/?term=137964	"1-AGPAT 6, AGPAT6, LPAAT-zeta, LPAATZ, TSARG7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003370	137964	GPAT4	http://www.ncbi.nlm.nih.gov/gene/?term=137964	"1-AGPAT 6, AGPAT6, LPAAT-zeta, LPAATZ, TSARG7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003371	13798	En1	http://www.ncbi.nlm.nih.gov/gene/?term=13798	"En-1, Mo-en.1 "	mRNA	Mus musculus	17399993	Dendrite	Ventral midBrain	In situ hybridization	"Here we report the presence of Engrailed protein and En1 mRNA in proximal dendrites of these neurons and of En1 mRNA in ventral midbrain synaptoneurosomes.  In contrast, the mRNA of En2 and HPRT (hypoxanthine phosphoribosyltransferase; a well-expressed soma-restricted mRNA) in the SN and VTA (Figs. 1G-J) are confined to the cell body, which confirms the specificity of En1 mRNA dendritic staining.  This finding, along with the absence of En2 mRNA in SNSs, confirms the in situ hybridization data and establishes that En1 mRNA is transported into the dendrites of ventral midbrain neurons. "
RLID00003372	1379	CR1L	http://www.ncbi.nlm.nih.gov/gene/?term=1379		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003373	13800	Enah	http://www.ncbi.nlm.nih.gov/gene/?term=13800	"Mena, NDPP-1, Ndpp1, WBP8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003374	13801	Enam	http://www.ncbi.nlm.nih.gov/gene/?term=13801	abte	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003375	13803	Enc1	http://www.ncbi.nlm.nih.gov/gene/?term=13803	"Nrpb, PIG10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003376	13804	Endog	http://www.ncbi.nlm.nih.gov/gene/?term=13804		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003377	13804	Endog	http://www.ncbi.nlm.nih.gov/gene/?term=13804		mRNA	Mus musculus	15280156	Cytosol	kidney	In situ hybridization	In situ hybridization and immunohistochemical studies localized the increased expression of Endo G mRNA to the cytosolic compartment and Endo G protein to the nuclear compartment of proximal tubules in cisplatin-treated mice.
RLID00003378	138050	HGSNAT	http://www.ncbi.nlm.nih.gov/gene/?term=138050	"HGNAT, MPS3C, RP73, TMEM76 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003379	13806	Eno1	http://www.ncbi.nlm.nih.gov/gene/?term=13806	"0610008I15, AL022784, Eno-1, MBP-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003380	13807	Eno2	http://www.ncbi.nlm.nih.gov/gene/?term=13807	"AI837106, D6Ertd375e, Eno-2, NSE "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003381	1380	CR2	http://www.ncbi.nlm.nih.gov/gene/?term=1380	"C3DR, CD21, CR, CVID7, SLEB9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003382	138151	NACC2	http://www.ncbi.nlm.nih.gov/gene/?term=138151	"BEND9, BTBD14, BTBD14A, BTBD31, NAC-2, RBB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003383	138199	CARNMT1	http://www.ncbi.nlm.nih.gov/gene/?term=138199	"C9orf41, UPF0586 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003384	138199	CARNMT1	http://www.ncbi.nlm.nih.gov/gene/?term=138199	"C9orf41, UPF0586 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003385	13822	Epb41l2	http://www.ncbi.nlm.nih.gov/gene/?term=13822	"4.1G, AW555191, D10Ertd398e, Epb4.1l2, NBL2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003386	13823	Epb41l3	http://www.ncbi.nlm.nih.gov/gene/?term=13823	"4.1B, DAL1P, Dal1, Epb4.1l3, NBL3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003387	138241	C9orf85	http://www.ncbi.nlm.nih.gov/gene/?term=138241		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003388	13829	Dmtn	http://www.ncbi.nlm.nih.gov/gene/?term=13829	"AI325486, Epb4.9, Epb49, dematin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003389	1382	CRABP2	http://www.ncbi.nlm.nih.gov/gene/?term=1382	"CRABP-II, RBP6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003390	13839	Epha5	http://www.ncbi.nlm.nih.gov/gene/?term=13839	"AI854630, AW125296, Cek7, Ehk1, Els1, Hek7, Rek7, bsk "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003391	13841	Epha7	http://www.ncbi.nlm.nih.gov/gene/?term=13841	"Cek11, Ebk, Ehk3, Hek11, Mdk1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003392	13841	Epha7	http://www.ncbi.nlm.nih.gov/gene/?term=13841	"Cek11, Ebk, Ehk3, Hek11, Mdk1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003393	138428	PTRH1	http://www.ncbi.nlm.nih.gov/gene/?term=138428	"C9orf115, PTH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003394	1384	CRAT	http://www.ncbi.nlm.nih.gov/gene/?term=1384	CAT1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003395	138639	PTPDC1	http://www.ncbi.nlm.nih.gov/gene/?term=138639	PTP9Q22	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003396	138639	PTPDC1	http://www.ncbi.nlm.nih.gov/gene/?term=138639	PTP9Q22	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003397	13865	Nr2f1	http://www.ncbi.nlm.nih.gov/gene/?term=13865	"COUP-TF1, COUP-TFI, COUPTFA, EAR3, Erbal3, SVP44, Tcfcoup1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003398	13869	Erbb4	http://www.ncbi.nlm.nih.gov/gene/?term=13869	"Her4, c-erbB-4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003399	13870	Ercc1	http://www.ncbi.nlm.nih.gov/gene/?term=13870	Ercc-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003400	138716	RPP25L	http://www.ncbi.nlm.nih.gov/gene/?term=138716	"C9orf23, bA296L22.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003401	13875	Erf	http://www.ncbi.nlm.nih.gov/gene/?term=13875		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003402	1387	CREBBP	http://www.ncbi.nlm.nih.gov/gene/?term=1387	"CBP, KAT3A, RSTS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003403	1387	CREBBP	http://www.ncbi.nlm.nih.gov/gene/?term=1387	"CBP, KAT3A, RSTS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003404	1387	CREBBP	http://www.ncbi.nlm.nih.gov/gene/?term=1387	"CBP, KAT3A, RSTS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003405	1389	CREBL2	http://www.ncbi.nlm.nih.gov/gene/?term=1389		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003406	1389	CREBL2	http://www.ncbi.nlm.nih.gov/gene/?term=1389		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003407	1390	CREM	http://www.ncbi.nlm.nih.gov/gene/?term=1390	"CREM-2, ICER, hCREM-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003408	1390	CREM	http://www.ncbi.nlm.nih.gov/gene/?term=1390	"CREM-2, ICER, hCREM-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003409	139105	BEND2	http://www.ncbi.nlm.nih.gov/gene/?term=139105	CXorf20	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003410	139105	BEND2	http://www.ncbi.nlm.nih.gov/gene/?term=139105	CXorf20	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003411	139231	FAM199X	http://www.ncbi.nlm.nih.gov/gene/?term=139231	CXorf39	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003412	13929	Amz2	http://www.ncbi.nlm.nih.gov/gene/?term=13929	"AA408420, ESTM12, X83328 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003413	1392	CRH	http://www.ncbi.nlm.nih.gov/gene/?term=1392	"CRF, CRH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003414	139322	APOOL	http://www.ncbi.nlm.nih.gov/gene/?term=139322	"CXorf33, FAM121A, Mic27, UNQ8193 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003415	139322	APOOL	http://www.ncbi.nlm.nih.gov/gene/?term=139322	"CXorf33, FAM121A, Mic27, UNQ8193 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003416	139322	APOOL	http://www.ncbi.nlm.nih.gov/gene/?term=139322	"CXorf33, FAM121A, Mic27, UNQ8193 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003417	139341	FUNDC1	http://www.ncbi.nlm.nih.gov/gene/?term=139341		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003418	1393	CRHBP	http://www.ncbi.nlm.nih.gov/gene/?term=1393	"CRF-BP, CRFBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003419	139422	MAGEB10	http://www.ncbi.nlm.nih.gov/gene/?term=139422		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003420	139422	MAGEB10	http://www.ncbi.nlm.nih.gov/gene/?term=139422		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003421	13957	X83313	http://www.ncbi.nlm.nih.gov/gene/?term=13957	ESTM4	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003422	139596	UPRT	http://www.ncbi.nlm.nih.gov/gene/?term=139596	"FUR1, UPP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003423	139596	UPRT	http://www.ncbi.nlm.nih.gov/gene/?term=139596	"FUR1, UPP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003424	1396	CRIP1	http://www.ncbi.nlm.nih.gov/gene/?term=1396	"CRHP, CRIP, CRP-1, CRP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003425	1396	CRIP1	http://www.ncbi.nlm.nih.gov/gene/?term=1396	"CRHP, CRIP, CRP-1, CRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003426	139716	GAB3	http://www.ncbi.nlm.nih.gov/gene/?term=139716		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003427	1397	CRIP2	http://www.ncbi.nlm.nih.gov/gene/?term=1397	"CRIP, CRP2, ESP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003428	139818	DOCK11	http://www.ncbi.nlm.nih.gov/gene/?term=139818	"ACG, ZIZ2, bB128O4.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003429	139886	SPIN4	http://www.ncbi.nlm.nih.gov/gene/?term=139886	TDRD28	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003430	1398	CRK	http://www.ncbi.nlm.nih.gov/gene/?term=1398	"CRKII, p38 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003431	13990	Smarcad1	http://www.ncbi.nlm.nih.gov/gene/?term=13990	"AV081750, AW226546, D6Pas1, Etl1, mKIAA1122 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003432	1399	CRKL	http://www.ncbi.nlm.nih.gov/gene/?term=1399		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003433	1399	CRKL	http://www.ncbi.nlm.nih.gov/gene/?term=1399		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003434	14000	Drosha	http://www.ncbi.nlm.nih.gov/gene/?term=14000	"1110013A17Rik, AI874853, Etohi2, Rn3, Rnasen "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003435	14004	Chchd2	http://www.ncbi.nlm.nih.gov/gene/?term=14004	"AL033347, Etohi6 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003436	14008	Etv2	http://www.ncbi.nlm.nih.gov/gene/?term=14008	Etsrp71	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003437	14017	Evi2a	http://www.ncbi.nlm.nih.gov/gene/?term=14017	"AW491894, Evi-2, Evi2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003438	14020	Evi5	http://www.ncbi.nlm.nih.gov/gene/?term=14020	NB4S	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003439	14030	Ewsr1	http://www.ncbi.nlm.nih.gov/gene/?term=14030	"Ews, Ewsh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003440	14042	Ext1	http://www.ncbi.nlm.nih.gov/gene/?term=14042	AA409028	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003441	140459	ASB6	http://www.ncbi.nlm.nih.gov/gene/?term=140459		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003442	140459	ASB6	http://www.ncbi.nlm.nih.gov/gene/?term=140459		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003443	140459	ASB6	http://www.ncbi.nlm.nih.gov/gene/?term=140459		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003444	140460	ASB7	http://www.ncbi.nlm.nih.gov/gene/?term=140460		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003445	140461	ASB8	http://www.ncbi.nlm.nih.gov/gene/?term=140461	PP14212	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003446	140465	MYL6B	http://www.ncbi.nlm.nih.gov/gene/?term=140465	MLC1SA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003447	140467	ZNF358	http://www.ncbi.nlm.nih.gov/gene/?term=140467	ZFEND	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003448	140486	Igf2bp1	http://www.ncbi.nlm.nih.gov/gene/?term=140486	"AL024068, AW549074, CRD-BP, Crdbp, D030026A21Rik, D11Moh40e, D11Moh45, IMP-1, Neilsen, ZBP-1, Zbp1, mir-3063 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003449	140486	Igf2bp1	http://www.ncbi.nlm.nih.gov/gene/?term=140486	"AL024068, AW549074, CRD-BP, Crdbp, D030026A21Rik, D11Moh40e, D11Moh45, IMP-1, Neilsen, ZBP-1, Zbp1, mir-3063 "	mRNA	Mus musculus	10875929	Cell leading edge	NIH 3T3 cell	In situ hybridization	"The results show that the distribution of full-length H19 RNA is similar to that of IMP-1 (21) by being either evenly distributed in areas with confluent growth-arrested cells (88% of transfected cells) or, as illustrated in Fig.8 B, localized to the leading edge of lamellipodia and perinuclear regions in dispersed proliferating cells (42% of transfected cells). "
RLID00003450	140486	Igf2bp1	http://www.ncbi.nlm.nih.gov/gene/?term=140486	"AL024068, AW549074, CRD-BP, Crdbp, D030026A21Rik, D11Moh40e, D11Moh45, IMP-1, Neilsen, ZBP-1, Zbp1, mir-3063 "	mRNA	Mus musculus	10875929	Lamellipodium	NIH 3T3 cell	In situ hybridization	"The results show that the distribution of full-length H19 RNA is similar to that of IMP-1 (21) by being either evenly distributed in areas with confluent growth-arrested cells (88% of transfected cells) or, as illustrated in Fig.8 B, localized to the leading edge of lamellipodia and perinuclear regions in dispersed proliferating cells (42% of transfected cells). "
RLID00003451	140486	Igf2bp1	http://www.ncbi.nlm.nih.gov/gene/?term=140486	"AL024068, AW549074, CRD-BP, Crdbp, D030026A21Rik, D11Moh40e, D11Moh45, IMP-1, Neilsen, ZBP-1, Zbp1, mir-3063 "	mRNA	Mus musculus	10875929	Perinuclear	NIH 3T3 cell	In situ hybridization	"The results show that the distribution of full-length H19 RNA is similar to that of IMP-1 (21) by being either evenly distributed in areas with confluent growth-arrested cells (88% of transfected cells) or, as illustrated in Fig.8 B, localized to the leading edge of lamellipodia and perinuclear regions in dispersed proliferating cells (42% of transfected cells). "
RLID00003452	14048	Eya1	http://www.ncbi.nlm.nih.gov/gene/?term=14048	bor	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003453	140492	Kcnn2	http://www.ncbi.nlm.nih.gov/gene/?term=140492	"KCa2.2, SK2, SKCA2, bc, fri "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003454	1404	HAPLN1	http://www.ncbi.nlm.nih.gov/gene/?term=1404	"CRT1, CRTL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003455	140545	RNF32	http://www.ncbi.nlm.nih.gov/gene/?term=140545	"FKSG33, HSD15, LMBR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003456	140564	APOBEC3D	http://www.ncbi.nlm.nih.gov/gene/?term=140564	"A3DE, APOBEC3E, ARP6, APOBEC3D "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003457	140564	APOBEC3D	http://www.ncbi.nlm.nih.gov/gene/?term=140564	"A3DE, APOBEC3E, ARP6, APOBEC3D "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003458	14056	Ezh2	http://www.ncbi.nlm.nih.gov/gene/?term=14056	"Enx-1, Enx1h, KMT6, mKIAA4065 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003459	140576	S100A16	http://www.ncbi.nlm.nih.gov/gene/?term=140576	"AAG13, DT1P1A7, S100F "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003460	14057	Sfxn1	http://www.ncbi.nlm.nih.gov/gene/?term=14057	"2810002O05Rik, A930015P12Rik, f "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003461	14057	Sfxn1	http://www.ncbi.nlm.nih.gov/gene/?term=14057	"2810002O05Rik, A930015P12Rik, f "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003462	14061	F2	http://www.ncbi.nlm.nih.gov/gene/?term=14061	"Cf-2, Cf2, FII "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003463	14062	F2r	http://www.ncbi.nlm.nih.gov/gene/?term=14062	"AI482343, Cf2r, Par1, ThrR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003464	140630	Ube4a	http://www.ncbi.nlm.nih.gov/gene/?term=140630	"4732444G18Rik, 9930123J21Rik, UFD2b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003465	140680	C20orf96	http://www.ncbi.nlm.nih.gov/gene/?term=140680	dJ1103G7.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003466	140688	NOL4L	http://www.ncbi.nlm.nih.gov/gene/?term=140688	"C20orf112, C20orf113, dJ1184F4.2, dJ1184F4.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003467	140691	TRIM69	http://www.ncbi.nlm.nih.gov/gene/?term=140691	"HSD-34, HSD34, RNF36, Trif "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003468	140691	TRIM69	http://www.ncbi.nlm.nih.gov/gene/?term=140691	"HSD-34, HSD34, RNF36, Trif "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003469	1406	CRX	http://www.ncbi.nlm.nih.gov/gene/?term=1406	"CORD2, CRD, LCA7, OTX3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003470	1406	CRX	http://www.ncbi.nlm.nih.gov/gene/?term=1406	"CORD2, CRD, LCA7, OTX3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003471	140707	BRI3BP	http://www.ncbi.nlm.nih.gov/gene/?term=140707	"BNAS1, HCCR-1, HCCR-2, HCCRBP-1, KG19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003472	14070	F8a	http://www.ncbi.nlm.nih.gov/gene/?term=14070	"AI852759, DXUcsf11, F8a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003473	140710	SOGA1	http://www.ncbi.nlm.nih.gov/gene/?term=140710	"C20orf117, KIAA0889, SOGA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003474	140735	DYNLL2	http://www.ncbi.nlm.nih.gov/gene/?term=140735	"DNCL1B, Dlc2, RSPH22 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003475	140735	DYNLL2	http://www.ncbi.nlm.nih.gov/gene/?term=140735	"DNCL1B, Dlc2, RSPH22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003476	140738	TMEM37	http://www.ncbi.nlm.nih.gov/gene/?term=140738	"PR, PR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003477	140739	UBE2F	http://www.ncbi.nlm.nih.gov/gene/?term=140739	NCE2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003478	140742	Sesn1	http://www.ncbi.nlm.nih.gov/gene/?term=140742	"1110002G11Rik, AU044290, Pa26, Sest1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003479	140767	NRSN1	http://www.ncbi.nlm.nih.gov/gene/?term=140767	"VMP, p24 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003480	140767	NRSN1	http://www.ncbi.nlm.nih.gov/gene/?term=140767	"VMP, p24 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003481	140780	Bmp2k	http://www.ncbi.nlm.nih.gov/gene/?term=140780	"4933417M22Rik, AA673486, AV128808, BIKE "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003482	1407	CRY1	http://www.ncbi.nlm.nih.gov/gene/?term=1407	PHLL1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003483	140803	TRPM6	http://www.ncbi.nlm.nih.gov/gene/?term=140803	"CHAK2, HMGX, HOMG, HOMG1, HSH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003484	140803	TRPM6	http://www.ncbi.nlm.nih.gov/gene/?term=140803	"CHAK2, HMGX, HOMG, HOMG1, HSH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003485	140809	SRXN1	http://www.ncbi.nlm.nih.gov/gene/?term=140809	"C20orf139, Npn3, SRX, SRX1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003486	140809	SRXN1	http://www.ncbi.nlm.nih.gov/gene/?term=140809	"C20orf139, Npn3, SRX, SRX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003487	140810	Ttbk2	http://www.ncbi.nlm.nih.gov/gene/?term=140810	"2610507N02Rik, AI326283, B930008N24Rik, TTK, Ttbk, Ttbk1, mKIAA0847 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003488	140823	ROMO1	http://www.ncbi.nlm.nih.gov/gene/?term=140823	"C20orf52, MTGM, MTGMP, bA353C18.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003489	140831	ZSWIM3	http://www.ncbi.nlm.nih.gov/gene/?term=140831	"C20orf164, PPP1R174 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003490	14083	Ptk2	http://www.ncbi.nlm.nih.gov/gene/?term=14083	"FAK, FRNK, Fadk, mKIAA4203, p125FAK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003491	14085	Fah	http://www.ncbi.nlm.nih.gov/gene/?term=14085		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003492	140883	ZNF280B	http://www.ncbi.nlm.nih.gov/gene/?term=140883	"5'OY11.1, D87009.C22.3, SUHW2, ZNF279, ZNF632 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003493	140883	ZNF280B	http://www.ncbi.nlm.nih.gov/gene/?term=140883	"5'OY11.1, D87009.C22.3, SUHW2, ZNF279, ZNF632 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003494	140883	ZNF280B	http://www.ncbi.nlm.nih.gov/gene/?term=140883	"5'OY11.1, D87009.C22.3, SUHW2, ZNF279, ZNF632 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003495	14088	Fancc	http://www.ncbi.nlm.nih.gov/gene/?term=14088	"Facc, mir-3074-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003496	140890	SREK1	http://www.ncbi.nlm.nih.gov/gene/?term=140890	"SFRS12, SRrp508, SRrp86 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003497	140901	STK35	http://www.ncbi.nlm.nih.gov/gene/?term=140901	"CLIK1L1, STK35 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003498	140901	STK35	http://www.ncbi.nlm.nih.gov/gene/?term=140901	"CLIK1, STK35L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003499	140917	Dclre1b	http://www.ncbi.nlm.nih.gov/gene/?term=140917	"AI452214, Apollo, SNMIB, mSNM1B "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003500	140931	Hnrnph1	http://www.ncbi.nlm.nih.gov/gene/?term=140931	"Hnrph, Hnrph1 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00003501	14105	Srsf10	http://www.ncbi.nlm.nih.gov/gene/?term=14105	"FUSIP2, Fusip1, NSSR1, NSSR2, Nssr, SRrp40, Sfrs13a, Srsf13a, TASR, TASR1, TASR2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003502	14105	Srsf10	http://www.ncbi.nlm.nih.gov/gene/?term=14105	"FUSIP2, Fusip1, NSSR1, NSSR2, Nssr, SRrp40, Sfrs13a, Srsf13a, TASR, TASR1, TASR2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003503	1410	CRYAB	http://www.ncbi.nlm.nih.gov/gene/?term=1410	"CMD1II, CRYA2, CTPP2, CTRCT16, HEL-S-101, HSPB5, MFM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003504	14115	Fbln2	http://www.ncbi.nlm.nih.gov/gene/?term=14115	"5730577E14Rik, FIBL-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003505	1411	CRYBA1	http://www.ncbi.nlm.nih.gov/gene/?term=1411	"CRYB1, CTRCT10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003506	1413	CRYBA4	http://www.ncbi.nlm.nih.gov/gene/?term=1413	"CTRCT23, MCOPCT4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003507	14155	Fem1b	http://www.ncbi.nlm.nih.gov/gene/?term=14155	mKIAA0396	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003508	14158	Fer	http://www.ncbi.nlm.nih.gov/gene/?term=14158	"AV082135, C330004K01Rikt, Fert2, Fer "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003509	14160	Lgr5	http://www.ncbi.nlm.nih.gov/gene/?term=14160	"FEX, Gpr49 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003510	14161	Fga	http://www.ncbi.nlm.nih.gov/gene/?term=14161	"ENSMUSG00000059807, Fib "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003511	14163	Fgd1	http://www.ncbi.nlm.nih.gov/gene/?term=14163	ZFYVE3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003512	14167	Fgf12	http://www.ncbi.nlm.nih.gov/gene/?term=14167	"AV114868, B230343J05Rik, FGF-12, FHF-1, Fhf1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003513	1416	CRYBB2P1	http://www.ncbi.nlm.nih.gov/gene/?term=1416	CRYB2B	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003514	14176	Fgf5	http://www.ncbi.nlm.nih.gov/gene/?term=14176	"Fgf-5, HBGF-5, angora, go "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003515	14186	Fgfr4	http://www.ncbi.nlm.nih.gov/gene/?term=14186	Fgfr-4	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003516	14201	Fhl3	http://www.ncbi.nlm.nih.gov/gene/?term=14201	SLIM2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003517	14211	Smc2	http://www.ncbi.nlm.nih.gov/gene/?term=14211	"5730502P04Rik, AI255214, AW545314, CAP-E, CAPE, Fin16, SMC-2l1, Smc2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003518	14217174	SPRRNA.42	http://www.ncbi.nlm.nih.gov/gene/?term=14217174	SPRRNA.42	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.42
RLID00003519	14217228	SPRRNA.46	http://www.ncbi.nlm.nih.gov/gene/?term=14217228	SPRRNA.46	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.46
RLID00003520	14217287	SPRRNA.45	http://www.ncbi.nlm.nih.gov/gene/?term=14217287	SPRRNA.45	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.45
RLID00003521	14217299	SPRRNA.47	http://www.ncbi.nlm.nih.gov/gene/?term=14217299	SPRRNA.47	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.47
RLID00003522	14217300	SPRRNA.48	http://www.ncbi.nlm.nih.gov/gene/?term=14217300	SPRRNA.48	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.48
RLID00003523	14217302	SPRRNA.52	http://www.ncbi.nlm.nih.gov/gene/?term=14217302	SPRRNA.52	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.52
RLID00003524	14217303	SPRRNA.50	http://www.ncbi.nlm.nih.gov/gene/?term=14217303	SPRRNA.50	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.50
RLID00003525	14217304	SPRRNA.51	http://www.ncbi.nlm.nih.gov/gene/?term=14217304	SPRRNA.51	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.51
RLID00003526	14217306	SPRRNA.43	http://www.ncbi.nlm.nih.gov/gene/?term=14217306	SPRRNA.43	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.43
RLID00003527	14217307	SPRRNA.44	http://www.ncbi.nlm.nih.gov/gene/?term=14217307	SPRRNA.44	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.44
RLID00003528	14217308	SPRRNA.49	http://www.ncbi.nlm.nih.gov/gene/?term=14217308	SPRRNA.49	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.49
RLID00003529	14217409	SPBTRNASER.05	http://www.ncbi.nlm.nih.gov/gene/?term=14217409	SPBTRNASER.05	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNASER.05
RLID00003530	14217707	SPBTRNASER.06	http://www.ncbi.nlm.nih.gov/gene/?term=14217707	SPBTRNASER.06	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNASER.06
RLID00003531	14218195	SPATRNAPRO.02	http://www.ncbi.nlm.nih.gov/gene/?term=14218195	SPATRNAPRO.02	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAPRO.02
RLID00003532	14219	Ctgf	http://www.ncbi.nlm.nih.gov/gene/?term=14219	"Ccn2, Fisp12, Hcs24, fisp-12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003533	14225	Fkbp1a	http://www.ncbi.nlm.nih.gov/gene/?term=14225	"FKBP12, Fkbp, Fkbp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003534	14228	Fkbp4	http://www.ncbi.nlm.nih.gov/gene/?term=14228	"59kDa, AL022792, AW208983, FKBP-4, FKBP-52, FKBP52, FKPB52, p59 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003535	14231	Fkbp7	http://www.ncbi.nlm.nih.gov/gene/?term=14231	"23kDa, FKBP-7, FKBP23 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003536	14254	Flt1	http://www.ncbi.nlm.nih.gov/gene/?term=14254	"AI323757, Flt-1, VEGFR-1, VEGFR1, sFlt1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003537	14262	Fmo3	http://www.ncbi.nlm.nih.gov/gene/?term=14262	AW111792	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003538	14265	Fmr1	http://www.ncbi.nlm.nih.gov/gene/?term=14265	"FMRP, Fmr-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003539	14265	Fmr1	http://www.ncbi.nlm.nih.gov/gene/?term=14265	"FMRP, Fmr-1 "	mRNA	Mus musculus	18539120	Dendrite	Neuron	Fluorescence in situ hybridization	Histogram showing dendritic Fmr1 mRNA abundance in KLC dominant negative-transfected neurons (n=13-15; *p<0.005; mean±SEM). Images above bars represent dendritic regions from images outlined at left.
RLID00003540	142678	MIB2	http://www.ncbi.nlm.nih.gov/gene/?term=142678	"ZZANK1, ZZZ5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003541	142678	MIB2	http://www.ncbi.nlm.nih.gov/gene/?term=142678	"ZZANK1, ZZZ5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003542	142679	DUSP19	http://www.ncbi.nlm.nih.gov/gene/?term=142679	"DUSP17, LMWDSP3, SKRP1, TS-DSP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003543	142679	DUSP19	http://www.ncbi.nlm.nih.gov/gene/?term=142679	"DUSP17, LMWDSP3, SKRP1, TS-DSP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003544	14268	Fn1	http://www.ncbi.nlm.nih.gov/gene/?term=14268	"E330027I09, Fn, Fn-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003545	14269	Fnbp1	http://www.ncbi.nlm.nih.gov/gene/?term=14269	"1110057E06Rik, 2210010H06Rik, FBP1, Fbp17 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003546	14270	Srgap2	http://www.ncbi.nlm.nih.gov/gene/?term=14270	"9930124L22Rik, AI448945, FBP2, Fnbp2, srGAP3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003547	14281	Fos	http://www.ncbi.nlm.nih.gov/gene/?term=14281	"D12Rfj1, c-fos, cFos "	mRNA	Mus musculus	1748285	Nucleus	NIH-3T3 cell	In situ hybridization|Electron microscopy	We have also compared the localization of c-fos transcripts with the speckled nuclear regions that are enriched in snRNPs and the non-snRNP splicing factor SC-35. Direct observations of three-dimensional rotations have revealed a close association between the c-fos transcripts and the nuclear speckles. This study demonstrates a direct link between specific nascent RNA transcripts and nuclear speckles that are enriched in pre-mRNA splicing factors.
RLID00003548	14281	Fos	http://www.ncbi.nlm.nih.gov/gene/?term=14281	"D12Rfj1, c-fos, cFos "	mRNA	Mus musculus	1748285	Nucleus	NIH-3T3 cell	In situ hybridization|Electron microscopy	"By using high-voltage electron microscopy, we have found that the c-fos path extends out and comes into direct contact with the nuclear envelope. "
RLID00003549	142940	TRUB1	http://www.ncbi.nlm.nih.gov/gene/?term=142940	PUS4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003550	142940	TRUB1	http://www.ncbi.nlm.nih.gov/gene/?term=142940	PUS4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003551	14297	Fxn	http://www.ncbi.nlm.nih.gov/gene/?term=14297	"FA, FARR, Frda, X25 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003552	1429	CRYZ	http://www.ncbi.nlm.nih.gov/gene/?term=1429		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003553	1429	CRYZ	http://www.ncbi.nlm.nih.gov/gene/?term=1429		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003554	1429	CRYZ	http://www.ncbi.nlm.nih.gov/gene/?term=1429		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003555	142	PARP1	http://www.ncbi.nlm.nih.gov/gene/?term=142	"ADPRT, ADPRT 1, ADPRT1, ARTD1, PARP, PARP-1, PPOL, pADPRT-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003556	14302	Frk	http://www.ncbi.nlm.nih.gov/gene/?term=14302	"BSK, BSK/IYK, C85044, GTK, RAK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003557	14313	Fst	http://www.ncbi.nlm.nih.gov/gene/?term=14313	"AL033346, FS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003558	14314	Fstl1	http://www.ncbi.nlm.nih.gov/gene/?term=14314	"AI316791, AW107808, Fstl, TSC-36 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003559	14314	Fstl1	http://www.ncbi.nlm.nih.gov/gene/?term=14314	"AI316791, AW107808, Fstl, TSC-36 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00003560	143187	VTI1A	http://www.ncbi.nlm.nih.gov/gene/?term=143187	"MMDS3, MVti1, VTI1RP2, Vti1-rp2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003561	1431	CS	http://www.ncbi.nlm.nih.gov/gene/?term=1431		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003562	143244	EIF5AL1	http://www.ncbi.nlm.nih.gov/gene/?term=143244	"EIF5AP1, bA342M3.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003563	143244	EIF5AL1	http://www.ncbi.nlm.nih.gov/gene/?term=143244	"EIF5AP1, bA342M3.3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003564	143244	EIF5AL1	http://www.ncbi.nlm.nih.gov/gene/?term=143244	"EIF5AP1, bA342M3.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003565	14325	Ftl1	http://www.ncbi.nlm.nih.gov/gene/?term=14325	"Ftl, Ftl-1, L-ferritin "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003566	143279	HECTD2	http://www.ncbi.nlm.nih.gov/gene/?term=143279		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003567	143279	HECTD2	http://www.ncbi.nlm.nih.gov/gene/?term=143279		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003568	143279	HECTD2	http://www.ncbi.nlm.nih.gov/gene/?term=143279		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003569	1432	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=1432	"CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2, PRKM14, PRKM15, RK, SAPK2A, p38, p38ALPHA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003570	1432	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=1432	"CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2, PRKM14, PRKM15, RK, SAPK2A, p38, p38ALPHA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003571	1432	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=1432	"CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2, PRKM14, PRKM15, RK, SAPK2A, p38, p38ALPHA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003572	1432	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=1432	"CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2, PRKM14, PRKM15, RK, SAPK2A, p38, p38ALPHA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003573	143379	C10orf82	http://www.ncbi.nlm.nih.gov/gene/?term=143379		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003574	143384	CACUL1	http://www.ncbi.nlm.nih.gov/gene/?term=143384	"C10orf46, CAC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003575	143384	CACUL1	http://www.ncbi.nlm.nih.gov/gene/?term=143384	"C10orf46, CAC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003576	143384	CACUL1	http://www.ncbi.nlm.nih.gov/gene/?term=143384	"C10orf46, CAC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003577	143384	CACUL1	http://www.ncbi.nlm.nih.gov/gene/?term=143384	"C10orf46, CAC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003578	14345	Fut4	http://www.ncbi.nlm.nih.gov/gene/?term=14345	"AI451562, CD15, FAL, FucT-IV, LeX, SSEA-1, Ssea1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003579	14349	Fv1	http://www.ncbi.nlm.nih.gov/gene/?term=14349	"Fv-1, Rv-1, Rv1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003580	1434	CSE1L	http://www.ncbi.nlm.nih.gov/gene/?term=1434	"CAS, CSE1, XPO2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003581	1434	CSE1L	http://www.ncbi.nlm.nih.gov/gene/?term=1434	"CAS, CSE1, XPO2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003582	1434	CSE1L	http://www.ncbi.nlm.nih.gov/gene/?term=1434	"CAS, CSE1, XPO2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003583	143570	XRRA1	http://www.ncbi.nlm.nih.gov/gene/?term=143570		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003584	14359	Fxr1	http://www.ncbi.nlm.nih.gov/gene/?term=14359	"1110050J02Rik, 9530073J07Rik, AI851072h, Fxr1p, Fxr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003585	14365	Fzd3	http://www.ncbi.nlm.nih.gov/gene/?term=14365	"AU020229, D930050A07Rik, Fz3 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003586	14365	Fzd3	http://www.ncbi.nlm.nih.gov/gene/?term=14365	"AU020229, D930050A07Rik, Fz3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003587	143662	MUC15	http://www.ncbi.nlm.nih.gov/gene/?term=143662	"MUC-15, PAS3, PASIII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003588	143684	FAM76B	http://www.ncbi.nlm.nih.gov/gene/?term=143684		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003589	1436	CSF1R	http://www.ncbi.nlm.nih.gov/gene/?term=1436	"C-FMS, CD115, CSF-1R, CSFR, FIM2, FMS, HDLS, M-CSF-R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003590	14375	Xrcc6	http://www.ncbi.nlm.nih.gov/gene/?term=14375	"70kDa, G22p1, Ku70 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003591	14376	Ganab	http://www.ncbi.nlm.nih.gov/gene/?term=14376	"AU042638, G2an, GluII, mKIAA0088 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003592	143872	ARHGAP42	http://www.ncbi.nlm.nih.gov/gene/?term=143872	GRAF3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003593	143884	CWF19L2	http://www.ncbi.nlm.nih.gov/gene/?term=143884		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003594	143888	KDELC2	http://www.ncbi.nlm.nih.gov/gene/?term=143888		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003595	14389	Gab2	http://www.ncbi.nlm.nih.gov/gene/?term=14389	"AI463667, D130058I17Rik, p97 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00003596	14390	Gabpa	http://www.ncbi.nlm.nih.gov/gene/?term=14390	GABPalpha	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003597	1439	CSF2RB	http://www.ncbi.nlm.nih.gov/gene/?term=1439	"CD131, CDw131, IL3RB, IL5RB, SMDP5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003598	143	PARP4	http://www.ncbi.nlm.nih.gov/gene/?term=143	"ADPRTL1, ARTD4, PARP-4, PARPL, PH5P, VAULT3, VPARP, VWA5C, p193 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003599	143	PARP4	http://www.ncbi.nlm.nih.gov/gene/?term=143	"ADPRTL1, ARTD4, PARP-4, PARPL, PH5P, VAULT3, VPARP, VWA5C, p193 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003600	143	PARP4	http://www.ncbi.nlm.nih.gov/gene/?term=143	"ADPRTL1, ARTD4, PARP-4, PARPL, PH5P, VAULT3, VPARP, VWA5C, p193 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003601	14402	Gabrb3	http://www.ncbi.nlm.nih.gov/gene/?term=14402	"A230092K12Rik, AW049585, Cp1, Gabrb-3, beta3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003602	144097	C11orf84	http://www.ncbi.nlm.nih.gov/gene/?term=144097		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003603	144108	SPTY2D1	http://www.ncbi.nlm.nih.gov/gene/?term=144108	Spt2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003604	144110	TMEM86A	http://www.ncbi.nlm.nih.gov/gene/?term=144110		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003605	144165	PRICKLE1	http://www.ncbi.nlm.nih.gov/gene/?term=144165	"EPM1B, RILP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003606	144193	AMDHD1	http://www.ncbi.nlm.nih.gov/gene/?term=144193	HMFT1272	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003607	1441	CSF3R	http://www.ncbi.nlm.nih.gov/gene/?term=1441	"CD114, GCSFR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003608	14420	Galc	http://www.ncbi.nlm.nih.gov/gene/?term=14420	"2310068B06Rik, A930008M05Rik, AW212969, AW413532, Gacy, twi, twitcher "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003609	144233	BCDIN3D	http://www.ncbi.nlm.nih.gov/gene/?term=144233		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003610	144233	BCDIN3D	http://www.ncbi.nlm.nih.gov/gene/?term=144233		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003611	144245	ALG10B	http://www.ncbi.nlm.nih.gov/gene/?term=144245	"ALG10, KCR1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003612	144245	ALG10B	http://www.ncbi.nlm.nih.gov/gene/?term=144245	"ALG10, KCR1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003613	14431	Gamt	http://www.ncbi.nlm.nih.gov/gene/?term=14431	"AA571402, Spintz1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003614	14432	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=14432	"B-50, Basp2, GAP-43 "	mRNA	Mus musculus	26512708	Axon	ForeBrain	Immunoprecipitation|RIP-Chip	The cis-element required for GAP-43 mRNA localization into PNS axons was mapped to the ARE/HuD binding site in its 3' UTR 
RLID00003615	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	16874305	Cytoplasm	Fibroblast	qRT-PCR|Northern blot	"Thus, an mRNA localized to the cytoplasm such as Gapdh shows no enrichment relative to CypA, and cytoplasmic and nuclear levels approximately equal 1 (Figure 6A). "
RLID00003616	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003617	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	12923260	Ribosome	B cell	Northern blot	"In this report, we use multiple cell fractionation protocols, in combination with cDNA microarray, nuclease protection, and Northern blot analyses, to assess the distribution of mRNAs between free and ER-bound ribosomes. We find a broad representation of mRNAs encoding soluble proteins in the ER fraction, with a subset of such mRNAs displaying substantial ER partitioning. In addition, we present evidence that membrane-bound ribosomes engage in the translation of mRNAs encoding soluble proteins. Single-cell in situ hybridization analysis of the subcellular distribution of mRNAs encoding ER-localized and soluble proteins identify two overall patterns of mRNA distribution in the cell-endoplasmic reticular and cytosolic. FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells.  "
RLID00003618	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00003619	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	26179904	Cytosol	Macrophage	qRT-PCR	"As expected, the mature IL-1a and Gapdh transcripts were localized to the cytosol, whereas 7SK RNA was confined to the nucleus. "
RLID00003620	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	For whole transcriptome profiling we used Gapdh for setting the number of PCR cycles for the amplification of somatodendritic and axonal RNA. In line with these qPCRs we detected Gapdh in both compartments of cultured motoneurons by FISH (Figure 7B). 
RLID00003621	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	26464439	Somatodendritic compartment	Motoneuron	In situ hybridization|qRT-PCR	For whole transcriptome profiling we used Gapdh for setting the number of PCR cycles for the amplification of somatodendritic and axonal RNA. In line with these qPCRs we detected Gapdh in both compartments of cultured motoneurons by FISH (Figure 7B). 
RLID00003622	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00003623	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	23898399	Cytoplasm	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00003624	14433	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=14433	Gapd	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00003625	144347	FAM101A	http://www.ncbi.nlm.nih.gov/gene/?term=144347	CFM2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003626	144348	ZNF664	http://www.ncbi.nlm.nih.gov/gene/?term=144348	"ZFOC1, ZNF176 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003627	144348	ZNF664	http://www.ncbi.nlm.nih.gov/gene/?term=144348	"ZFOC1, ZNF176 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003628	144348	ZNF664	http://www.ncbi.nlm.nih.gov/gene/?term=144348	"ZFOC1, ZNF176 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003629	144363	LYRM5	http://www.ncbi.nlm.nih.gov/gene/?term=144363		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003630	144402	CPNE8	http://www.ncbi.nlm.nih.gov/gene/?term=144402		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003631	144404	TMEM120B	http://www.ncbi.nlm.nih.gov/gene/?term=144404		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003632	144423	GLT1D1	http://www.ncbi.nlm.nih.gov/gene/?term=144423		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003633	14450	Gart	http://www.ncbi.nlm.nih.gov/gene/?term=14450	"Gaps, Prgs "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003634	1445	CSK	http://www.ncbi.nlm.nih.gov/gene/?term=1445		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003635	14460	Gata1	http://www.ncbi.nlm.nih.gov/gene/?term=14460	"Gata-1, Gf-1, eryf1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003636	14467	Gbas	http://www.ncbi.nlm.nih.gov/gene/?term=14467	"AV006093, Nipsnap2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003637	144699	FBXL14	http://www.ncbi.nlm.nih.gov/gene/?term=144699	Fbl14	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003638	144699	FBXL14	http://www.ncbi.nlm.nih.gov/gene/?term=144699	Fbl14	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003639	144717	FAM109A	http://www.ncbi.nlm.nih.gov/gene/?term=144717	"IPIP27A, SES1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003640	14479	Usp15	http://www.ncbi.nlm.nih.gov/gene/?term=14479	"4921514G19Rik, AI327321, E430033I05Rik, Gcap18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003641	144809	FAM216B	http://www.ncbi.nlm.nih.gov/gene/?term=144809	C13orf30	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003642	144983	HNRNPA1L2	http://www.ncbi.nlm.nih.gov/gene/?term=144983		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003643	145173	B3GLCT	http://www.ncbi.nlm.nih.gov/gene/?term=145173	"B3GALTL, B3GTL, B3Glc-T, Gal-T, beta3Glc-T "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003644	145173	B3GLCT	http://www.ncbi.nlm.nih.gov/gene/?term=145173	"B3GALTL, B3GTL, B3Glc-T, Gal-T, beta3Glc-T "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003645	145200	LINC00239	http://www.ncbi.nlm.nih.gov/gene/?term=145200	"C14orf72, NCRNA00239 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003646	1452	CSNK1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1452	"CK1, CK1a, CKIa, HEL-S-77p, HLCDGP1, PRO2975 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003647	1452	CSNK1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1452	"CK1, CK1a, CKIa, HEL-S-77p, HLCDGP1, PRO2975 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003648	1452	CSNK1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1452	"CK1, CK1a, CKIa, HEL-S-77p, HLCDGP1, PRO2975 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003649	145389	SLC38A6	http://www.ncbi.nlm.nih.gov/gene/?term=145389	"NAT-1, SNAT6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003650	1453	CSNK1D	http://www.ncbi.nlm.nih.gov/gene/?term=1453	"ASPS, CKIdelta, FASPS2, HCKID "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003651	145407	C14orf37	http://www.ncbi.nlm.nih.gov/gene/?term=145407	c14_5376	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003652	145447	ABHD12B	http://www.ncbi.nlm.nih.gov/gene/?term=145447	"BEM46L3, C14orf29, c14_5314 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003653	14545	Gdap1	http://www.ncbi.nlm.nih.gov/gene/?term=14545		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003654	1454	CSNK1E	http://www.ncbi.nlm.nih.gov/gene/?term=1454	"CKIepsilon, HCKIE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003655	1454	CSNK1E	http://www.ncbi.nlm.nih.gov/gene/?term=1454	"CKIepsilon, HCKIE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003656	14554	Gdap9	http://www.ncbi.nlm.nih.gov/gene/?term=14554		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003657	145567	TTC7B	http://www.ncbi.nlm.nih.gov/gene/?term=145567	"TTC7L1, c14_5685 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003658	1455	CSNK1G2	http://www.ncbi.nlm.nih.gov/gene/?term=1455	CK1g2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003659	1455	CSNK1G2	http://www.ncbi.nlm.nih.gov/gene/?term=1455	CK1g2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003660	1455	CSNK1G2	http://www.ncbi.nlm.nih.gov/gene/?term=1455	CK1g2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003661	1456	CSNK1G3	http://www.ncbi.nlm.nih.gov/gene/?term=1456	"CKI-gamma 3L, CSNK1G3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003662	1456	CSNK1G3	http://www.ncbi.nlm.nih.gov/gene/?term=1456	"CKI-gamma 3, CSNK1G3L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003663	14570	Arhgdig	http://www.ncbi.nlm.nih.gov/gene/?term=14570	"Gdi5, RIP2, Rho-GDI-3, Rho-GDI2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003664	14573	Gdnf	http://www.ncbi.nlm.nih.gov/gene/?term=14573	AI385739	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003665	145741	C2CD4A	http://www.ncbi.nlm.nih.gov/gene/?term=145741	"FAM148A, NLF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003666	145741	C2CD4A	http://www.ncbi.nlm.nih.gov/gene/?term=145741	"FAM148A, NLF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003667	145741	C2CD4A	http://www.ncbi.nlm.nih.gov/gene/?term=145741	"FAM148A, NLF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003668	145773	FAM81A	http://www.ncbi.nlm.nih.gov/gene/?term=145773		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003669	145781	GCOM1	http://www.ncbi.nlm.nih.gov/gene/?term=145781	"GRINL1A, Gcom2, MYZAP, MYZAP-POLR2M, gcom "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003670	145781	GCOM1	http://www.ncbi.nlm.nih.gov/gene/?term=145781	"GRINL1A, Gcom2, MYZAP, MYZAP-POLR2M, gcom "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003671	145781	GCOM1	http://www.ncbi.nlm.nih.gov/gene/?term=145781	"GRINL1A, Gcom2, MYZAP, MYZAP-POLR2M, gcom "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003672	1457	CSNK2A1	http://www.ncbi.nlm.nih.gov/gene/?term=1457	"CK2A1, CKII, CSNK2A3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003673	145853	C15orf61	http://www.ncbi.nlm.nih.gov/gene/?term=145853		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003674	145853	C15orf61	http://www.ncbi.nlm.nih.gov/gene/?term=145853		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003675	14593	Ggps1	http://www.ncbi.nlm.nih.gov/gene/?term=14593	"1810026C22Rik, 9530089B04Rik, AI843169, C79210 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003676	14593	Ggps1	http://www.ncbi.nlm.nih.gov/gene/?term=14593	"1810026C22Rik, 9530089B04Rik, AI843169, C79210 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003677	14593	Ggps1	http://www.ncbi.nlm.nih.gov/gene/?term=14593	"1810026C22Rik, 9530089B04Rik, AI843169, C79210 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003678	14599	Gh	http://www.ncbi.nlm.nih.gov/gene/?term=14599	"Gh1b1, Gh "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003679	1459	CSNK2A2	http://www.ncbi.nlm.nih.gov/gene/?term=1459	"CK2A2, CK2alpha', CSNK2A1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003680	1459	CSNK2A2	http://www.ncbi.nlm.nih.gov/gene/?term=1459	"CK2A2, CK2alpha', CSNK2A1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003681	14600	Ghr	http://www.ncbi.nlm.nih.gov/gene/?term=14600	"GHBP, GHR/BP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003682	14603	Gif	http://www.ncbi.nlm.nih.gov/gene/?term=14603	AV073125	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003683	146050	ZSCAN29	http://www.ncbi.nlm.nih.gov/gene/?term=146050	"ZNF690, Zfp690 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003684	146050	ZSCAN29	http://www.ncbi.nlm.nih.gov/gene/?term=146050	"ZNF690, Zfp690 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003685	146050	ZSCAN29	http://www.ncbi.nlm.nih.gov/gene/?term=146050	"ZNF690, Zfp690 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003686	1460	CSNK2B	http://www.ncbi.nlm.nih.gov/gene/?term=1460	"CK2B, CK2N, CSK2B, G5A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003687	1460	CSNK2B	http://www.ncbi.nlm.nih.gov/gene/?term=1460	"CK2B, CK2N, CSK2B, G5A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003688	1460	CSNK2B	http://www.ncbi.nlm.nih.gov/gene/?term=1460	"CK2B, CK2N, CSK2B, G5A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003689	14615	Gjc1	http://www.ncbi.nlm.nih.gov/gene/?term=14615	"C130009G16Rik, Cnx45, Cx45, Gja-7, Gja7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003690	146177	VWA3A	http://www.ncbi.nlm.nih.gov/gene/?term=146177		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003691	146198	ZFP90	http://www.ncbi.nlm.nih.gov/gene/?term=146198	"FIK, NK10, ZNF756, zfp-90 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003692	146223	CMTM4	http://www.ncbi.nlm.nih.gov/gene/?term=146223	CKLFSF4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003693	14625	Gykl1	http://www.ncbi.nlm.nih.gov/gene/?term=14625	"AI449806, Gk-rs1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003694	14629	Gclc	http://www.ncbi.nlm.nih.gov/gene/?term=14629	"D9Wsu168e, GLCL-H, Ggcs-hs, Glclc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003695	1462	VCAN	http://www.ncbi.nlm.nih.gov/gene/?term=1462	"CSPG2, ERVR, GHAP, PG-M, WGN, WGN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003696	1462	VCAN	http://www.ncbi.nlm.nih.gov/gene/?term=1462	"CSPG2, ERVR, GHAP, PG-M, WGN, WGN1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003697	146330	FBXL16	http://www.ncbi.nlm.nih.gov/gene/?term=146330	"C16orf22, Fbl16, c380A1.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003698	14634	Gli3	http://www.ncbi.nlm.nih.gov/gene/?term=14634	"AI854843, AU023367, Bph, GLI3-190, GLI3FL, Pdn, Xt, add "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003699	146439	BICDL2	http://www.ncbi.nlm.nih.gov/gene/?term=146439	BICDR-2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003700	14645	Glul	http://www.ncbi.nlm.nih.gov/gene/?term=14645	"GS, Glns "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003701	1464	CSPG4	http://www.ncbi.nlm.nih.gov/gene/?term=1464	"HMW-MAA, MCSP, MCSPG, MEL-CSPG, MSK16, NG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003702	14651	Hagh	http://www.ncbi.nlm.nih.gov/gene/?term=14651	"BC019817, Glo-2, Glo2, Rsp29 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003703	146540	ZNF785	http://www.ncbi.nlm.nih.gov/gene/?term=146540		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003704	146540	ZNF785	http://www.ncbi.nlm.nih.gov/gene/?term=146540		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003705	146542	ZNF688	http://www.ncbi.nlm.nih.gov/gene/?term=146542		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003706	146556	C16orf89	http://www.ncbi.nlm.nih.gov/gene/?term=146556		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003707	146556	C16orf89	http://www.ncbi.nlm.nih.gov/gene/?term=146556		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003708	14658	Glrb	http://www.ncbi.nlm.nih.gov/gene/?term=14658	"AI853901, Glyrb, spa, spastic "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003709	1465	CSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=1465	"CRP, CRP1, CSRP, CYRP, D1S181E, HEL-141, HEL-S-286 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003710	14661	Glud1	http://www.ncbi.nlm.nih.gov/gene/?term=14661	"AI118167, Gdh-X, Glud, Gludl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003711	1466	CSRP2	http://www.ncbi.nlm.nih.gov/gene/?term=1466	"CRP2, LMO5, SmLIM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003712	14674	Gna13	http://www.ncbi.nlm.nih.gov/gene/?term=14674	"AU024132, AU043124, Galpha13 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003713	14674	Gna13	http://www.ncbi.nlm.nih.gov/gene/?term=14674	"AU024132, AU043124, Galpha13 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003714	14678	Gnai2	http://www.ncbi.nlm.nih.gov/gene/?term=14678	"C76432, Galphai2, Gia, Gnai-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003715	14679	Gnai3	http://www.ncbi.nlm.nih.gov/gene/?term=14679	"AI158965, AW537698, Galphai3, Gnai-3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003716	14681	Gnao1	http://www.ncbi.nlm.nih.gov/gene/?term=14681	"AW050213, Galphao, Gnao, alphaO "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003717	146862	UNC45B	http://www.ncbi.nlm.nih.gov/gene/?term=146862	"CMYA4, CTRCT43, SMUNC45, UNC-45B, UNC45 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003718	146862	UNC45B	http://www.ncbi.nlm.nih.gov/gene/?term=146862	"CMYA4, CTRCT43, SMUNC45, UNC-45B, UNC45 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003719	14688	Gnb1	http://www.ncbi.nlm.nih.gov/gene/?term=14688	"AA409223, C77571, Gnb-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003720	146894	CD300LG	http://www.ncbi.nlm.nih.gov/gene/?term=146894	"CLM-9, CLM9, NEPMUCIN, TREM-4, TREM4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003721	146894	CD300LG	http://www.ncbi.nlm.nih.gov/gene/?term=146894	"CLM-9, CLM9, NEPMUCIN, TREM-4, TREM4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003722	1468	SLC25A10	http://www.ncbi.nlm.nih.gov/gene/?term=1468	DIC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003723	147007	TMEM199	http://www.ncbi.nlm.nih.gov/gene/?term=147007	"C17orf32, CDG2P, VMA12, VPH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003724	147007	TMEM199	http://www.ncbi.nlm.nih.gov/gene/?term=147007	"C17orf32, VMA12, VPH2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003725	147015	DHRS13	http://www.ncbi.nlm.nih.gov/gene/?term=147015	SDR7C5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003726	147015	DHRS13	http://www.ncbi.nlm.nih.gov/gene/?term=147015	SDR7C5	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003727	14704	Gng3	http://www.ncbi.nlm.nih.gov/gene/?term=14704		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003728	14705	Bscl2	http://www.ncbi.nlm.nih.gov/gene/?term=14705	"2900097C17Rik, AI046355, Gng3lg "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003729	14707	Gng5	http://www.ncbi.nlm.nih.gov/gene/?term=14707	G(y)5	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003730	14710	Gngt2	http://www.ncbi.nlm.nih.gov/gene/?term=14710	AV096488	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003731	147111	NOTUM	http://www.ncbi.nlm.nih.gov/gene/?term=147111	hNOTUM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003732	147166	TRIM16L	http://www.ncbi.nlm.nih.gov/gene/?term=147166	TRIM70	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003733	147166	TRIM16L	http://www.ncbi.nlm.nih.gov/gene/?term=147166	TRIM70	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003734	147179	WIPF2	http://www.ncbi.nlm.nih.gov/gene/?term=147179	"WICH, WIRE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003735	147179	WIPF2	http://www.ncbi.nlm.nih.gov/gene/?term=147179	"WICH, WIRE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003736	147179	WIPF2	http://www.ncbi.nlm.nih.gov/gene/?term=147179	"WICH, WIRE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003737	147184	TMEM99	http://www.ncbi.nlm.nih.gov/gene/?term=147184		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003738	147184	TMEM99	http://www.ncbi.nlm.nih.gov/gene/?term=147184		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003739	1471	CST3	http://www.ncbi.nlm.nih.gov/gene/?term=1471	"ARMD11, HEL-S-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003740	1471	CST3	http://www.ncbi.nlm.nih.gov/gene/?term=1471	"ARMD11, HEL-S-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003741	147339	C18orf25	http://www.ncbi.nlm.nih.gov/gene/?term=147339	"ARKL1, RNF111L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003742	147339	C18orf25	http://www.ncbi.nlm.nih.gov/gene/?term=147339	"ARKL1, RNF111L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003743	14735	Gpc4	http://www.ncbi.nlm.nih.gov/gene/?term=14735	"9530073D23Rik, AF311610, AI385680, AI661372, K-glypican "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003744	147381	CBLN2	http://www.ncbi.nlm.nih.gov/gene/?term=147381		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003745	14745	Lpar1	http://www.ncbi.nlm.nih.gov/gene/?term=14745	"AI326300, Edg2, Gpcr26, Kdt2, lpA1, vzg-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003746	147495	APCDD1	http://www.ncbi.nlm.nih.gov/gene/?term=147495	"B7323, DRAPC1, FP7019, HHS, HTS, HYPT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003747	1474	CST6	http://www.ncbi.nlm.nih.gov/gene/?term=1474		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003748	14751	Gpi1	http://www.ncbi.nlm.nih.gov/gene/?term=14751	"Amf, Gpi, Gpi-1, Gpi-1r, Gpi-1s, Gpi-1t-r, Gpi1-s, Gpi1-t, Gpi1s, MF, NK, NK/GPI, Nlk, Org, Pgi, Phi, Gpi1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003749	14756	Gpld1	http://www.ncbi.nlm.nih.gov/gene/?term=14756	"6330541J12Rik, AW546131 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003750	14758	Gpm6b	http://www.ncbi.nlm.nih.gov/gene/?term=14758	"AI593561, Gpm6, M6B "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003751	147657	ZNF480	http://www.ncbi.nlm.nih.gov/gene/?term=147657		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003752	147660	ZNF578	http://www.ncbi.nlm.nih.gov/gene/?term=147660		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003753	147687	ZNF417	http://www.ncbi.nlm.nih.gov/gene/?term=147687		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003754	147687	ZNF417	http://www.ncbi.nlm.nih.gov/gene/?term=147687		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003755	147694	ZNF548	http://www.ncbi.nlm.nih.gov/gene/?term=147694		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003756	147694	ZNF548	http://www.ncbi.nlm.nih.gov/gene/?term=147694		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003757	1476	CSTB	http://www.ncbi.nlm.nih.gov/gene/?term=1476	"CST6, EPM1, EPM1A, PME, STFB, ULD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003758	1476	CSTB	http://www.ncbi.nlm.nih.gov/gene/?term=1476	"CST6, EPM1, EPM1A, PME, STFB, ULD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003759	1476	CSTB	http://www.ncbi.nlm.nih.gov/gene/?term=1476	"CST6, EPM1, EPM1A, PME, STFB, ULD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003760	147727	ILF3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=147727		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003761	14773	Grk5	http://www.ncbi.nlm.nih.gov/gene/?term=14773	Gprk5	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003762	1477	CSTF1	http://www.ncbi.nlm.nih.gov/gene/?term=1477	"CstF-50, CstFp50 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003763	1477	CSTF1	http://www.ncbi.nlm.nih.gov/gene/?term=1477	"CstF-50, CstFp50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003764	147841	SPC24	http://www.ncbi.nlm.nih.gov/gene/?term=147841	SPBC24	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003765	14789	P3h3	http://www.ncbi.nlm.nih.gov/gene/?term=14789	"BC016431, Grcb, Leprel2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003766	1478	CSTF2	http://www.ncbi.nlm.nih.gov/gene/?term=1478	CstF-64	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003767	1478	CSTF2	http://www.ncbi.nlm.nih.gov/gene/?term=1478	CstF-64	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003768	147920	IGFL2	http://www.ncbi.nlm.nih.gov/gene/?term=147920	"UNQ645, VPRI645 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003769	147920	IGFL2	http://www.ncbi.nlm.nih.gov/gene/?term=147920	"UNQ645, VPRI645 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003770	14794	Spsb2	http://www.ncbi.nlm.nih.gov/gene/?term=14794	"AI461677, C9, Grcc9, SSB2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003771	147965	FAM98C	http://www.ncbi.nlm.nih.gov/gene/?term=147965		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003772	147968	CAPN12	http://www.ncbi.nlm.nih.gov/gene/?term=147968		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003773	14797	Aes	http://www.ncbi.nlm.nih.gov/gene/?term=14797	"AL024115, Esp1, Grg, Grg-5, Grg5, Tle5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003774	1479	CSTF3	http://www.ncbi.nlm.nih.gov/gene/?term=1479	CSTF-77	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003775	14805	Grik1	http://www.ncbi.nlm.nih.gov/gene/?term=14805	"A830007B11Rik, D16Ium24, D16Ium24e, GluK1, GluK5, Glur-5, Glur5, Glurbeta1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003776	148103	ZNF599	http://www.ncbi.nlm.nih.gov/gene/?term=148103		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003777	14810	Grin1	http://www.ncbi.nlm.nih.gov/gene/?term=14810	"GluN1, GluRdelta1, GluRzeta1, M100174, NMD-R1, NMDAR1, NR1, Nmdar, Rgsc174 "	mRNA	Mus musculus	12853299	Endoplasmic reticulum	Cortical neuron	-	"Subcellular fractionation studies show that all detectable NR1 mRNA is associated with rough endoplasmic reticulum, indicating that subcellular distribution of NR1 mRNA in fetal cortical neurons does not play a role in ethanol-mediated NR1 mRNA stabilization. "
RLID00003778	148156	ZNF558	http://www.ncbi.nlm.nih.gov/gene/?term=148156		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003779	14815	Nr3c1	http://www.ncbi.nlm.nih.gov/gene/?term=14815	"GR, Grl-1, Grl1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003780	148170	CDC42EP5	http://www.ncbi.nlm.nih.gov/gene/?term=148170	"Borg3, CEP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003781	148206	ZNF714	http://www.ncbi.nlm.nih.gov/gene/?term=148206		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003782	148206	ZNF714	http://www.ncbi.nlm.nih.gov/gene/?term=148206		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003783	148206	ZNF714	http://www.ncbi.nlm.nih.gov/gene/?term=148206		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003784	148213	ZNF681	http://www.ncbi.nlm.nih.gov/gene/?term=148213		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003785	148213	ZNF681	http://www.ncbi.nlm.nih.gov/gene/?term=148213		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003786	148223	C19orf25	http://www.ncbi.nlm.nih.gov/gene/?term=148223		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003787	148254	ZNF555	http://www.ncbi.nlm.nih.gov/gene/?term=148254		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003788	14825	Cxcl1	http://www.ncbi.nlm.nih.gov/gene/?term=14825	"Fsp, Gro1, KC, Mgsa, N51, Scyb1, gro "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003789	14825	Cxcl1	http://www.ncbi.nlm.nih.gov/gene/?term=14825	"Fsp, Gro1, KC, Mgsa, N51, Scyb1, gro "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003790	14827	Pdia3	http://www.ncbi.nlm.nih.gov/gene/?term=14827	"58kDa, ERp57, ERp60, ERp61, Erp, Grp58, PDI, PDI-Q2, PI-PLC, PLC[a], Plca "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003791	148281	SYT6	http://www.ncbi.nlm.nih.gov/gene/?term=148281	sytVI	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00003792	148281	SYT6	http://www.ncbi.nlm.nih.gov/gene/?term=148281	sytVI	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003793	14828	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=14828	"AL022860, AU019543, Bip, D2Wsu141e, D2Wsu17e, Grp78, Hsce70, SEZ-7, Sez7, baffled, mBiP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003794	14828	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=14828	"AL022860, AU019543, Bip, D2Wsu141e, D2Wsu17e, Grp78, Hsce70, SEZ-7, Sez7, baffled, mBiP "	mRNA	Mus musculus	12923260	Endoplasmic reticulum	B cell	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00003795	14828	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=14828	"AL022860, AU019543, Bip, D2Wsu141e, D2Wsu17e, Grp78, Hsce70, SEZ-7, Sez7, baffled, mBiP "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. mRNAs for resident proteins of the ER lumen, including BiP, calreticulin, and GRP94, were also highly enriched on membrane-bound polysomes. "
RLID00003796	14828	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=14828	"Bip, Sez7, mBiP, Grp78, SEZ-7, Hsce70, baffled, AL022860, AU019543, D2Wsu17e, D2Wsu141e "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00003797	148413	LOC148413	http://www.ncbi.nlm.nih.gov/gene/?term=148413		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003798	14852	Gspt1	http://www.ncbi.nlm.nih.gov/gene/?term=14852	"AI314175, AI326449, AV307676, C79774, G1st, Gst-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003799	148534	TMEM56	http://www.ncbi.nlm.nih.gov/gene/?term=148534		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003800	14854	Gss	http://www.ncbi.nlm.nih.gov/gene/?term=14854	"AI314904, GS-A/GS-B, GSH-S "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003801	14862	Gstm1	http://www.ncbi.nlm.nih.gov/gene/?term=14862	"Gstb-1, Gstb1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003802	1486	CTBS	http://www.ncbi.nlm.nih.gov/gene/?term=1486	CTB	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003803	1486	CTBS	http://www.ncbi.nlm.nih.gov/gene/?term=1486	CTB	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003804	1486	CTBS	http://www.ncbi.nlm.nih.gov/gene/?term=1486	CTB	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003805	1487364	BICP0	http://www.ncbi.nlm.nih.gov/gene/?term=1487364	BoHV1_gp35	mRNA	Bovine herpesvirus 1	25529439	Cytoplasm	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00003806	1487364	BICP0	http://www.ncbi.nlm.nih.gov/gene/?term=1487364	BoHV1_gp35	mRNA	Bovine herpesvirus 1	25529439	Nucleus	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00003807	148738	HFE2	http://www.ncbi.nlm.nih.gov/gene/?term=148738	"HFE2A, HJV, JH, RGMC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003808	14873	Gsto1	http://www.ncbi.nlm.nih.gov/gene/?term=14873	"AA407097, AI194287, AU018802, Gsto-1, Gstx, Spg-r, p28 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003809	148789	B3GALNT2	http://www.ncbi.nlm.nih.gov/gene/?term=148789	"B3GalNAc-T2, MDDGA11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003810	1487	CTBP1	http://www.ncbi.nlm.nih.gov/gene/?term=1487	BARS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003811	1487	CTBP1	http://www.ncbi.nlm.nih.gov/gene/?term=1487	BARS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003812	1487	CTBP1	http://www.ncbi.nlm.nih.gov/gene/?term=1487	BARS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003813	148808	MFSD4A	http://www.ncbi.nlm.nih.gov/gene/?term=148808	"MFSD4, UNQ3064 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003814	148808	MFSD4A	http://www.ncbi.nlm.nih.gov/gene/?term=148808	"MFSD4, UNQ3064 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003815	14884	Gtf2h1	http://www.ncbi.nlm.nih.gov/gene/?term=14884	"62kDa, AW743425, AW822074, BTF2 p62, C77871, p62 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003816	14885	Gtf2h4	http://www.ncbi.nlm.nih.gov/gene/?term=14885	"AW545633, BTF2 p52, p52 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003817	148867	SLC30A7	http://www.ncbi.nlm.nih.gov/gene/?term=148867	"ZNT7, ZnT-7, ZnTL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003818	148867	SLC30A7	http://www.ncbi.nlm.nih.gov/gene/?term=148867	"ZNT7, ZnT-7, ZnTL2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003819	148867	SLC30A7	http://www.ncbi.nlm.nih.gov/gene/?term=148867	"ZNT7, ZnT-7, ZnTL2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003820	148867	SLC30A7	http://www.ncbi.nlm.nih.gov/gene/?term=148867	"ZNT7, ZnT-7, ZnTL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003821	148898	ZNF436-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=148898	C1orf213	lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00003822	1488	CTBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1488		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003823	148932	MOB3C	http://www.ncbi.nlm.nih.gov/gene/?term=148932	"MOB1E, MOBKL2C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003824	148979	GLIS1	http://www.ncbi.nlm.nih.gov/gene/?term=148979		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003825	1489	CTF1	http://www.ncbi.nlm.nih.gov/gene/?term=1489	"CT-1, CT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003826	148	ADRA1A	http://www.ncbi.nlm.nih.gov/gene/?term=148	"ADRA1C, ADRA1L1, ALPHA1AAR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003827	148	ADRA1A	http://www.ncbi.nlm.nih.gov/gene/?term=148	"ADRA1C, ADRA1L1, ALPHA1AAR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003828	149041	RC3H1	http://www.ncbi.nlm.nih.gov/gene/?term=149041	"RNF198, ROQUIN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003829	149041	RC3H1	http://www.ncbi.nlm.nih.gov/gene/?term=149041	"RNF198, ROQUIN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003830	1490	CTGF	http://www.ncbi.nlm.nih.gov/gene/?term=1490	"CCN2, HCS24, IGFBP8, NOV2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003831	14910	Gt(ROSA)26Sor	http://www.ncbi.nlm.nih.gov/gene/?term=14910	"AV258896, Gtrgeo26, Gtrosa26, R26, ROSA26, Thumpd3as1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003832	14913	Guca1a	http://www.ncbi.nlm.nih.gov/gene/?term=14913	"GC-A, Gcap1, Guca1, mGCAP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003833	149175	MANEAL	http://www.ncbi.nlm.nih.gov/gene/?term=149175		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003834	149175	MANEAL	http://www.ncbi.nlm.nih.gov/gene/?term=149175		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003835	149175	MANEAL	http://www.ncbi.nlm.nih.gov/gene/?term=149175		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003836	149175	MANEAL	http://www.ncbi.nlm.nih.gov/gene/?term=149175		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003837	1491	CTH	http://www.ncbi.nlm.nih.gov/gene/?term=1491		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003838	14924	Magi1	http://www.ncbi.nlm.nih.gov/gene/?term=14924	"AIP3, BAP1, Baiap1, Gukmi1, MAGI1c, Magi-1, TNRC19, WWP3, mKIAA4129 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003839	149345	SHISA4	http://www.ncbi.nlm.nih.gov/gene/?term=149345	"C1orf40, TMEM58 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003840	14936	Gys1	http://www.ncbi.nlm.nih.gov/gene/?term=14936	"Gys3, MGS "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003841	149371	EXOC8	http://www.ncbi.nlm.nih.gov/gene/?term=149371	"EXO84, Exo84p, SEC84 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003842	149371	EXOC8	http://www.ncbi.nlm.nih.gov/gene/?term=149371	"EXO84, Exo84p, SEC84 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003843	149428	BNIPL	http://www.ncbi.nlm.nih.gov/gene/?term=149428	"BNIP-S-1, BNIPL-2, BNIPL1, BNIPL2, BNIPS, PP753, BNIPL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003844	149428	BNIPL	http://www.ncbi.nlm.nih.gov/gene/?term=149428	"BNIP-S-1, BNIPL-2, BNIPL1, BNIPL2, BNIPS, PP753, BNIPL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003845	149466	C1orf210	http://www.ncbi.nlm.nih.gov/gene/?term=149466	TEMP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003846	149466	C1orf210	http://www.ncbi.nlm.nih.gov/gene/?term=149466	TEMP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003847	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	16874305	Cytoplasm	Fibroblast	qRT-PCR|Northern blot	"The imprinted H19 ncRNA shows a mean nuclear/cytoplasmic ratio of 1.0:1, confirming a previous report that it is exported to the cytoplasm (Brannan et al, 1990) (Figure 6A). "
RLID00003848	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/H19/
RLID00003849	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	17948025	Cytoplasm	Fibroblast	In situ hybridization|qRT-PCR	"We sought to determine the subcellular localization of the non-coding H19 ICR transcripts. We separated nuclear and cytoplasmic RNA fractions from mouse embryonic fibroblasts. Igf2 and H19 gene transcripts were found both in the nucleus and in the cytoplasm, whereas the ncICR transcripts were almost exclusively detected in the nuclear fraction (Fig 1D), which is consistent with a function in gene expression. "
RLID00003850	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	22684254	Cytoplasm	Embryonic Fibroblast	qRT-PCR|Northern blot	"The H19 locus expresses high levels of a 2.5 kb RNA Polymerase II dependent transcript, which is spliced, capped, polyadenylated, and exported into the cytoplasm. "
RLID00003851	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	17948025	Nucleus	Fibroblast	In situ hybridization|qRT-PCR	"We sought to determine the subcellular localization of the non-coding H19 ICR transcripts. We separated nuclear and cytoplasmic RNA fractions from mouse embryonic fibroblasts. Igf2 and H19 gene transcripts were found both in the nucleus and in the cytoplasm, whereas the ncICR transcripts were almost exclusively detected in the nuclear fraction (Fig 1D), which is consistent with a function in gene expression. "
RLID00003852	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	10875929	Lamellipodium	NIH 3T3 cell	In situ hybridization	"The results show that the distribution of full-length H19 RNA is similar to that of IMP-1 (21) by being either evenly distributed in areas with confluent growth-arrested cells (88% of transfected cells) or, as illustrated in Fig.8 B, localized to the leading edge of lamellipodia and perinuclear regions in dispersed proliferating cells (42% of transfected cells). "
RLID00003853	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	10875929	Cell leading edge	NIH 3T3 cell	In situ hybridization	"The results show that the distribution of full-length H19 RNA is similar to that of IMP-1 (21) by being either evenly distributed in areas with confluent growth-arrested cells (88% of transfected cells) or, as illustrated in Fig.8 B, localized to the leading edge of lamellipodia and perinuclear regions in dispersed proliferating cells (42% of transfected cells). "
RLID00003854	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	10875929	Perinuclear	NIH 3T3 cell	In situ hybridization	"The results show that the distribution of full-length H19 RNA is similar to that of IMP-1 (21) by being either evenly distributed in areas with confluent growth-arrested cells (88% of transfected cells) or, as illustrated in Fig.8 B, localized to the leading edge of lamellipodia and perinuclear regions in dispersed proliferating cells (42% of transfected cells). "
RLID00003855	14955	H19	http://www.ncbi.nlm.nih.gov/gene/?term=14955	AI747191	lncRNA	Mus musculus	15094229	Cytoplasm	Hepatocyte	In situ hybridization	"Similar to albumin mRNA, H19 mRNA appeared to be localized mainly in the cytoplasm. "
RLID00003856	149563	C1orf64	http://www.ncbi.nlm.nih.gov/gene/?term=149563	ERRF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003857	1495	CTNNA1	http://www.ncbi.nlm.nih.gov/gene/?term=1495	"CAP102, MDPT2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003858	1495	CTNNA1	http://www.ncbi.nlm.nih.gov/gene/?term=1495	"CAP102, MDPT2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003859	1495	CTNNA1	http://www.ncbi.nlm.nih.gov/gene/?term=1495	CAP102	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003860	149603	RNF187	http://www.ncbi.nlm.nih.gov/gene/?term=149603	"RACO-1, RACO1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003861	149603	RNF187	http://www.ncbi.nlm.nih.gov/gene/?term=149603	"RACO-1, RACO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003862	1497	CTNS	http://www.ncbi.nlm.nih.gov/gene/?term=1497	"CTNS-LSB, PQLC4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003863	149840	C20orf196	http://www.ncbi.nlm.nih.gov/gene/?term=149840		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003864	149951	COMMD7	http://www.ncbi.nlm.nih.gov/gene/?term=149951	"C20orf92, dJ1085F17.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003865	149986	LSM14B	http://www.ncbi.nlm.nih.gov/gene/?term=149986	"C20orf40, FAM61B, FT005, LSM13, RAP55B, bA11M20.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003866	1499	CTNNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1499	"CTNNB, MRD19, armadillo "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003867	1499	CTNNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1499	"CTNNB, MRD19, armadillo "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00003868	1499	CTNNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1499	"CTNNB, MRD19, armadillo "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003869	1499	CTNNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1499	"CTNNB, MRD19, armadillo "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003870	1499	CTNNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1499	"CTNNB, MRD19, armadillo "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00003871	14	AAMP	http://www.ncbi.nlm.nih.gov/gene/?term=14		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003872	14	AAMP	http://www.ncbi.nlm.nih.gov/gene/?term=14		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003873	14	AAMP	http://www.ncbi.nlm.nih.gov/gene/?term=14		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003874	150094	SIK1	http://www.ncbi.nlm.nih.gov/gene/?term=150094	"EIEE30, MSK, SIK, SNF1LK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003875	1500	CTNND1	http://www.ncbi.nlm.nih.gov/gene/?term=1500	"CAS, CTNND, P120CAS, P120CTN, p120, p120(CAS), p120(CTN) "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003876	1500	CTNND1	http://www.ncbi.nlm.nih.gov/gene/?term=1500	"CAS, CTNND, P120CAS, P120CTN, p120, p120(CAS), p120(CTN) "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003877	1501	CTNND2	http://www.ncbi.nlm.nih.gov/gene/?term=1501	"GT24, NPRAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003878	150223	YDJC	http://www.ncbi.nlm.nih.gov/gene/?term=150223		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003879	150223	YDJC	http://www.ncbi.nlm.nih.gov/gene/?term=150223		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003880	150274	HSCB	http://www.ncbi.nlm.nih.gov/gene/?term=150274	"DNAJC20, HSC20, JAC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003881	150275	CCDC117	http://www.ncbi.nlm.nih.gov/gene/?term=150275	dJ366L4.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003882	150275	CCDC117	http://www.ncbi.nlm.nih.gov/gene/?term=150275	dJ366L4.1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003883	150275	CCDC117	http://www.ncbi.nlm.nih.gov/gene/?term=150275	dJ366L4.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003884	150356	CHADL	http://www.ncbi.nlm.nih.gov/gene/?term=150356	SLRR4B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003885	150383	CDPF1	http://www.ncbi.nlm.nih.gov/gene/?term=150383	C22orf40	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003886	150383	CDPF1	http://www.ncbi.nlm.nih.gov/gene/?term=150383	C22orf40	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003887	1503	CTPS1	http://www.ncbi.nlm.nih.gov/gene/?term=1503	"CTPS, IMD24 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003888	150465	TTL	http://www.ncbi.nlm.nih.gov/gene/?term=150465		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003889	15064	Mr1	http://www.ncbi.nlm.nih.gov/gene/?term=15064	H2ls	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003890	150678	MYEOV2	http://www.ncbi.nlm.nih.gov/gene/?term=150678		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003891	150684	COMMD1	http://www.ncbi.nlm.nih.gov/gene/?term=150684	"C2orf5, MURR1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003892	150684	COMMD1	http://www.ncbi.nlm.nih.gov/gene/?term=150684	"C2orf5, MURR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003893	150684	COMMD1	http://www.ncbi.nlm.nih.gov/gene/?term=150684	"C2orf5, MURR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003894	150696	PROM2	http://www.ncbi.nlm.nih.gov/gene/?term=150696	PROML2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003895	150696	PROM2	http://www.ncbi.nlm.nih.gov/gene/?term=150696	PROML2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003896	150696	PROM2	http://www.ncbi.nlm.nih.gov/gene/?term=150696	PROML2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003897	150763	GPAT2	http://www.ncbi.nlm.nih.gov/gene/?term=150763	CT123	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003898	150771	ITPRIPL1	http://www.ncbi.nlm.nih.gov/gene/?term=150771	KIAA1754L	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003899	15078	H3f3a	http://www.ncbi.nlm.nih.gov/gene/?term=15078	H3.3A	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003900	15081	H3f3b	http://www.ncbi.nlm.nih.gov/gene/?term=15081	"9430068D06Rik, H3.3B "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003901	150864	FAM117B	http://www.ncbi.nlm.nih.gov/gene/?term=150864	ALS2CR13	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003902	150864	FAM117B	http://www.ncbi.nlm.nih.gov/gene/?term=150864	ALS2CR13	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003903	1508	CTSB	http://www.ncbi.nlm.nih.gov/gene/?term=1508	"APPS, CPSB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003904	1508	CTSB	http://www.ncbi.nlm.nih.gov/gene/?term=1508	"APPS, CPSB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003905	1508	CTSB	http://www.ncbi.nlm.nih.gov/gene/?term=1508	"APPS, CPSB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003906	1508	CTSB	http://www.ncbi.nlm.nih.gov/gene/?term=1508	"APPS, CPSB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003907	150946	GAREM2	http://www.ncbi.nlm.nih.gov/gene/?term=150946	"FAM59B, GAREML "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00003908	150946	GAREM2	http://www.ncbi.nlm.nih.gov/gene/?term=150946	"FAM59B, GAREML "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003909	1509	CTSD	http://www.ncbi.nlm.nih.gov/gene/?term=1509	"CLN10, CPSD, HEL-S-130P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003910	1509	CTSD	http://www.ncbi.nlm.nih.gov/gene/?term=1509	"CLN10, CPSD, HEL-S-130P "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003911	1509	CTSD	http://www.ncbi.nlm.nih.gov/gene/?term=1509	"CLN10, CPSD, HEL-S-130P "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003912	151011	SEPT10	http://www.ncbi.nlm.nih.gov/gene/?term=151011		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003913	151050	KANSL1L	http://www.ncbi.nlm.nih.gov/gene/?term=151050	"C2orf67, MSL1v2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003914	15108	Hsd17b10	http://www.ncbi.nlm.nih.gov/gene/?term=15108	"17bHSD10, Ads9, ERAB, Hadh2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003915	1510	CTSE	http://www.ncbi.nlm.nih.gov/gene/?term=1510	CATE	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003916	15115	Hars	http://www.ncbi.nlm.nih.gov/gene/?term=15115	MMHRS	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003917	151176	FAM132B	http://www.ncbi.nlm.nih.gov/gene/?term=151176	"C1QTNF15, CTRP15 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003918	15117	Has2	http://www.ncbi.nlm.nih.gov/gene/?term=15117		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003919	151188	ARL6IP6	http://www.ncbi.nlm.nih.gov/gene/?term=151188	"AIP-6, AIP6, PFAAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003920	151188	ARL6IP6	http://www.ncbi.nlm.nih.gov/gene/?term=151188	"AIP-6, AIP6, PFAAP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003921	151194	METTL21A	http://www.ncbi.nlm.nih.gov/gene/?term=151194	"FAM119A, HCA557b, HSPA-KMT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003922	151195	CCNYL1	http://www.ncbi.nlm.nih.gov/gene/?term=151195		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003923	151230	KLHL23	http://www.ncbi.nlm.nih.gov/gene/?term=151230	DITHP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003924	151230	KLHL23	http://www.ncbi.nlm.nih.gov/gene/?term=151230	DITHP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003925	1512	CTSH	http://www.ncbi.nlm.nih.gov/gene/?term=1512	"ACC-4, ACC-5, ACC4, ACC5, CPSB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003926	1512	CTSH	http://www.ncbi.nlm.nih.gov/gene/?term=1512	"ACC-4, ACC-5, ACC4, ACC5, CPSB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003927	151354	FAM84A	http://www.ncbi.nlm.nih.gov/gene/?term=151354	"NSE1, PP11517 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003928	151393	RMDN2	http://www.ncbi.nlm.nih.gov/gene/?term=151393	"BLOCK18, FAM82A, FAM82A1, PRO34163, PYST9371, RMD-2, RMD2, RMD4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003929	1514	CTSL	http://www.ncbi.nlm.nih.gov/gene/?term=1514	"CATL1, MEP, CTSL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003930	1514	CTSL	http://www.ncbi.nlm.nih.gov/gene/?term=1514	"CATL, CTSL1, MEP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003931	151516	ASPRV1	http://www.ncbi.nlm.nih.gov/gene/?term=151516	"MUNO, SASP, SASPase, Taps "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003932	151531	UPP2	http://www.ncbi.nlm.nih.gov/gene/?term=151531	"UDRPASE2, UP2, UPASE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003933	15159	Hccs	http://www.ncbi.nlm.nih.gov/gene/?term=15159		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003934	151613	TTC14	http://www.ncbi.nlm.nih.gov/gene/?term=151613	"DRDL5813, PRO19630 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003935	151636	DTX3L	http://www.ncbi.nlm.nih.gov/gene/?term=151636	BBAP	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003936	151636	DTX3L	http://www.ncbi.nlm.nih.gov/gene/?term=151636	BBAP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003937	151636	DTX3L	http://www.ncbi.nlm.nih.gov/gene/?term=151636	BBAP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003938	151636	DTX3L	http://www.ncbi.nlm.nih.gov/gene/?term=151636	BBAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003939	15182	Hdac2	http://www.ncbi.nlm.nih.gov/gene/?term=15182	"D10Wsu179e, YAF1, Yy1bp, mRPD3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003940	15183	Hdac3	http://www.ncbi.nlm.nih.gov/gene/?term=15183	AW537363	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003941	151887	CCDC80	http://www.ncbi.nlm.nih.gov/gene/?term=151887	"DRO1, SSG1, URB, okuribin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003942	151903	CCDC12	http://www.ncbi.nlm.nih.gov/gene/?term=151903		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003943	151903	CCDC12	http://www.ncbi.nlm.nih.gov/gene/?term=151903		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003944	151987	PPP4R2	http://www.ncbi.nlm.nih.gov/gene/?term=151987	PP4R2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003945	15199	Hebp1	http://www.ncbi.nlm.nih.gov/gene/?term=15199	"Hebp, p22HBP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003946	1519	CTSO	http://www.ncbi.nlm.nih.gov/gene/?term=1519	CTSO1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003947	151	ADRA2B	http://www.ncbi.nlm.nih.gov/gene/?term=151	"ADRA2L1, ADRA2RL1, ADRARL1, ALPHA2BAR, FAME2, alpha-2BAR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003948	152002	XXYLT1	http://www.ncbi.nlm.nih.gov/gene/?term=152002	C3orf21	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003949	152006	RNF38	http://www.ncbi.nlm.nih.gov/gene/?term=152006		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003950	152007	GLIPR2	http://www.ncbi.nlm.nih.gov/gene/?term=152007	"C9orf19, GAPR-1, GAPR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003951	152007	GLIPR2	http://www.ncbi.nlm.nih.gov/gene/?term=152007	"C9orf19, GAPR-1, GAPR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003952	15201	Hells	http://www.ncbi.nlm.nih.gov/gene/?term=15201	"AI323785, E130115I21Rik, LSH, Lysh, PASG, YFK8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003953	15201	Hells	http://www.ncbi.nlm.nih.gov/gene/?term=15201	"AI323785, E130115I21Rik, LSH, Lysh, PASG, YFK8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003954	1520	CTSS	http://www.ncbi.nlm.nih.gov/gene/?term=1520		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003955	1520	CTSS	http://www.ncbi.nlm.nih.gov/gene/?term=1520		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003956	1520	CTSS	http://www.ncbi.nlm.nih.gov/gene/?term=1520		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003957	152100	CMC1	http://www.ncbi.nlm.nih.gov/gene/?term=152100	C3orf68	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003958	15212	Hexb	http://www.ncbi.nlm.nih.gov/gene/?term=15212		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00003959	152137	CCDC50	http://www.ncbi.nlm.nih.gov/gene/?term=152137	"C3orf6, DFNA44, YMER "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003960	152137	CCDC50	http://www.ncbi.nlm.nih.gov/gene/?term=152137	"C3orf6, DFNA44, YMER "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003961	152137	CCDC50	http://www.ncbi.nlm.nih.gov/gene/?term=152137	"C3orf6, DFNA44, YMER "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003962	152137	CCDC50	http://www.ncbi.nlm.nih.gov/gene/?term=152137	"C3orf6, DFNA44, YMER "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00003963	152137	CCDC50	http://www.ncbi.nlm.nih.gov/gene/?term=152137	"C3orf6, DFNA44, YMER "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003964	152195	NUDT16P1	http://www.ncbi.nlm.nih.gov/gene/?term=152195	NUDT16P	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003965	15220	Foxq1	http://www.ncbi.nlm.nih.gov/gene/?term=15220	"HFH-1, Hfh1, Hfh1l, sa "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003966	152217	NCBP2-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=152217		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003967	152273	FGD5	http://www.ncbi.nlm.nih.gov/gene/?term=152273	ZFYVE23	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003968	1522	CTSZ	http://www.ncbi.nlm.nih.gov/gene/?term=1522	CTSX	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003969	1522	CTSZ	http://www.ncbi.nlm.nih.gov/gene/?term=1522	CTSX	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003970	1522	CTSZ	http://www.ncbi.nlm.nih.gov/gene/?term=1522	CTSX	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003971	15235	Mst1	http://www.ncbi.nlm.nih.gov/gene/?term=15235	"D3F15S2h, D9H3F15S2, DNF15S2h, Hgfl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003972	1523	CUX1	http://www.ncbi.nlm.nih.gov/gene/?term=1523	"CASP, CDP, CDP/Cut, CDP1, COY1, CUTL1, CUX, Clox, Cux/CDP, GOLIM6, Nbla10317, p100, p110, p200, p75 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00003973	1523	CUX1	http://www.ncbi.nlm.nih.gov/gene/?term=1523	"CASP, CDP, CDP/Cut, CDP1, COY1, CUTL1, CUX, Clox, Cux/CDP, GOLIM6, Nbla10317, p100, p110, p200, p75 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003974	15247	Mfsd14a	http://www.ncbi.nlm.nih.gov/gene/?term=15247	Hiat1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003975	152519	NIPAL1	http://www.ncbi.nlm.nih.gov/gene/?term=152519	NPAL1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003976	15251	Hif1a	http://www.ncbi.nlm.nih.gov/gene/?term=15251	"AA959795, HIF-1-alpha, HIF1-alpha, HIF1alpha, MOP1, bHLHe78 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003977	15251	Hif1a	http://www.ncbi.nlm.nih.gov/gene/?term=15251	"AA959795, HIF-1-alpha, HIF1-alpha, HIF1alpha, MOP1, bHLHe78 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003978	152559	PAQR3	http://www.ncbi.nlm.nih.gov/gene/?term=152559	RKTG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003979	152579	SCFD2	http://www.ncbi.nlm.nih.gov/gene/?term=152579	STXBP1L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003980	15257	Hipk1	http://www.ncbi.nlm.nih.gov/gene/?term=15257	"1110062K04Rik, Myak "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003981	15257	Hipk1	http://www.ncbi.nlm.nih.gov/gene/?term=15257	"1110062K04Rik, Myak "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003982	15259	Hipk3	http://www.ncbi.nlm.nih.gov/gene/?term=15259	"DYRK6, FIST3, PKY, mir-1902 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003983	15259	Hipk3	http://www.ncbi.nlm.nih.gov/gene/?term=15259	"DYRK6, FIST3, PKY, mir-1902 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003984	1525	CXADR	http://www.ncbi.nlm.nih.gov/gene/?term=1525	"CAR, CAR4/6, HCAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003985	1525	CXADR	http://www.ncbi.nlm.nih.gov/gene/?term=1525	"CAR, CAR4/6, HCAR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003986	15277	Hk2	http://www.ncbi.nlm.nih.gov/gene/?term=15277	"AI642394, HKII "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003987	152815	THAP6	http://www.ncbi.nlm.nih.gov/gene/?term=152815		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003988	152831	KLB	http://www.ncbi.nlm.nih.gov/gene/?term=152831	BKL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003989	15284	Hlx	http://www.ncbi.nlm.nih.gov/gene/?term=15284	Hlx1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00003990	15289	Hmgb1	http://www.ncbi.nlm.nih.gov/gene/?term=15289	"HMG-1, Hmg1, SBP-1, p30 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00003991	15289	Hmgb1	http://www.ncbi.nlm.nih.gov/gene/?term=15289	"HMG-1, Hmg1, SBP-1, p30 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00003992	1528	CYB5A	http://www.ncbi.nlm.nih.gov/gene/?term=1528	"CYB5, MCB5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003993	1528	CYB5A	http://www.ncbi.nlm.nih.gov/gene/?term=1528	"CYB5, MCB5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00003994	1528	CYB5A	http://www.ncbi.nlm.nih.gov/gene/?term=1528	"CYB5, MCB5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003995	152926	PPM1K	http://www.ncbi.nlm.nih.gov/gene/?term=152926	"BDP, MSUDMV, PP2Ckappa, PP2Cm, PTMP, UG0882E07 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003996	152992	TRMT44	http://www.ncbi.nlm.nih.gov/gene/?term=152992	"C4orf23, METTL19, TRM44 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00003997	152	ADRA2C	http://www.ncbi.nlm.nih.gov/gene/?term=152	"ADRA2L2, ADRA2RL2, ADRARL2, ALPHA2CAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003998	153090	DAB2IP	http://www.ncbi.nlm.nih.gov/gene/?term=153090	"AF9Q34, AIP-1, AIP1, DIP1/2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00003999	153090	DAB2IP	http://www.ncbi.nlm.nih.gov/gene/?term=153090	"AF9Q34, AIP-1, AIP1, DIP1/2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004000	153129	SLC38A9	http://www.ncbi.nlm.nih.gov/gene/?term=153129	URLC11	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004001	15312	Hmgn1	http://www.ncbi.nlm.nih.gov/gene/?term=15312	"HMG-14, Hmg14 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004002	153201	SLC36A2	http://www.ncbi.nlm.nih.gov/gene/?term=153201	"PAT2, TRAMD1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004003	153201	SLC36A2	http://www.ncbi.nlm.nih.gov/gene/?term=153201	"PAT2, TRAMD1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004004	153222	CREBRF	http://www.ncbi.nlm.nih.gov/gene/?term=153222	"C5orf41, LRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004005	153241	CEP120	http://www.ncbi.nlm.nih.gov/gene/?term=153241	"CCDC100, SRTD13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004006	15331	Hmgn2	http://www.ncbi.nlm.nih.gov/gene/?term=15331	"HMG-17, Hmg17 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004007	153328	SLC25A48	http://www.ncbi.nlm.nih.gov/gene/?term=153328		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004008	153339	TMEM167A	http://www.ncbi.nlm.nih.gov/gene/?term=153339	TMEM167	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004009	153443	SRFBP1	http://www.ncbi.nlm.nih.gov/gene/?term=153443	"BUD22, P49, Rlb1, STRAP, p49/STRAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004010	153443	SRFBP1	http://www.ncbi.nlm.nih.gov/gene/?term=153443	"BUD22, P49, Rlb1, STRAP, p49/STRAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004011	1534	CYB561	http://www.ncbi.nlm.nih.gov/gene/?term=1534	"CYB561A1, FRRS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004012	1534	CYB561	http://www.ncbi.nlm.nih.gov/gene/?term=1534	"CYB561A1, FRRS2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004013	153527	ZMAT2	http://www.ncbi.nlm.nih.gov/gene/?term=153527	"Ptg-12, Snu23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004014	153562	MARVELD2	http://www.ncbi.nlm.nih.gov/gene/?term=153562	"DFNB49, MARVD2, MRVLDC2, Tric "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004015	153562	MARVELD2	http://www.ncbi.nlm.nih.gov/gene/?term=153562	"DFNB49, MARVD2, MRVLDC2, Tric "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004016	153562	MARVELD2	http://www.ncbi.nlm.nih.gov/gene/?term=153562	"DFNB49, MARVD2, MRVLDC2, Tric "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004017	153579	BTNL9	http://www.ncbi.nlm.nih.gov/gene/?term=153579	"BTN3, BTN8, VDLS1900 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004018	15357	Hmgcr	http://www.ncbi.nlm.nih.gov/gene/?term=15357	"HMG-CoAR, Red "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004019	1535	CYBA	http://www.ncbi.nlm.nih.gov/gene/?term=1535	p22-PHOX	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004020	1535	CYBA	http://www.ncbi.nlm.nih.gov/gene/?term=1535	p22-PHOX	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004021	153642	ARSK	http://www.ncbi.nlm.nih.gov/gene/?term=153642	TSULF	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004022	15369	Hmox2	http://www.ncbi.nlm.nih.gov/gene/?term=15369	"HO-2, HO2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004023	1536	CYBB	http://www.ncbi.nlm.nih.gov/gene/?term=1536	"AMCBX2, CGD, GP91-1, GP91-PHOX, GP91PHOX, IMD34, NOX2, p91-PHOX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004024	15372	Hmx2	http://www.ncbi.nlm.nih.gov/gene/?term=15372	"Nkx-5.2, Nkx5-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004025	153768	PRELID2	http://www.ncbi.nlm.nih.gov/gene/?term=153768		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004026	1537	CYC1	http://www.ncbi.nlm.nih.gov/gene/?term=1537	"MC3DN6, UQCR4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004027	1537	CYC1	http://www.ncbi.nlm.nih.gov/gene/?term=1537	"MC3DN6, UQCR4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004028	15382	Hnrnpa1	http://www.ncbi.nlm.nih.gov/gene/?term=15382	"HDP-1, Hdp, Hnrpa1, hnRNP A1, hnrnp-A1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004029	153830	RNF145	http://www.ncbi.nlm.nih.gov/gene/?term=153830		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004030	15384	Hnrnpab	http://www.ncbi.nlm.nih.gov/gene/?term=15384	"3010025C11Rik, CBF-A, Cgbfa, Hnrpab "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004031	15384	Hnrnpab	http://www.ncbi.nlm.nih.gov/gene/?term=15384	"3010025C11Rik, CBF-A, Cgbfa, Hnrpab "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004032	15387	Hnrnpk	http://www.ncbi.nlm.nih.gov/gene/?term=15387	"Hnrpk, KBBP, NOVA "	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00004033	15397	Hoxa11os	http://www.ncbi.nlm.nih.gov/gene/?term=15397	"Hoxa11as, Hoxa11s "	lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00004034	15397	Hoxa11os	http://www.ncbi.nlm.nih.gov/gene/15397	"Hoxa11s, Hoxa11as "	lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00004035	15397	Hoxa11os	http://www.ncbi.nlm.nih.gov/gene/15397	"Hoxa11s, Hoxa11as "	lncRNA	Mus musculus	23898399	Cytoplasm	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00004036	153	ADRB1	http://www.ncbi.nlm.nih.gov/gene/?term=153	"ADRB1R, B1AR, BETA1AR, RHR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004037	153	ADRB1	http://www.ncbi.nlm.nih.gov/gene/?term=153	"ADRB1R, B1AR, BETA1AR, RHR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004038	154007	SNRNP48	http://www.ncbi.nlm.nih.gov/gene/?term=154007	"C6orf151, dJ336K20B.1, dJ512B11.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004039	154007	SNRNP48	http://www.ncbi.nlm.nih.gov/gene/?term=154007	"C6orf151, dJ336K20B.1, dJ512B11.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004040	154007	SNRNP48	http://www.ncbi.nlm.nih.gov/gene/?term=154007	"C6orf151, dJ336K20B.1, dJ512B11.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004041	15401	Hoxa4	http://www.ncbi.nlm.nih.gov/gene/?term=15401	"AV206827, Hox-1.4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004042	154091	SLC2A12	http://www.ncbi.nlm.nih.gov/gene/?term=154091	"GLUT12, GLUT8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004043	1540	CYLD	http://www.ncbi.nlm.nih.gov/gene/?term=1540	"BRSS, CDMT1, CYLDI, EAC, MFT, MFT1, SBS, TEM, USPL2, CYLD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004044	1540	CYLD	http://www.ncbi.nlm.nih.gov/gene/?term=1540	"BRSS, CDMT, CYLD1, CYLDI, EAC, MFT, MFT1, SBS, TEM, USPL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004045	154141	MBOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=154141	"LPEAT1, LPLAT, LPLAT 1, LPSAT, OACT1, dJ434O11.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004046	154141	MBOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=154141	"LPEAT1, LPLAT, LPLAT 1, LPSAT, OACT1, dJ434O11.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004047	154141	MBOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=154141	"LPEAT1, LPLAT, LPLAT 1, LPSAT, OACT1, dJ434O11.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004048	154214	RNF217	http://www.ncbi.nlm.nih.gov/gene/?term=154214	"C6orf172, IBRDC1, dJ84N20.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004049	15423	Hoxc4	http://www.ncbi.nlm.nih.gov/gene/?term=15423	Hox-3.5	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004050	154313	CFAP206	http://www.ncbi.nlm.nih.gov/gene/?term=154313	"C6orf165, dJ382I10.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004051	154313	CFAP206	http://www.ncbi.nlm.nih.gov/gene/?term=154313	"C6orf165, dJ382I10.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004052	15444	Hpca	http://www.ncbi.nlm.nih.gov/gene/?term=15444		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004053	154467	CCDC167	http://www.ncbi.nlm.nih.gov/gene/?term=154467	"C6orf129, HSPC265 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004054	1544	CYP1A2	http://www.ncbi.nlm.nih.gov/gene/?term=1544	"CP12, P3-450, P450(PA) "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004055	1544	CYP1A2	http://www.ncbi.nlm.nih.gov/gene/?term=1544	"CP12, P3-450, P450(PA) "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004056	15461	Hras	http://www.ncbi.nlm.nih.gov/gene/?term=15461	"H-ras, Ha-ras, Harvey-ras-1, Hras1, Kras2, c-H-ras, c-Ha-ras, c-rasHa, ras, Hras "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004057	15463	Agfg1	http://www.ncbi.nlm.nih.gov/gene/?term=15463	"AU045498, C130049H11Rik, C85612, D730048C23Rik, Hrb, RAB, Rip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004058	154664	ABCA13	http://www.ncbi.nlm.nih.gov/gene/?term=154664		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004059	154664	ABCA13	http://www.ncbi.nlm.nih.gov/gene/?term=154664		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004060	154664	ABCA13	http://www.ncbi.nlm.nih.gov/gene/?term=154664		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004061	154743	BMT2	http://www.ncbi.nlm.nih.gov/gene/?term=154743		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004062	154791	C7orf55	http://www.ncbi.nlm.nih.gov/gene/?term=154791	"FMC1, HSPC268 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004063	154807	VKORC1L1	http://www.ncbi.nlm.nih.gov/gene/?term=154807		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004064	15481	Hspa8	http://www.ncbi.nlm.nih.gov/gene/?term=15481	"2410008N15Rik, Hsc70, Hsc71, Hsc73, Hsp73, Hspa10 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004065	15483	Hsd11b1	http://www.ncbi.nlm.nih.gov/gene/?term=15483		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004066	15486	Hsd17b2	http://www.ncbi.nlm.nih.gov/gene/?term=15486	"AI194836, AI194967, AI255511 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004067	1548	CYP2A6	http://www.ncbi.nlm.nih.gov/gene/?term=1548	"CPA6, CYP2A, CYP2A3, CYPIIA6, P450C2A, P450PB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004068	15490	Hsd17b7	http://www.ncbi.nlm.nih.gov/gene/?term=15490	"AI266814, ERG27 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004069	154	ADRB2	http://www.ncbi.nlm.nih.gov/gene/?term=154	"ADRB2R, ADRBR, B2AR, BAR, BETA2AR "	mRNA	Homo sapiens	23351737	Cytoplasm	Smooth muscle cell	Fluorescence in situ hybridization	Fluorescent in situ hybridization (FISH) analysis to localize endogenous mRNA in DDT1-MF2 cells showed that β2-AR mRNA is localized to the peripheral cytoplasmic regions of DDT1-MF2 cells. The results of immunofluorescence staining and FISH analysis in control and HuR knockdown cells emphasize the spatiotemporal relationship between β2-AR mRNA localization and translation and its importance in receptor localization to the plasma membrane.
RLID00004070	154	ADRB2	http://www.ncbi.nlm.nih.gov/gene/?term=154	"ADRB2R, ADRBR, B2AR, BAR, BETA2AR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004071	15500	Hsf2	http://www.ncbi.nlm.nih.gov/gene/?term=15500	AI661205	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004072	15505	Hsph1	http://www.ncbi.nlm.nih.gov/gene/?term=15505	"105kDa, AI790491, Hsp105, Hsp110, hsp-E7I, hsp110/105 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004073	155060	LOC155060	http://www.ncbi.nlm.nih.gov/gene/?term=155060		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004074	155066	ATP6V0E2	http://www.ncbi.nlm.nih.gov/gene/?term=155066	"ATP6V0E2L, C7orf32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004075	15516	Hsp90ab1	http://www.ncbi.nlm.nih.gov/gene/?term=15516	"90kDa, AL022974, C81438, Hsp84, Hsp84-1, Hsp90, Hspcb "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00004076	15519	Hsp90aa1	http://www.ncbi.nlm.nih.gov/gene/?term=15519	"86kDa, 89kDa, AL024080, AL024147, Hsp86-1, Hsp89, Hsp90, Hspca, hsp4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004077	15519	Hsp90aa1	http://www.ncbi.nlm.nih.gov/gene/?term=15519	"86kDa, 89kDa, AL024080, AL024147, Hsp86-1, Hsp89, Hsp90, Hspca, hsp4 "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00004078	15525	Hspa4	http://www.ncbi.nlm.nih.gov/gene/?term=15525	"70kDa, AI317151, APG-2, Hsp110, Hsp70RY, mKIAA4025 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004079	15526	Hspa9	http://www.ncbi.nlm.nih.gov/gene/?term=15526	"74kDa, Csa, Grp75, Hsc74, Hsp74, Hsp74aa, Mortalin, Mot-2, Mot2, Mthsp70, Pbp74, Hspa9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004080	15530	Hspg2	http://www.ncbi.nlm.nih.gov/gene/?term=15530	"AI852380, Pcn, Plc, per "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004081	15530	Hspg2	http://www.ncbi.nlm.nih.gov/gene/?term=15530	"AI852380, Pcn, Plc, per "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004082	155370	SBDSP1	http://www.ncbi.nlm.nih.gov/gene/?term=155370	SBDSP	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004083	155400	NSUN5P1	http://www.ncbi.nlm.nih.gov/gene/?term=155400	"NSUN5B, WBSCR20B "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004084	155435	RBM33	http://www.ncbi.nlm.nih.gov/gene/?term=155435	PRR8	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004085	155435	RBM33	http://www.ncbi.nlm.nih.gov/gene/?term=155435	PRR8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004086	15551	Htr1b	http://www.ncbi.nlm.nih.gov/gene/?term=15551		mRNA	Mus musculus	8159291	Cell body	Pyramidal cell	In situ hybridization	"In the hippocampus, 5-hydroxytryptamine1B messenger RNA is localized in the cell bodies of pyramidal cells of the CA1 field. "
RLID00004087	1555	CYP2B6	http://www.ncbi.nlm.nih.gov/gene/?term=1555	"CPB6, CYP2B, CYP2B7, CYP2B7P, CYPIIB6, EFVM, IIB1, P450 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004088	1555	CYP2B6	http://www.ncbi.nlm.nih.gov/gene/?term=1555	"CPB6, CYP2B, CYP2B7, CYP2B7P, CYPIIB6, EFVM, IIB1, P450 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004089	1555	CYP2B6	http://www.ncbi.nlm.nih.gov/gene/?term=1555	"CPB6, CYP2B, CYP2B7, CYP2B7P, CYPIIB6, EFVM, IIB1, P450 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004090	1555	CYP2B6	http://www.ncbi.nlm.nih.gov/gene/1555	"CPB6, EFVM, IIB1, P450, CYP2B, CYP2B7, CYP2B7P, CYPIIB6 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00004091	15566	Htr7	http://www.ncbi.nlm.nih.gov/gene/?term=15566	5-HT7	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004092	15568	Elavl1	http://www.ncbi.nlm.nih.gov/gene/?term=15568	"2410055N02Rik, HUR, Hua, W91709 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004093	15571	Elavl3	http://www.ncbi.nlm.nih.gov/gene/?term=15571	"2600009P04Rik, Huc, PLE21, mHuC "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004094	15572	Elavl4	http://www.ncbi.nlm.nih.gov/gene/?term=15572	"Elav, Hud, PNEM "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004095	15574	Hus1	http://www.ncbi.nlm.nih.gov/gene/?term=15574		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004096	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Nucleus	HeLa cell	Confocal microscopy	Subsequent optical Z sectioning by confocal microscopy confirmed that the signal for unspliced env mRNA was detectable throughout the nucleus in the presence of Rev (data not shown). 
RLID00004097	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Cytoplasm	HeLa cell	S1 protection experiments	"The HeLa CMV*Rev/pgEnv Hygro cells were grown in the presence or absence of tetracycline and subsequently fractionated into matrix, nucleoplasmic, and cytoplasmic fractions. S1 protection of the env unspliced RNA from each of these fractions revealed that the RNA was indeed associated with the nuclear matrix in both the absence (Fig.3A) and presence (Fig.3B) of Rev. "
RLID00004098	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Nucleoplasm	HeLa cell	S1 protection experiments	"The HeLa CMV*Rev/pgEnv Hygro cells were grown in the presence or absence of tetracycline and subsequently fractionated into matrix, nucleoplasmic, and cytoplasmic fractions. S1 protection of the env unspliced RNA from each of these fractions revealed that the RNA was indeed associated with the nuclear matrix in both the absence (Fig.3A) and presence (Fig.3B) of Rev. "
RLID00004099	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Nucleus	HeLa cell	S1 protection experiments	"The HeLa CMV*Rev/pgEnv Hygro cells were grown in the presence or absence of tetracycline and subsequently fractionated into matrix, nucleoplasmic, and cytoplasmic fractions. S1 protection of the env unspliced RNA from each of these fractions revealed that the RNA was indeed associated with the nuclear matrix in both the absence (Fig.3A) and presence (Fig.3B) of Rev. "
RLID00004100	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Nucleoplasm	HeLa cell	In situ hybridization	"Using in situ hybridization, we demonstrated that in the absence of Rev, unspliced RNA generated with an HIV-1 env expression construct displayed discrete localization in the nucleus, coincident with the location of the gene and not associated with SC35-containing nuclear speckles. Expression of Rev resulted in a disperse signal for the unspliced RNA throughout both the nucleus and the cytoplasm. Subsequent fractionation of the nucleus revealed that the majority of unspliced viral RNA within the nucleus is associated with the nuclear matrix and that upon expression of Rev, a small proportion of the unspliced RNA is found within the nucleoplasm. "
RLID00004101	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Cytoplasm	HeLa cell	In situ hybridization	"In contrast, upon induction of Rev expression, we detected unspliced and spliced RNA in the nucleoplasm and in the cytoplasm, consistent with the export of unspliced RNA (Fig. (Fig.3B).3B). "
RLID00004102	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Nucleus	HeLa cell	In situ hybridization	Hybridization to unspliced HIV-1 env mRNA (pseudocolored in green) in the absence of Rev expression revealed that the unspliced RNA was located in the nucleus as a discrete signal (Fig. (Fig.1A).1A). 
RLID00004103	155971	env	http://www.ncbi.nlm.nih.gov/gene/?term=155971	HIV1gp8	mRNA	Human immunodeficiency virus 1	9811683	Nucleus	HeLa cell	In situ hybridization	"Using in situ hybridization, we demonstrated that in the absence of Rev, unspliced RNA generated with an HIV-1 env expression construct displayed discrete localization in the nucleus, coincident with the location of the gene and not associated with SC35-containing nuclear speckles. Expression of Rev resulted in a disperse signal for the unspliced RNA throughout both the nucleus and the cytoplasm. Subsequent fractionation of the nucleus revealed that the majority of unspliced viral RNA within the nucleus is associated with the nuclear matrix and that upon expression of Rev, a small proportion of the unspliced RNA is found within the nucleoplasm. "
RLID00004104	156	ADRBK1	http://www.ncbi.nlm.nih.gov/gene/?term=156	"BARK1, BETA-ARK1, GRK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004105	156	ADRBK1	http://www.ncbi.nlm.nih.gov/gene/?term=156	"BARK1, BETA-ARK1, GRK2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004106	156	ADRBK1	http://www.ncbi.nlm.nih.gov/gene/?term=156	"BARK1, BETA-ARK1, GRK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004107	157285	SGK223	http://www.ncbi.nlm.nih.gov/gene/?term=157285	PRAGMIN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004108	157313	CDCA2	http://www.ncbi.nlm.nih.gov/gene/?term=157313	"PPP1R81, Repo-Man "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004109	157378	TMEM65	http://www.ncbi.nlm.nih.gov/gene/?term=157378		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004110	157506	RDH10	http://www.ncbi.nlm.nih.gov/gene/?term=157506	SDR16C4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004111	157506	RDH10	http://www.ncbi.nlm.nih.gov/gene/?term=157506	SDR16C4	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004112	157506	RDH10	http://www.ncbi.nlm.nih.gov/gene/?term=157506	SDR16C4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004113	157506	RDH10	http://www.ncbi.nlm.nih.gov/gene/?term=157506	SDR16C4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004114	157506	RDH10	http://www.ncbi.nlm.nih.gov/gene/?term=157506	SDR16C4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004115	157567	ANKRD46	http://www.ncbi.nlm.nih.gov/gene/?term=157567	"ANK-S, GENX-115279 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004116	157567	ANKRD46	http://www.ncbi.nlm.nih.gov/gene/?term=157567	"ANK-S, GENX-115279 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004117	157570	ESCO2	http://www.ncbi.nlm.nih.gov/gene/?term=157570	"2410004I17Rik, EFO2, RBS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004118	157638	FAM84B	http://www.ncbi.nlm.nih.gov/gene/?term=157638	"BCMP101, NSE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004119	157697	ERICH1	http://www.ncbi.nlm.nih.gov/gene/?term=157697	HSPC319	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004120	157697	ERICH1	http://www.ncbi.nlm.nih.gov/gene/?term=157697	HSPC319	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004121	157769	FAM91A1	http://www.ncbi.nlm.nih.gov/gene/?term=157769		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004122	1577	CYP3A5	http://www.ncbi.nlm.nih.gov/gene/?term=1577	"CP35, CYPIIIA5, P450PCN3, PCN3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004123	157807	CLVS1	http://www.ncbi.nlm.nih.gov/gene/?term=157807	"CRALBPL, RLBP1L1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004124	157922	CAMSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=157922		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004125	157	ADRBK2	http://www.ncbi.nlm.nih.gov/gene/?term=157	"BARK2, GRK3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004126	157	ADRBK2	http://www.ncbi.nlm.nih.gov/gene/?term=157	"BARK2, GRK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004127	158046	NXNL2	http://www.ncbi.nlm.nih.gov/gene/?term=158046	"C9orf121, RDCVF2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004128	158046	NXNL2	http://www.ncbi.nlm.nih.gov/gene/?term=158046	"C9orf121, RDCVF2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004129	158135	TTLL11	http://www.ncbi.nlm.nih.gov/gene/?term=158135	"C9orf20, bA244O19.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004130	158158	RASEF	http://www.ncbi.nlm.nih.gov/gene/?term=158158	RAB45	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004131	158293	FAM120AOS	http://www.ncbi.nlm.nih.gov/gene/?term=158293	C9orf10OS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004132	158293	FAM120AOS	http://www.ncbi.nlm.nih.gov/gene/?term=158293	C9orf10OS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004133	158297	SAXO1	http://www.ncbi.nlm.nih.gov/gene/?term=158297	"C9orf138, FAM154A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004134	158381	ATP8B5P	http://www.ncbi.nlm.nih.gov/gene/?term=158381	FetA	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004135	1584	CYP11B1	http://www.ncbi.nlm.nih.gov/gene/?term=1584	"CPN1, CYP11B, FHI, P450C11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004136	158511	CSAG1	http://www.ncbi.nlm.nih.gov/gene/?term=158511	"CSAGE, CT24.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004137	158586	ZXDB	http://www.ncbi.nlm.nih.gov/gene/?term=158586	"ZNF905, dJ83L6.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004138	158747	MOSPD2	http://www.ncbi.nlm.nih.gov/gene/?term=158747		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004139	158830	CXorf65	http://www.ncbi.nlm.nih.gov/gene/?term=158830		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004140	15893	Ica1	http://www.ncbi.nlm.nih.gov/gene/?term=15893	"69kDa, ICA69 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004141	1589	CYP21A2	http://www.ncbi.nlm.nih.gov/gene/?term=1589	"CA21H, CAH1, CPS1, CYP21, CYP21B, P450c21B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004142	158	ADSL	http://www.ncbi.nlm.nih.gov/gene/?term=158	"AMPS, ASASE, ASL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004143	158	ADSL	http://www.ncbi.nlm.nih.gov/gene/?term=158	"AMPS, ASASE, ASL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004144	158	ADSL	http://www.ncbi.nlm.nih.gov/gene/?term=158	"AMPS, ASASE, ASL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004145	159090	FAM122B	http://www.ncbi.nlm.nih.gov/gene/?term=159090	SPACIA2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004146	159091	FAM122C	http://www.ncbi.nlm.nih.gov/gene/?term=159091		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004147	159195	USP54	http://www.ncbi.nlm.nih.gov/gene/?term=159195	"C10orf29, bA137L10.3, bA137L10.4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004148	15925	Ide	http://www.ncbi.nlm.nih.gov/gene/?term=15925	"1300012G03Rik, 4833415K22Rik, AA675336, AI507533 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004149	15926	Idh1	http://www.ncbi.nlm.nih.gov/gene/?term=15926	"AI314845, AI788952, E030024J03Rik, Id-1, Idh-1, Idpc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004150	1592	CYP26A1	http://www.ncbi.nlm.nih.gov/gene/?term=1592	"CP26, CYP26, P450RAI, P450RAI1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004151	15944	Irgm1	http://www.ncbi.nlm.nih.gov/gene/?term=15944	"Ifggd3, Ifi1, Iigp3, Iipg3, Irgm, LRG-47 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004152	1595	CYP51A1	http://www.ncbi.nlm.nih.gov/gene/?term=1595	"CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004153	1595	CYP51A1	http://www.ncbi.nlm.nih.gov/gene/?term=1595	"CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004154	1595	CYP51A1	http://www.ncbi.nlm.nih.gov/gene/?term=1595	"CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004155	1595	CYP51A1	http://www.ncbi.nlm.nih.gov/gene/?term=1595	"CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004156	1595	CYP51A1	http://www.ncbi.nlm.nih.gov/gene/?term=1595	"CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004157	15979	Ifngr1	http://www.ncbi.nlm.nih.gov/gene/?term=15979	"CD119, IFN-gammaR, Ifgr, Ifngr, Nktar "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004158	159	ADSS	http://www.ncbi.nlm.nih.gov/gene/?term=159	"ADEH 2, ADSS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004159	159	ADSS	http://www.ncbi.nlm.nih.gov/gene/?term=159	"ADEH 2, ADSS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004160	159	ADSS	http://www.ncbi.nlm.nih.gov/gene/?term=159	"ADEH, ADSS 2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004161	16000	Igf1	http://www.ncbi.nlm.nih.gov/gene/?term=16000	"C730016P09Rik, Igf-1, Igf-I "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004162	16002	Igf2	http://www.ncbi.nlm.nih.gov/gene/?term=16002	"AL033362, Igf-2, Igf-II, M6pr, Mpr, Peg2 "	mRNA	Mus musculus	17948025	Cytoplasm	Fibroblast	In situ hybridization|qRT-PCR	"We sought to determine the subcellular localization of the non-coding H19 ICR transcripts. We separated nuclear and cytoplasmic RNA fractions from mouse embryonic fibroblasts. Igf2 and H19 gene transcripts were found both in the nucleus and in the cytoplasm, whereas the ncICR transcripts were almost exclusively detected in the nuclear fraction (Fig 1D), which is consistent with a function in gene expression. "
RLID00004163	16002	Igf2	http://www.ncbi.nlm.nih.gov/gene/?term=16002	"AL033362, Igf-2, Igf-II, M6pr, Mpr, Peg2 "	mRNA	Mus musculus	17948025	Nucleus	Fibroblast	In situ hybridization|qRT-PCR	"We sought to determine the subcellular localization of the non-coding H19 ICR transcripts. We separated nuclear and cytoplasmic RNA fractions from mouse embryonic fibroblasts. Igf2 and H19 gene transcripts were found both in the nucleus and in the cytoplasm, whereas the ncICR transcripts were almost exclusively detected in the nuclear fraction (Fig 1D), which is consistent with a function in gene expression. "
RLID00004164	16004	Igf2r	http://www.ncbi.nlm.nih.gov/gene/?term=16004	"AI661837, CD222, CI-MPR, M6P/IGF2R, Mpr300 "	mRNA	Mus musculus	16874305	Cytoplasm	Fibroblast	qRT-PCR|Northern blot	"In contrast to Air, however, Igf2r mRNA is clearly exported to the cytoplasm (Figure 6B and C). "
RLID00004165	16011	Igfbp5	http://www.ncbi.nlm.nih.gov/gene/?term=16011	"AI256729, AW208790, IGFBP-5, IGFBP-5P "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004166	16012	Igfbp6	http://www.ncbi.nlm.nih.gov/gene/?term=16012	IGFBP-6	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004167	1601	DAB2	http://www.ncbi.nlm.nih.gov/gene/?term=1601	"DOC-2, DOC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004168	160287	LDHAL6A	http://www.ncbi.nlm.nih.gov/gene/?term=160287	LDH6A	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004169	160287	LDHAL6A	http://www.ncbi.nlm.nih.gov/gene/?term=160287	LDH6A	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004170	1603	DAD1	http://www.ncbi.nlm.nih.gov/gene/?term=1603	OST2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004171	1603	DAD1	http://www.ncbi.nlm.nih.gov/gene/?term=1603	OST2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004172	160418	TMTC3	http://www.ncbi.nlm.nih.gov/gene/?term=160418	SMILE	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004173	160428	ALDH1L2	http://www.ncbi.nlm.nih.gov/gene/?term=160428	mtFDH	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004174	1604	CD55	http://www.ncbi.nlm.nih.gov/gene/?term=1604	"CR, CROM, DAF, TC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004175	160518	DENND5B	http://www.ncbi.nlm.nih.gov/gene/?term=160518		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004176	1605	DAG1	http://www.ncbi.nlm.nih.gov/gene/?term=1605	"156DAG, A3a, AGRNR, DAG, MDDGA9, MDDGC7, MDDGC9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004177	1605	DAG1	http://www.ncbi.nlm.nih.gov/gene/?term=1605	"156DAG, A3a, AGRNR, DAG, MDDGA9, MDDGC7, MDDGC9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004178	16065	Igh-VS107	http://www.ncbi.nlm.nih.gov/gene/?term=16065	"IgG, IgH, VhNZA6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004179	16068	Il18bp	http://www.ncbi.nlm.nih.gov/gene/?term=16068	"IL-18BP, Igifbp, MC54L "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004180	1606	DGKA	http://www.ncbi.nlm.nih.gov/gene/?term=1606	"DAGK, DAGK1, DGK-alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004181	160857	CCDC122	http://www.ncbi.nlm.nih.gov/gene/?term=160857		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004182	160857	CCDC122	http://www.ncbi.nlm.nih.gov/gene/?term=160857		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004183	1609	DGKQ	http://www.ncbi.nlm.nih.gov/gene/?term=1609	"DAGK, DAGK4, DAGK7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004184	160	AP2A1	http://www.ncbi.nlm.nih.gov/gene/?term=160	"ADTAA, AP2-ALPHA, CLAPA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004185	1610	DAO	http://www.ncbi.nlm.nih.gov/gene/?term=1610	"DAAO, DAMOX, OXDA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004186	1611	DAP	http://www.ncbi.nlm.nih.gov/gene/?term=1611		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004187	1611	DAP	http://www.ncbi.nlm.nih.gov/gene/?term=1611		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004188	161291	TMEM30B	http://www.ncbi.nlm.nih.gov/gene/?term=161291	CDC50B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004189	1612	DAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=1612	DAPK	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004190	1612	DAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=1612	DAPK	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004191	161357	MDGA2	http://www.ncbi.nlm.nih.gov/gene/?term=161357	"MAMDC1, c14_5286 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004192	1613	DAPK3	http://www.ncbi.nlm.nih.gov/gene/?term=1613	"DLK, ZIP, ZIPK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004193	161424	NOP9	http://www.ncbi.nlm.nih.gov/gene/?term=161424	C14orf21	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004194	161436	EML5	http://www.ncbi.nlm.nih.gov/gene/?term=161436	EMAP-2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004195	161436	EML5	http://www.ncbi.nlm.nih.gov/gene/?term=161436	EMAP-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004196	161497	STRC	http://www.ncbi.nlm.nih.gov/gene/?term=161497	DFNB16	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004197	16150	Ikbkb	http://www.ncbi.nlm.nih.gov/gene/?term=16150	"AI132552, IKK-2, IKK-beta, IKK2, IKK[b], IKKbeta "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004198	16150	Ikbkb	http://www.ncbi.nlm.nih.gov/gene/?term=16150	"AI132552, IKK-2, IKK-beta, IKK2, IKK[b], IKKbeta "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004199	1615	DARS	http://www.ncbi.nlm.nih.gov/gene/?term=1615	"HBSL, aspRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004200	1615	DARS	http://www.ncbi.nlm.nih.gov/gene/?term=1615	"HBSL, aspRS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004201	1615	DARS	http://www.ncbi.nlm.nih.gov/gene/?term=1615	"HBSL, aspRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004202	16164	Il13ra1	http://www.ncbi.nlm.nih.gov/gene/?term=16164	"AI882074, CD213a1, IL-13R-alpha-1, IL-13r[a], Il13ra, NR4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004203	1616	DAXX	http://www.ncbi.nlm.nih.gov/gene/?term=1616	"BING2, DAP6, EAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004204	1616	DAXX	http://www.ncbi.nlm.nih.gov/gene/?term=1616	"BING2, DAP6, EAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004205	1616	DAXX	http://www.ncbi.nlm.nih.gov/gene/?term=1616	"BING2, DAP6, EAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004206	161742	SPRED1	http://www.ncbi.nlm.nih.gov/gene/?term=161742	"NFLS, PPP1R147, hSpred1, spred-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004207	161742	SPRED1	http://www.ncbi.nlm.nih.gov/gene/?term=161742	"NFLS, PPP1R147, hSpred1, spred-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004208	16175	Il1a	http://www.ncbi.nlm.nih.gov/gene/?term=16175	Il-1a	mRNA	Mus musculus	26179904	Cytosol	Macrophage	qRT-PCR	"As expected, the mature IL-1a and Gapdh transcripts were localized to the cytosol, whereas 7SK RNA was confined to the nucleus. "
RLID00004209	161829	EXD1	http://www.ncbi.nlm.nih.gov/gene/?term=161829	EXDL1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004210	161829	EXD1	http://www.ncbi.nlm.nih.gov/gene/?term=161829	EXDL1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004211	16182	Il18r1	http://www.ncbi.nlm.nih.gov/gene/?term=16182	"Il18ralpha, Il1rrp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004212	1618	DAZL	http://www.ncbi.nlm.nih.gov/gene/?term=1618	"DAZH, DAZL1, DAZLA, SPGYLA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004213	16192	Il5ra	http://www.ncbi.nlm.nih.gov/gene/?term=16192	"CD125, CDw125, Il5r "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004214	16195	Il6st	http://www.ncbi.nlm.nih.gov/gene/?term=16195	"5133400A03Rik, AA389424, BB405851, CD130, D13Ertd699e, gp130 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004215	161	AP2A2	http://www.ncbi.nlm.nih.gov/gene/?term=161	"ADTAB, CLAPA2, HIP-9, HIP9, HYPJ "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004216	16201	Ilf3	http://www.ncbi.nlm.nih.gov/gene/?term=16201	"MBII-26, MPHOSPH4, NF90, NFAR "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004217	162073	ITPRIPL2	http://www.ncbi.nlm.nih.gov/gene/?term=162073		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004218	162073	ITPRIPL2	http://www.ncbi.nlm.nih.gov/gene/?term=162073		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004219	162073	ITPRIPL2	http://www.ncbi.nlm.nih.gov/gene/?term=162073		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004220	162073	ITPRIPL2	http://www.ncbi.nlm.nih.gov/gene/?term=162073		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004221	16210	Impact	http://www.ncbi.nlm.nih.gov/gene/?term=16210	E430016J11Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004222	16211	Kpnb1	http://www.ncbi.nlm.nih.gov/gene/?term=16211	"AA409963, IPOB, Impnb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004223	16211	Kpnb1	http://www.ncbi.nlm.nih.gov/gene/?term=16211	"AA409963, IPOB, Impnb "	mRNA	Mus musculus	22841314	Axon	Sciatic nerves	In situ hybridization	Here we show that a long 3' untranslated region (3' UTR) directs axonal localization of Importin β1. 
RLID00004224	1622	DBI	http://www.ncbi.nlm.nih.gov/gene/?term=1622	"ACBD1, ACBP, CCK-RP, EP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004225	162417	NAGS	http://www.ncbi.nlm.nih.gov/gene/?term=162417	"AGAS, ARGA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004226	162427	FAM134C	http://www.ncbi.nlm.nih.gov/gene/?term=162427		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004227	162427	FAM134C	http://www.ncbi.nlm.nih.gov/gene/?term=162427		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004228	162427	FAM134C	http://www.ncbi.nlm.nih.gov/gene/?term=162427		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004229	162427	FAM134C	http://www.ncbi.nlm.nih.gov/gene/?term=162427		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004230	162605	KRT28	http://www.ncbi.nlm.nih.gov/gene/?term=162605	"K25IRS4, KRT25D "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004231	1627	DBN1	http://www.ncbi.nlm.nih.gov/gene/?term=1627	D0S117E	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004232	1628	DBP	http://www.ncbi.nlm.nih.gov/gene/?term=1628	DABP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004233	1628	DBP	http://www.ncbi.nlm.nih.gov/gene/?term=1628	DABP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004234	162966	ZNF600	http://www.ncbi.nlm.nih.gov/gene/?term=162966	KR-ZNF1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004235	162967	ZNF320	http://www.ncbi.nlm.nih.gov/gene/?term=162967	ZFPL	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004236	162967	ZNF320	http://www.ncbi.nlm.nih.gov/gene/?term=162967	ZFPL	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004237	162968	ZNF497	http://www.ncbi.nlm.nih.gov/gene/?term=162968		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004238	162968	ZNF497	http://www.ncbi.nlm.nih.gov/gene/?term=162968		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004239	162989	DEDD2	http://www.ncbi.nlm.nih.gov/gene/?term=162989	FLAME-3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004240	162998	OR7D2	http://www.ncbi.nlm.nih.gov/gene/?term=162998	"HTPCRH03, OR19-10, OR19-4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004241	162998	OR7D2	http://www.ncbi.nlm.nih.gov/gene/?term=162998	"HTPCRH03, OR19-10, OR19-4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004242	1629	DBT	http://www.ncbi.nlm.nih.gov/gene/?term=1629	"BCATE2, BCKAD-E2, BCKADE2, BCOADC-E2, E2, E2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004243	162	AP1B1	http://www.ncbi.nlm.nih.gov/gene/?term=162	"ADTB1, AP105A, BAM22, CLAPB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004244	162	AP1B1	http://www.ncbi.nlm.nih.gov/gene/?term=162	"ADTB1, AP105A, BAM22, CLAPB2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004245	163033	ZNF579	http://www.ncbi.nlm.nih.gov/gene/?term=163033		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004246	163049	ZNF791	http://www.ncbi.nlm.nih.gov/gene/?term=163049		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004247	163051	ZNF709	http://www.ncbi.nlm.nih.gov/gene/?term=163051		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004248	163051	ZNF709	http://www.ncbi.nlm.nih.gov/gene/?term=163051		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004249	163126	EID2	http://www.ncbi.nlm.nih.gov/gene/?term=163126	"CRI2, EID-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004250	16319	Incenp	http://www.ncbi.nlm.nih.gov/gene/?term=16319	"2700067E22Rik, AU019509, C130081E20, C77457 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004251	163227	ZNF100	http://www.ncbi.nlm.nih.gov/gene/?term=163227		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004252	163227	ZNF100	http://www.ncbi.nlm.nih.gov/gene/?term=163227		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004253	16329	Inpp1	http://www.ncbi.nlm.nih.gov/gene/?term=16329	"2300002C06Rik, AV137389 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00004254	1632	ECI1	http://www.ncbi.nlm.nih.gov/gene/?term=1632	DCI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004255	1632	ECI1	http://www.ncbi.nlm.nih.gov/gene/?term=1632	DCI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004256	16333	Ins1	http://www.ncbi.nlm.nih.gov/gene/?term=16333	"Ins-1, Ins2-rs1 "	mRNA	Mus musculus	25018104	Endoplasmic reticulum	INS-1 cell	qRT-PCR	"Preceding apoptosis, increasing ER stress agent levels progressively increases IRE1α phosphorylation, XBP1 mRNA splicing, endonucleolytic decay of the ER-localized mRNA, Ins1 mRNA (which encodes proinsulin), induction of thioredoxin-interacting protein (TXNIP) mRNA (whose product activates the NLRP3 inflammasome), and downstream c-Jun terminal kinase phosphorylation (JNKs) (Figure S1E,F). "
RLID00004257	16333	Ins1	http://www.ncbi.nlm.nih.gov/gene/?term=16333	"Ins-1, Ins2-rs1 "	mRNA	Mus musculus	15972000	Endoplasmic reticulum	MIN6 cell	Northern blot	"In conclusion, our results provide evidence that the selective recruitment of proinsulin mRNA to the ER, together with increases in the rate of initiation are important mediators of glucose-stimulated proinsulin synthesis in pancreatic beta-cells.  "
RLID00004258	16334	Ins2	http://www.ncbi.nlm.nih.gov/gene/?term=16334	"AA986540, Ins-2, InsII, Mody, Mody4 "	mRNA	Mus musculus	15972000	Endoplasmic reticulum	MIN6 cell	Northern blot	"In conclusion, our results provide evidence that the selective recruitment of proinsulin mRNA to the ER, together with increases in the rate of initiation are important mediators of glucose-stimulated proinsulin synthesis in pancreatic beta-cells.  "
RLID00004259	16337	Insr	http://www.ncbi.nlm.nih.gov/gene/?term=16337	"4932439J01Rik, CD220, D630014A15Rik, IR, IR-A, IR-B "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004260	1633	DCK	http://www.ncbi.nlm.nih.gov/gene/?term=1633		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004261	16341	Eif3e	http://www.ncbi.nlm.nih.gov/gene/?term=16341	"48kDa, Eif3s6, Int6, eIF3-p46, eIF3-p48 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004262	16341	Eif3e	http://www.ncbi.nlm.nih.gov/gene/?term=16341	"48kDa, Eif3s6, Int6, eIF3-p46, eIF3-p48 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004263	163486	DENND1B	http://www.ncbi.nlm.nih.gov/gene/?term=163486	"C1ORF18, C1orf218, FAM31B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004264	16351	Ipp	http://www.ncbi.nlm.nih.gov/gene/?term=16351	"D4Jhu8, Mipp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004265	16353	Ipw	http://www.ncbi.nlm.nih.gov/gene/?term=16353		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004266	163590	TOR1AIP2	http://www.ncbi.nlm.nih.gov/gene/?term=163590	"IFRG15, LULL1, NET9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004267	163590	TOR1AIP2	http://www.ncbi.nlm.nih.gov/gene/?term=163590	"IFRG15, LULL1, NET9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004268	163590	TOR1AIP2	http://www.ncbi.nlm.nih.gov/gene/?term=163590	"IFRG15, LULL1, NET9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004269	1635	DCTD	http://www.ncbi.nlm.nih.gov/gene/?term=1635		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004270	1635	DCTD	http://www.ncbi.nlm.nih.gov/gene/?term=1635		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004271	163702	IFNLR1	http://www.ncbi.nlm.nih.gov/gene/?term=163702	"CRF2/12, IFNLR, IL-28R1, IL28RA, LICR2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004272	163702	IFNLR1	http://www.ncbi.nlm.nih.gov/gene/?term=163702	"CRF2/12, IFNLR, IL-28R1, IL28RA, LICR2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004273	16372	Irx2	http://www.ncbi.nlm.nih.gov/gene/?term=16372		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004274	163732	CITED4	http://www.ncbi.nlm.nih.gov/gene/?term=163732		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004275	16373	Irx3	http://www.ncbi.nlm.nih.gov/gene/?term=16373	AI894186	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004276	163859	SDE2	http://www.ncbi.nlm.nih.gov/gene/?term=163859	"C1orf55, dJ671D7.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004277	163859	SDE2	http://www.ncbi.nlm.nih.gov/gene/?term=163859	"C1orf55, dJ671D7.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004278	163859	SDE2	http://www.ncbi.nlm.nih.gov/gene/?term=163859	"C1orf55, dJ671D7.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004279	163859	SDE2	http://www.ncbi.nlm.nih.gov/gene/?term=163859	"C1orf55, dJ671D7.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004280	163882	CNST	http://www.ncbi.nlm.nih.gov/gene/?term=163882	"C1orf71, PPP1R64 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004281	16392	Isl1	http://www.ncbi.nlm.nih.gov/gene/?term=16392		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004282	1639	DCTN1	http://www.ncbi.nlm.nih.gov/gene/?term=1639	"DAP-150, DP-150, P135 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004283	163	AP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=163	"ADTB2, AP105B, AP2-BETA, CLAPB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004284	163	AP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=163	"ADTB2, AP105B, AP2-BETA, CLAPB1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004285	16401	Itga4	http://www.ncbi.nlm.nih.gov/gene/?term=16401	"CD49DB, Itga4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004286	16403	Itga6	http://www.ncbi.nlm.nih.gov/gene/?term=16403	"5033401O05Rik, AI115430, Cd49f, VLA-6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004287	16407	Itgae	http://www.ncbi.nlm.nih.gov/gene/?term=16407	"A530055J10, CD103, aM290, alpha-E1, alpha-M290 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004288	164091	PAQR7	http://www.ncbi.nlm.nih.gov/gene/?term=164091	"MPRA, PGLP, mSR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004289	164091	PAQR7	http://www.ncbi.nlm.nih.gov/gene/?term=164091	"MPRA, PGLP, mSR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004290	16410	Itgav	http://www.ncbi.nlm.nih.gov/gene/?term=16410	"1110004F14Rik, 2610028E01Rik, CD51, D430040G12Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004291	16410	Itgav	http://www.ncbi.nlm.nih.gov/gene/?term=16410	"1110004F14Rik, 2610028E01Rik, CD51, D430040G12Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004292	16412	Itgb1	http://www.ncbi.nlm.nih.gov/gene/?term=16412	"4633401G24Rik, AA409975, AA960159, CD29, ENSMUSG00000051907, Fnrb, Gm9863, gpIIa "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004293	16412	Itgb1	http://www.ncbi.nlm.nih.gov/gene/?term=16412	"4633401G24Rik, AA409975, AA960159, CD29, ENSMUSG00000051907, Fnrb, Gm9863, gpIIa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004294	16415	Itgb2l	http://www.ncbi.nlm.nih.gov/gene/?term=16415	"5033406G21Rik, pactolus "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004295	1641	DCX	http://www.ncbi.nlm.nih.gov/gene/?term=1641	"DBCN, DC, LISX, SCLH, XLIS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004296	1641	DCX	http://www.ncbi.nlm.nih.gov/gene/?term=1641	"DBCN, DC, LISX, SCLH, XLIS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004297	16423	Cd47	http://www.ncbi.nlm.nih.gov/gene/?term=16423	"9130415E20Rik, AA407862, AI848868, AW108519, B430305P08Rik, IAP, Itgp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004298	16428	Itk	http://www.ncbi.nlm.nih.gov/gene/?term=16428	"Emt, Tcsk, Tsk "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004299	1642	DDB1	http://www.ncbi.nlm.nih.gov/gene/?term=1642	"DDBA, UV-DDB1, XAP1, XPCE, XPE, XPE-BF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004300	1642	DDB1	http://www.ncbi.nlm.nih.gov/gene/?term=1642	"DDBA, UV-DDB1, XAP1, XPCE, XPE, XPE-BF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004301	1642	DDB1	http://www.ncbi.nlm.nih.gov/gene/?term=1642	"DDBA, UV-DDB1, XAP1, XPCE, XPE, XPE-BF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004302	16430	Stt3a	http://www.ncbi.nlm.nih.gov/gene/?term=16430	"AA408947, BB081708, Itm1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004303	16432	Itm2b	http://www.ncbi.nlm.nih.gov/gene/?term=16432	"AI256040, Bri, Bri2, Bricd2b, D14Sel6, E25BMM, imBRI2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004304	16438	Itpr1	http://www.ncbi.nlm.nih.gov/gene/?term=16438	"D6Pas2, ENSMUSG00000072853, Gm10429, IP3R1, InsP3R, Ip3r, Itpr-1, P400, Pcp-1, Pcp1, opt, wblo "	mRNA	Mus musculus	25821909	Dendrite	Neuron	Fluorescence in situ hybridization	"DISC1 colocalizes with HZF and ITPR1 mRNA in hippocampal dendrites and directly associates with neuronal mRNAs, including ITPR1 mRNA.  DISC1 colocalized with HZF and Itpr1 mRNA in hippocampal dendrites. "
RLID00004305	1643	DDB2	http://www.ncbi.nlm.nih.gov/gene/?term=1643	"DDBB, UV-DDB2, XPE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004306	1643	DDB2	http://www.ncbi.nlm.nih.gov/gene/?term=1643	"DDBB, UV-DDB2, XPE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004307	16443	Itsn1	http://www.ncbi.nlm.nih.gov/gene/?term=16443	"AA517634, AA545208, AI316805, AI839402, AI848451, Ehsh1, Ese1, Itsn, Sh3p17 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004308	16443	Itsn1	http://www.ncbi.nlm.nih.gov/gene/?term=16443	"AA517634, AA545208, AI316805, AI839402, AI848451, Ehsh1, Ese1, Itsn, Sh3p17 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004309	16447	Ivl	http://www.ncbi.nlm.nih.gov/gene/?term=16447	1110019C06Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004310	16452	Jak2	http://www.ncbi.nlm.nih.gov/gene/?term=16452	Fd17	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004311	1645	AKR1C1	http://www.ncbi.nlm.nih.gov/gene/?term=1645	"2-ALPHA-HSD, 20-ALPHA-HSD, C9, DD1, DD1/DD2, DDH, DDH1, H-37, HAKRC, HBAB, MBAB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004312	16467	Atcay	http://www.ncbi.nlm.nih.gov/gene/?term=16467	"3322401A10Rik, BB077577, BNIP-H, CLAC, hes, ji "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004313	16476	Jun	http://www.ncbi.nlm.nih.gov/gene/?term=16476	"AP-1c, c-jun, Jun "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004314	16478	Jund	http://www.ncbi.nlm.nih.gov/gene/?term=16478	Jund1	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004315	1647	GADD45A	http://www.ncbi.nlm.nih.gov/gene/?term=1647	"DDIT1, GADD45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004316	16480	Jup	http://www.ncbi.nlm.nih.gov/gene/?term=16480	"Ctnng, D930025P04Rik, PG "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004317	164832	LONRF2	http://www.ncbi.nlm.nih.gov/gene/?term=164832	RNF192	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004318	16485	Kcna1	http://www.ncbi.nlm.nih.gov/gene/?term=16485	"AI840627, Kca1-1, Kv1.1, MBK1, Mk-1, Shak, mceph "	mRNA	Mus musculus	21233214	Axon	Neuron	RT-PCR	"Figure 3: Presynaptic localization of Kv1.1, -1.2, -.3, and -1.6 on dopamine axons of the dorsal striatum.  Data are collected from Figure 3. "
RLID00004319	16485	Kcna1	http://www.ncbi.nlm.nih.gov/gene/?term=16485	"AI840627, Kca1-1, Kv1.1, MBK1, Mk-1, Shak, mceph "	mRNA	Mus musculus	26512708	Axon	ForeBrain	Immunoprecipitation|RIP-Chip	"HuD has also been implicated in axonal localization of other neuronal mRNAs including Tau, Neuritin/CPG15, Kv.1.1 and CaMKIIα mRNAs "
RLID00004320	16490	Kcna2	http://www.ncbi.nlm.nih.gov/gene/?term=16490	"Akr6a4, ENSMUSG00000074335, Gm10672, Kca1-2, Kv1.2, Mk-2 "	mRNA	Mus musculus	21233214	Axon	Neuron	RT-PCR	"Figure 3: Presynaptic localization of Kv1.1, -1.2, -.3, and -1.6 on dopamine axons of the dorsal striatum.  Data are collected from Figure 3. "
RLID00004321	16491	Kcna3	http://www.ncbi.nlm.nih.gov/gene/?term=16491	"Kca1-3, Kv1.3, Mk-3 "	mRNA	Mus musculus	21233214	Axon	Neuron	RT-PCR	"Figure 3: Presynaptic localization of Kv1.1, -1.2, -.3, and -1.6 on dopamine axons of the dorsal striatum.  Data are collected from Figure 3. "
RLID00004322	16494	Kcna6	http://www.ncbi.nlm.nih.gov/gene/?term=16494	"Kv1.6, MK1.6 "	mRNA	Mus musculus	21233214	Axon	Neuron	RT-PCR	"Figure 3: Presynaptic localization of Kv1.1, -1.2, -.3, and -1.6 on dopamine axons of the dorsal striatum.  Data are collected from Figure 3. "
RLID00004323	16497	Kcnab1	http://www.ncbi.nlm.nih.gov/gene/?term=16497	"Akr8a8, Kvbeta1.1, mKv(beta)1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004324	16498	Kcnab2	http://www.ncbi.nlm.nih.gov/gene/?term=16498	"F5, I2rf5, Kcnb3, kv-beta-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004325	1649	DDIT3	http://www.ncbi.nlm.nih.gov/gene/?term=1649	"CEBPZ, CHOP, CHOP-10, CHOP10, GADD153 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004326	1649	DDIT3	http://www.ncbi.nlm.nih.gov/gene/?term=1649	"CEBPZ, CHOP, CHOP-10, CHOP10, GADD153 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004327	1649	DDIT3	http://www.ncbi.nlm.nih.gov/gene/?term=1649	"CEBPZ, CHOP, CHOP-10, CHOP10, GADD153 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004328	1649	DDIT3	http://www.ncbi.nlm.nih.gov/gene/?term=1649	"CEBPZ, CHOP, CHOP-10, CHOP10, GADD153 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004329	164	AP1G1	http://www.ncbi.nlm.nih.gov/gene/?term=164	"ADTG, CLAPG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004330	164	AP1G1	http://www.ncbi.nlm.nih.gov/gene/?term=164	"ADTG, CLAPG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004331	164	AP1G1	http://www.ncbi.nlm.nih.gov/gene/?term=164	"ADTG, CLAPG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004332	16500	Kcnb1	http://www.ncbi.nlm.nih.gov/gene/?term=16500	"Kcr1-1, Kv2.1, Shab "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004333	16508	Kcnd2	http://www.ncbi.nlm.nih.gov/gene/?term=16508	"AI839615, AW555701, Kv4.2, R75121, mKIAA1044 "	mRNA	Mus musculus	22099464	Dendrite	Hippocampus	Fluorescence in situ hybridization	"Moreover, we found dendritic localization of Kv4.2 mRNA in the CA1 dendritic field of the hippocampus (Figure 1A). "
RLID00004334	1650	DDOST	http://www.ncbi.nlm.nih.gov/gene/?term=1650	"AGER1, CDG1R, OKSWcl45, OST, OST48, WBP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004335	1650	DDOST	http://www.ncbi.nlm.nih.gov/gene/?term=1650	"AGER1, CDG1R, OKSWcl45, OST, OST48, WBP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004336	1650	DDOST	http://www.ncbi.nlm.nih.gov/gene/?term=1650	"AGER1, CDG1R, OKSWcl45, OST, OST48, WBP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004337	16514	Kcnj11	http://www.ncbi.nlm.nih.gov/gene/?term=16514	"Kir6.2, mBIR "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004338	16516	Kcnj15	http://www.ncbi.nlm.nih.gov/gene/?term=16516	"4930414N08Rik, AI182284, AI267127, IRKK, Kir4.2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004339	1652	DDT	http://www.ncbi.nlm.nih.gov/gene/?term=1652	DDCT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004340	1652	DDT	http://www.ncbi.nlm.nih.gov/gene/?term=1652	DDCT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004341	1652	DDT	http://www.ncbi.nlm.nih.gov/gene/?term=1652	DDCT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004342	165324	UBXN2A	http://www.ncbi.nlm.nih.gov/gene/?term=165324	UBXD4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004343	165324	UBXN2A	http://www.ncbi.nlm.nih.gov/gene/?term=165324	UBXD4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004344	16536	Kcnq2	http://www.ncbi.nlm.nih.gov/gene/?term=16536	"HNSPC, KQT2, Nmf134 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004345	1653	DDX1	http://www.ncbi.nlm.nih.gov/gene/?term=1653	"DBP-RB, UKVH5d "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004346	1653	DDX1	http://www.ncbi.nlm.nih.gov/gene/?term=1653	"DBP-RB, UKVH5d "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004347	16543	Mdfic	http://www.ncbi.nlm.nih.gov/gene/?term=16543	"Kdt1, Mdfid "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004348	16548	Khk	http://www.ncbi.nlm.nih.gov/gene/?term=16548		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004349	1654	DDX3X	http://www.ncbi.nlm.nih.gov/gene/?term=1654	"CAP-Rf, DBX, DDX14, DDX3, HLP2, MRX102 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004350	1654	DDX3X	http://www.ncbi.nlm.nih.gov/gene/?term=1654	"CAP-Rf, DBX, DDX14, DDX3, HLP2, MRX102 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004351	1654	DDX3X	http://www.ncbi.nlm.nih.gov/gene/?term=1654	"CAP-Rf, DBX, DDX14, DDX3, HLP2, MRX102 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004352	1655	DDX5	http://www.ncbi.nlm.nih.gov/gene/?term=1655	"G17P1, HLR1, HUMP68, p68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004353	1655	DDX5	http://www.ncbi.nlm.nih.gov/gene/?term=1655	"G17P1, HLR1, HUMP68, p68 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004354	16561	Kif1b	http://www.ncbi.nlm.nih.gov/gene/?term=16561	"A530096N05Rik, AI448212, AI506502, D4Mil1e, KIF1Bp130, KIF1Bp204 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004355	16563	Kif2a	http://www.ncbi.nlm.nih.gov/gene/?term=16563	"C530030B14Rik, Kif2, Kns2, M-kinesin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004356	16568	Kif3a	http://www.ncbi.nlm.nih.gov/gene/?term=16568	"Kif3, Kifl, Kns3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004357	1656	DDX6	http://www.ncbi.nlm.nih.gov/gene/?term=1656	"HLR2, P54, RCK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004358	1656	DDX6	http://www.ncbi.nlm.nih.gov/gene/?term=1656	"HLR2, P54, RCK "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004359	1656	DDX6	http://www.ncbi.nlm.nih.gov/gene/?term=1656	"HLR2, P54, RCK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004360	16570	Kif3c	http://www.ncbi.nlm.nih.gov/gene/?term=16570	mKIAA4058	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004361	16573	Kif5b	http://www.ncbi.nlm.nih.gov/gene/?term=16573	"AL022807, Khc, Khcs, Kns1, Ukhc "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00004362	16574	Kif5c	http://www.ncbi.nlm.nih.gov/gene/?term=16574	"KINN, Khc, NKHC, NKHC2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004363	16579	Kifap3	http://www.ncbi.nlm.nih.gov/gene/?term=16579	"KAP-3, KAP3, SMAP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004364	1657	DMXL1	http://www.ncbi.nlm.nih.gov/gene/?term=1657		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004365	1657	DMXL1	http://www.ncbi.nlm.nih.gov/gene/?term=1657		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004366	16588	Kin	http://www.ncbi.nlm.nih.gov/gene/?term=16588	Kin17	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004367	16589	Uhmk1	http://www.ncbi.nlm.nih.gov/gene/?term=16589	"4732477C12Rik, 4930500M09Rik, AA673513, AI449218, AU021979, KIS, Kist, P-CIP2 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004368	165918	RNF168	http://www.ncbi.nlm.nih.gov/gene/?term=165918	hRNF168	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004369	16592	Fabp5	http://www.ncbi.nlm.nih.gov/gene/?term=16592	"E-FABP, Fabpe, Klbp, PA-FABP, mal1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004370	16594	Klc2	http://www.ncbi.nlm.nih.gov/gene/?term=16594	"8030455F02Rik, AW212649, KLC 2, KLC-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004371	16598	Klf2	http://www.ncbi.nlm.nih.gov/gene/?term=16598	Lklf	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004372	16599	Klf3	http://www.ncbi.nlm.nih.gov/gene/?term=16599	"9930027G08Rik, AL024007, Bklf, Tef-2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004373	1659	DHX8	http://www.ncbi.nlm.nih.gov/gene/?term=1659	"DDX8, HRH1, PRP22, PRPF22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004374	1659	DHX8	http://www.ncbi.nlm.nih.gov/gene/?term=1659	"DDX8, HRH1, PRP22, PRPF22 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004375	165	AEBP1	http://www.ncbi.nlm.nih.gov/gene/?term=165	ACLP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004376	16600	Klf4	http://www.ncbi.nlm.nih.gov/gene/?term=16600	"EZF, Gklf, Zie "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004377	166012	CHST13	http://www.ncbi.nlm.nih.gov/gene/?term=166012	C4ST3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004378	1660	DHX9	http://www.ncbi.nlm.nih.gov/gene/?term=1660	"DDX9, LKP, NDH2, NDHII, RHA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004379	1660	DHX9	http://www.ncbi.nlm.nih.gov/gene/?term=1660	"DDX9, LKP, NDH2, NDHII, RHA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004380	1660	DHX9	http://www.ncbi.nlm.nih.gov/gene/?term=1660	"DDX9, LKP, NDH2, NDHII, RHA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004381	16612	Klk1	http://www.ncbi.nlm.nih.gov/gene/?term=16612	"0610007D04Rik, KAL-B, Kalb6, Klk6, mGk-6, Klk1 "	mRNA	Mus musculus	2033241	Nucleus	Submandibular gland	Autoradiography	Resolution obtained with this 3H-labeled probe showed mGK-6 mRNA in striated duct cells to be located on RER and in the nucleus and perinuclear area of the cell.
RLID00004382	16612	Klk1	http://www.ncbi.nlm.nih.gov/gene/?term=16612	"0610007D04Rik, KAL-B, Kalb6, Klk6, mGk-6, Klk1 "	mRNA	Mus musculus	2033241	Perinuclear	Submandibular gland	Autoradiography	Resolution obtained with this 3H-labeled probe showed mGK-6 mRNA in striated duct cells to be located on RER and in the nucleus and perinuclear area of the cell.
RLID00004383	16612	Klk1	http://www.ncbi.nlm.nih.gov/gene/?term=16612	"0610007D04Rik, KAL-B, Kalb6, Klk6, mGk-6, Klk1 "	mRNA	Mus musculus	2033241	Endoplasmic reticulum	Submandibular gland	Autoradiography	Resolution obtained with this 3H-labeled probe showed mGK-6 mRNA in striated duct cells to be located on RER and in the nucleus and perinuclear area of the cell.
RLID00004384	16619	Klk1b27	http://www.ncbi.nlm.nih.gov/gene/?term=16619	"Gk27, Klk21l, Klk27, mGK-27 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004385	1662	DDX10	http://www.ncbi.nlm.nih.gov/gene/?term=1662	HRH-J8	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004386	1662	DDX10	http://www.ncbi.nlm.nih.gov/gene/?term=1662	HRH-J8	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004387	166336	PRICKLE2	http://www.ncbi.nlm.nih.gov/gene/?term=166336	EPM5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004388	166378	SPATA5	http://www.ncbi.nlm.nih.gov/gene/?term=166378	"AFG2, EHLMRS, SPAF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004389	166378	SPATA5	http://www.ncbi.nlm.nih.gov/gene/?term=166378	"AFG2, EHLMRS, SPAF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004390	166379	BBS12	http://www.ncbi.nlm.nih.gov/gene/?term=166379	C4orf24	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004391	1663	DDX11	http://www.ncbi.nlm.nih.gov/gene/?term=1663	"CHL1, CHLR1, KRG2, WABS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004392	1663	DDX11	http://www.ncbi.nlm.nih.gov/gene/?term=1663	"CHL1, CHLR1, KRG2, WABS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004393	16643	Klrd1	http://www.ncbi.nlm.nih.gov/gene/?term=16643	CD94	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004394	16656	Hivep3	http://www.ncbi.nlm.nih.gov/gene/?term=16656	"2900056N03Rik, A130075N07, AI848000, E030045D18Rik, KBP-1, KBP1, Krc, Rc, Schnurri-3, Shn3, Zas3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004395	1665	DHX15	http://www.ncbi.nlm.nih.gov/gene/?term=1665	"DBP1, DDX15, HRH2, PRP43, PRPF43, PrPp43p "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004396	16661	Krt10	http://www.ncbi.nlm.nih.gov/gene/?term=16661	"D130054E02Rik, K10, K1C1, Krt-1.10, Krt1-10 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004397	16666	Krt16	http://www.ncbi.nlm.nih.gov/gene/?term=16666	"AI324768, CK-16, K16, Krt1-16 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004398	1666	DECR1	http://www.ncbi.nlm.nih.gov/gene/?term=1666	"DECR, NADPH, SDR18C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004399	1666	DECR1	http://www.ncbi.nlm.nih.gov/gene/?term=1666	"DECR, NADPH, SDR18C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004400	16670	Krt32	http://www.ncbi.nlm.nih.gov/gene/?term=16670	"Ha3, Hka2, K32, Krt1-2, Krtha2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004401	16675	Krt27	http://www.ncbi.nlm.nih.gov/gene/?term=16675	"CK-27, Krt1-c29, mIRSa3.1, stpm "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004402	166815	TIGD2	http://www.ncbi.nlm.nih.gov/gene/?term=166815	HEL106	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004403	166929	SGMS2	http://www.ncbi.nlm.nih.gov/gene/?term=166929	SMS2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004404	166968	MIER3	http://www.ncbi.nlm.nih.gov/gene/?term=166968		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004405	166	AES	http://www.ncbi.nlm.nih.gov/gene/?term=166	"AES-1, AES-2, ESP1, GRG, GRG5, Grg-5, TLE5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004406	166	AES	http://www.ncbi.nlm.nih.gov/gene/?term=166	"AES-1-2, ESP1, GRG, GRG5, Grg-5, TLE5, AES "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004407	16709	Ktn1	http://www.ncbi.nlm.nih.gov/gene/?term=16709		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004408	167153	PAPD4	http://www.ncbi.nlm.nih.gov/gene/?term=167153	"GLD2, TUT2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004409	167153	PAPD4	http://www.ncbi.nlm.nih.gov/gene/?term=167153	"GLD2, TUT2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004410	167153	PAPD4	http://www.ncbi.nlm.nih.gov/gene/?term=167153	"GLD2, TUT2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004411	167227	DCP2	http://www.ncbi.nlm.nih.gov/gene/?term=167227	NUDT20	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004412	167227	DCP2	http://www.ncbi.nlm.nih.gov/gene/?term=167227	NUDT20	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004413	167227	DCP2	http://www.ncbi.nlm.nih.gov/gene/?term=167227	NUDT20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004414	16728	L1cam	http://www.ncbi.nlm.nih.gov/gene/?term=16728	"CD171, L1, N-CAM-L1, NCAM-L1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004415	1672	DEFB1	http://www.ncbi.nlm.nih.gov/gene/?term=1672	"BD1, DEFB-1, DEFB101, HBD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004416	1675	CFD	http://www.ncbi.nlm.nih.gov/gene/?term=1675	"ADIPSIN, ADN, DF, PFD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004417	1675	CFD	http://www.ncbi.nlm.nih.gov/gene/?term=1675	"ADIPSIN, ADN, DF, PFD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004418	16765	Stmn1	http://www.ncbi.nlm.nih.gov/gene/?term=16765	"19k, Lag, Lap18, Op18, P18, P19, Pig, Pp17, Pp18, Pp19, Pr22, Smn "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004419	167691	LCA5	http://www.ncbi.nlm.nih.gov/gene/?term=167691	C6orf152	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004420	1676	DFFA	http://www.ncbi.nlm.nih.gov/gene/?term=1676	"DFF-45, DFF1, ICAD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004421	1676	DFFA	http://www.ncbi.nlm.nih.gov/gene/?term=1676	"DFF-45, DFF1, ICAD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004422	1676	DFFA	http://www.ncbi.nlm.nih.gov/gene/?term=1676	"DFF-45, DFF1, ICAD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004423	1676	DFFA	http://www.ncbi.nlm.nih.gov/gene/?term=1676	"DFF-45, DFF1, ICAD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004424	16775	Lama4	http://www.ncbi.nlm.nih.gov/gene/?term=16775		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004425	1677	DFFB	http://www.ncbi.nlm.nih.gov/gene/?term=1677	"CAD, CPAN, DFF-40, DFF2, DFF40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004426	16780	Lamb3	http://www.ncbi.nlm.nih.gov/gene/?term=16780		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004427	16782	Lamc2	http://www.ncbi.nlm.nih.gov/gene/?term=16782	AA589349	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004428	16785	Rpsa	http://www.ncbi.nlm.nih.gov/gene/?term=16785	"67kDa, 67lr, AL022858, Lamr, Lamr1, Lamrl1, MLR, P40, P40-3, P40-8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004429	16785	Rpsa	http://www.ncbi.nlm.nih.gov/gene/?term=16785	"67kDa, 67lr, AL022858, Lamr, Lamr1, Lamrl1, MLR, P40, P40-3, P40-8 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004430	16792	Laptm5	http://www.ncbi.nlm.nih.gov/gene/?term=16792	E3	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004431	16795	Large	http://www.ncbi.nlm.nih.gov/gene/?term=16795	"BPFD#36, Gyltl1a, Mbp-1, Mbp1, enr, fg, froggy, myd "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004432	16815	Lbx2	http://www.ncbi.nlm.nih.gov/gene/?term=16815	Lbx2h	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004433	16818	Lck	http://www.ncbi.nlm.nih.gov/gene/?term=16818	"Hck-3, Lsk, Lskt, p56<lck>, p56Lck "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004434	16828	Ldha	http://www.ncbi.nlm.nih.gov/gene/?term=16828	"Ldh1, Ldhm, l7R2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004435	16828	Ldha	http://www.ncbi.nlm.nih.gov/gene/?term=16828	"Ldh1, Ldhm, l7R2 "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00004436	16828	Ldha	http://www.ncbi.nlm.nih.gov/gene/?term=16828	"Ldh1, Ldhm, l7R2 "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00004437	16832	Ldhb	http://www.ncbi.nlm.nih.gov/gene/?term=16832	"AI790582, H-Ldh, LDH-B, LDH-H, Ldh-2, Ldh2 "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00004438	16832	Ldhb	http://www.ncbi.nlm.nih.gov/gene/?term=16832	"AI790582, H-Ldh, LDH-B, LDH-H, Ldh-2, Ldh2 "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00004439	16833	Ldhc	http://www.ncbi.nlm.nih.gov/gene/?term=16833	"LDH-C4, Ldh-3, Ldh-x, Ldh34, Ldhc "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00004440	16833	Ldhc	http://www.ncbi.nlm.nih.gov/gene/?term=16833	"LDH-C4, Ldh-3, Ldh-x, Ldh34, Ldhc "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00004441	16834	Cog1	http://www.ncbi.nlm.nih.gov/gene/?term=16834	"6030445I15, Ldlb, mKIAA1381 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004442	16835	Ldlr	http://www.ncbi.nlm.nih.gov/gene/?term=16835	Hlb301	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004443	168374	ZNF92	http://www.ncbi.nlm.nih.gov/gene/?term=168374	"HEL-203, HPF12, HTF12, TF12 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004444	168374	ZNF92	http://www.ncbi.nlm.nih.gov/gene/?term=168374	"HEL-203, HPF12, HTF12, TF12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004445	16842	Lef1	http://www.ncbi.nlm.nih.gov/gene/?term=16842	"3000002B05, AI451430, Lef-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004446	168451	THAP5	http://www.ncbi.nlm.nih.gov/gene/?term=168451		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004447	168451	THAP5	http://www.ncbi.nlm.nih.gov/gene/?term=168451		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004448	16846	Lep	http://www.ncbi.nlm.nih.gov/gene/?term=16846	"ob, obese "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004449	168544	ZNF467	http://www.ncbi.nlm.nih.gov/gene/?term=168544	"EZI, Zfp467 "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00004450	16855	Lgals4	http://www.ncbi.nlm.nih.gov/gene/?term=16855	gal-4	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004451	16865	Eif2d	http://www.ncbi.nlm.nih.gov/gene/?term=16865	"D1Ertd5e, Lgtn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004452	16870	Lhx2	http://www.ncbi.nlm.nih.gov/gene/?term=16870	"LH2A, Lh-2, Lim2, ap, apterous "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004453	16874	Lhx6	http://www.ncbi.nlm.nih.gov/gene/?term=16874	Lhx6.1	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004454	168850	ZNF800	http://www.ncbi.nlm.nih.gov/gene/?term=168850		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004455	168850	ZNF800	http://www.ncbi.nlm.nih.gov/gene/?term=168850		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004456	16898	Rps2	http://www.ncbi.nlm.nih.gov/gene/?term=16898	"Llrep3, S4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004457	16898	Rps2	http://www.ncbi.nlm.nih.gov/gene/?term=16898	"Llrep3, S4 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004458	16905	Lmna	http://www.ncbi.nlm.nih.gov/gene/?term=16905	Dhe	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004459	16905	Lmna	http://www.ncbi.nlm.nih.gov/gene/?term=16905	Dhe	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004460	1690	COCH	http://www.ncbi.nlm.nih.gov/gene/?term=1690	"COCH-5B2, COCH5B2, DFNA9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004461	1690	COCH	http://www.ncbi.nlm.nih.gov/gene/?term=1690	"COCH-5B25B2, DFNA9, COCH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004462	169166	SNX31	http://www.ncbi.nlm.nih.gov/gene/?term=169166		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004463	169200	TMEM64	http://www.ncbi.nlm.nih.gov/gene/?term=169200		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004464	16939	Lor	http://www.ncbi.nlm.nih.gov/gene/?term=16939	"AI036317, S77319 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004465	16952	Anxa1	http://www.ncbi.nlm.nih.gov/gene/?term=16952	"Anx-1, Anx-A1, C430014K04Rik, Lpc-1, Lpc1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004466	169611	OLFML2A	http://www.ncbi.nlm.nih.gov/gene/?term=169611	PRO34319	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004467	169611	OLFML2A	http://www.ncbi.nlm.nih.gov/gene/?term=169611	PRO34319	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004468	169714	QSOX2	http://www.ncbi.nlm.nih.gov/gene/?term=169714	"QSCN6L1, SOXN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004469	169714	QSOX2	http://www.ncbi.nlm.nih.gov/gene/?term=169714	"QSCN6L1, SOXN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004470	169714	QSOX2	http://www.ncbi.nlm.nih.gov/gene/?term=169714	"QSCN6L1, SOXN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004471	16974	Lrp6	http://www.ncbi.nlm.nih.gov/gene/?term=16974	"C030016K15Rik, Cd, Gw, ska26, ska<m26Jus>, skax26 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004472	16975	Lrp8	http://www.ncbi.nlm.nih.gov/gene/?term=16975	"4932703M08Rik, AA921429, AI848122, ApoER2, Lr8b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004473	16979	Lrrn1	http://www.ncbi.nlm.nih.gov/gene/?term=16979	"2810047E21Rik, NLRR-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004474	16981	Lrrn3	http://www.ncbi.nlm.nih.gov/gene/?term=16981	NLRR-3	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004475	169841	ZNF169	http://www.ncbi.nlm.nih.gov/gene/?term=169841		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004476	16985	Lsp1	http://www.ncbi.nlm.nih.gov/gene/?term=16985	"Lsp-1, WP34, p50, pp52 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004477	16994	Ltb	http://www.ncbi.nlm.nih.gov/gene/?term=16994	"AI662801, LTbeta, Tnfc, Tnfsf3, Tnlg1c, p33 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004478	16	AARS	http://www.ncbi.nlm.nih.gov/gene/?term=16	"CMT2N, EIEE29 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004479	16	AARS	http://www.ncbi.nlm.nih.gov/gene/?term=16	"CMT2N, EIEE29 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004480	16	AARS	http://www.ncbi.nlm.nih.gov/gene/?term=16	"CMT2N, EIEE29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004481	17005	Ltk	http://www.ncbi.nlm.nih.gov/gene/?term=17005		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004482	170082	TCEANC	http://www.ncbi.nlm.nih.gov/gene/?term=170082		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004483	170384	FUT11	http://www.ncbi.nlm.nih.gov/gene/?term=170384		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004484	170392	OIT3	http://www.ncbi.nlm.nih.gov/gene/?term=170392	LZP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004485	170439	Elovl6	http://www.ncbi.nlm.nih.gov/gene/?term=170439	"C77826, FAE, LCE "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004486	170463	SSBP4	http://www.ncbi.nlm.nih.gov/gene/?term=170463		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004487	170463	SSBP4	http://www.ncbi.nlm.nih.gov/gene/?term=170463		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004488	170506	DHX36	http://www.ncbi.nlm.nih.gov/gene/?term=170506	"DDX36, G4R1, MLEL1, RHAU "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004489	170506	DHX36	http://www.ncbi.nlm.nih.gov/gene/?term=170506	"DDX36, G4R1, MLEL1, RHAU "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004490	17057	Klrb1a	http://www.ncbi.nlm.nih.gov/gene/?term=17057	"Ly55a, NKR-P1.7, NKR-P1A, NKRP12, Nkrp1-a, Nkrp1a, ly-55A "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004491	170622	COMMD6	http://www.ncbi.nlm.nih.gov/gene/?term=170622	Acrg	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004492	170622	COMMD6	http://www.ncbi.nlm.nih.gov/gene/?term=170622	Acrg	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004493	170622	COMMD6	http://www.ncbi.nlm.nih.gov/gene/?term=170622	Acrg	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004494	170626	XAGE3	http://www.ncbi.nlm.nih.gov/gene/?term=170626	"CT12.3a, CT12.3b, GAGED4, PLAC6, XAGE-3, pp9012 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004495	170639	Olfr78	http://www.ncbi.nlm.nih.gov/gene/?term=170639	"4633402A21Rik, MOL2.3, MOR18-2, Or51e2, PSGR, RA1c "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004496	170679	PSORS1C1	http://www.ncbi.nlm.nih.gov/gene/?term=170679	"C6orf16, SEEK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004497	170691	ADAMTS17	http://www.ncbi.nlm.nih.gov/gene/?term=170691		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004498	170691	ADAMTS17	http://www.ncbi.nlm.nih.gov/gene/?term=170691		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004499	170691	ADAMTS17	http://www.ncbi.nlm.nih.gov/gene/?term=170691		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004500	170707	Usp48	http://www.ncbi.nlm.nih.gov/gene/?term=170707	"2810449C13Rik, AI115503, BC021769, D330022K21Rik, Usp31 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004501	170740	Zfp287	http://www.ncbi.nlm.nih.gov/gene/?term=170740	"B230333C16Rik, SKAT-2, Skat2, Znf287, mszf16, mszf74 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004502	170742	Sertad3	http://www.ncbi.nlm.nih.gov/gene/?term=170742	"AW124805, D1Mgi51, Rbt1, Sei3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004503	170758	Rac3	http://www.ncbi.nlm.nih.gov/gene/?term=170758	Rac1B	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004504	170760	Acbd3	http://www.ncbi.nlm.nih.gov/gene/?term=170760	"60kDa, 8430407O11Rik, D1Ertd10e, GCP60, GOLPH1, Gocap1, Pap7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004505	170762	Nup155	http://www.ncbi.nlm.nih.gov/gene/?term=170762	"D930027M19Rik, mKIAA0791 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004506	17076	Ly75	http://www.ncbi.nlm.nih.gov/gene/?term=17076	"CD205, DEC-205, DEC205 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004507	170770	Bbc3	http://www.ncbi.nlm.nih.gov/gene/?term=170770	"PUMA, PUMA/JFY1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004508	170789	Acot8	http://www.ncbi.nlm.nih.gov/gene/?term=170789	"PTE-2, Pte1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004509	170791	Rbm39	http://www.ncbi.nlm.nih.gov/gene/?term=170791	"1500012C14Rik, 2310040E03Rik, B330012G18Rik, C79248, R75070, Rnpc2, caper "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004510	170822	Usp33	http://www.ncbi.nlm.nih.gov/gene/?term=170822	"9830169D19Rik, AA409780, Vdu1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004511	170823	Glmn	http://www.ncbi.nlm.nih.gov/gene/?term=170823	"9330160J16Rik, AW227515, Fap48, Fap68 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004512	17082	Il1rl1	http://www.ncbi.nlm.nih.gov/gene/?term=17082	"DER4, Fit-1, Ly84, ST2L, St2, St2-rs1, T1, T1/ST2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004513	17085	Ly9	http://www.ncbi.nlm.nih.gov/gene/?term=17085	"AI893573, CD229, Lgp100, Ly-9, SLAMF3, T100 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004514	17087	Ly96	http://www.ncbi.nlm.nih.gov/gene/?term=17087	"ESOP-1, MD-2, MD2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004515	170930	Sumo2	http://www.ncbi.nlm.nih.gov/gene/?term=170930	"SUMO-2, Smt3A, Smt3b, Smt3h2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004516	170930	Sumo2	http://www.ncbi.nlm.nih.gov/gene/?term=170930	"Smt3A, Smt3b, SUMO-2, Smt3h2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004517	170938	Zfp617	http://www.ncbi.nlm.nih.gov/gene/?term=170938	Zfps11-6	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004518	170942	Erdr1	http://www.ncbi.nlm.nih.gov/gene/?term=170942	edr	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004519	170954	PPP1R18	http://www.ncbi.nlm.nih.gov/gene/?term=170954	"HKMT1098, KIAA1949 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004520	170958	ZNF525	http://www.ncbi.nlm.nih.gov/gene/?term=170958		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004521	171017	ZNF384	http://www.ncbi.nlm.nih.gov/gene/?term=171017	"CAGH1, CAGH1A, CIZ, ERDA2, NMP4, NP, TNRC1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004522	171017	ZNF384	http://www.ncbi.nlm.nih.gov/gene/?term=171017	"CAGH1, CAGH1A, CIZ, ERDA2, NMP4, NP, TNRC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004523	17101	Lyst	http://www.ncbi.nlm.nih.gov/gene/?term=17101	"D13Sfk13, beige, bg "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004524	171023	ASXL1	http://www.ncbi.nlm.nih.gov/gene/?term=171023	"BOPS, MDS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004525	171023	ASXL1	http://www.ncbi.nlm.nih.gov/gene/?term=171023	"BOPS, MDS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004526	171024	SYNPO2	http://www.ncbi.nlm.nih.gov/gene/?term=171024		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004527	171024	SYNPO2	http://www.ncbi.nlm.nih.gov/gene/?term=171024		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004528	171024	SYNPO2	http://www.ncbi.nlm.nih.gov/gene/?term=171024		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004529	171162	Reg3a	http://www.ncbi.nlm.nih.gov/gene/?term=171162	"Pap2, PapII "	mRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"By quantitative fluorescent in situ hybridization combined with immunofluorescence to unambiguously distinguish intra-axonal mRNAs, we show that regenerating spinal cord axons contain β-actin, GAP-43, Neuritin, Reg3a, Hamp, and Importin β1 mRNAs.  "
RLID00004530	171166	Mcoln3	http://www.ncbi.nlm.nih.gov/gene/?term=171166	"6720490O21Rik, TRPML3, Va "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004531	17118	Marcks	http://www.ncbi.nlm.nih.gov/gene/?term=17118	"Macs, PKCSL "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004532	171199	Vmn1r18	http://www.ncbi.nlm.nih.gov/gene/?term=171199	V1rc26	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004533	171212	Galnt10	http://www.ncbi.nlm.nih.gov/gene/?term=171212	"AU018154, C330012K04Rik, GalNAc-T10, GalNAc-T9, Galnt9, ppGaNTase "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004534	171228	Vmn1r225	http://www.ncbi.nlm.nih.gov/gene/?term=171228	V1re5	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004535	17122	Mxd4	http://www.ncbi.nlm.nih.gov/gene/?term=17122	"2810410A03Rik, Mad4, bHLHc12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004536	17122	Mxd4	http://www.ncbi.nlm.nih.gov/gene/?term=17122	"2810410A03Rik, Mad4, bHLHc12 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004537	171230	Vmn1r231	http://www.ncbi.nlm.nih.gov/gene/?term=171230	"V1re5, V1re7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004538	171236	Vmn1r233	http://www.ncbi.nlm.nih.gov/gene/?term=171236	V1rf5	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004539	171244	Vmn1r81	http://www.ncbi.nlm.nih.gov/gene/?term=171244	V1rg9	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004540	171250	Vmn1r206	http://www.ncbi.nlm.nih.gov/gene/?term=171250	V1rh7	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004541	171269	Vmn1r210	http://www.ncbi.nlm.nih.gov/gene/?term=171269	V1rh10	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004542	171271	Vmn1r220	http://www.ncbi.nlm.nih.gov/gene/?term=171271	V1rh12	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004543	171274	Vmn1r222	http://www.ncbi.nlm.nih.gov/gene/?term=171274	V1rh16	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004544	171285	Havcr2	http://www.ncbi.nlm.nih.gov/gene/?term=171285	"TIM-3, Tim3, Timd3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004545	17128	Smad4	http://www.ncbi.nlm.nih.gov/gene/?term=17128	"AW743858, D18Wsu70e, DPC4, Madh4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004546	17132	Maf	http://www.ncbi.nlm.nih.gov/gene/?term=17132	"2810401A20Rik, A230108G15Rik, AW047063, c-maf "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004547	17133	Maff	http://www.ncbi.nlm.nih.gov/gene/?term=17133		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004548	17134	Mafg	http://www.ncbi.nlm.nih.gov/gene/?term=17134	"AA545192, C630022N07Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004549	171361	Eef1a1	http://www.ncbi.nlm.nih.gov/gene/?term=171361	"EEF-1, EEF1A, EF1A, Eef1a2, Eef1a2l1, SI "	mRNA	Rattus norvegicus	16079402	Dendrite	Hippocampus	In situ hybridization|Immunofluorescence assay	"We demonstrate here that the mRNA for the elongation factor 1 alpha (EF1alpha) is present in vivo in the dendrites of neurons that exhibit LTP and LTD, and that its translation is locally regulated. "
RLID00004550	171381	Psd	http://www.ncbi.nlm.nih.gov/gene/?term=171381	EFA6	mRNA	Rattus norvegicus	15009133	Cell body	Hippocampus	In situ hybridization	"Our results provided definitive evidence for somatodendritic localization of EFA6A mRNA in both cultured and in vivo hyppocampal neurons by nonradioactive in situ hybridization.  In both in vivo and cultured hyppocampal neurons, the signal for EFA6A mRNA was detected in the dendrites as well as cell bodies.(Fig.2B and D) "
RLID00004551	171381	Psd	http://www.ncbi.nlm.nih.gov/gene/?term=171381	EFA6	mRNA	Rattus norvegicus	15009133	Dendrite	Hippocampus	In situ hybridization	"Our results provided definitive evidence for somatodendritic localization of EFA6A mRNA in both cultured and in vivo hyppocampal neurons by nonradioactive in situ hybridization.  In both in vivo and cultured hyppocampal neurons, the signal for EFA6A mRNA was detected in the dendrites as well as cell bodies.(Fig.2B and D) "
RLID00004552	171392	ZNF675	http://www.ncbi.nlm.nih.gov/gene/?term=171392	"TBZF, TIZ "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004553	171425	CLYBL	http://www.ncbi.nlm.nih.gov/gene/?term=171425	CLB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004554	171463	Il17rd	http://www.ncbi.nlm.nih.gov/gene/?term=171463	"2810004A10Rik, AI428510, Sef, Sef-S "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004555	171504	Apobr	http://www.ncbi.nlm.nih.gov/gene/?term=171504	"Apob-48r, Apob48r "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004556	171546	SPTSSA	http://www.ncbi.nlm.nih.gov/gene/?term=171546	"C14orf147, SSSPTA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004557	171546	SPTSSA	http://www.ncbi.nlm.nih.gov/gene/?term=171546	"C14orf147, SSSPTA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004558	171568	POLR3H	http://www.ncbi.nlm.nih.gov/gene/?term=171568	"RPC22.9, RPC8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004559	17156	Man1a2	http://www.ncbi.nlm.nih.gov/gene/?term=17156	"AI428775, AI528764, AI854422, Man1b, PCR2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004560	17156	Man1a2	http://www.ncbi.nlm.nih.gov/gene/?term=17156	"AI428775, AI528764, AI854422, Man1b, PCR2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004561	171586	ABHD3	http://www.ncbi.nlm.nih.gov/gene/?term=171586	LABH3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004562	17158	Man2a1	http://www.ncbi.nlm.nih.gov/gene/?term=17158	"Mana-2, Mana2, Map-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004563	17164	Mapkapk2	http://www.ncbi.nlm.nih.gov/gene/?term=17164	"AA960234, MAPKAP-K2, MK-2, MK2, Rps6kc1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004564	17164	Mapkapk2	http://www.ncbi.nlm.nih.gov/gene/?term=17164	"AA960234, MAPKAP-K2, MK-2, MK2, Rps6kc1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004565	17165	Mapkapk5	http://www.ncbi.nlm.nih.gov/gene/?term=17165	"MK5, PRAK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004566	17168	Nprl3	http://www.ncbi.nlm.nih.gov/gene/?term=17168	"Aag, CGTHBA, HS-26, HS-40, Mare, Phg, Prox1, m(alpha)RE "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004567	1716	DGUOK	http://www.ncbi.nlm.nih.gov/gene/?term=1716	"MTDPS3, dGK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004568	1716	DGUOK	http://www.ncbi.nlm.nih.gov/gene/?term=1716	"MTDPS3, dGK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004569	1716	DGUOK	http://www.ncbi.nlm.nih.gov/gene/?term=1716	"MTDPS3, dGK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004570	17175	Masp2	http://www.ncbi.nlm.nih.gov/gene/?term=17175	"MASP-2, MAp19 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004571	1717	DHCR7	http://www.ncbi.nlm.nih.gov/gene/?term=1717	SLOS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004572	1717	DHCR7	http://www.ncbi.nlm.nih.gov/gene/?term=1717	SLOS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004573	17180	Matn1	http://www.ncbi.nlm.nih.gov/gene/?term=17180	"CMP, Crtm, Mat1, matrilin-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004574	17181	Matn2	http://www.ncbi.nlm.nih.gov/gene/?term=17181	"Crtm2, matrilin-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004575	17183	Matn4	http://www.ncbi.nlm.nih.gov/gene/?term=17183	matrilin-4	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004576	17184	Matr3	http://www.ncbi.nlm.nih.gov/gene/?term=17184	"1110061A14Rik, 2810017I02Rik, AI841759, AW555618, D030046F20Rik, mKIAA0723 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004577	1718	DHCR24	http://www.ncbi.nlm.nih.gov/gene/?term=1718	"DCE, Nbla03646, SELADIN1, seladin-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004578	1718	DHCR24	http://www.ncbi.nlm.nih.gov/gene/?term=1718	"DCE, Nbla03646, SELADIN1, seladin-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004579	1718	DHCR24	http://www.ncbi.nlm.nih.gov/gene/?term=1718	"DCE, Nbla03646, SELADIN1, seladin-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004580	17192	Mbd3	http://www.ncbi.nlm.nih.gov/gene/?term=17192	"AI181826, AU019209 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004581	17196	Mbp	http://www.ncbi.nlm.nih.gov/gene/?term=17196	"C76307, Hmbpr, R75289, golli-mbp, jve, mld, shi "	mRNA	Mus musculus	7877439	Cytoplasm	Brain	In situ hybridization	This mRNA distribution pattern was maintained into adulthood and was consistent with the presence of MBP mRNA in distal cytoplasmic regions. 
RLID00004582	1719	DHFR	http://www.ncbi.nlm.nih.gov/gene/?term=1719	"DHFRP1, DYR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004583	1719	DHFR	http://www.ncbi.nlm.nih.gov/gene/?term=1719	"DHFRP1, DYR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004584	17217	Mcm4	http://www.ncbi.nlm.nih.gov/gene/?term=17217	"19G, AI325074, AU045576, Cdc21, Mcmd4, mKIAA4003, mcdc21 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004585	17220	Mcm7	http://www.ncbi.nlm.nih.gov/gene/?term=17220	"AI747533, Mcmd7, mCDC47 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004586	17222	Anapc1	http://www.ncbi.nlm.nih.gov/gene/?term=17222	"2610021O03Rik, AI047775, AI853536, AW547281, Apc1, Mcpr, tsg24 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004587	1723	DHODH	http://www.ncbi.nlm.nih.gov/gene/?term=1723	"DHOdehase, POADS, URA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004588	17240	Mdfi	http://www.ncbi.nlm.nih.gov/gene/?term=17240	"I-mf, I-mfa "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004589	17240	Mdfi	http://www.ncbi.nlm.nih.gov/gene/?term=17240	"I-mf, I-mfa "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004590	17246	Mdm2	http://www.ncbi.nlm.nih.gov/gene/?term=17246	"1700007J15Rik, AA415488, Mdm-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004591	17248	Mdm4	http://www.ncbi.nlm.nih.gov/gene/?term=17248	"4933417N07Rik, AA414968, AL023055, AU018793, AU021806, C85810, Mdmx "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004592	17250	Abcc1	http://www.ncbi.nlm.nih.gov/gene/?term=17250	"Abcc1ab, MRP, Mdrap, Mrp1, Abcc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004593	17256	Mea1	http://www.ncbi.nlm.nih.gov/gene/?term=17256	Mea-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004594	17258	Mef2a	http://www.ncbi.nlm.nih.gov/gene/?term=17258	A430079H05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004595	17259	Mef2b	http://www.ncbi.nlm.nih.gov/gene/?term=17259	AI451606	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004596	1725	DHPS	http://www.ncbi.nlm.nih.gov/gene/?term=1725	"DHS, DS, MIG13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004597	1725	DHPS	http://www.ncbi.nlm.nih.gov/gene/?term=1725	"DHS, DS, MIG13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004598	17260	Mef2c	http://www.ncbi.nlm.nih.gov/gene/?term=17260	"5430401D19Rik, 9930028G15Rik, AV011172, Mef2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004599	17261	Mef2d	http://www.ncbi.nlm.nih.gov/gene/?term=17261	C80750	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004600	17263	Meg3	http://www.ncbi.nlm.nih.gov/gene/?term=17263	"2900016C05Rik, 3110050O07Rik, 6330408G06Rik, AI425946, AW108224, D12Bwg1266e, Gtl2, R74756, R75394 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004601	17263	Meg3	http://www.ncbi.nlm.nih.gov/gene/?term=17263	"2900016C05Rik, 3110050O07Rik, 6330408G06Rik, AI425946, AW108224, D12Bwg1266e, Gtl2, R74756, R75394 "	lncRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"We then analyzed the abundance of several lncRNAs, namely Malat1, Meg3, Rmst, Xist and Miat. All of these lncRNAs were present in the axonal compartment.  "
RLID00004602	17268	Meis1	http://www.ncbi.nlm.nih.gov/gene/?term=17268	"C530044H18Rik, Evi8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004603	17268	Meis1	http://www.ncbi.nlm.nih.gov/gene/?term=17268	"C530044H18Rik, Evi8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004604	17276	Mela	http://www.ncbi.nlm.nih.gov/gene/?term=17276	"80kDa, Ag, env, gag, gag-pol, pol "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004605	1727	CYB5R3	http://www.ncbi.nlm.nih.gov/gene/?term=1727	"B5R, DIA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004606	1727	CYB5R3	http://www.ncbi.nlm.nih.gov/gene/?term=1727	"B5R, DIA1 "	mRNA	Homo sapiens	21266463	Endoplasmic reticulum	Foreskin fibroblast	RT-PCR	The combined results from our multiple approaches consistently demonstrate that Dia1 mRNA is localized on the ER membrane. Fig. 3. Dia1 mRNA is localized on the ER.
RLID00004607	17283	Men1	http://www.ncbi.nlm.nih.gov/gene/?term=17283	AW045611	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004608	17285	Meox1	http://www.ncbi.nlm.nih.gov/gene/?term=17285	"AI385561, D330041M02Rik, Mox-1, Mox1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004609	17289	Mertk	http://www.ncbi.nlm.nih.gov/gene/?term=17289	"Eyk, Mer, Nyk, nmf12 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004610	1728	NQO1	http://www.ncbi.nlm.nih.gov/gene/?term=1728	"DHQU, DIA4, DTD, NMOR1, NMORI, QR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004611	1728	NQO1	http://www.ncbi.nlm.nih.gov/gene/?term=1728	"DHQU, DIA4, DTD, NMOR1, NMORI, QR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004612	1728	NQO1	http://www.ncbi.nlm.nih.gov/gene/?term=1728	"DHQU, DIA4, DTD, NMOR1, NMORI, QR1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004613	1728	NQO1	http://www.ncbi.nlm.nih.gov/gene/?term=1728	"DHQU, DIA4, DTD, NMOR1, NMORI, QR1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004614	17295	Met	http://www.ncbi.nlm.nih.gov/gene/?term=17295	"AI838057, HGF, HGFR, Par4, c-Met "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004615	1729	DIAPH1	http://www.ncbi.nlm.nih.gov/gene/?term=1729	"DFNA1, DIA1, DRF1, LFHL1, SCBMS, hDIA1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004616	17305	Mfng	http://www.ncbi.nlm.nih.gov/gene/?term=17305	AW546563	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004617	17318	Mid1	http://www.ncbi.nlm.nih.gov/gene/?term=17318	"61B3-R, DXHXS1141, Fxy, Trim18 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004618	17330	Minpp1	http://www.ncbi.nlm.nih.gov/gene/?term=17330	AA408516	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004619	17347	Mknk2	http://www.ncbi.nlm.nih.gov/gene/?term=17347	"2010016G11Rik, Gprk7, Mnk2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004620	17356	Mllt4	http://www.ncbi.nlm.nih.gov/gene/?term=17356	"5033403D15Rik, AF6, Af-6, Afadin, Gm314, I-afadin, S-afadin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004621	1735	DIO3	http://www.ncbi.nlm.nih.gov/gene/?term=1735	"5DIII, D3, DIOIII, TXDI3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004622	1736	DKC1	http://www.ncbi.nlm.nih.gov/gene/?term=1736	"CBF5, DKC, DKCX, NAP57, NOLA4, XAP101 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004623	1736	DKC1	http://www.ncbi.nlm.nih.gov/gene/?term=1736	"CBF5, DKC, DKCX, NAP57, NOLA4, XAP101 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004624	1737	DLAT	http://www.ncbi.nlm.nih.gov/gene/?term=1737	"DLTA, PDC-E2, PDCE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004625	1737	DLAT	http://www.ncbi.nlm.nih.gov/gene/?term=1737	"DLTA, PDC-E2, PDCE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004626	1738	DLD	http://www.ncbi.nlm.nih.gov/gene/?term=1738	"DLDD, DLDH, E3, GCSL, LAD, PHE3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004627	1738	DLD	http://www.ncbi.nlm.nih.gov/gene/?term=1738	"DLDDH, E3, GCSL, LAD, PHE3, DLD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004628	17390	Mmp2	http://www.ncbi.nlm.nih.gov/gene/?term=17390	"Clg4a, GelA, MMP-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004629	17395	Mmp9	http://www.ncbi.nlm.nih.gov/gene/?term=17395	"AW743869, B/MMP9, Clg4b, Gel B, MMP-9, pro-MMP-9 "	mRNA	Mus musculus	24227732	Dendrite	Oocyte	In situ hybridization	Here we show that MMP-9 mRNA is part of the FMRP complex and colocalizes in dendrites. Endogenous MMP-9 mRNA was revealed by in situ hybridization combined with immunodetection of FMRP. MMP-9 mRNA was localized in granules along the dendrites and exhibited abundant colocalization with FMRP (Fig. 3C). 
RLID00004630	1739	DLG1	http://www.ncbi.nlm.nih.gov/gene/?term=1739	"DLGH1, SAP-97, SAP97, dJ1061C18.1.1, hdlg "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004631	1739	DLG1	http://www.ncbi.nlm.nih.gov/gene/?term=1739	"DLGH1, SAP-97, SAP97, dJ1061C18.1.1, hdlg "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004632	1741	DLG3	http://www.ncbi.nlm.nih.gov/gene/?term=1741	"MRX, MRX90, NEDLG, PPP1R82, SAP102, XLMR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004633	17420	Mnat1	http://www.ncbi.nlm.nih.gov/gene/?term=17420	"E130115E11Rik, MAT1, P36 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004634	1742	DLG4	http://www.ncbi.nlm.nih.gov/gene/?term=1742	"PSD95, SAP-90, SAP90 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004635	1743	DLST	http://www.ncbi.nlm.nih.gov/gene/?term=1743	DLTS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004636	17450	Morc1	http://www.ncbi.nlm.nih.gov/gene/?term=17450	Morc	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004637	17472	Gbp4	http://www.ncbi.nlm.nih.gov/gene/?term=17472	"AW228052, Mag-2, Mpa-2, Mpa2, mKIAA4245 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004638	17475	Mpdz	http://www.ncbi.nlm.nih.gov/gene/?term=17475	"AI225843, B930003D11Rik, MUPP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004639	1748	DLX4	http://www.ncbi.nlm.nih.gov/gene/?term=1748	"BP1, DLX7, DLX8, DLX9, OFC15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004640	1749	DLX5	http://www.ncbi.nlm.nih.gov/gene/?term=1749	SHFM1D	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004641	174	AFP	http://www.ncbi.nlm.nih.gov/gene/?term=174	"AFPD, FETA, HPAFP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004642	17532	Mras	http://www.ncbi.nlm.nih.gov/gene/?term=17532	"2900078C09Rik, AI326250 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004643	17535	Mre11a	http://www.ncbi.nlm.nih.gov/gene/?term=17535	"Mre11, Mre11b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004644	17537	Meis3	http://www.ncbi.nlm.nih.gov/gene/?term=17537	"AI573393, Mrg2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004645	1759	DNM1	http://www.ncbi.nlm.nih.gov/gene/?term=1759	"DNM, EIEE31 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004646	175	AGA	http://www.ncbi.nlm.nih.gov/gene/?term=175	"AGU, ASRG, GA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004647	1760	DMPK	http://www.ncbi.nlm.nih.gov/gene/?term=1760	"DM, DM1, DM1PK, DMK, MDPK, MT-PK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004648	1762	DMWD	http://www.ncbi.nlm.nih.gov/gene/?term=1762	"D19S593E, DMR-N9, DMRN9, gene59 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004649	1763	DNA2	http://www.ncbi.nlm.nih.gov/gene/?term=1763	"DNA2L, hDNA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004650	1763	DNA2	http://www.ncbi.nlm.nih.gov/gene/?term=1763	"DNA2L, hDNA2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004651	17686	Msh3	http://www.ncbi.nlm.nih.gov/gene/?term=17686	"D13Em1, Rep-3, Rep3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004652	17688	Msh6	http://www.ncbi.nlm.nih.gov/gene/?term=17688	"AU044881, AW550279, GTBP, Gtmbp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004653	1768	DNAH6	http://www.ncbi.nlm.nih.gov/gene/?term=1768	"DNHL1, Dnahc6, HL-2, HL2 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00004654	17692	Msl3	http://www.ncbi.nlm.nih.gov/gene/?term=17692	"AU0189311, Msl3l1, Msl3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004655	1773	DNASE1	http://www.ncbi.nlm.nih.gov/gene/?term=1773	"DNL1, DRNI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004656	1774	DNASE1L1	http://www.ncbi.nlm.nih.gov/gene/?term=1774	"DNAS1L1, DNASEX, DNL1L, G4.8, XIB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004657	17751	Mt3	http://www.ncbi.nlm.nih.gov/gene/?term=17751	Mt-3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004658	17754	Map1a	http://www.ncbi.nlm.nih.gov/gene/?term=17754	"6330416M19Rik, AI853608, Mtap-1, Mtap1, Mtap1a, moth1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004659	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004660	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004661	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	mRNA	Mus musculus	16631377	Growth cone	Hippocampus	Fluorescence in situ hybridization	"MAP1b mRNA, a known FMRP target, was also localized to axon growth cones. "
RLID00004662	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	mRNA	Mus musculus	18539120	Dendrite	Neuron	Fluorescence in situ hybridization	"Fig. 1 Fluorescence in situ hybridization (FISH) of hippocampal neurons. (a-d) Neurons from wild-type (WT, right panels) or FMRP-knockout (KO, left panels) were cultured for 10 days and either not stimulated ('unstim', upper panels') or stimulated with 50uM DHPG for 15 minutes ('DHPG' lower panels). Corresponding histograms showing dendritic quantification of FISH experiments are shown to the right. Results for WT (black bars) and KO (white bars) are labeled on the x-axis. Close-up images of dendritic signals are shown to the right (in same order). (a) MAP1b mRNA (n=15-16; *p<0.001 for unstimulated vs. DHPG in WT, P>0.25 for KO). (b)CaMKIIa mRNA (n=15-17; *p<0.01 for WT, p>0.2 for KO). There was no significant difference in CaMKIIa abundance of unstimulated neurons between WT and KO (n=15, p>0.1). (c) Beta-actin mRNA (n=11-13; p>0.2). Scale bars=12um. (d-e) FISH for other mRNA targets of FMRP in both WT (right image panels) and KO (left image panels). Representative images shown for unstimulated (upper panels; 'unstim' and stimulated (lower panels; DHPG, 50uM), and close-up images of dendrites are displayed above the histograms (in same order). Histograms (right) showing dendritic fluorescence quantification are shown for WT (green) and KO (red) using probes to (d) SAPAP4 (n=16-17; p<0.01 for WT, p>25 for KO) and (e) GABA-A receptor delta (n=13-15; *, ***p<0.01 for unstimulated vs. DHPG in WT and for DHPG in WT and KO, **p<0.05 for unstimulated vs. DHPG in KO). (c) Dendritic CaMKIIa mRNA localization in response to DHPG (11DIV). (d) Dendritic SAPAP4 mRNA localization in response to DHPG (11DIV). "
RLID00004663	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	mRNA	Mus musculus	18539120	Synapse	Brain	qRT-PCR	"The mRNA targets reduced in Kif5 association included genes involved in actin remodeling at synapses (cofilin phosphatase (PP2Ac); p116-RIP), synapse-associated signaling (DAG1;RGS5) and synapse structure (SAPAP4; CaMKIIa; MAP1b). Not all mRNAs were significantly reduced in Kif5 IPs, as OCRL1 mRNA was similar in KO brain (P>0.05, n=8). "
RLID00004664	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	mRNA	Mus musculus	16098134	Synapse	Hippocampus	In situ hybridization|Immunofluorescence assay	"MAP1B mRNA [Fig. 3(a), green] was dendritically localized in granules and exhibited abundant colocalization with FMRP (red, inset). A Z-series followed by deconvolution and volume rendering of the boxed dendrite in Fig. 3(a) depicts FMRP and MAP1B mRNA that colocalized in granules (yellow) at synapses (synapsin staining, blue) [Fig. 3(b), insets a, b]. "
RLID00004665	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5 "	mRNA	Mus musculus	16098134	Dendrite	Hippocampus	In situ hybridization|Immunofluorescence assay	"MAP1B mRNA [Fig. 3(a), green] was dendritically localized in granules and exhibited abundant colocalization with FMRP (red, inset). A Z-series followed by deconvolution and volume rendering of the boxed dendrite in Fig. 3(a) depicts FMRP and MAP1B mRNA that colocalized in granules (yellow) at synapses (synapsin staining, blue) [Fig. 3(b), insets a, b]. "
RLID00004666	17756	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=17756	"G1-397-34, MAP-2, Mtap-2, Mtap2, repro4 "	mRNA	Mus musculus	15328607	Dendrite	Retina	In situ hybridization	"We found that in contrast to rodent MAP2 mRNAs, which are highly enriched in dendritic regions of the retina, chicken MAP2 transcripts are virtually absent from such areas and are rather connected to neuronal somata.  The combined data suggest that in the mouse retina, MAP2 mRNA is located predominantly in layers rich in dendrites whereas in the chicken retina, MAP2 mRNA is largely con?ned to neuronal somata. "
RLID00004667	17756	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=17756	"G1-397-34, MAP-2, Mtap-2, Mtap2, repro4 "	mRNA	Mus musculus	8647897	Dendrite	Mature neuron	In situ hybridization	"Initially, each was detected in axons and dendrites, although tau persisted only in axons, whereas MAP2C and MAP2 were restricted to cell bodies and dendrites. "
RLID00004668	17756	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=17756	"G1-397-34, MAP-2, Mtap-2, Mtap2, repro4 "	mRNA	Mus musculus	8647897	Cell body	Mature neuron	In situ hybridization	"Initially, each was detected in axons and dendrites, although tau persisted only in axons, whereas MAP2C and MAP2 were restricted to cell bodies and dendrites. "
RLID00004669	17762	Mapt	http://www.ncbi.nlm.nih.gov/gene/?term=17762	"AI413597, AW045860, Mtapt, Tau "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004670	17762	Mapt	http://www.ncbi.nlm.nih.gov/gene/?term=17762	"AI413597, AW045860, Mtapt, Tau "	mRNA	Mus musculus	11517247	Axon	Embryo	In situ hybridization	We demonstrated colocalization of the targeted tau mRNA and its translated protein in the axon and growth cone.
RLID00004671	17762	Mapt	http://www.ncbi.nlm.nih.gov/gene/?term=17762	"AI413597, AW045860, Mtapt, Tau "	mRNA	Mus musculus	11517247	Cell body	Embryo	In situ hybridization	Both tau mRNA and tau protein remained in the cell body.
RLID00004672	17762	Mapt	http://www.ncbi.nlm.nih.gov/gene/?term=17762	"AI413597, AW045860, Mtapt, Tau "	mRNA	Mus musculus	26512708	Axon	ForeBrain	Immunoprecipitation|RIP-Chip	"HuD has also been implicated in axonal localization of other neuronal mRNAs including Tau, Neuritin/CPG15, Kv.1.1 and CaMKIIα mRNAs "
RLID00004673	17762	Mapt	http://www.ncbi.nlm.nih.gov/gene/?term=17762	"AI413597, AW045860, Mtapt, Tau "	mRNA	Mus musculus	8647897	Axon	Mature neuron	In situ hybridization	"Initially, each was detected in axons and dendrites, although tau persisted only in axons, whereas MAP2C and MAP2 were restricted to cell bodies and dendrites. "
RLID00004674	17763	Mtcp1	http://www.ncbi.nlm.nih.gov/gene/?term=17763	P13MTCP1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004675	17764	Mtf1	http://www.ncbi.nlm.nih.gov/gene/?term=17764	"MTF-1, Thyls "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004676	17764	Mtf1	http://www.ncbi.nlm.nih.gov/gene/?term=17764	"MTF-1, Thyls "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004677	17765	Mtf2	http://www.ncbi.nlm.nih.gov/gene/?term=17765	"9230112N11Rik, AA537621, C76717, M96, Pcl2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004678	17766	Nudt1	http://www.ncbi.nlm.nih.gov/gene/?term=17766	Mth1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004679	17772	Mtm1	http://www.ncbi.nlm.nih.gov/gene/?term=17772	"AF073996, Mtm, mKIAA4176 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004680	17772	Mtm1	http://www.ncbi.nlm.nih.gov/gene/?term=17772	"AF073996, Mtm, mKIAA4176 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004681	1777	DNASE2	http://www.ncbi.nlm.nih.gov/gene/?term=1777	"DNASE2A, DNL, DNL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004682	1778	DYNC1H1	http://www.ncbi.nlm.nih.gov/gene/?term=1778	"CMT2O, DHC1, DHC1a, DNCH1, DNCL, DNECL, DYHC, Dnchc1, HL-3, SMALED1, p22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004683	1778	DYNC1H1	http://www.ncbi.nlm.nih.gov/gene/?term=1778	"CMT2O, DHC1, DHC1a, DNCH1, DNCL, DNECL, DYHC, Dnchc1, HL-3, SMALED1, p22 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004684	1778	DYNC1H1	http://www.ncbi.nlm.nih.gov/gene/?term=1778	"CMT2O, DHC1, DHC1a, DNCH1, DNCL, DNECL, DYHC, Dnchc1, HL-3, SMALED1, p22 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004685	177	AGER	http://www.ncbi.nlm.nih.gov/gene/?term=177	RAGE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004686	1780	DYNC1I1	http://www.ncbi.nlm.nih.gov/gene/?term=1780	"DNCI1, DNCIC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004687	1780	DYNC1I1	http://www.ncbi.nlm.nih.gov/gene/?term=1780	"DNCI1, DNCIC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004688	1781	DYNC1I2	http://www.ncbi.nlm.nih.gov/gene/?term=1781	"DIC74, DNCI2, IC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004689	1781	DYNC1I2	http://www.ncbi.nlm.nih.gov/gene/?term=1781	"DIC74, DNCI2, IC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004690	17827	Mtx1	http://www.ncbi.nlm.nih.gov/gene/?term=17827	"Gcap6, Mtx "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004691	1783	DYNC1LI2	http://www.ncbi.nlm.nih.gov/gene/?term=1783	"DNCLI2, LIC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004692	1783	DYNC1LI2	http://www.ncbi.nlm.nih.gov/gene/?term=1783	"DNCLI2, LIC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004693	17840	Mup1	http://www.ncbi.nlm.nih.gov/gene/?term=17840	"Ltn-1, Lvtn-1, Mup-1, Mup-a0, Mup7, Up-1, Mup1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004694	17841	Mup2	http://www.ncbi.nlm.nih.gov/gene/?term=17841	"AA589603, Mup-2, Mup18, Mup4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004695	17847	Usp34	http://www.ncbi.nlm.nih.gov/gene/?term=17847	"A530081C03Rik, Murr2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004696	17847	Usp34	http://www.ncbi.nlm.nih.gov/gene/?term=17847	"A530081C03Rik, Murr2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004697	17850	Mut	http://www.ncbi.nlm.nih.gov/gene/?term=17850	"D230010K02Rik, Mcm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004698	17855	Mvk	http://www.ncbi.nlm.nih.gov/gene/?term=17855	"2310010A05Rik, AI256848, AI414037, MK "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004699	17858	Mx2	http://www.ncbi.nlm.nih.gov/gene/?term=17858	"AI528743, Mx-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004700	1785	DNM2	http://www.ncbi.nlm.nih.gov/gene/?term=1785	"CMT2M, CMTDI1, CMTDIB, DI-CMTB, DYN2, DYNII, LCCS5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004701	17869	Myc	http://www.ncbi.nlm.nih.gov/gene/?term=17869	"AU0167572, Niard, Nird, bHLHe39, Myc "	mRNA	Mus musculus	19003354	Ribosome	Fibroblast	Hybridisation|Northern blot	Globin transcripts with the native globin 3'untranslated region or with the 3'untranslated region of c-myc are present in free/cytoskeletal-bound polysomes.
RLID00004702	1786	DNMT1	http://www.ncbi.nlm.nih.gov/gene/?term=1786	"ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT, m.HsaI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004703	1786	DNMT1	http://www.ncbi.nlm.nih.gov/gene/?term=1786	"ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT, m.HsaI "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004704	17874	Myd88	http://www.ncbi.nlm.nih.gov/gene/?term=17874		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004705	1787	TRDMT1	http://www.ncbi.nlm.nih.gov/gene/?term=1787	"DMNT2, DNMT2, MHSAIIP, PUMET, RNMT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004706	1787	TRDMT1	http://www.ncbi.nlm.nih.gov/gene/?term=1787	"DMNT2, DNMT2, MHSAIIP, PUMET, RNMT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004707	1787	TRDMT1	http://www.ncbi.nlm.nih.gov/gene/?term=1787	"DMNT2, DNMT2, MHSAIIP, PUMET, RNMT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004708	17883	Myh3	http://www.ncbi.nlm.nih.gov/gene/?term=17883	"MyHC-emb, Myhs-e, Myhse "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004709	1788	DNMT3A	http://www.ncbi.nlm.nih.gov/gene/?term=1788	"DNMT3A2, M.HsaIIIA, TBRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004710	178	AGL	http://www.ncbi.nlm.nih.gov/gene/?term=178	GDE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004711	178	AGL	http://www.ncbi.nlm.nih.gov/gene/?term=178	GDE	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004712	17906	Myl2	http://www.ncbi.nlm.nih.gov/gene/?term=17906	"MLC-2, MLC-2s/v, MLC-2v, Mlc2v, Mylpc "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004713	17910	Myo15	http://www.ncbi.nlm.nih.gov/gene/?term=17910	"Myo15a, sh-2, sh2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004714	17930	Myom2	http://www.ncbi.nlm.nih.gov/gene/?term=17930	AW146149	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004715	17931	Ppp1r12a	http://www.ncbi.nlm.nih.gov/gene/?term=17931	"1200015F06Rik, 5730577I22Rik, AA792106, AV099298, D10Ertd625e, Mypt1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004716	17931	Ppp1r12a	http://www.ncbi.nlm.nih.gov/gene/?term=17931	"1200015F06Rik, 5730577I22Rik, AA792106, AV099298, D10Ertd625e, Mypt1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004717	17936	Nab1	http://www.ncbi.nlm.nih.gov/gene/?term=17936		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004718	17937	Nab2	http://www.ncbi.nlm.nih.gov/gene/?term=17937	AI451907	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004719	17938	Naca	http://www.ncbi.nlm.nih.gov/gene/?term=17938	"AL022831, AL024382, Gm1878, mKIAA0363, skNAC "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004720	1793	DOCK1	http://www.ncbi.nlm.nih.gov/gene/?term=1793	"DOCK180, ced5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004721	17940	Naip1	http://www.ncbi.nlm.nih.gov/gene/?term=17940	"AV364616, Birc1a, D13Lsd1, Naip, Naip-rs1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004722	1794	DOCK2	http://www.ncbi.nlm.nih.gov/gene/?term=1794	IMD40	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004723	1795	DOCK3	http://www.ncbi.nlm.nih.gov/gene/?term=1795	"MOCA, PBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004724	17965	Nbl1	http://www.ncbi.nlm.nih.gov/gene/?term=17965	"D4H1S1733E, DAN, Dana, NO3 "	mRNA	Mus musculus	11134349	Axon	Fetus	In situ hybridization	"In order to understand better the in vivo roles of DAN, we designed bioassays for BMP blockade within the Xenopus embryo, examined Dan expression in the mouse, and generated mice that lacked DAN function. In this way, we have shown that DAN may bind GDF-5 in vivo, that Dan mRNA is localized in many developing axon tracts, and that Dan mutant mice have only subtle defects. "
RLID00004725	1796	DOK1	http://www.ncbi.nlm.nih.gov/gene/?term=1796	"P62DOK, pp62 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004726	17973	Nck1	http://www.ncbi.nlm.nih.gov/gene/?term=17973	"6330586M15Rik, D230010O13Rik, Nck, Nck-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004727	17975	Ncl	http://www.ncbi.nlm.nih.gov/gene/?term=17975	"B530004O11Rik, C23, D0Nds28, D1Nds28, Nucl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004728	17979	Ncoa3	http://www.ncbi.nlm.nih.gov/gene/?term=17979	"2010305B15Rik, AW321064, Actr, Aib1, KAT13B, Rac3, Src3, Tram-1, Tram1, bHLHe42, p/Cip, pCip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004729	1797	DXO	http://www.ncbi.nlm.nih.gov/gene/?term=1797	"DOM3L, DOM3Z, NG6, RAI1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004730	1798	DPAGT1	http://www.ncbi.nlm.nih.gov/gene/?term=1798	"ALG7, CDG-Ij, CDG1J, CMS13, CMSTA2, D11S366, DGPT, DPAGT, DPAGT2, G1PT, GPT, UAGT, UGAT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004731	1798	DPAGT1	http://www.ncbi.nlm.nih.gov/gene/?term=1798	"ALG7, CDG-Ij, CDG1J, CMS13, CMSTA2, D11S366, DGPT, DPAGT, DPAGT2, G1PT, GPT, UAGT, UGAT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004732	17996	Neb	http://www.ncbi.nlm.nih.gov/gene/?term=17996	AI595938	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004733	17997	Nedd1	http://www.ncbi.nlm.nih.gov/gene/?term=17997		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004734	18004	Nek1	http://www.ncbi.nlm.nih.gov/gene/?term=18004	"D8Ertd790e, kat "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004735	18007	Neo1	http://www.ncbi.nlm.nih.gov/gene/?term=18007	"2610028H22Rik, AI327052, D930014N22Rik, Igdcc2 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004736	18007	Neo1	http://www.ncbi.nlm.nih.gov/gene/?term=18007	"2610028H22Rik, AI327052, D930014N22Rik, Igdcc2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004737	1800	DPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=1800	"MBD1, MDP, RDP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004738	18012	Neurod1	http://www.ncbi.nlm.nih.gov/gene/?term=18012	"BETA2, BHF-1, Neurod, bHLHa3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004739	18012	Neurod1	http://www.ncbi.nlm.nih.gov/gene/?term=18012	"BETA2, BHF-1, Neurod, bHLHa3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004740	18013	Neurod2	http://www.ncbi.nlm.nih.gov/gene/?term=18013	"Ndrf, bHLHa1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004741	18015	Nf1	http://www.ncbi.nlm.nih.gov/gene/?term=18015	"AW494271, Dsk9, E030030H24Rik, Mhdadsk9, Nf-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004742	18018	Nfatc1	http://www.ncbi.nlm.nih.gov/gene/?term=18018	"2210017P03Rik, AI449492, AV076380, NF-ATc, NFAT2, NFATc, Nfatcb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004743	1801	DPH1	http://www.ncbi.nlm.nih.gov/gene/?term=1801	"DPH2L, DPH2L1, OVCA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004744	1801	DPH1	http://www.ncbi.nlm.nih.gov/gene/?term=1801	"DPH2L, DPH2L1, OVCA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004745	1801	DPH1	http://www.ncbi.nlm.nih.gov/gene/?term=1801	"DPH2L, DPH2L1, OVCA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004746	18020	Nfatc2ip	http://www.ncbi.nlm.nih.gov/gene/?term=18020	"D7Ertd304e, NIP45 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004747	18021	Nfatc3	http://www.ncbi.nlm.nih.gov/gene/?term=18021	"C80703, D8Ertd281e, NFAT4, NFATx "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004748	18028	Nfib	http://www.ncbi.nlm.nih.gov/gene/?term=18028	"6720429L07Rik, CTF, E030026I10Rik, NF-I/B, NF1-B, NFI-B "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004749	18030	Nfil3	http://www.ncbi.nlm.nih.gov/gene/?term=18030	"AV225605, E4BP4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004750	18035	Nfkbia	http://www.ncbi.nlm.nih.gov/gene/?term=18035	"AI462015, Nfkbi "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004751	18036	Nfkbib	http://www.ncbi.nlm.nih.gov/gene/?term=18036	"I(Kappa)B(beta), I-kappa-B-beta, IKB-beta, IKappaBbeta, IkB, IkBb, NF-kappa-BIB, ikB-B "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004752	18038	Nfkbil1	http://www.ncbi.nlm.nih.gov/gene/?term=18038	"Def-7, IKBL "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004753	18045	Nfyb	http://www.ncbi.nlm.nih.gov/gene/?term=18045	"AA985999, Cbf-A "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004754	18046	Nfyc	http://www.ncbi.nlm.nih.gov/gene/?term=18046		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004755	1804	DPP6	http://www.ncbi.nlm.nih.gov/gene/?term=1804	"DPL1, DPPX, MRD33, VF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004756	18072	Nhlh2	http://www.ncbi.nlm.nih.gov/gene/?term=18072	"6230401I09Rik, Hen2, NSCL2, Nscl-2, bHLHa34 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004757	18080	Nin	http://www.ncbi.nlm.nih.gov/gene/?term=18080	"3110068G20Rik, AI385615, AU024711, mKIAA1565 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004758	18081	Ninj1	http://www.ncbi.nlm.nih.gov/gene/?term=18081	AU024536	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004759	18087	Nktr	http://www.ncbi.nlm.nih.gov/gene/?term=18087	"5330401F18Rik, D9Wsu172e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004760	1808	DPYSL2	http://www.ncbi.nlm.nih.gov/gene/?term=1808	"CRMP-2, CRMP2, DHPRP2, DRP-2, DRP2, N2A3, ULIP-2, ULIP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004761	18091	Nkx2-5	http://www.ncbi.nlm.nih.gov/gene/?term=18091	"Csx, Nkx-2.5, Nkx2.5, tinman "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004762	18099	Nlk	http://www.ncbi.nlm.nih.gov/gene/?term=18099	AI194375	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004763	18101	Nmbr	http://www.ncbi.nlm.nih.gov/gene/?term=18101	BB182387	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004764	18103	Nme2	http://www.ncbi.nlm.nih.gov/gene/?term=18103	"NM23-H2, NM23B, nm23-M2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004765	18103	Nme2	http://www.ncbi.nlm.nih.gov/gene/?term=18103	"NM23-H2, NM23B, nm23-M2 "	mRNA	Mus musculus	11891645	Nucleus	Dorsal root ganglia	In situ hybridization	"Moreover, in situ hybridization also displayed a specific nuclear localization for nm23-M2 mRNA. "
RLID00004766	18108	Nmt2	http://www.ncbi.nlm.nih.gov/gene/?term=18108	"A930001K02Rik, AI605445, AU044698, hNMT-2 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004767	18109	Mycn	http://www.ncbi.nlm.nih.gov/gene/?term=18109	"N-myc, Nmyc, Nmyc-1, Nmyc1, bHLHe37, c-nmyc "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004768	1810	DR1	http://www.ncbi.nlm.nih.gov/gene/?term=1810	"NC2, NC2-BETA, NC2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004769	1810	DR1	http://www.ncbi.nlm.nih.gov/gene/?term=1810	"NC2, NC2-BETA, NC2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004770	18113	Nnmt	http://www.ncbi.nlm.nih.gov/gene/?term=18113		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004771	18115	Nnt	http://www.ncbi.nlm.nih.gov/gene/?term=18115	"4930423F13Rik, AI323702, BB168308 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004772	18117	Emc8	http://www.ncbi.nlm.nih.gov/gene/?term=18117	"Cox4nb, Fam158b, Noc4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004773	18128	Notch1	http://www.ncbi.nlm.nih.gov/gene/?term=18128	"9930111A19Rik, Mis6, N1, Tan1, lin-12 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004774	18130	Ints6	http://www.ncbi.nlm.nih.gov/gene/?term=18130	"2900075H24Rik, AI480962, DICE1, Ddx26, HDB, Notch2l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004775	18139	Zfp638	http://www.ncbi.nlm.nih.gov/gene/?term=18139	"AI323587, Np220, Zfml, Znf638, mNP220 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004776	1813	DRD2	http://www.ncbi.nlm.nih.gov/gene/?term=1813	"D2DR, D2R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004777	18140	Uhrf1	http://www.ncbi.nlm.nih.gov/gene/?term=18140	"AL022808, ICBP90, Np95, RNF106 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004778	18141	Nup50	http://www.ncbi.nlm.nih.gov/gene/?term=18141	"1700030K07Rik, AI413123, Npap60 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004779	18142	Npas1	http://www.ncbi.nlm.nih.gov/gene/?term=18142	"MOP5, bHLHe11 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004780	18145	Npc1	http://www.ncbi.nlm.nih.gov/gene/?term=18145	"A430089E03Rik, C85354, D18Ertd139e, D18Ertd723e, lcsd, nmf164, spm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004781	18148	Npm1	http://www.ncbi.nlm.nih.gov/gene/?term=18148	"B23, NO38, Npm "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004782	18148	Npm1	http://www.ncbi.nlm.nih.gov/gene/?term=18148	"B23, NO38, Npm "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004783	18162	Npr3	http://www.ncbi.nlm.nih.gov/gene/?term=18162	"ANP-C, ANPR-C, EF-2, NPR-C, lgj, stri "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004784	18173	Slc11a1	http://www.ncbi.nlm.nih.gov/gene/?term=18173	"Bcg, Ity, Ity1, Lsh, Nramp, Nramp1, ity "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004785	18175	Nrap	http://www.ncbi.nlm.nih.gov/gene/?term=18175		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004786	18181	Nrf1	http://www.ncbi.nlm.nih.gov/gene/?term=18181	"C87038, D6Ertd415e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004787	18186	Nrp1	http://www.ncbi.nlm.nih.gov/gene/?term=18186	"C530029I03, NP-1, NPN-1, Npn1, Nrp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004788	18187	Nrp2	http://www.ncbi.nlm.nih.gov/gene/?term=18187	"1110048P06Rik, Np-2, Np2, Npn-2, Npn2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004789	18190	Nrxn2	http://www.ncbi.nlm.nih.gov/gene/?term=18190	"6430591O13Rik, mKIAA0921 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004790	18191	Nrxn3	http://www.ncbi.nlm.nih.gov/gene/?term=18191		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004791	18197	Nsg2	http://www.ncbi.nlm.nih.gov/gene/?term=18197		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004792	1819	DRG2	http://www.ncbi.nlm.nih.gov/gene/?term=1819		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004793	1819	DRG2	http://www.ncbi.nlm.nih.gov/gene/?term=1819		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004794	1819	DRG2	http://www.ncbi.nlm.nih.gov/gene/?term=1819		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004795	18201	Nsmaf	http://www.ncbi.nlm.nih.gov/gene/?term=18201	"AA959567, C630007J05, Fan "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004796	18207	Nthl1	http://www.ncbi.nlm.nih.gov/gene/?term=18207	"Nth1, Octs3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004797	1820	ARID3A	http://www.ncbi.nlm.nih.gov/gene/?term=1820	"BRIGHT, DRIL1, DRIL3, E2FBP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004798	18213	Ntrk3	http://www.ncbi.nlm.nih.gov/gene/?term=18213	"AW125844_tv3, TrkC, Ntrk3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004799	18214	Ddr2	http://www.ncbi.nlm.nih.gov/gene/?term=18214	"AW495251, Ntrkr3, tyro10 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004800	18214	Ddr2	http://www.ncbi.nlm.nih.gov/gene/?term=18214	"AW495251, Ntrkr3, tyro10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004801	18214	Ddr2	http://www.ncbi.nlm.nih.gov/gene/?term=18214	"AW495251, Ntrkr3, tyro10 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00004802	18217	Ntsr2	http://www.ncbi.nlm.nih.gov/gene/?term=18217	"NT2R, NTRL "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004803	1822	ATN1	http://www.ncbi.nlm.nih.gov/gene/?term=1822	"B37, D12S755E, DRPLA, HRS, NOD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004804	18230	Nxn	http://www.ncbi.nlm.nih.gov/gene/?term=18230	l11Jus13	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004805	18247	Oaz2	http://www.ncbi.nlm.nih.gov/gene/?term=18247	"AZ-2, AZ2-ps, Sez15, Oaz2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004806	1824	DSC2	http://www.ncbi.nlm.nih.gov/gene/?term=1824	"ARVD11, CDHF2, DG2, DGII/III, DSC3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004807	1824	DSC2	http://www.ncbi.nlm.nih.gov/gene/?term=1824	"ARVD11, CDHF2, DG2, DGII/III, DSC3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004808	1825	DSC3	http://www.ncbi.nlm.nih.gov/gene/?term=1825	"CDHF3, DSC, DSC1, DSC2, DSC4, HT-CP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004809	1825	DSC3	http://www.ncbi.nlm.nih.gov/gene/?term=1825	"CDHF3, DSC, DSC1, DSC2, DSC4, HT-CP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004810	18263	Odc1	http://www.ncbi.nlm.nih.gov/gene/?term=18263	ODC	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004811	1826	DSCAM	http://www.ncbi.nlm.nih.gov/gene/?term=1826	"CHD2, CHD2-42, CHD2-52 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004812	1827	RCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=1827	"ADAPT78, CSP1, DSC1, DSCR1, MCIP1, RCN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004813	1827	RCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=1827	"ADAPT78, CSP1, DSC1, DSCR1, MCIP1, RCN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004814	1827	RCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=1827	"ADAPT78, CSP1, DSC1, DSCR1, MCIP1, RCN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004815	18292	Sebox	http://www.ncbi.nlm.nih.gov/gene/?term=18292	"OG9, Og9x "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004816	1829	DSG2	http://www.ncbi.nlm.nih.gov/gene/?term=1829	"CDHF5, HDGC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004817	1829	DSG2	http://www.ncbi.nlm.nih.gov/gene/?term=1829	"CDHF5, HDGC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004818	182	JAG1	http://www.ncbi.nlm.nih.gov/gene/?term=182	"AGS, AHD, AWS, CD339, HJ1, JAGL1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004819	182	JAG1	http://www.ncbi.nlm.nih.gov/gene/?term=182	"AGS, AHD, AWS, CD339, HJ1, JAGL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004820	1830	DSG3	http://www.ncbi.nlm.nih.gov/gene/?term=1830	"CDHF6, PVA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004821	1830	DSG3	http://www.ncbi.nlm.nih.gov/gene/?term=1830	"CDHF6, PVA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004822	18312	Olfr15	http://www.ncbi.nlm.nih.gov/gene/?term=18312	"MOR256-17, OR3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004823	1831	TSC22D3	http://www.ncbi.nlm.nih.gov/gene/?term=1831	"DIP, DSIPI, GILZ, TSC-22R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004824	1832	DSP	http://www.ncbi.nlm.nih.gov/gene/?term=1832	"DCWHKTA, DP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004825	18356	Olfr56	http://www.ncbi.nlm.nih.gov/gene/?term=18356	"IF7, MOR276-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004826	18363	Olfr62	http://www.ncbi.nlm.nih.gov/gene/?term=18363	"H12, IH12, MOR258-5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004827	1836	SLC26A2	http://www.ncbi.nlm.nih.gov/gene/?term=1836	"D5S1708, DTD, DTDST, EDM4, MST153, MSTP157 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004828	1836	SLC26A2	http://www.ncbi.nlm.nih.gov/gene/?term=1836	"D5S1708, DTD, DTDST, EDM4, MST153, MSTP157 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004829	18377	Omg	http://www.ncbi.nlm.nih.gov/gene/?term=18377		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004830	1838	DTNB	http://www.ncbi.nlm.nih.gov/gene/?term=1838		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004831	18392	Orc1	http://www.ncbi.nlm.nih.gov/gene/?term=18392	"AA545195, MmORC1l, Orc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004832	1839	HBEGF	http://www.ncbi.nlm.nih.gov/gene/?term=1839	"DTR, DTS, DTSF, HEGFL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004833	1840	DTX1	http://www.ncbi.nlm.nih.gov/gene/?term=1840	hDx-1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004834	18412	Sqstm1	http://www.ncbi.nlm.nih.gov/gene/?term=18412	"A170, OSF-6, Osi, STAP, STONE14, p62 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004835	18415	Hspa4l	http://www.ncbi.nlm.nih.gov/gene/?term=18415	"94kDa, AI461691, APG-1, Osp94 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004836	1841	DTYMK	http://www.ncbi.nlm.nih.gov/gene/?term=1841	"CDC8, PP3731, TMPK, TYMK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004837	1841	DTYMK	http://www.ncbi.nlm.nih.gov/gene/?term=1841	"CDC8, PP3731, TMPK, TYMK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004838	1842	ECM2	http://www.ncbi.nlm.nih.gov/gene/?term=1842		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004839	18439	P2rx7	http://www.ncbi.nlm.nih.gov/gene/?term=18439	"AI467586, P2X(7), P2X7R "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004840	1843	DUSP1	http://www.ncbi.nlm.nih.gov/gene/?term=1843	"CL100, HVH1, MKP-1, MKP1, PTPN10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004841	18451	P4ha1	http://www.ncbi.nlm.nih.gov/gene/?term=18451	"AL022634, P4ha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004842	18458	Pabpc1	http://www.ncbi.nlm.nih.gov/gene/?term=18458	"PABP, Pabp1, PabpI, Pabpl1, ePAB "	mRNA	Mus musculus	25370180	Cytoplasm	Oocyte	In situ hybridization	"However, Pabpc1 transcript was highly generated in the prepubertal and pubertal mouse ovaries except for 1-week old ovary than those of other developmental terms. In the prepubertal mouse ovaries, RNA in situ hybridization localized both Epab and Pabpc1 transcripts in the cytoplasm of oocytes and granulosa cells of all follicular stages. "
RLID00004843	1845	DUSP3	http://www.ncbi.nlm.nih.gov/gene/?term=1845	VHR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004844	1845	DUSP3	http://www.ncbi.nlm.nih.gov/gene/?term=1845	VHR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004845	18472	Pafah1b1	http://www.ncbi.nlm.nih.gov/gene/?term=18472	"LIS-1, Lis1, MMS10-U, Mdsh, Ms10u, Pafaha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004846	18475	Pafah1b2	http://www.ncbi.nlm.nih.gov/gene/?term=18475	"AI747451, AU021353, Pafahb, mus[b] "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004847	18477	Prdx1	http://www.ncbi.nlm.nih.gov/gene/?term=18477	"MSP23, NkefA, OSF-3, OSF3, PAG, Paga, PrdxI, PrxI, TDX2, TPxA, Tdpx2, prx1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004848	1847	DUSP5	http://www.ncbi.nlm.nih.gov/gene/?term=1847	"DUSP, HVH3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004849	1847	DUSP5	http://www.ncbi.nlm.nih.gov/gene/?term=1847	"DUSP, HVH3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004850	1847	DUSP5	http://www.ncbi.nlm.nih.gov/gene/?term=1847	"DUSP, HVH3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004851	18491	Pappa	http://www.ncbi.nlm.nih.gov/gene/?term=18491	"8430414N03Rik, IGFBP-4ase, PAG1, PAPP-A "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004852	1849	DUSP7	http://www.ncbi.nlm.nih.gov/gene/?term=1849	"MKPX, PYST2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004853	1849	DUSP7	http://www.ncbi.nlm.nih.gov/gene/?term=1849	"MKPX, PYST2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004854	1849	DUSP7	http://www.ncbi.nlm.nih.gov/gene/?term=1849	"MKPX, PYST2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004855	18510	Pax8	http://www.ncbi.nlm.nih.gov/gene/?term=18510	Pax-8	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004856	18514	Pbx1	http://www.ncbi.nlm.nih.gov/gene/?term=18514	"2310056B04Rik, D230003C07Rik, Pbx-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004857	18516	Pbx3	http://www.ncbi.nlm.nih.gov/gene/?term=18516		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004858	18519	Kat2b	http://www.ncbi.nlm.nih.gov/gene/?term=18519	"A930006P13Rik, AI461839, AW536563, Pcaf, p/CAF "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004859	18536	Pcm1	http://www.ncbi.nlm.nih.gov/gene/?term=18536	"2600002H09Rik, 9430077F19Rik, C030044G17Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004860	18541	Pcnt	http://www.ncbi.nlm.nih.gov/gene/?term=18541	"AW476095, C86676, KEN2, kendrin, m239Asp, m275Asp, Pcnt "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004861	18545	Pcp2	http://www.ncbi.nlm.nih.gov/gene/?term=18545	"L7, Pcp-2 "	mRNA	Mus musculus	9387927	Dendrite	Purkinje cell	In situ hybridizationq|Immunocytochemistry	"L7 mRNA is localized in clusters within the proximal and distal branches of dendrites, but also in the proximal part of Purkinje cell axons. "
RLID00004862	18545	Pcp2	http://www.ncbi.nlm.nih.gov/gene/?term=18545	"L7, Pcp-2 "	mRNA	Mus musculus	9387927	Axon	Purkinje cell	In situ hybridizationq|Immunocytochemistry	"L7 mRNA is localized in clusters within the proximal and distal branches of dendrites, but also in the proximal part of Purkinje cell axons. "
RLID00004863	18545	Pcp2	http://www.ncbi.nlm.nih.gov/gene/?term=18545	"L7, Pcp-2 "	mRNA	Mus musculus	12399102	Cell body	Purkinje cell	In situ hybridization	In mouse both mRNA forms are detectable in dendrites but their relative proportions change during development. In order to determine the subcellular distribution of the two forms of L7 mRNA we performed in situ hybridization using exon 1A- and 1B-specific probes. Both mRNA forms were found to be abundantly localized in both the cell body and dendrites of Purkinje cells (Fig. 2).
RLID00004864	18545	Pcp2	http://www.ncbi.nlm.nih.gov/gene/?term=18545	"L7, Pcp-2 "	mRNA	Mus musculus	12399102	Dendrite	Purkinje cell	In situ hybridization	In mouse both mRNA forms are detectable in dendrites but their relative proportions change during development. In order to determine the subcellular distribution of the two forms of L7 mRNA we performed in situ hybridization using exon 1A- and 1B-specific probes. Both mRNA forms were found to be abundantly localized in both the cell body and dendrites of Purkinje cells (Fig. 2).
RLID00004865	18549	Pcsk2	http://www.ncbi.nlm.nih.gov/gene/?term=18549	"6330411F23Rik, AI839700, Nec-2, Nec2, PC2, Phpp-2, SPC2 "	mRNA	Mus musculus	15972000	Endoplasmic reticulum	MIN6 cell	Northern blot	"Figure 2: Glucose stimulates the recruitment of mRNAs encoding secretory membrane proteins to the ER: subcellular fractionation using the digitonin method. MIN6 cells were preincubated in KRB containing 2 mM glucose for 1 h followed by incubation in KRB containing 2 or 20 mM glucose for a further period of 1 h. (a) Cells were permeabilized with digitonin and pelleted resulting in a membrane fraction (Mem) and a cytosolic fraction (Cyt). The 10% refers to 10% of total RNA/protein. RNA was isolated from each fraction and run on a 1% agarose formaldehyde gel, transferred on to a nylon membrane and probed for proinsulin (PI), PC2, CPH and actin mRNAs. The intensities of the bands were quantified using ImageJ and the mRNA levels were expressed as a percentage of total mRNA. (b) Protein samples from each fraction were run on SDS/PAGE (20% of membrane fraction and 20% of cytosolic fraction) and subjected to immunoblotting with anti-ERK2, calreticulin and SRP54 antibodies. Detection was by enhanced chemiluminescence. The results presented are representative of three separate experiments. Data are collected from Figure 2. "
RLID00004866	1854	DUT	http://www.ncbi.nlm.nih.gov/gene/?term=1854	dUTPase	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004867	1854	DUT	http://www.ncbi.nlm.nih.gov/gene/?term=1854	dUTPase	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004868	1855	DVL1	http://www.ncbi.nlm.nih.gov/gene/?term=1855	"DRS2, DVLL1, DVL1P1, DVL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004869	18563	Pcx	http://www.ncbi.nlm.nih.gov/gene/?term=18563	"Pc, Pcb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004870	18569	Pdcd4	http://www.ncbi.nlm.nih.gov/gene/?term=18569	"D19Ucla1, Ma3, Tis "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004871	1856	DVL2	http://www.ncbi.nlm.nih.gov/gene/?term=1856		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004872	1856	DVL2	http://www.ncbi.nlm.nih.gov/gene/?term=1856		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004873	18572	Pdcd11	http://www.ncbi.nlm.nih.gov/gene/?term=18572	"1110021I22Rik, ALG-4, Pdcd7, mKIAA0185 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004874	18576	Pde3b	http://www.ncbi.nlm.nih.gov/gene/?term=18576	"9830102A01Rik, AI847709 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004875	18577	Pde4a	http://www.ncbi.nlm.nih.gov/gene/?term=18577	"D9Ertd60e, Dpde2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004876	18578	Pde4b	http://www.ncbi.nlm.nih.gov/gene/?term=18578	"Dpde4, R74983, dunce "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004877	1857	DVL3	http://www.ncbi.nlm.nih.gov/gene/?term=1857		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004878	1857	DVL3	http://www.ncbi.nlm.nih.gov/gene/?term=1857	DRS3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004879	18583	Pde7a	http://www.ncbi.nlm.nih.gov/gene/?term=18583	"AU015378, AW047537 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004880	18595	Pdgfra	http://www.ncbi.nlm.nih.gov/gene/?term=18595	"AI115593, CD140a, Pdgfr-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004881	18597	Pdha1	http://www.ncbi.nlm.nih.gov/gene/?term=18597	Pdha-1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004882	1859	DYRK1A	http://www.ncbi.nlm.nih.gov/gene/?term=1859	"DYRK, DYRK1, HP86, MNB, MNBH, MRD7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004883	1859	DYRK1A	http://www.ncbi.nlm.nih.gov/gene/?term=1859	"DYRK, DYRK1, HP86, MNB, MNBH, MRD7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004884	185	AGTR1	http://www.ncbi.nlm.nih.gov/gene/?term=185	"AG2S, AGTR1B, AT1, AT1AR, AT1B, AT1BR, AT1R, AT2R1, HAT1R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004885	18605	Enpp1	http://www.ncbi.nlm.nih.gov/gene/?term=18605	"4833416E15Rik, AI428932, C76301, CD203c, E-NPP 1, E-NPP1, Ly-41, M6S1, NPP1, Npps, PC-1, Pca, Pca-1, Pdnp1, ttw, twy "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004886	18607	Pdpk1	http://www.ncbi.nlm.nih.gov/gene/?term=18607	Pdk1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004887	18610	Pdyn	http://www.ncbi.nlm.nih.gov/gene/?term=18610	Dyn	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004888	18613	Pecam1	http://www.ncbi.nlm.nih.gov/gene/?term=18613	"C85791, Cd31, PECAM-1, Pecam "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004889	18616	Peg3	http://www.ncbi.nlm.nih.gov/gene/?term=18616	"AL022617, ASF-1, End4, Gcap4, Pw1, Zfp102, mKIAA0287 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004890	18618	Pemt	http://www.ncbi.nlm.nih.gov/gene/?term=18618	"PEAMT, PEMT2, Pempt, Pempt2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004891	1861	TOR1A	http://www.ncbi.nlm.nih.gov/gene/?term=1861	"DQ2, DYT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004892	1861	TOR1A	http://www.ncbi.nlm.nih.gov/gene/?term=1861	"DQ2, DYT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004893	1861	TOR1A	http://www.ncbi.nlm.nih.gov/gene/?term=1861	"DQ2, DYT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004894	18628	Per3	http://www.ncbi.nlm.nih.gov/gene/?term=18628	"2810049O06Rik, mPer3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004895	18628	Per3	http://www.ncbi.nlm.nih.gov/gene/?term=18628	"2810049O06Rik, mPer3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004896	18633	Pex16	http://www.ncbi.nlm.nih.gov/gene/?term=18633		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004897	18636	Cfp	http://www.ncbi.nlm.nih.gov/gene/?term=18636	"BCFG, Pfc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004898	18639	Pfkfb1	http://www.ncbi.nlm.nih.gov/gene/?term=18639	PFK/FBPase 1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004899	18640	Pfkfb2	http://www.ncbi.nlm.nih.gov/gene/?term=18640	4930568D07Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004900	18641	Pfkl	http://www.ncbi.nlm.nih.gov/gene/?term=18641	"AA407869, ATP-PFK, PFK-L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004901	18645	Pfn2	http://www.ncbi.nlm.nih.gov/gene/?term=18645	Pfn	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004902	18655	Pgk1	http://www.ncbi.nlm.nih.gov/gene/?term=18655	Pgk-1	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004903	18669	Abcb1b	http://www.ncbi.nlm.nih.gov/gene/?term=18669	"Abcb1, Mdr1, Mdr1b, Pgy-1, Pgy1, mdr "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004904	18674	Slc25a3	http://www.ncbi.nlm.nih.gov/gene/?term=18674	"5730556H19Rik, PTP, Phc "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004905	18685	Phtf1	http://www.ncbi.nlm.nih.gov/gene/?term=18685	"AU041898, AW049785, Phft, Phtf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004906	1869	E2F1	http://www.ncbi.nlm.nih.gov/gene/?term=1869	"E2F-1, RBAP1, RBBP3, RBP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004907	1869	E2F1	http://www.ncbi.nlm.nih.gov/gene/?term=1869	"E2F-1, RBAP1, RBBP3, RBP3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004908	1869	E2F1	http://www.ncbi.nlm.nih.gov/gene/?term=1869	"E2F-1, RBAP1, RBBP3, RBP3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004909	18700	Piga	http://www.ncbi.nlm.nih.gov/gene/?term=18700	"AI194334, Pig-a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004910	18701	Pigf	http://www.ncbi.nlm.nih.gov/gene/?term=18701		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004911	18704	Pik3c2a	http://www.ncbi.nlm.nih.gov/gene/?term=18704	"Cpk-m, PI3KC2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004912	18706	Pik3ca	http://www.ncbi.nlm.nih.gov/gene/?term=18706	"6330412C24Rik, caPI3K, p110, p110alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004913	18708	Pik3r1	http://www.ncbi.nlm.nih.gov/gene/?term=18708	"PI3K, p50alpha, p55alpha, p85alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004914	18709	Pik3r2	http://www.ncbi.nlm.nih.gov/gene/?term=18709	p85beta	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004915	1870	E2F2	http://www.ncbi.nlm.nih.gov/gene/?term=1870	E2F-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004916	1870	E2F2	http://www.ncbi.nlm.nih.gov/gene/?term=1870	E2F-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004917	1870	E2F2	http://www.ncbi.nlm.nih.gov/gene/?term=1870	E2F-2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004918	1870	E2F2	http://www.ncbi.nlm.nih.gov/gene/?term=1870	E2F-2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004919	18712	Pim1	http://www.ncbi.nlm.nih.gov/gene/?term=18712	Pim-1	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00004920	18718	Pip4k2a	http://www.ncbi.nlm.nih.gov/gene/?term=18718	"AW742916, Pip5k2a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004921	1871	E2F3	http://www.ncbi.nlm.nih.gov/gene/?term=1871	E2F-3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004922	18741	Pitx2	http://www.ncbi.nlm.nih.gov/gene/?term=18741	"9430085M16Rik, Brx1, Brx1b, Munc30, Otlx2, Ptx2, Rieg "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004923	18747	Prkaca	http://www.ncbi.nlm.nih.gov/gene/?term=18747	"PKCD, Pkaca "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004924	1874	E2F4	http://www.ncbi.nlm.nih.gov/gene/?term=1874	E2F-4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004925	1874	E2F4	http://www.ncbi.nlm.nih.gov/gene/?term=1874	E2F-4	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004926	18750	Prkca	http://www.ncbi.nlm.nih.gov/gene/?term=18750	"AI875142, Pkca "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004927	18754	Prkce	http://www.ncbi.nlm.nih.gov/gene/?term=18754	"5830406C15Rik, PKC[e], PKCepsilon, Pkce, R75156 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004928	1875	E2F5	http://www.ncbi.nlm.nih.gov/gene/?term=1875	E2F-5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004929	1875	E2F5	http://www.ncbi.nlm.nih.gov/gene/?term=1875	E2F-5	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00004930	18762	Prkcz	http://www.ncbi.nlm.nih.gov/gene/?term=18762	"AI098070, C80388, Pkcz, R74924, aPKCzeta, nPKC-zeta, zetaPKC "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004931	18763	Pkd1	http://www.ncbi.nlm.nih.gov/gene/?term=18763	"PC1, mFLJ00285 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004932	18764	Pkd2	http://www.ncbi.nlm.nih.gov/gene/?term=18764	"C030034P18Rik, PC2, TRPP2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004933	18786	Plaa	http://www.ncbi.nlm.nih.gov/gene/?term=18786	"2410007N06, AI536418, AU018445, AW208417, D4Ertd618e, PLA2P, PLAP, Ufd3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004934	18789	Papola	http://www.ncbi.nlm.nih.gov/gene/?term=18789	"Pap, PapIII, Plap "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004935	18791	Plat	http://www.ncbi.nlm.nih.gov/gene/?term=18791	"AU020998, AW212668, D8Ertd2e, tPA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004936	18798	Plcb4	http://www.ncbi.nlm.nih.gov/gene/?term=18798	"A930039J07Rik, AI854601, C230058B11Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004937	18805	Pld1	http://www.ncbi.nlm.nih.gov/gene/?term=18805	"AA536939, C85393a, Pld1b, Pld1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004938	18810	Plec	http://www.ncbi.nlm.nih.gov/gene/?term=18810	"AA591047, AU042537, EBS1, PCN, PLTN1, Plec "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004939	18817	Plk1	http://www.ncbi.nlm.nih.gov/gene/?term=18817	"Plk, STPK13 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004940	18823	Plp1	http://www.ncbi.nlm.nih.gov/gene/?term=18823	"DM20, Plp, jimpy, jp, msd, rsh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004941	18823	Plp1	http://www.ncbi.nlm.nih.gov/gene/?term=18823	"DM20, Plp, jimpy, jp, msd, rsh "	mRNA	Mus musculus	7877439	Cytoplasm	Brain	In situ hybridization	A similar staining pattern was evident in sections hybridized with CNP riboprobe (Fig. 4C) suggesting that the distribution of both CNP and PLP mRNA was primarily perinuclear.
RLID00004942	18845	Plxna2	http://www.ncbi.nlm.nih.gov/gene/?term=18845	"2810428A13Rik, AA589422, AW457381, OCT, PlexA2, Plxn2, mKIAA0463 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004943	18854	Pml	http://www.ncbi.nlm.nih.gov/gene/?term=18854	"1200009E24Rik, AI661194, Trim19 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004944	18857	Pmp2	http://www.ncbi.nlm.nih.gov/gene/?term=18857	P2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004945	18861	Pms2	http://www.ncbi.nlm.nih.gov/gene/?term=18861	"AW555130, Pmsl2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004946	1889	ECE1	http://www.ncbi.nlm.nih.gov/gene/?term=1889	ECE	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004947	1891	ECH1	http://www.ncbi.nlm.nih.gov/gene/?term=1891	HPXEL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004948	1891	ECH1	http://www.ncbi.nlm.nih.gov/gene/?term=1891	HPXEL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004949	1892	ECHS1	http://www.ncbi.nlm.nih.gov/gene/?term=1892	"ECHS1D, SCEH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004950	1892	ECHS1	http://www.ncbi.nlm.nih.gov/gene/?term=1892	"ECHS1D, SCEH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004951	1893	ECM1	http://www.ncbi.nlm.nih.gov/gene/?term=1893	URBWD	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004952	18949	Pnn	http://www.ncbi.nlm.nih.gov/gene/?term=18949	"AU045199, D12Ertd512e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004953	1894	ECT2	http://www.ncbi.nlm.nih.gov/gene/?term=1894	ARHGEF31	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004954	18968	Pola1	http://www.ncbi.nlm.nih.gov/gene/?term=18968	"AW321876, Pola "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004955	18972	Pold2	http://www.ncbi.nlm.nih.gov/gene/?term=18972	"50kDa, p50, po1D2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004956	18973	Pole	http://www.ncbi.nlm.nih.gov/gene/?term=18973		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004957	18974	Pole2	http://www.ncbi.nlm.nih.gov/gene/?term=18974		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004958	18983	Cnot7	http://www.ncbi.nlm.nih.gov/gene/?term=18983	"AU022737, CAF-1, Caf1, Pop2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004959	18986	Pou2f1	http://www.ncbi.nlm.nih.gov/gene/?term=18986	"2810482H01Rik, NF-A1, Oct-1, Oct1, Otf-1, Otf1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004960	18988	Pou2f3	http://www.ncbi.nlm.nih.gov/gene/?term=18988	"Epoc-1, Oct-11a, Oct11, Otf-11, Otf11, Skin, Skin-1a, Skn-1a, Skn-li "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004961	18996	Pou4f1	http://www.ncbi.nlm.nih.gov/gene/?term=18996	"Brn-3, Brn-3.0, Brn3, Brn3.0, Brn3a, E130119J07Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004962	18998	Pou4f3	http://www.ncbi.nlm.nih.gov/gene/?term=18998	"Brn3.1, Brn3c, ddl, dreidel "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004963	189	AGXT	http://www.ncbi.nlm.nih.gov/gene/?term=189	"AGT, AGT1, AGXT1, PH1, SPAT, SPT, TLH6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004964	19014	Med1	http://www.ncbi.nlm.nih.gov/gene/?term=19014	"AI480703, CRSP210, DRIP205, PBP, Pparbp, TRAP220, l11Jus15 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004965	19015	Ppard	http://www.ncbi.nlm.nih.gov/gene/?term=19015	"NUC-1, NUC1, Nr1c2, PPAR-beta, PPAR-delta, PPAR[b], PPARdelta, Pparb, Pparb/d "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004966	19017	Ppargc1a	http://www.ncbi.nlm.nih.gov/gene/?term=19017	"A830037N07Rik, ENSMUSG00000079510, Gm11133, PGC-1, PPARGC-1-alpha, Pgc-1alpha, Pgc1, Pgco1, Ppargc1 "	mRNA	Mus musculus	12234291	Nucleus	LLCPK1 cell	In situ hybridization|qRT-PCR	"PGC-1 was localized to the nuclei. At low levels of expression, nuclear staining was diffuse. At higher levels of expression, GFP-PGC-1 localized to nuclear speckles. "
RLID00004967	1901	S1PR1	http://www.ncbi.nlm.nih.gov/gene/?term=1901	"CD363, CHEDG1, D1S3362, ECGF1, EDG-1, EDG1, S1P1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004968	19024	Ppfibp2	http://www.ncbi.nlm.nih.gov/gene/?term=19024	Cclp1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004969	19027	Sypl	http://www.ncbi.nlm.nih.gov/gene/?term=19027	"AI314763, AI604763, D12Ertd446e, PanI, Pphn1, Sypl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004970	19027	Sypl	http://www.ncbi.nlm.nih.gov/gene/?term=19027	"AI314763, AI604763, D12Ertd446e, PanI, Pphn1, Sypl "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004971	19045	Ppp1ca	http://www.ncbi.nlm.nih.gov/gene/?term=19045	"Ppp1c, dism2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004972	19047	Ppp1cc	http://www.ncbi.nlm.nih.gov/gene/?term=19047	"PP-1G, PP1, dis2m1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004973	19053	Ppp2cb	http://www.ncbi.nlm.nih.gov/gene/?term=19053	"AI115466, D8Ertd766e, PP2Ac "	mRNA	Mus musculus	18539120	Synapse	Brain	qRT-PCR	"The mRNA targets reduced in Kif5 association included genes involved in actin remodeling at synapses (cofilin phosphatase (PP2Ac); p116-RIP), synapse-associated signaling (DAG1;RGS5) and synapse structure (SAPAP4; CaMKIIa; MAP1b). Not all mRNAs were significantly reduced in Kif5 IPs, as OCRL1 mRNA was similar in KO brain (P>0.05, n=8). "
RLID00004974	19056	Ppp3cb	http://www.ncbi.nlm.nih.gov/gene/?term=19056	"1110063J16Rik, Calnb, CnAbeta, Cnab "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004975	19058	Ppp3r1	http://www.ncbi.nlm.nih.gov/gene/?term=19058	"CaNB1, Cnb1, MCIP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004976	19063	Ppt1	http://www.ncbi.nlm.nih.gov/gene/?term=19063	"9530043G02Rik, AA960502, C77813, CLN1, D4Ertd184e, INCL, PPT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004977	19069	Nup88	http://www.ncbi.nlm.nih.gov/gene/?term=19069	"Nup84, Prei2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004978	19070	Mob4	http://www.ncbi.nlm.nih.gov/gene/?term=19070	"2610109B12Rik, Mobkl3, Phocn, Prei3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004979	19075	Prim1	http://www.ncbi.nlm.nih.gov/gene/?term=19075	AI324982	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004980	19084	Prkar1a	http://www.ncbi.nlm.nih.gov/gene/?term=19084	"1300018C22Rik, RIalpha, Tse-1, Tse1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004981	19085	Prkar1b	http://www.ncbi.nlm.nih.gov/gene/?term=19085	"AI385716, RIbeta "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004982	19090	Prkdc	http://www.ncbi.nlm.nih.gov/gene/?term=19090	"AI326420, AU019811, DNA-PKcs, DNAPDcs, DNAPK, DNPK1, DOXNPH, HYRC1, XRCC7, dxnph, p460, scid, slip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004983	19091	Prkg1	http://www.ncbi.nlm.nih.gov/gene/?term=19091	"AW125416, CGKI, Gm19690b, Prkgr1b, Prkg1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004984	19094	Mapk11	http://www.ncbi.nlm.nih.gov/gene/?term=19094	"P38b, Prkm11, Sapk2, Sapk2b, p38-2, p38beta, p38beta2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004985	19099	Mapk8ip1	http://www.ncbi.nlm.nih.gov/gene/?term=19099	"IB1, JIP-1, Jip1, Prkm8ip, Skip, mjip-2a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004986	19106	Eif2ak2	http://www.ncbi.nlm.nih.gov/gene/?term=19106	"2310047A08Rik, 4732414G15Rik, AI467567, AI747578, Pkr, Prkr, Tik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00004987	1910	EDNRB	http://www.ncbi.nlm.nih.gov/gene/?term=1910	"ABCDS, ET-B, ET-BR, ETB, ETB1, ETBR, ETRB, HSCR, HSCR2, WS4A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004988	19110	Prl4a1	http://www.ncbi.nlm.nih.gov/gene/?term=19110	"AA409771, Ghd23, PLP-A, Prlpa "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004989	19118	Prm1	http://www.ncbi.nlm.nih.gov/gene/?term=19118	Prm-1	mRNA	Mus musculus	26071953	Nucleus	Sperm	RT-PCR	"Within this set of RNAs, the Prm1 transcript, as well as Erich2 and Fam71e2 (formerly 4933404M02Rik and 4930401F20Rik, respectively), were previously identified within the mouse sperm nucleus by RT-PCR though their preferential localization within the gamete could not be inferred from that study (15).  "
RLID00004990	1911	PHC1	http://www.ncbi.nlm.nih.gov/gene/?term=1911	"EDR1, HPH1, MCPH11, RAE28 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004991	1912	PHC2	http://www.ncbi.nlm.nih.gov/gene/?term=1912	"EDR2, HPH2, PH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00004992	1912	PHC2	http://www.ncbi.nlm.nih.gov/gene/?term=1912	"EDR2, HPH2, PH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00004993	19134	Prpf4b	http://www.ncbi.nlm.nih.gov/gene/?term=19134	"2610037H07, Prp4, Prp4k, Prpk, cbp143 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004994	19139	Prps1	http://www.ncbi.nlm.nih.gov/gene/?term=19139	"2310010D17Rik, C76571, C76678, PRS-I, Prps-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004995	19143	St14	http://www.ncbi.nlm.nih.gov/gene/?term=19143	"Epithin, MT-SP1, Prss14, Tmprss14, mCAP3, matriptase "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004996	19155	Npepps	http://www.ncbi.nlm.nih.gov/gene/?term=19155	"AAP-S, MP100, Psa, R74825, goku "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004997	191578	Helq	http://www.ncbi.nlm.nih.gov/gene/?term=191578	"AU021725, D430018E21Rik, Hel308 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00004998	191585	PLAC4	http://www.ncbi.nlm.nih.gov/gene/?term=191585	"C21orf115, PRED78 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00004999	191585	PLAC4	http://www.ncbi.nlm.nih.gov/gene/?term=191585	"C21orf115, PRED78 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005000	1915	EEF1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1915	"CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005001	1915	EEF1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1915	"CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005002	1915	EEF1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1915	"CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005003	1915	EEF1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1915	"CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005004	1915	EEF1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1915	"CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005005	19164	Psen1	http://www.ncbi.nlm.nih.gov/gene/?term=19164	"Ad3h, PS-1, PS1, S182 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005006	19167	Psma3	http://www.ncbi.nlm.nih.gov/gene/?term=19167	Lmpc8	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005007	19167	Psma3	http://www.ncbi.nlm.nih.gov/gene/?term=19167	Lmpc8	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005008	19171	Psmb10	http://www.ncbi.nlm.nih.gov/gene/?term=19171	"Mecl-1, Mecl1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005009	191	AHCY	http://www.ncbi.nlm.nih.gov/gene/?term=191	"SAHH, adoHcyase "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005010	191	AHCY	http://www.ncbi.nlm.nih.gov/gene/?term=191	"SAHH, adoHcyase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005011	191	AHCY	http://www.ncbi.nlm.nih.gov/gene/?term=191	"SAHH, adoHcyase "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005012	19204	Ptafr	http://www.ncbi.nlm.nih.gov/gene/?term=19204	PAFR	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005013	19210	Ptdss1	http://www.ncbi.nlm.nih.gov/gene/?term=19210	"AU044268, AW539008, PSS-1, mKIAA0024 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005014	192111	PGAM5	http://www.ncbi.nlm.nih.gov/gene/?term=192111	BXLBV68	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005015	192111	PGAM5	http://www.ncbi.nlm.nih.gov/gene/?term=192111	BXLBV68	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005016	192119	Dicer1	http://www.ncbi.nlm.nih.gov/gene/?term=192119	"1110006F08Rik, D12Ertd7e, mKIAA0928 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005017	19211	Pten	http://www.ncbi.nlm.nih.gov/gene/?term=19211	"2310035O07Rik, A130070J02Rik, AI463227, B430203M17Rik, MMAC1, TEP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005018	192156	Mvd	http://www.ncbi.nlm.nih.gov/gene/?term=192156	"C78718, Mpd "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005019	192161	Pcdha9	http://www.ncbi.nlm.nih.gov/gene/?term=192161		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005020	192166	Sardh	http://www.ncbi.nlm.nih.gov/gene/?term=192166		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005021	192169	Ufsp2	http://www.ncbi.nlm.nih.gov/gene/?term=192169	1810047C23Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005022	192173	Fam195b	http://www.ncbi.nlm.nih.gov/gene/?term=192173		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005023	192174	Rwdd4a	http://www.ncbi.nlm.nih.gov/gene/?term=192174	"BC016198, Gm1942, Rwdd4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005024	192187	Stab1	http://www.ncbi.nlm.nih.gov/gene/?term=192187	"FEEL-1, FELE-1, MFEEL-1, MS-1, STAB-1, mKIAA0246 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005025	192191	Med9	http://www.ncbi.nlm.nih.gov/gene/?term=192191	"BC019367, Med25 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005026	192192	Shkbp1	http://www.ncbi.nlm.nih.gov/gene/?term=192192	"B930062H15Rik, Sb1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005027	192193	Edem1	http://www.ncbi.nlm.nih.gov/gene/?term=192193	"A130059K23Rik, EDEM, mKIAA0212 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005028	192195	Ash1l	http://www.ncbi.nlm.nih.gov/gene/?term=192195	"8030453L17Rik, Ash1, E430018P19Rik, Kmt2h "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005029	192197	Bcas3	http://www.ncbi.nlm.nih.gov/gene/?term=192197	"1500019F07Rik, 2610028P08Rik, AU021018, BC028339, K20D4, rudhira "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005030	19219	Ptger4	http://www.ncbi.nlm.nih.gov/gene/?term=19219	"EP4, Ptgerep4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005031	19221	Ptgfrn	http://www.ncbi.nlm.nih.gov/gene/?term=19221	"4833445A08Rik, AU042434, CD9P-1, FPRP, Trim45 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005032	19222	Ptgir	http://www.ncbi.nlm.nih.gov/gene/?term=19222	"IP, PGI2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005033	19223	Ptgis	http://www.ncbi.nlm.nih.gov/gene/?term=19223	"Cyp8, Cyp8a1, Pgis "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005034	19224	Ptgs1	http://www.ncbi.nlm.nih.gov/gene/?term=19224	"COX1, Cox-1, Cox-3, PGHS-1, PHS 1, Pghs1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005035	192285	Phf21a	http://www.ncbi.nlm.nih.gov/gene/?term=192285	"80kDa, Bhc, Bhc80, D030065N23Rik, PFTF1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005036	192286	HIGD2A	http://www.ncbi.nlm.nih.gov/gene/?term=192286	RCF1b	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005037	192286	HIGD2A	http://www.ncbi.nlm.nih.gov/gene/?term=192286	RCF1b	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005038	19230	Twf1	http://www.ncbi.nlm.nih.gov/gene/?term=19230	"A6, Ptk9, twinfilin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005039	19231	Ptma	http://www.ncbi.nlm.nih.gov/gene/?term=19231	Thym	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005040	19231	Ptma	http://www.ncbi.nlm.nih.gov/gene/?term=19231	Thym	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005041	19240	Tmsb10	http://www.ncbi.nlm.nih.gov/gene/?term=19240	"Ptmb10, Tb10 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005042	19240	Tmsb10	http://www.ncbi.nlm.nih.gov/gene/?term=19240	"Ptmb10, Tb10 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005043	19242	Ptn	http://www.ncbi.nlm.nih.gov/gene/?term=19242	"HARP, HB-GAM, HBBN, HBGF-8, HBNF, OSF, Osf-1, Osf1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005044	19243	Ptp4a1	http://www.ncbi.nlm.nih.gov/gene/?term=19243	"AA415290, AU019864, C130021B01, Prl-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005045	19244	Ptp4a2	http://www.ncbi.nlm.nih.gov/gene/?term=19244	Prl-2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005046	19245	Ptp4a3	http://www.ncbi.nlm.nih.gov/gene/?term=19245	"AV088979, Prl-3, pPtp4a3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005047	19246	Ptpn1	http://www.ncbi.nlm.nih.gov/gene/?term=19246	"PTP-1B, PTP-HA2, PTP1B "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005048	19248	Ptpn12	http://www.ncbi.nlm.nih.gov/gene/?term=19248	"P19-PTP, PTP-P19, PTP-PEST, PTPG1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005049	19255	Ptpn2	http://www.ncbi.nlm.nih.gov/gene/?term=19255	"AI325124, Ptpt, TC-PTP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005050	19261	Sirpa	http://www.ncbi.nlm.nih.gov/gene/?term=19261	"AI835480, Bit, CD172a, P84, Ptpns1, SHP-1, SHPS-1, SIRP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005051	19262	Ptpra	http://www.ncbi.nlm.nih.gov/gene/?term=19262	"Ptpa, Ptpalpha, Rptpalpha, Rptra, Rptralpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005052	192662	Arhgdia	http://www.ncbi.nlm.nih.gov/gene/?term=192662	"5330430M07Rik, Gdi-1, Rho-GDI, RhoDGI, RhoGDI-1 "	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00005053	192669	AGO3	http://www.ncbi.nlm.nih.gov/gene/?term=192669	EIF2C3	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005054	19267	Ptpre	http://www.ncbi.nlm.nih.gov/gene/?term=19267	"PTPe, PTPepsilon, RPTPepsilon "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005055	19268	Ptprf	http://www.ncbi.nlm.nih.gov/gene/?term=19268	"AA591035, LAR, LARS, RPTP-LAR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005056	19272	Ptprk	http://www.ncbi.nlm.nih.gov/gene/?term=19272	"AI853699, PTPk, RPTPkappa "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005057	19275	Ptprn	http://www.ncbi.nlm.nih.gov/gene/?term=19275	"IA-2, mIA-A, mKIAA4064 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005058	192786	Rapgef6	http://www.ncbi.nlm.nih.gov/gene/?term=192786	"A530068K01, AI844632, BB085664, C030018K18Rik, PDZ-GEF2, Pdzgef2, RA-GEF-2, Ragef2, mKIAA4052 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005059	19288	Ptx3	http://www.ncbi.nlm.nih.gov/gene/?term=19288	"AI607804, TSG-14 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005060	19291	Purb	http://www.ncbi.nlm.nih.gov/gene/?term=19291	"2310015K15Rik, AA114818, Cager-2, D11Bwg0414e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005061	19296	Pvt1	http://www.ncbi.nlm.nih.gov/gene/?term=19296	"Ayu21-84Imeg, Gt(pU21)84Imeg, Mis-1, Mlvi-1, Pvt-1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005062	192976	Lrrc75a	http://www.ncbi.nlm.nih.gov/gene/?term=192976	Fam211a	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005063	19298	Pex19	http://www.ncbi.nlm.nih.gov/gene/?term=19298	Pxf	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005064	19299	Abcd3	http://www.ncbi.nlm.nih.gov/gene/?term=19299	"AI313901, AU018866, AW146054, PMP68, PMP70, Pxmp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005065	19300	Abcd4	http://www.ncbi.nlm.nih.gov/gene/?term=19300	"P69r, P70R, Pxmp1l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005066	193116	Slu7	http://www.ncbi.nlm.nih.gov/gene/?term=193116	"AU018913, D11Ertd730e, D3Bwg0878e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005067	19317	Qk	http://www.ncbi.nlm.nih.gov/gene/?term=19317	"1110003F05Rik, 1500005P18I, l(17)-1Wis, l17Wis1, Qk "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005068	19317	Qk	http://www.ncbi.nlm.nih.gov/gene/?term=19317	"1110003F05Rik, 1500005P18I, l(17)-1Wis, l17Wis1, Qk "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005069	19325	Rab10	http://www.ncbi.nlm.nih.gov/gene/?term=19325	AW107754	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005070	19330	Rab18	http://www.ncbi.nlm.nih.gov/gene/?term=19330	AA959686	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005071	19334	Rab22a	http://www.ncbi.nlm.nih.gov/gene/?term=19334	"3732413A17Rik, AI662177, AW319644, AW550514, E130120E14Rik, Rab22 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005072	19339	Rab3a	http://www.ncbi.nlm.nih.gov/gene/?term=19339		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005073	19341	Rab4a	http://www.ncbi.nlm.nih.gov/gene/?term=19341	"AI848268, Rab4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005074	19342	Rab4b	http://www.ncbi.nlm.nih.gov/gene/?term=19342	1500031G17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005075	19352	Rabggtb	http://www.ncbi.nlm.nih.gov/gene/?term=19352		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005076	19357	Rad21	http://www.ncbi.nlm.nih.gov/gene/?term=19357	"SCC1, mKIAA0078 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005077	19360	Rad50	http://www.ncbi.nlm.nih.gov/gene/?term=19360	"Mrelll, Rad50 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005078	19364	Rad51d	http://www.ncbi.nlm.nih.gov/gene/?term=19364	"R51H3, Rad51l3, TRAD, Trad-d5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005079	19364	Rad51d	http://www.ncbi.nlm.nih.gov/gene/?term=19364	"R51H3, Rad51l3, TRAD, Trad-d5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005080	19366	Rad54l	http://www.ncbi.nlm.nih.gov/gene/?term=19366	RAD54	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005081	1936	EEF1D	http://www.ncbi.nlm.nih.gov/gene/?term=1936	"EF-1D, EF1D, FP1047 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005082	1936	EEF1D	http://www.ncbi.nlm.nih.gov/gene/?term=1936	"EF-1D, EF1D, FP1047 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005083	1936	EEF1D	http://www.ncbi.nlm.nih.gov/gene/?term=1936	"EF-1D, EF1D, FP1047 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005084	1936	EEF1D	http://www.ncbi.nlm.nih.gov/gene/?term=1936	"EF-1D, EF1D, FP1047 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005085	193740	Hspa1a	http://www.ncbi.nlm.nih.gov/gene/?term=193740	"Hsp70-3, Hsp70.3, Hsp72, hsp68, hsp70A1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005086	193742	Abhd16a	http://www.ncbi.nlm.nih.gov/gene/?term=193742	"AI326074, Bat-5, Bat5, D17H6S82E, NG26 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005087	19374	Rag2	http://www.ncbi.nlm.nih.gov/gene/?term=19374	Rag-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005088	19377	Rai1	http://www.ncbi.nlm.nih.gov/gene/?term=19377	Gt1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005089	1937	EEF1G	http://www.ncbi.nlm.nih.gov/gene/?term=1937	"EF1G, GIG35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005090	1937	EEF1G	http://www.ncbi.nlm.nih.gov/gene/?term=1937	"EF1G, GIG35 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005091	1937	EEF1G	http://www.ncbi.nlm.nih.gov/gene/?term=1937	"EF1G, GIG35 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005092	193813	Mcfd2	http://www.ncbi.nlm.nih.gov/gene/?term=193813	"1810021C21Rik, F5f8d, Lman1ip, Sdnsf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005093	19384	Ran	http://www.ncbi.nlm.nih.gov/gene/?term=19384		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005094	19386	Ranbp2	http://www.ncbi.nlm.nih.gov/gene/?term=19386	"A430087B05Rik, AI256741, NUP358 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005095	1938	EEF2	http://www.ncbi.nlm.nih.gov/gene/?term=1938	"EEF-2, EF-2, EF2, SCA26 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005096	1938	EEF2	http://www.ncbi.nlm.nih.gov/gene/?term=1938	"EEF-2, EF-2, EF2, SCA26 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005097	1938	EEF2	http://www.ncbi.nlm.nih.gov/gene/?term=1938	"EEF-2, EF-2, EF2, SCA26 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005098	19400	Rapsn	http://www.ncbi.nlm.nih.gov/gene/?term=19400	"43kDa, Nraps, Raps, rapsyn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005099	19411	Rarg	http://www.ncbi.nlm.nih.gov/gene/?term=19411	"Nr1b3, RAR-gamma, RARD, RARgamma2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005100	19416	Rasd1	http://www.ncbi.nlm.nih.gov/gene/?term=19416	Dexras1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005101	1942	EFNA1	http://www.ncbi.nlm.nih.gov/gene/?term=1942	"B61, ECKLG, EFL1, EPLG1, LERK-1, LERK1, TNFAIP4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005102	194433	Olfr707	http://www.ncbi.nlm.nih.gov/gene/?term=194433	MOR260-8P	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005103	1945	EFNA4	http://www.ncbi.nlm.nih.gov/gene/?term=1945	"EFL4, EPLG4, LERK4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005104	194738	Rhox11	http://www.ncbi.nlm.nih.gov/gene/?term=194738	"BC049711, Gm39 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005105	1947	EFNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1947	"CFND, CFNS, EFB1, EFL3, EPLG2, Elk-L, LERK2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005106	1947	EFNB1	http://www.ncbi.nlm.nih.gov/gene/?term=1947	"CFND, CFNS, EFB1, EFL3, EPLG2, Elk-L, LERK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005107	1948	EFNB2	http://www.ncbi.nlm.nih.gov/gene/?term=1948	"EPLG5, HTKL, Htk-L, LERK5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005108	1948	EFNB2	http://www.ncbi.nlm.nih.gov/gene/?term=1948	"EPLG5, HTKL, Htk-L, LERK5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005109	1948	EFNB2	http://www.ncbi.nlm.nih.gov/gene/?term=1948	"EPLG5, HTKL, Htk-L, LERK5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005110	195018	Zzef1	http://www.ncbi.nlm.nih.gov/gene/?term=195018	"8430405D05Rik, BC051585, C130099L13Rik, C85424, NSPA, mKIAA0399 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005111	195018	Zzef1	http://www.ncbi.nlm.nih.gov/gene/?term=195018	"8430405D05Rik, BC051585, C130099L13Rik, C85424, NSPA, mKIAA0399 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005112	1951	CELSR3	http://www.ncbi.nlm.nih.gov/gene/?term=1951	"ADGRC3, CDHF11, EGFL1, FMI1, HFMI1, MEGF2, RESDA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005113	1952	CELSR2	http://www.ncbi.nlm.nih.gov/gene/?term=1952	"ADGRC2, CDHF10, EGFL2, Flamingo1, MEGF3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005114	1953	MEGF6	http://www.ncbi.nlm.nih.gov/gene/?term=1953	EGFL3	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005115	1954	MEGF8	http://www.ncbi.nlm.nih.gov/gene/?term=1954	"C19orf49, CRPT2, EGFL4, SBP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005116	1955	MEGF9	http://www.ncbi.nlm.nih.gov/gene/?term=1955	EGFL5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005117	1956	EGFR	http://www.ncbi.nlm.nih.gov/gene/?term=1956	"ERBB, ERBB1, HER1, NISBD2, PIG61, mENA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005118	1956	EGFR	http://www.ncbi.nlm.nih.gov/gene/?term=1956	"ERBB, ERBB1, HER1, NISBD2, PIG61, mENA "	mRNA	Homo sapiens	1983869	Cytoplasm	Breast cell cancer	In situ hybridization	"EGF-R mRNA was observed principally at the cytoplasmic level, on organelles involved in the protein synthesis process. Labeling was also located on the microvilli which extend into the intercellular space, suggesting that some mRNA would be located in sites where EGF-R is utilized. Some mRNA was observed in the nucleus. "
RLID00005119	1956	EGFR	http://www.ncbi.nlm.nih.gov/gene/?term=1956	"ERBB, ERBB1, HER1, NISBD2, PIG61, mENA "	mRNA	Homo sapiens	20453113	Endoplasmic reticulum	NCI/ADR-RES cell	qRT-PCR	"The relative partitioning of both cytosolic (ACTB, H3.3) and ER-bound (MDR1, CANX) transcripts between both fractions was marked, despite the small carryover of cytosol in the ER fraction (Fig. 2B). Polysome profile analyses from the isolated fractions indicated that these transcripts migrated in polyribosome-containing fractions (Fig. 2C). Notably, the distribution of ER-bound transcripts between the ER and cytosol did not change on arsenite treatment of NCI/ADR-RES cells (Fig. 2D). Data are collected from Figure 2. "
RLID00005120	1956	EGFR	http://www.ncbi.nlm.nih.gov/gene/?term=1956	"ERBB, ERBB1, HER1, NISBD2, PIG61, mENA "	mRNA	Homo sapiens	1983869	Nucleus	Breast cell cancer	In situ hybridization	"EGF-R mRNA was observed principally at the cytoplasmic level, on organelles involved in the protein synthesis process. Labeling was also located on the microvilli which extend into the intercellular space, suggesting that some mRNA would be located in sites where EGF-R is utilized. Some mRNA was observed in the nucleus. "
RLID00005121	195827	AAED1	http://www.ncbi.nlm.nih.gov/gene/?term=195827	C9orf21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005122	195828	ZNF367	http://www.ncbi.nlm.nih.gov/gene/?term=195828	"AFF29, CDC14B, ZFF29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005123	195828	ZNF367	http://www.ncbi.nlm.nih.gov/gene/?term=195828	"AFF29, CDC14B, ZFF29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005124	1958	EGR1	http://www.ncbi.nlm.nih.gov/gene/?term=1958	"AT225, G0S30, KROX-24, NGFI-A, TIS8, ZIF-268, ZNF225 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005125	1958	EGR1	http://www.ncbi.nlm.nih.gov/gene/?term=1958	"AT225, G0S30, KROX-24, NGFI-A, TIS8, ZIF-268, ZNF225 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005126	1958	EGR1	http://www.ncbi.nlm.nih.gov/gene/?term=1958	"AT225, G0S30, KROX-24, NGFI-A, TIS8, ZIF-268, ZNF225 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005127	196047	EMX2OS	http://www.ncbi.nlm.nih.gov/gene/?term=196047	"EMX2-AS1, NCRNA00045 "	lncRNA	Homo sapiens	21128942	Nucleus	Brain tissue	qRT-PCR|Microarray	Table 2: Long noncoding RNAs represented on Affymetrix U133 arrays that were reliably detected in human nucleus accumbens. An lncRNA was considered reliably detected in human NAcc if at least one probe corresponding to the transcript gave a specific signal in all control subjects. No transcripts undetected in the controls were consistently detected in drug abusers. Data are collected from Talbe 2.
RLID00005128	196051	PLPP4	http://www.ncbi.nlm.nih.gov/gene/?term=196051	"DPPL2, PPAPDC1, PPAPDC1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005129	1960	EGR3	http://www.ncbi.nlm.nih.gov/gene/?term=1960	"EGR-3, PILOT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005130	1961	EGR4	http://www.ncbi.nlm.nih.gov/gene/?term=1961	"NGFI-C, NGFIC, PAT133 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005131	196264	MPZL3	http://www.ncbi.nlm.nih.gov/gene/?term=196264		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005132	196383	RILPL2	http://www.ncbi.nlm.nih.gov/gene/?term=196383	RLP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005133	196383	RILPL2	http://www.ncbi.nlm.nih.gov/gene/?term=196383	RLP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005134	196383	RILPL2	http://www.ncbi.nlm.nih.gov/gene/?term=196383	RLP2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005135	196410	METTL7B	http://www.ncbi.nlm.nih.gov/gene/?term=196410	ALDI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005136	196441	ZFC3H1	http://www.ncbi.nlm.nih.gov/gene/?term=196441	"CCDC131, PSRC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005137	196441	ZFC3H1	http://www.ncbi.nlm.nih.gov/gene/?term=196441	"CCDC131, CSRC2, PSRC2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005138	196441	ZFC3H1	http://www.ncbi.nlm.nih.gov/gene/?term=196441	"CCDC131, CSRC2, PSRC2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005139	19646	Rbbp4	http://www.ncbi.nlm.nih.gov/gene/?term=19646	"RBAP48, mRbAp48 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005140	196475	RMST	http://www.ncbi.nlm.nih.gov/gene/?term=196475	"LINC00054, NCRMS, NCRNA00054 "	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00005141	196483	EEF2KMT	http://www.ncbi.nlm.nih.gov/gene/?term=196483	"FAM86A, SB153, eEF2-KMT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005142	1964	EIF1AX	http://www.ncbi.nlm.nih.gov/gene/?term=1964	"EIF1A, EIF1AP1, EIF4C, eIF-1A, eIF-4C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005143	1964	EIF1AX	http://www.ncbi.nlm.nih.gov/gene/?term=1964	"EIF1A, EIF1AP1, EIF4C, eIF-1A, eIF-4C "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005144	1964	EIF1AX	http://www.ncbi.nlm.nih.gov/gene/?term=1964	"EIF1A, EIF1AP1, EIF4C, eIF-1A, eIF-4C "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005145	19650	Rbl1	http://www.ncbi.nlm.nih.gov/gene/?term=19650	"AW547426, PRB1, p107 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005146	196513	DCP1B	http://www.ncbi.nlm.nih.gov/gene/?term=196513	DCP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005147	196513	DCP1B	http://www.ncbi.nlm.nih.gov/gene/?term=196513	DCP1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005148	19651	Rbl2	http://www.ncbi.nlm.nih.gov/gene/?term=19651	"PRB2, RBR-2, Rb2, p130 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005149	196527	ANO6	http://www.ncbi.nlm.nih.gov/gene/?term=196527	"BDPLT7, SCTS, TMEM16F "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005150	196528	ARID2	http://www.ncbi.nlm.nih.gov/gene/?term=196528	"BAF200, p200 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005151	19652	Rbm3	http://www.ncbi.nlm.nih.gov/gene/?term=19652	2600016C11Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005152	19653	Rbm4	http://www.ncbi.nlm.nih.gov/gene/?term=19653	"4921506I22Rik, Lark1, Mlarka, lark, Rbm4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005153	19656	Rbmxl1	http://www.ncbi.nlm.nih.gov/gene/?term=19656	"Hnrpg, Rbmx, Rbmxrt "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005154	1965	EIF2S1	http://www.ncbi.nlm.nih.gov/gene/?term=1965	"EIF-2, EIF-2A, EIF-2alpha, EIF2, EIF2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005155	1965	EIF2S1	http://www.ncbi.nlm.nih.gov/gene/?term=1965	"EIF-2, EIF-2A, EIF-2alpha, EIF2, EIF2A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005156	1965	EIF2S1	http://www.ncbi.nlm.nih.gov/gene/?term=1965	"EIF-2, EIF-2A, EIF-2alpha, EIF2, EIF2A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005157	19663	Rbpms	http://www.ncbi.nlm.nih.gov/gene/?term=19663	"2010300K22Rik, 2700019M19Rik, AU017537, RBP-MS, hermes "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005158	19663	Rbpms	http://www.ncbi.nlm.nih.gov/gene/?term=19663	"2010300K22Rik, 2700019M19Rik, AU017537, RBP-MS, hermes "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005159	19664	Rbpj	http://www.ncbi.nlm.nih.gov/gene/?term=19664	"AI843960, CBF1, Igkjrb, Igkrsbp, RBP-J, RBP-J kappa, RBP-Jkappa, RBPjk, Rbpsuh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005160	196740	VSTM4	http://www.ncbi.nlm.nih.gov/gene/?term=196740	C10orf72	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005161	196740	VSTM4	http://www.ncbi.nlm.nih.gov/gene/?term=196740	C10orf72	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005162	1967	EIF2B1	http://www.ncbi.nlm.nih.gov/gene/?term=1967	"EIF2B, EIF2BA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005163	1967	EIF2B1	http://www.ncbi.nlm.nih.gov/gene/?term=1967	"EIF2B, EIF2BA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005164	1967	EIF2B1	http://www.ncbi.nlm.nih.gov/gene/?term=1967	"EIF2B, EIF2BA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005165	19684	Rdx	http://www.ncbi.nlm.nih.gov/gene/?term=19684	AA516625	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005166	1968	EIF2S3	http://www.ncbi.nlm.nih.gov/gene/?term=1968	"EIF2, EIF2G, EIF2gamma, eIF-2gA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005167	1968	EIF2S3	http://www.ncbi.nlm.nih.gov/gene/?term=1968	"EIF2, EIF2G, EIF2gamma, eIF-2gA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005168	1968	EIF2S3	http://www.ncbi.nlm.nih.gov/gene/?term=1968	"EIF2, EIF2G, EIF2gamma, eIF-2gA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005169	19691	Recql	http://www.ncbi.nlm.nih.gov/gene/?term=19691	RecQ1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005170	19691	Recql	http://www.ncbi.nlm.nih.gov/gene/?term=19691	RecQ1	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005171	19698	Relb	http://www.ncbi.nlm.nih.gov/gene/?term=19698	shep	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005172	196	AHR	http://www.ncbi.nlm.nih.gov/gene/?term=196	bHLHe76	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005173	196	AHR	http://www.ncbi.nlm.nih.gov/gene/?term=196	bHLHe76	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005174	196	AHR	http://www.ncbi.nlm.nih.gov/gene/?term=196	bHLHe76	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005175	196	AHR	http://www.ncbi.nlm.nih.gov/gene/?term=196	bHLHe76	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005176	196	AHR	http://www.ncbi.nlm.nih.gov/gene/?term=196	bHLHe76	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005177	19712	Rest	http://www.ncbi.nlm.nih.gov/gene/?term=19712	"2610008J04Rik, AA407358, NRSF, REST4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005178	197131	UBR1	http://www.ncbi.nlm.nih.gov/gene/?term=197131	JBS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005179	197131	UBR1	http://www.ncbi.nlm.nih.gov/gene/?term=197131	JBS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005180	19713	Ret	http://www.ncbi.nlm.nih.gov/gene/?term=19713	"PTC, RET51, RET9, c-Ret "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005181	19714	Rev3l	http://www.ncbi.nlm.nih.gov/gene/?term=19714	"Rev, Rev3, Sez4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005182	19726	Rfx3	http://www.ncbi.nlm.nih.gov/gene/?term=19726	"C230093O12Rik, MRFX3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005183	197335	WDR90	http://www.ncbi.nlm.nih.gov/gene/?term=197335	"C16orf15, C16orf16, C16orf17, C16orf18, C16orf19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005184	197335	WDR90	http://www.ncbi.nlm.nih.gov/gene/?term=197335	"C16orf15, C16orf16, C16orf17, C16orf18, C16orf19 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005185	19734	Rgs16	http://www.ncbi.nlm.nih.gov/gene/?term=19734	"Rgs14, Rgsr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005186	197358	NLRC3	http://www.ncbi.nlm.nih.gov/gene/?term=197358	"CLR16.2, NOD3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005187	197358	NLRC3	http://www.ncbi.nlm.nih.gov/gene/?term=197358	"CLR16.2, NOD3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005188	19735	Rgs2	http://www.ncbi.nlm.nih.gov/gene/?term=19735	GOS8	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005189	197370	NSMCE1	http://www.ncbi.nlm.nih.gov/gene/?term=197370	NSE1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005190	197370	NSMCE1	http://www.ncbi.nlm.nih.gov/gene/?term=197370	NSE1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005191	197370	NSMCE1	http://www.ncbi.nlm.nih.gov/gene/?term=197370	NSE1	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00005192	1973	EIF4A1	http://www.ncbi.nlm.nih.gov/gene/?term=1973	"DDX2A, EIF-4A, EIF4A, eIF-4A-I, eIF4A-I "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005193	197407	ZNF48	http://www.ncbi.nlm.nih.gov/gene/?term=197407	ZNF553	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005194	1974	EIF4A2	http://www.ncbi.nlm.nih.gov/gene/?term=1974	"BM-010, DDX2B, EIF4A, EIF4F, eIF-4A-II, eIF4A-II "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005195	1975	EIF4B	http://www.ncbi.nlm.nih.gov/gene/?term=1975	"EIF-4B, PRO1843 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005196	19775	Xpr1	http://www.ncbi.nlm.nih.gov/gene/?term=19775	"Rmc-1, Rmc1, Sxv, Syg1, XR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005197	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP, EIF4E1, EIF4EL1, EIF4F, eIF-4E "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005198	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP1, EIF4EL1, EIF4F, eIF-4E, EIF4E "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005199	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP1, EIF4EL1, EIF4F, eIF-4E, EIF4E "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005200	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP1, EIF4EL1, EIF4F, eIF-4E, EIF4E "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005201	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP1, EIF4EL1, EIF4F, eIF-4E, EIF4E "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005202	1978	EIF4EBP1	http://www.ncbi.nlm.nih.gov/gene/?term=1978	"4E-BP1, 4EBP1, BP-1, PHAS-I "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005203	19791	Rn18s	http://www.ncbi.nlm.nih.gov/gene/?term=19791		rRNA	Mus musculus	26178919	Nucleolus	Embryo	In situ hybridization	"Furthermore, at the morula stage, whereas 18S rRNA and ribosomal protein S6 (rpS7), which are components of the ribosome, were distributed to the cytoplasm in WT embryos, they were mainly localized in the nucleoli in Nepro KO embryos.  At the 4-cell stage, the expression of 18S rRNA and rpS6 were detected in the nucleolus and cytoplasm at low level in both Nepro +/ and Nepro -/- (Fig. 4A). The majority of 18S rRNA and rpS6 was detected in nucleoli but not the cytoplasm in Nepro embryos at the morula stage.  "
RLID00005204	19791	Rn18s	http://www.ncbi.nlm.nih.gov/gene/?term=19791		rRNA	Mus musculus	26178919	Cytoplasm	Embryo	In situ hybridization	"Furthermore, at the morula stage, whereas 18S rRNA and ribosomal protein S6 (rpS6), which are components of the ribosome, were distributed to the cytoplasm in WT embryos, they were mainly localized in the nucleoli in Nepro KO embryos. At the morula stage, whereas 18S rRNA and rpS6 were distributed in the cytoplasm in Nepro +/ embryos, they were mainly restricted in nucleoli in Nepro -/- embryos (Fig. 4B). "
RLID00005205	19791	Rn18s	http://www.ncbi.nlm.nih.gov/gene/?term=19791		rRNA	Mus musculus	26464439	Cytoplasm	Motoneuron	In situ hybridization|qRT-PCR	"18S rRNA, a component of ribosomes, was similarly present in the cytoplasm and in motor axons. "
RLID00005206	19791	Rn18s	http://www.ncbi.nlm.nih.gov/gene/?term=19791		rRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"18S rRNA, a component of ribosomes, was similarly present in the cytoplasm and in motor axons. "
RLID00005207	19791	Rn18s	http://www.ncbi.nlm.nih.gov/gene/?term=19791		rRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR	"We noted that levels of all RNAs measured, including ribosomal 18S RNA, U6, CAMK2a and BC1, as well as mature microRNAs and their precursors, were lower in synaptosomes relative to that observed in synaptoneurosomes. "
RLID00005208	1979	EIF4EBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1979	"4EBP2, PHASII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005209	1979	EIF4EBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1979	"4EBP2, PHASII "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005210	1979	EIF4EBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1979	"4EBP2, PHASII "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005211	1979	EIF4EBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1979	"4EBP2, PHASII "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005212	197	AHSG	http://www.ncbi.nlm.nih.gov/gene/?term=197	"A2HS, AHS, FETUA, HSGA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005213	19817	Rn7sk	http://www.ncbi.nlm.nih.gov/gene/?term=19817		snRNA	Mus musculus	26179904	Nucleus	Macrophage	qRT-PCR	"As expected, the mature IL-1a and Gapdh transcripts were localized to the cytosol, whereas 7SK RNA was confined to the nucleus. "
RLID00005214	19817	Rn7sk	http://www.ncbi.nlm.nih.gov/gene/?term=19817		snRNA	Mus musculus	26464439	Somatodendritic compartment	Motoneuron	In situ hybridization|qRT-PCR	"The somatodendritic compartment was enriched for transcripts with post-synaptic functions as well as for certain nuclear non-coding RNAs such as 7SK. We found 7SK relatively more abundant in the somatodendritic compartment, but also detectable in motor axons, which we validated by qPCR (see Figure 8A). In our motoneuron dataset we found 7SK more abundant in the somatodendritic compared to the axonal cytoplasm in line with its nuclear function in transcriptional regulation (33). "
RLID00005215	19817	Rn7sk	http://www.ncbi.nlm.nih.gov/gene/?term=19817		snRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"We found 7SK relatively more abundant in the somatodendritic compartment, but also detectable in motor axons, which we validated by qPCR (see Figure 8A).  In our motoneuron dataset we found 7SK more abundant in the somatodendritic compared to the axonal cytoplasm in line with its nuclear function in transcriptional regulation (33). "
RLID00005216	1981	EIF4G1	http://www.ncbi.nlm.nih.gov/gene/?term=1981	"EIF-4G1, EIF4F, EIF4G, EIF4GI, P220, PARK18 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005217	19821	Rnf2	http://www.ncbi.nlm.nih.gov/gene/?term=19821	"AI326319, AI450156, AU019207, Ring1B, dinG "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005218	19822	Rnf4	http://www.ncbi.nlm.nih.gov/gene/?term=19822	"AU018689, Gtrgeo8, SNURF "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005219	19826	Rnps1	http://www.ncbi.nlm.nih.gov/gene/?term=19826		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005220	1982	EIF4G2	http://www.ncbi.nlm.nih.gov/gene/?term=1982	"AAG1, DAP5, NAT1, P97 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005221	19835230	tRNA:CR45107	http://www.ncbi.nlm.nih.gov/gene/?term=19835230	"Dmel_CR45107, AE002787.trna24-ThrTGT, CR30261, CR30505, CR45107, Dmel\CR45107, chr2R.trna83-ThrTGT, tRNA:CR30505, tRNA:T3:47F, tRNA:T:TGT:AE002787-a, tRNA:thr3:47F, tRNA[Thr][[3]], tRNA[[Thr]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0266574.html
RLID00005222	19836221	tRNA:CR45106	http://www.ncbi.nlm.nih.gov/gene/?term=19836221	"Dmel_CR45106, AE002787.trna33-ThrTGT, CR30260, CR45106, Dmel\CR45106, chr2R.trna15-ThrTGT, tRNA:CR30260, tRNA:T3:47F, tRNA:T:TGT:AE002787-d, tRNA:thr3:47F, tRNA[Thr][[3]], tRNA[[Thr]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0266573.html
RLID00005223	1983	EIF5	http://www.ncbi.nlm.nih.gov/gene/?term=1983	"EIF-5, EIF-5A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005224	1983	EIF5	http://www.ncbi.nlm.nih.gov/gene/?term=1983	"EIF-5, EIF-5A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005225	1983	EIF5	http://www.ncbi.nlm.nih.gov/gene/?term=1983	"EIF-5, EIF-5A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005226	1984	EIF5A	http://www.ncbi.nlm.nih.gov/gene/?term=1984	"EIF-5A1, eIF5AI, EIF5A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005227	19876	Robo1	http://www.ncbi.nlm.nih.gov/gene/?term=19876	"AW494633, AW742721, DUTT1, Gm310 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005228	19877	Rock1	http://www.ncbi.nlm.nih.gov/gene/?term=19877	"1110055K06Rik, Rock-I "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005229	19878	Rock2	http://www.ncbi.nlm.nih.gov/gene/?term=19878	"B230113H15Rik, ROKalpha, Rho-kinase, Rock-IIm, mKIAA0619, Rock2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005230	19883	Rora	http://www.ncbi.nlm.nih.gov/gene/?term=19883	"9530021D13Rik, Nr1f1, ROR1, ROR2, ROR3, nmf267, sg, staggerer, tmgc26 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005231	19889	Rp2	http://www.ncbi.nlm.nih.gov/gene/?term=19889	"AI662636h, Rp2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005232	19896	Rpl10a	http://www.ncbi.nlm.nih.gov/gene/?term=19896	"CsA-19, Nedd6 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005233	19896	Rpl10a	http://www.ncbi.nlm.nih.gov/gene/?term=19896	"CsA-19, Nedd6 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005234	19899	Rpl18	http://www.ncbi.nlm.nih.gov/gene/?term=19899	"L18a, Rpl18 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005235	19921	Rpl19	http://www.ncbi.nlm.nih.gov/gene/?term=19921		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005236	1992	SERPINB1	http://www.ncbi.nlm.nih.gov/gene/?term=1992	"EI, ELANH2, HEL-S-27, HEL57, LEI, M/NEI, MNEI, PI-2, PI2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005237	1992	SERPINB1	http://www.ncbi.nlm.nih.gov/gene/?term=1992	"EI, ELANH2, HEL-S-27, HEL57, LEI, M/NEI, MNEI, PI-2, PI2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005238	1992	SERPINB1	http://www.ncbi.nlm.nih.gov/gene/?term=1992	"EI, ELANH2, HEL-S-27, HEL57, LEI, M/NEI, MNEI, PI-2, PI2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005239	19933	Rpl21	http://www.ncbi.nlm.nih.gov/gene/?term=19933	"8430440E03Rik, L21 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005240	19933	Rpl21	http://www.ncbi.nlm.nih.gov/gene/?term=19933	"8430440E03Rik, L21 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005241	19934	Rpl22	http://www.ncbi.nlm.nih.gov/gene/?term=19934	2700038K18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005242	19934	Rpl22	http://www.ncbi.nlm.nih.gov/gene/?term=19934	2700038K18Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005243	19941	Rpl26	http://www.ncbi.nlm.nih.gov/gene/?term=19941	SIG-20	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005244	19942	Rpl27	http://www.ncbi.nlm.nih.gov/gene/?term=19942		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005245	19942	Rpl27	http://www.ncbi.nlm.nih.gov/gene/?term=19942		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005246	19943	Rpl28	http://www.ncbi.nlm.nih.gov/gene/?term=19943	D7Wsu21e	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005247	19943	Rpl28	http://www.ncbi.nlm.nih.gov/gene/?term=19943	D7Wsu21e	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005248	19944	Rpl29	http://www.ncbi.nlm.nih.gov/gene/?term=19944	Rpl43	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005249	19946	Rpl30	http://www.ncbi.nlm.nih.gov/gene/?term=19946		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005250	1994	ELAVL1	http://www.ncbi.nlm.nih.gov/gene/?term=1994	"ELAV1, HUR, Hua, MelG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005251	1994	ELAVL1	http://www.ncbi.nlm.nih.gov/gene/?term=1994	"ELAV1, HUR, Hua, MelG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005252	19951	Rpl32	http://www.ncbi.nlm.nih.gov/gene/?term=19951	"AU020185, rpL32-3A "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005253	199675	MCEMP1	http://www.ncbi.nlm.nih.gov/gene/?term=199675	C19orf59	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005254	199692	ZNF627	http://www.ncbi.nlm.nih.gov/gene/?term=199692		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005255	199699	DAND5	http://www.ncbi.nlm.nih.gov/gene/?term=199699	"CER2, CERL2, CKTSF1B3, COCO, CRL2, DANTE, GREM3, SP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005256	199699	DAND5	http://www.ncbi.nlm.nih.gov/gene/?term=199699	"CER2, CERL2, CKTSF1B3, COCO, CRL2, DANTE, GREM3, SP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005257	199720	GGN	http://www.ncbi.nlm.nih.gov/gene/?term=199720		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005258	199731	CADM4	http://www.ncbi.nlm.nih.gov/gene/?term=199731	"IGSF4C, NECL4, Necl-4, TSLL2, synCAM4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005259	199746	U2AF1L4	http://www.ncbi.nlm.nih.gov/gene/?term=199746	"U2AF1-RS3, U2AF1L3, U2AF1L3V1, U2AF1RS3, U2af26 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005260	1997	ELF1	http://www.ncbi.nlm.nih.gov/gene/?term=1997		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005261	19981	Rpl37a	http://www.ncbi.nlm.nih.gov/gene/?term=19981		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005262	19982	Rpl36a	http://www.ncbi.nlm.nih.gov/gene/?term=19982	"L44L, Rpl44 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005263	199857	ALG14	http://www.ncbi.nlm.nih.gov/gene/?term=199857	CMS15	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005264	19989	Rpl7	http://www.ncbi.nlm.nih.gov/gene/?term=19989	"Rpl7a, Surf-3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005265	19989	Rpl7	http://www.ncbi.nlm.nih.gov/gene/?term=19989	"Rpl7a, Surf-3 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005266	1998	ELF2	http://www.ncbi.nlm.nih.gov/gene/?term=1998	"EU32, NERF, NERF-1A, NERF-1B, NERF-1a, b, NERF-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005267	1998	ELF2	http://www.ncbi.nlm.nih.gov/gene/?term=1998	"EU32, NERF, NERF-1A, NERF-1B, NERF-1a, b, NERF-2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005268	1998	ELF2	http://www.ncbi.nlm.nih.gov/gene/?term=1998	"EU32, NERF, NERF-1A, NERF-1B, NERF-1a, b, NERF-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005269	199953	TMEM201	http://www.ncbi.nlm.nih.gov/gene/?term=199953	NET5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005270	199964	TMEM61	http://www.ncbi.nlm.nih.gov/gene/?term=199964		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005271	199990	FAAP20	http://www.ncbi.nlm.nih.gov/gene/?term=199990	"C1orf86, FP7162 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005272	199990	FAAP20	http://www.ncbi.nlm.nih.gov/gene/?term=199990	"C1orf86, FP7162 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005273	1999	ELF3	http://www.ncbi.nlm.nih.gov/gene/?term=1999	"EPR-1, ERT, ESE-1, ESX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005274	199	AIF1	http://www.ncbi.nlm.nih.gov/gene/?term=199	"AIF-1, IBA1, IRT-1, IRT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005275	200014	CC2D1B	http://www.ncbi.nlm.nih.gov/gene/?term=200014		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005276	200014	CC2D1B	http://www.ncbi.nlm.nih.gov/gene/?term=200014		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005277	200014	CC2D1B	http://www.ncbi.nlm.nih.gov/gene/?term=200014		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005278	20005	Rpl9	http://www.ncbi.nlm.nih.gov/gene/?term=20005		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005279	200081	TXLNA	http://www.ncbi.nlm.nih.gov/gene/?term=200081	"IL14, TXLN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005280	200081	TXLNA	http://www.ncbi.nlm.nih.gov/gene/?term=200081	"IL14, TXLN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005281	2000	ELF4	http://www.ncbi.nlm.nih.gov/gene/?term=2000	"ELFR, MEF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005282	200162	SPAG17	http://www.ncbi.nlm.nih.gov/gene/?term=200162	"CT143, PF6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005283	200172	SLFNL1	http://www.ncbi.nlm.nih.gov/gene/?term=200172		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005284	200185	KRTCAP2	http://www.ncbi.nlm.nih.gov/gene/?term=200185	KCP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005285	20019	Polr1a	http://www.ncbi.nlm.nih.gov/gene/?term=20019	"194kDa, 3010014K16Rik, RPA194, Rpo1-4, mRPA1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005286	20019	Polr1a	http://www.ncbi.nlm.nih.gov/gene/?term=20019	"194kDa, 3010014K16Rik, RPA194, Rpo1-4, mRPA1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005287	200205	IBA57	http://www.ncbi.nlm.nih.gov/gene/?term=200205	"C1orf69, MMDS3, SPG74 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005288	200205	IBA57	http://www.ncbi.nlm.nih.gov/gene/?term=200205	"C1orf69, MMDS3, SPG74 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005289	200205	IBA57	http://www.ncbi.nlm.nih.gov/gene/?term=200205	"C1orf69, MMDS3, SPG74 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005290	20020	Polr2a	http://www.ncbi.nlm.nih.gov/gene/?term=20020	"220kDa, Rpb1, Rpo2-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005291	2002	ELK1	http://www.ncbi.nlm.nih.gov/gene/?term=2002		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005292	200312	RNF215	http://www.ncbi.nlm.nih.gov/gene/?term=200312		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005293	200315	APOBEC3A	http://www.ncbi.nlm.nih.gov/gene/?term=200315	"A3A, ARP3, PHRBN, bK150C2.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005294	200315	APOBEC3A	http://www.ncbi.nlm.nih.gov/gene/?term=200315	"A3A, ARP3, PHRBN, bK150C2.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005295	200316	APOBEC3F	http://www.ncbi.nlm.nih.gov/gene/?term=200316	"A3F, ARP8, BK150C2.4.MRNA, KA6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005296	200316	APOBEC3F	http://www.ncbi.nlm.nih.gov/gene/?term=200316	"A3F, ARP8, BK150C2.4.MRNA, KA6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005297	200424	TET3	http://www.ncbi.nlm.nih.gov/gene/?term=200424	hCG_40738	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005298	20042	Rps12	http://www.ncbi.nlm.nih.gov/gene/?term=20042		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005299	20042	Rps12	http://www.ncbi.nlm.nih.gov/gene/?term=20042		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005300	20044	Rps14	http://www.ncbi.nlm.nih.gov/gene/?term=20044	"2600014J02Rik, AL023078 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005301	20044	Rps14	http://www.ncbi.nlm.nih.gov/gene/?term=20044	"2600014J02Rik, AL023078 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005302	200504	GKN2	http://www.ncbi.nlm.nih.gov/gene/?term=200504	"BRICD1B, GDDR, PRO813, TFIZ1, VLTI465 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005303	20054	Rps15	http://www.ncbi.nlm.nih.gov/gene/?term=20054	rig	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005304	20055	Rps16	http://www.ncbi.nlm.nih.gov/gene/?term=20055	"AA420385, AI317031 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005305	200576	PIKFYVE	http://www.ncbi.nlm.nih.gov/gene/?term=200576	"CFD, FAB1, HEL37, PIP5K, PIP5K3, ZFYVE29 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005306	2005	ELK4	http://www.ncbi.nlm.nih.gov/gene/?term=2005	SAP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005307	200634	KRTCAP3	http://www.ncbi.nlm.nih.gov/gene/?term=200634	"KCP3, MRV222, PRO9898 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005308	200634	KRTCAP3	http://www.ncbi.nlm.nih.gov/gene/?term=200634	KCP3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005309	20068	Rps17	http://www.ncbi.nlm.nih.gov/gene/?term=20068		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005310	200728	TMEM17	http://www.ncbi.nlm.nih.gov/gene/?term=200728		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005311	200728	TMEM17	http://www.ncbi.nlm.nih.gov/gene/?term=200728		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005312	200728	TMEM17	http://www.ncbi.nlm.nih.gov/gene/?term=200728		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005313	20084	Rps18	http://www.ncbi.nlm.nih.gov/gene/?term=20084	"H-2Ke3, H2-Ke3, Ke-3, ke3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005314	20084	Rps18	http://www.ncbi.nlm.nih.gov/gene/?term=20084	"H-2Ke3, H2-Ke3, Ke-3, ke3 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005315	200879	LIPH	http://www.ncbi.nlm.nih.gov/gene/?term=200879	"AH, ARWH2, HYPT7, LAH2, LPDLR, PLA1B, mPA-PLA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005316	20088	Rps24	http://www.ncbi.nlm.nih.gov/gene/?term=20088		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005317	200894	ARL13B	http://www.ncbi.nlm.nih.gov/gene/?term=200894	"ARL2L1, JBTS8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005318	200895	DHFRL1	http://www.ncbi.nlm.nih.gov/gene/?term=200895	DHFRP4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005319	20090	Rps29	http://www.ncbi.nlm.nih.gov/gene/?term=20090		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005320	200916	RPL22L1	http://www.ncbi.nlm.nih.gov/gene/?term=200916		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005321	200916	RPL22L1	http://www.ncbi.nlm.nih.gov/gene/?term=200916		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005322	200916	RPL22L1	http://www.ncbi.nlm.nih.gov/gene/?term=200916		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005323	200916	RPL22L1	http://www.ncbi.nlm.nih.gov/gene/?term=200916		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005324	20091	Rps3a1	http://www.ncbi.nlm.nih.gov/gene/?term=20091	Rps3a	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005325	200933	FBXO45	http://www.ncbi.nlm.nih.gov/gene/?term=200933	Fbx45	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005326	200933	FBXO45	http://www.ncbi.nlm.nih.gov/gene/?term=200933	Fbx45	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005327	200942	KLHDC8B	http://www.ncbi.nlm.nih.gov/gene/?term=200942	CHL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005328	200942	KLHDC8B	http://www.ncbi.nlm.nih.gov/gene/?term=200942	CHL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005329	200958	MUC20	http://www.ncbi.nlm.nih.gov/gene/?term=200958	MUC-20	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005330	200958	MUC20	http://www.ncbi.nlm.nih.gov/gene/?term=200958	MUC-20	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005331	20102	Rps4x	http://www.ncbi.nlm.nih.gov/gene/?term=20102	"Rps4, Rps4-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005332	20102	Rps4x	http://www.ncbi.nlm.nih.gov/gene/?term=20102	"Rps4, Rps4-1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005333	20104	Rps6	http://www.ncbi.nlm.nih.gov/gene/?term=20104	S6R	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005334	2010	EMD	http://www.ncbi.nlm.nih.gov/gene/?term=2010	"EDMD, LEMD5, STA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005335	20112	Rps6ka2	http://www.ncbi.nlm.nih.gov/gene/?term=20112	"90kDa, D17Wsu134e, Rps6ka-rs1, Rsk3, p90rsk, pp90rsk "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005336	201158	TVP23C	http://www.ncbi.nlm.nih.gov/gene/?term=201158	FAM18B2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005337	201158	TVP23C	http://www.ncbi.nlm.nih.gov/gene/?term=201158	FAM18B2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005338	20115	Rps7	http://www.ncbi.nlm.nih.gov/gene/?term=20115	"MtuA, S7, Rps7 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005339	201161	CENPV	http://www.ncbi.nlm.nih.gov/gene/?term=201161	"3110013H01Rik, CENP-V, PRR6, p30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005340	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005341	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005342	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005343	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005344	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005345	201164	PLD6	http://www.ncbi.nlm.nih.gov/gene/?term=201164	ZUC	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005346	201164	PLD6	http://www.ncbi.nlm.nih.gov/gene/?term=201164	ZUC	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005347	20116	Rps8	http://www.ncbi.nlm.nih.gov/gene/?term=20116		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005348	20116	Rps8	http://www.ncbi.nlm.nih.gov/gene/?term=20116		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005349	201176	ARHGAP27	http://www.ncbi.nlm.nih.gov/gene/?term=201176	"CAMGAP1, PP905, SH3D20, SH3P20 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005350	201229	LYRM9	http://www.ncbi.nlm.nih.gov/gene/?term=201229	"C17orf108, HSD24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005351	201254	STRA13	http://www.ncbi.nlm.nih.gov/gene/?term=201254	"CENP-X, CENPX, D9, FAAP10, MHF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005352	201254	STRA13	http://www.ncbi.nlm.nih.gov/gene/?term=201254	"CENP-X, CENPX, D9, FAAP10, MHF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005353	201255	LRRC45	http://www.ncbi.nlm.nih.gov/gene/?term=201255		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005354	201266	SLC39A11	http://www.ncbi.nlm.nih.gov/gene/?term=201266	"C17orf26, ZIP11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005355	201292	TRIM65	http://www.ncbi.nlm.nih.gov/gene/?term=201292	4732463G12Rik	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005356	201292	TRIM65	http://www.ncbi.nlm.nih.gov/gene/?term=201292	4732463G12Rik	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005357	201294	UNC13D	http://www.ncbi.nlm.nih.gov/gene/?term=201294	"FHL3, HLH3, HPLH3, Munc13-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005358	20130	Rras	http://www.ncbi.nlm.nih.gov/gene/?term=20130	AI573426	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005359	20133	Rrm1	http://www.ncbi.nlm.nih.gov/gene/?term=20133	RnrM1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005360	2013	EMP2	http://www.ncbi.nlm.nih.gov/gene/?term=2013	XMP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005361	2013	EMP2	http://www.ncbi.nlm.nih.gov/gene/?term=2013	XMP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005362	2013	EMP2	http://www.ncbi.nlm.nih.gov/gene/?term=2013	XMP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005363	201475	RAB12	http://www.ncbi.nlm.nih.gov/gene/?term=201475		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005364	2014	EMP3	http://www.ncbi.nlm.nih.gov/gene/?term=2014	YMP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005365	201562	HACD2	http://www.ncbi.nlm.nih.gov/gene/?term=201562	PTPLB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005366	201562	HACD2	http://www.ncbi.nlm.nih.gov/gene/?term=201562	PTPLB	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005367	201595	STT3B	http://www.ncbi.nlm.nih.gov/gene/?term=201595	"CDG1X, SIMP, STT3-B "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005368	201595	STT3B	http://www.ncbi.nlm.nih.gov/gene/?term=201595	"CDG1X, SIMP, STT3-B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005369	201626	PDE12	http://www.ncbi.nlm.nih.gov/gene/?term=201626	2'-PDE	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005370	201626	PDE12	http://www.ncbi.nlm.nih.gov/gene/?term=201626	"2'-PDE, 2-PDE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005371	201626	PDE12	http://www.ncbi.nlm.nih.gov/gene/?term=201626	"2'-PDE, 2-PDE "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005372	201626	PDE12	http://www.ncbi.nlm.nih.gov/gene/?term=201626	"2'-PDE, 2-PDE "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005373	201627	DENND6A	http://www.ncbi.nlm.nih.gov/gene/?term=201627	"AFI1A, FAM116A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005374	201627	DENND6A	http://www.ncbi.nlm.nih.gov/gene/?term=201627	"AFI1A, FAM116A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005375	201627	DENND6A	http://www.ncbi.nlm.nih.gov/gene/?term=201627	"AFI1A, FAM116A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005376	20166	Rtkn	http://www.ncbi.nlm.nih.gov/gene/?term=20166		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005377	20168	Rtn3	http://www.ncbi.nlm.nih.gov/gene/?term=20168	RTN3-A1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005378	201725	C4orf46	http://www.ncbi.nlm.nih.gov/gene/?term=201725	RCDG1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005379	2017	CTTN	http://www.ncbi.nlm.nih.gov/gene/?term=2017	EMS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005380	20184	Uimc1	http://www.ncbi.nlm.nih.gov/gene/?term=20184	"9430016E08Rik, D330018D10Rik, D630032M02Rik, RIP110, Rxrip110 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005381	201895	SMIM14	http://www.ncbi.nlm.nih.gov/gene/?term=201895	C4orf34	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005382	201931	TMEM192	http://www.ncbi.nlm.nih.gov/gene/?term=201931		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005383	201931	TMEM192	http://www.ncbi.nlm.nih.gov/gene/?term=201931		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005384	201931	TMEM192	http://www.ncbi.nlm.nih.gov/gene/?term=201931		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005385	20193	S100a1	http://www.ncbi.nlm.nih.gov/gene/?term=20193	"AI266795, S100, S100a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005386	20195	S100a11	http://www.ncbi.nlm.nih.gov/gene/?term=20195	"EMAPI, Emap1, S100a14, S100c, cal "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005387	201965	RWDD4	http://www.ncbi.nlm.nih.gov/gene/?term=201965	"FAM28A, RWDD4A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005388	20196	S100a13	http://www.ncbi.nlm.nih.gov/gene/?term=20196		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005389	20197	S100a3	http://www.ncbi.nlm.nih.gov/gene/?term=20197	S100E	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005390	20197	S100a3	http://www.ncbi.nlm.nih.gov/gene/?term=20197	S100E	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005391	2019	EN1	http://www.ncbi.nlm.nih.gov/gene/?term=2019		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005392	202018	TAPT1	http://www.ncbi.nlm.nih.gov/gene/?term=202018	CMVFR	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005393	202018	TAPT1	http://www.ncbi.nlm.nih.gov/gene/?term=202018	"CMVFR, OCLSBG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005394	2020	EN2	http://www.ncbi.nlm.nih.gov/gene/?term=2020		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005395	20218	Khdrbs1	http://www.ncbi.nlm.nih.gov/gene/?term=20218	"Sam68, p62, p68 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005396	2021	ENDOG	http://www.ncbi.nlm.nih.gov/gene/?term=2021		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005397	2021	ENDOG	http://www.ncbi.nlm.nih.gov/gene/?term=2021		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005398	202243	CCDC125	http://www.ncbi.nlm.nih.gov/gene/?term=202243	KENAE	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005399	202243	CCDC125	http://www.ncbi.nlm.nih.gov/gene/?term=202243	KENAE	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005400	20224	Sar1a	http://www.ncbi.nlm.nih.gov/gene/?term=20224	"1600019H17Rik, Sara, Sara1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005401	20229	Sat1	http://www.ncbi.nlm.nih.gov/gene/?term=20229	"AA617398, SSAT, Sat "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005402	20230	Satb1	http://www.ncbi.nlm.nih.gov/gene/?term=20230	"2610306G12Rik, AW413156 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005403	20239	Atxn2	http://www.ncbi.nlm.nih.gov/gene/?term=20239	"9630045M23Rik, ATX2, AW544490, Sca2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005404	2023	ENO1	http://www.ncbi.nlm.nih.gov/gene/?term=2023	"ENO1L1, HEL-S-17, MPB1, NNE, PPH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005405	2023	ENO1	http://www.ncbi.nlm.nih.gov/gene/?term=2023	"ENO1L1, HEL-S-17, MPB1, NNE, PPH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005406	2023	ENO1	http://www.ncbi.nlm.nih.gov/gene/?term=2023	"ENO1L1, HEL-S-17, MPB1, NNE, PPH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005407	20249	Scd1	http://www.ncbi.nlm.nih.gov/gene/?term=20249	"AA589638, AI265570, Scd, Scd-1, ab "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005408	20250	Scd2	http://www.ncbi.nlm.nih.gov/gene/?term=20250	"Mir5114, Scd-2, mir-5114, swty "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005409	20254	Scg2	http://www.ncbi.nlm.nih.gov/gene/?term=20254	"Chgc, SgII "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005410	20255	Scg3	http://www.ncbi.nlm.nih.gov/gene/?term=20255	"1B1075, AI385542, Chgd, SgIII "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005411	20257	Stmn2	http://www.ncbi.nlm.nih.gov/gene/?term=20257	"AI159727, SCG10, Scgn10, Stmb2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005412	20266	Scn1b	http://www.ncbi.nlm.nih.gov/gene/?term=20266		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005413	20269	Scn3a	http://www.ncbi.nlm.nih.gov/gene/?term=20269	"Gm1000, Nav1.3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005414	20269	Scn3a	http://www.ncbi.nlm.nih.gov/gene/?term=20269	"Gm1000, Nav1.3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005415	2026	ENO2	http://www.ncbi.nlm.nih.gov/gene/?term=2026	"HEL-S-279, NSE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005416	2026	ENO2	http://www.ncbi.nlm.nih.gov/gene/?term=2026	"HEL-S-279, NSE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005417	2026	ENO2	http://www.ncbi.nlm.nih.gov/gene/?term=2026	"HEL-S-279, NSE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005418	2026	ENO2	http://www.ncbi.nlm.nih.gov/gene/?term=2026	"HEL-S-279, NSE "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00005419	20273	Scn8a	http://www.ncbi.nlm.nih.gov/gene/?term=20273	"AI853486, C630029C19Rik, NaCh6, Nav1.6, dmu, med, mnd-2, mnd2, nmf2, nmf335, nmf58, nur14, seal "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005420	20273	Scn8a	http://www.ncbi.nlm.nih.gov/gene/?term=20273	"AI853486, C630029C19Rik, NaCh6, Nav1.6, dmu, med, mnd-2, mnd2, nmf2, nmf335, nmf58, nur14, seal "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005421	20274	Scn9a	http://www.ncbi.nlm.nih.gov/gene/?term=20274	"Nav1.7, PN1, mKIAA4197 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005422	20296	Ccl2	http://www.ncbi.nlm.nih.gov/gene/?term=20296	"AI323594, HC11, JE, MCAF, MCP-1, MCP1, SMC-CF, Scya2, Sigje "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005423	2029	ENSA	http://www.ncbi.nlm.nih.gov/gene/?term=2029	ARPP-19e	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005424	2029	ENSA	http://www.ncbi.nlm.nih.gov/gene/?term=2029	ARPP-19e	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005425	2029	ENSA	http://www.ncbi.nlm.nih.gov/gene/?term=2029	ARPP-19e	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005426	202	AIM1	http://www.ncbi.nlm.nih.gov/gene/?term=202	"CRYBG1, ST4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005427	202	AIM1	http://www.ncbi.nlm.nih.gov/gene/?term=202	"CRYBG1, ST4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005428	202	AIM1	http://www.ncbi.nlm.nih.gov/gene/?term=202	"CRYBG1, ST4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005429	20300	Ccl25	http://www.ncbi.nlm.nih.gov/gene/?term=20300	"A130072A22Rik, AI852536, CKb15, Scya25, TECK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005430	203062	TSNARE1	http://www.ncbi.nlm.nih.gov/gene/?term=203062		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005431	203068	TUBB	http://www.ncbi.nlm.nih.gov/gene/?term=203068	"CDCBM6, CSCSC1, M40, OK/SW-cl.56, TUBB1, TUBB5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005432	203068	TUBB	http://www.ncbi.nlm.nih.gov/gene/?term=203068	"CDCBM6, CSCSC1, M40, OK/SW-cl.561, TUBB5, TUBB "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005433	203069	R3HCC1	http://www.ncbi.nlm.nih.gov/gene/?term=203069		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005434	203069	R3HCC1	http://www.ncbi.nlm.nih.gov/gene/?term=203069		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005435	20306	Ccl7	http://www.ncbi.nlm.nih.gov/gene/?term=20306	"MCP-3, Scya7, fic, marc, mcp3 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005436	2030	SLC29A1	http://www.ncbi.nlm.nih.gov/gene/?term=2030	ENT1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005437	2030	SLC29A1	http://www.ncbi.nlm.nih.gov/gene/?term=2030	ENT1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005438	20311	Cxcl5	http://www.ncbi.nlm.nih.gov/gene/?term=20311	"AMCF-II, Cxcl6, ENA-78, GCP-2, LIX, Scyb5, Scyb6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005439	20318	Sdf4	http://www.ncbi.nlm.nih.gov/gene/?term=20318	Cab45	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005440	203197	C9orf91	http://www.ncbi.nlm.nih.gov/gene/?term=203197		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005441	203197	C9orf91	http://www.ncbi.nlm.nih.gov/gene/?term=203197		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005442	203197	C9orf91	http://www.ncbi.nlm.nih.gov/gene/?term=203197		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005443	20320	Nptn	http://www.ncbi.nlm.nih.gov/gene/?term=20320	"AW554172, SDR-1, Sdfr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005444	203245	NAIF1	http://www.ncbi.nlm.nih.gov/gene/?term=203245	"C9orf90, bA379C10.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005445	20324	Sdpr	http://www.ncbi.nlm.nih.gov/gene/?term=20324		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005446	20324	Sdpr	http://www.ncbi.nlm.nih.gov/gene/?term=20324		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005447	203260	CCDC107	http://www.ncbi.nlm.nih.gov/gene/?term=203260	PSEC0222	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005448	203286	ANKS6	http://www.ncbi.nlm.nih.gov/gene/?term=203286	"ANKRD14, NPHP16, PKDR1, SAMD6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005449	203286	ANKS6	http://www.ncbi.nlm.nih.gov/gene/?term=203286	"ANKRD14, NPHP16, PKDR1, SAMD6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005450	203328	SUSD3	http://www.ncbi.nlm.nih.gov/gene/?term=203328		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005451	20334	Sec23a	http://www.ncbi.nlm.nih.gov/gene/?term=20334	"Msec23, Sec23r "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005452	20336	Exoc4	http://www.ncbi.nlm.nih.gov/gene/?term=20336	"C78892, Sec8, Sec8l1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005453	2033	EP300	http://www.ncbi.nlm.nih.gov/gene/?term=2033	"KAT3B, RSTS2, p300 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005454	2033	EP300	http://www.ncbi.nlm.nih.gov/gene/?term=2033	"KAT3B, RSTS2, p300 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005455	2033	EP300	http://www.ncbi.nlm.nih.gov/gene/?term=2033	"KAT3B, RSTS2, p300 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005456	2033	EP300	http://www.ncbi.nlm.nih.gov/gene/?term=2033	"KAT3B, RSTS2, p300 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005457	20340	Glg1	http://www.ncbi.nlm.nih.gov/gene/?term=20340	"AI593353, AW537898, CFR, CFR-1, ESL-1, MG-160, MG160, Selel "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005458	203427	SLC25A43	http://www.ncbi.nlm.nih.gov/gene/?term=203427		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005459	20346	Sema3a	http://www.ncbi.nlm.nih.gov/gene/?term=20346	"Hsema-I, SEMA1, SemD, Semad, coll-1 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005460	2034	EPAS1	http://www.ncbi.nlm.nih.gov/gene/?term=2034	"ECYT4, HIF2A, HLF, MOP2, PASD2, bHLHe73 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005461	2034	EPAS1	http://www.ncbi.nlm.nih.gov/gene/?term=2034	"ECYT4, HIF2A, HLF, MOP2, PASD2, bHLHe73 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005462	203522	INTS6L	http://www.ncbi.nlm.nih.gov/gene/?term=203522	DDX26B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005463	20352	Sema4b	http://www.ncbi.nlm.nih.gov/gene/?term=20352	"SemC, Semac, mKIAA1745 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005464	203547	VMA21	http://www.ncbi.nlm.nih.gov/gene/?term=203547	"MEAX, XMEA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005465	203547	VMA21	http://www.ncbi.nlm.nih.gov/gene/?term=203547	"MEAX, XMEA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005466	203547	VMA21	http://www.ncbi.nlm.nih.gov/gene/?term=203547	"MEAX, XMEA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005467	203569	PAGE2	http://www.ncbi.nlm.nih.gov/gene/?term=203569	"CT16.4, GAGEC2, GAGEE2, PAGE-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005468	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005469	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005470	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005471	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005472	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005473	20360	Sema6c	http://www.ncbi.nlm.nih.gov/gene/?term=20360	"Semay, mKIAA1869 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005474	20361	Sema7a	http://www.ncbi.nlm.nih.gov/gene/?term=20361	"2900057C09Rik, CDw108, H-Sema-L, M-Sema-L, Semal "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005475	20364	Sepw1	http://www.ncbi.nlm.nih.gov/gene/?term=20364	selW	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005476	20365	Serf1	http://www.ncbi.nlm.nih.gov/gene/?term=20365	"4F5, Msmac1, m4F5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005477	20371	Foxp3	http://www.ncbi.nlm.nih.gov/gene/?term=20371	"JM2, scurfin, sf "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005478	20379	Sfrp4	http://www.ncbi.nlm.nih.gov/gene/?term=20379		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005479	2037	EPB41L2	http://www.ncbi.nlm.nih.gov/gene/?term=2037	"4.1-G, 4.1G "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005480	2037	EPB41L2	http://www.ncbi.nlm.nih.gov/gene/?term=2037	"4.1-G, 4.1G "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005481	2037	EPB41L2	http://www.ncbi.nlm.nih.gov/gene/?term=2037	"4.1-G, 4.1G "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005482	20384	Srsf5	http://www.ncbi.nlm.nih.gov/gene/?term=20384	Sfrs5	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005483	20384	Srsf5	http://www.ncbi.nlm.nih.gov/gene/?term=20384	Sfrs5	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005484	20387	Sftpa1	http://www.ncbi.nlm.nih.gov/gene/?term=20387	"SP-A, Sftp-1, Sftp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005485	20390	Sftpd	http://www.ncbi.nlm.nih.gov/gene/?term=20390	"AI573415, SP-D, Sftp4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005486	20394	Scg5	http://www.ncbi.nlm.nih.gov/gene/?term=20394	"7B2, AI325031, Sgne-1, Sgne1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005487	20397	Sgpl1	http://www.ncbi.nlm.nih.gov/gene/?term=20397	"AI428538, D10Xrf456, S1PL, Spl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005488	20399	Sh2b1	http://www.ncbi.nlm.nih.gov/gene/?term=20399	"AI425885, C530001K22Rik, Irip, Psm, SH2-B, SH2-Bb, Sh2bpsm1, mKIAA1299 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005489	2039	DMTN	http://www.ncbi.nlm.nih.gov/gene/?term=2039	"DMT, EPB49 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005490	2039	DMTN	http://www.ncbi.nlm.nih.gov/gene/?term=2039	"DMT, EPB49 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005491	203	AK1	http://www.ncbi.nlm.nih.gov/gene/?term=203	HTL-S-58j	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005492	203	AK1	http://www.ncbi.nlm.nih.gov/gene/?term=203	HTL-S-58j	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005493	20401	Sh3bp1	http://www.ncbi.nlm.nih.gov/gene/?term=20401	3BP-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005494	20402	Zfp106	http://www.ncbi.nlm.nih.gov/gene/?term=20402	"Cd-1, D2Dcr28, H3a, Sh3bp3, Znf106, sirm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005495	20403	Itsn2	http://www.ncbi.nlm.nih.gov/gene/?term=20403	"AI327390, Ese2, Sh3d1B, Sh3p18, mKIAA1256 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005496	20409	Ostf1	http://www.ncbi.nlm.nih.gov/gene/?term=20409	"C78236, SH3P2, Sh3d3 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005497	2040	STOM	http://www.ncbi.nlm.nih.gov/gene/?term=2040	"BND7, EPB7, EPB72 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005498	2040	STOM	http://www.ncbi.nlm.nih.gov/gene/?term=2040	"BND7, EPB7, EPB72 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005499	2040	STOM	http://www.ncbi.nlm.nih.gov/gene/?term=2040	"BND7, EPB7, EPB72 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005500	2040	STOM	http://www.ncbi.nlm.nih.gov/gene/?term=2040	"BND7, EPB7, EPB72 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005501	20419	Shcbp1	http://www.ncbi.nlm.nih.gov/gene/?term=20419	mPAL	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005502	20425	Shmt1	http://www.ncbi.nlm.nih.gov/gene/?term=20425	"AI324848, AI385541, C81125, Shmt, mshmt, mshmt1, mshmt2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005503	20429	Shox2	http://www.ncbi.nlm.nih.gov/gene/?term=20429	"6330543G17Rik, OG12, Og12x, Prx3, SHOT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005504	2042	EPHA3	http://www.ncbi.nlm.nih.gov/gene/?term=2042	"EK4, ETK, ETK1, HEK, HEK4, TYRO4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005505	2042	EPHA3	http://www.ncbi.nlm.nih.gov/gene/?term=2042	"EK4, ETK, ETK1, HEK, HEK4, TYRO4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005506	2042	EPHA3	http://www.ncbi.nlm.nih.gov/gene/?term=2042	"EK4, ETK, ETK1, HEK, HEK4, TYRO4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005507	20437	Siah1a	http://www.ncbi.nlm.nih.gov/gene/?term=20437	"AA982064, AI853500, Sinh1a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005508	20438	Siah1b	http://www.ncbi.nlm.nih.gov/gene/?term=20438	"AA960570, Sinh1b, siah-1b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005509	2043	EPHA4	http://www.ncbi.nlm.nih.gov/gene/?term=2043	"HEK8, SEK, TYRO1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005510	20441	St3gal3	http://www.ncbi.nlm.nih.gov/gene/?term=20441	"ST3GalIII, ST3N, Siat3, Siat6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005511	2044	EPHA5	http://www.ncbi.nlm.nih.gov/gene/?term=2044	"CEK7, EHK-1, EHK1, EK7, HEK7, TYRO4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005512	20462	Tra2b	http://www.ncbi.nlm.nih.gov/gene/?term=20462	"5730405G21Rik, D16Ertd266e, SIG-41, Sfrs10, Silg41, TRA2beta "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005513	20467	Sin3b	http://www.ncbi.nlm.nih.gov/gene/?term=20467	2810430C10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005514	20473	Six3	http://www.ncbi.nlm.nih.gov/gene/?term=20473	"E130112M24Rika, Six3alpha, Six3b, Six3beta, Six3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005515	20476	Six6	http://www.ncbi.nlm.nih.gov/gene/?term=20476	"Optx2, Six9 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005516	20479	Vps4b	http://www.ncbi.nlm.nih.gov/gene/?term=20479	"8030489C12Rik, Skd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005517	20482	Skil	http://www.ncbi.nlm.nih.gov/gene/?term=20482	"Skir, SnoN, sno "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005518	204851	HIPK1	http://www.ncbi.nlm.nih.gov/gene/?term=204851	"Myak, Nbak2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005519	204851	HIPK1	http://www.ncbi.nlm.nih.gov/gene/?term=204851	"Myak, Nbak2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005520	204851	HIPK1	http://www.ncbi.nlm.nih.gov/gene/?term=204851	"Myak, Nbak2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005521	2048	EPHB2	http://www.ncbi.nlm.nih.gov/gene/?term=2048	"CAPB, DRT, EK5, EPHT3, ERK, Hek5, PCBC, Tyro5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005522	2048	EPHB2	http://www.ncbi.nlm.nih.gov/gene/?term=2048	"CAPB, DRT, EK5, EPHT3, ERK, Hek5, PCBC, Tyro5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005523	20492	Slbp	http://www.ncbi.nlm.nih.gov/gene/?term=20492		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005524	20492	Slbp	http://www.ncbi.nlm.nih.gov/gene/?term=20492		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005525	20494	Slc10a2	http://www.ncbi.nlm.nih.gov/gene/?term=20494	"ASBT, ISBT "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005526	2049	EPHB3	http://www.ncbi.nlm.nih.gov/gene/?term=2049	"ETK2, HEK2, TYRO6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005527	204	AK2	http://www.ncbi.nlm.nih.gov/gene/?term=204	ADK2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005528	204	AK2	http://www.ncbi.nlm.nih.gov/gene/?term=204	ADK2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005529	20501	Slc16a1	http://www.ncbi.nlm.nih.gov/gene/?term=20501	"AL022710, Mct1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005530	2050	EPHB4	http://www.ncbi.nlm.nih.gov/gene/?term=2050	"HTK, MYK1, TYRO11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005531	2050	EPHB4	http://www.ncbi.nlm.nih.gov/gene/?term=2050	"HTK, MYK1, TYRO11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005532	20511	Slc1a2	http://www.ncbi.nlm.nih.gov/gene/?term=20511	"1700091C19Rik, 2900019G14Rik, AI159670, Eaat2, GLT-1, GLT1, MGLT1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005533	205147	AMER3	http://www.ncbi.nlm.nih.gov/gene/?term=205147	FAM123C	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005534	20515	Slc20a1	http://www.ncbi.nlm.nih.gov/gene/?term=20515	"AI607883, Glvr-1, Glvr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005535	2051	EPHB6	http://www.ncbi.nlm.nih.gov/gene/?term=2051	HEP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005536	2051	EPHB6	http://www.ncbi.nlm.nih.gov/gene/?term=2051	HEP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005537	205251	LINC00116	http://www.ncbi.nlm.nih.gov/gene/?term=205251	NCRNA00116	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005538	20527	Slc2a3	http://www.ncbi.nlm.nih.gov/gene/?term=20527	"AA408729, AL023014, AL024341, AU040424, C78366, Glut-3, Glut3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005539	20529	Slc31a1	http://www.ncbi.nlm.nih.gov/gene/?term=20529	"4930445G01Rik, AI787263, AU016967, Ctr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005540	2052	EPHX1	http://www.ncbi.nlm.nih.gov/gene/?term=2052	"EPHX, EPOX, HYL1, MEH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005541	20534	Slc4a1ap	http://www.ncbi.nlm.nih.gov/gene/?term=20534	kanadaptin	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005542	20538	Slc6a2	http://www.ncbi.nlm.nih.gov/gene/?term=20538	"NE-T, NET, Slc6a5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005543	2053	EPHX2	http://www.ncbi.nlm.nih.gov/gene/?term=2053	"CEH, SEH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005544	205428	C3orf58	http://www.ncbi.nlm.nih.gov/gene/?term=205428	"DIA1, GoPro49, HASF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005545	2054	STX2	http://www.ncbi.nlm.nih.gov/gene/?term=2054	"EPIM, EPM, STX2A, STX2B, STX2C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005546	2054	STX2	http://www.ncbi.nlm.nih.gov/gene/?term=2054	"EPIM, EPMA, STX2B, STX2C, STX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005547	2054	STX2	http://www.ncbi.nlm.nih.gov/gene/?term=2054	"EPIM, EPMA, STX2B, STX2C, STX2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005548	2054	STX2	http://www.ncbi.nlm.nih.gov/gene/?term=2054	"EPIM, EPMA, STX2B, STX2C, STX2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005549	205564	SENP5	http://www.ncbi.nlm.nih.gov/gene/?term=205564		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005550	205564	SENP5	http://www.ncbi.nlm.nih.gov/gene/?term=205564		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005551	20557	Slfn3	http://www.ncbi.nlm.nih.gov/gene/?term=20557		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005552	2055	CLN8	http://www.ncbi.nlm.nih.gov/gene/?term=2055	"C8orf61, EPMR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005553	205717	USF3	http://www.ncbi.nlm.nih.gov/gene/?term=205717	KIAA2018	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005554	205717	USF3	http://www.ncbi.nlm.nih.gov/gene/?term=205717	KIAA2018	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005555	2057	EPOR	http://www.ncbi.nlm.nih.gov/gene/?term=2057	EPO-R	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005556	20585	Hltf	http://www.ncbi.nlm.nih.gov/gene/?term=20585	"AF010600, BC057116, P113, Smarca3, Snf2l3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005557	20585	Hltf	http://www.ncbi.nlm.nih.gov/gene/?term=20585	"AF010600, BC057116, P113, Smarca3, Snf2l3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005558	20589	Ighmbp2	http://www.ncbi.nlm.nih.gov/gene/?term=20589	"AEP, nmd, sma, Catf1, Smbp2, Smbp-2, Smubp2, RIPE3b1 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00005559	20589	Ighmbp2	http://www.ncbi.nlm.nih.gov/gene/?term=20589	"AEP, Catf1, RIPE3b1, Smbp-2, Smbp2, Smubp2, nmd, sma "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005560	20589	Ighmbp2	http://www.ncbi.nlm.nih.gov/gene/?term=20589	"AEP, Catf1, RIPE3b1, Smbp-2, Smbp2, Smubp2, nmd, sma "	mRNA	Mus musculus	12923260	Ribosome	B cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00005561	2058	EPRS	http://www.ncbi.nlm.nih.gov/gene/?term=2058	"EARS, GLUPRORS, PARS, PIG32, QARS, QPRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005562	2058	EPRS	http://www.ncbi.nlm.nih.gov/gene/?term=2058	"EARS, GLUPRORS, PARS, PIG32, QARS, QPRS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005563	2058	EPRS	http://www.ncbi.nlm.nih.gov/gene/?term=2058	"EARS, GLUPRORS, PARS, PIG32, QARS, QPRS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005564	20592	Kdm5d	http://www.ncbi.nlm.nih.gov/gene/?term=20592	"HY, Jarid1d, Smcy "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005565	2059	EPS8	http://www.ncbi.nlm.nih.gov/gene/?term=2059	DFNB102	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005566	20603	Sms	http://www.ncbi.nlm.nih.gov/gene/?term=20603	"AI427066, Gy, SPMSY, SpmST, gyro "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005567	20605	Sstr1	http://www.ncbi.nlm.nih.gov/gene/?term=20605	"SRIF-2, SS-1-R, SS1-R, SS1R, Smstr-1, Smstr1, sst1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005568	2060	EPS15	http://www.ncbi.nlm.nih.gov/gene/?term=2060	"AF-1P, AF1P, MLLT5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005569	2060	EPS15	http://www.ncbi.nlm.nih.gov/gene/?term=2060	"AF-1P, AF1P, MLLT5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005570	2060	EPS15	http://www.ncbi.nlm.nih.gov/gene/?term=2060	"AF-1P, AF1P, MLLT5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005571	20610	Sumo3	http://www.ncbi.nlm.nih.gov/gene/?term=20610	"2810014B19Rik, D10Ertd345e, SMT3A, SUMO-3, Smt3h1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005572	20611	Ssty1	http://www.ncbi.nlm.nih.gov/gene/?term=20611	"Smy, Ssty "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005573	20614	Snap25	http://www.ncbi.nlm.nih.gov/gene/?term=20614	"Bdr, GENA70, SNAP-25, SUP, sp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005574	20614	Snap25	http://www.ncbi.nlm.nih.gov/gene/?term=20614	"Bdr, GENA70, SNAP-25, SUP, sp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005575	20616	Snap91	http://www.ncbi.nlm.nih.gov/gene/?term=20616	"91kDa, AP180, F1-20, mKIAA0656 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005576	20618	Sncg	http://www.ncbi.nlm.nih.gov/gene/?term=20618	"C79089, persyn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005577	20619	Snap23	http://www.ncbi.nlm.nih.gov/gene/?term=20619	"23kDa, AA408749, SNAP-23, Sndt, Syndet "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005578	20620	Plk2	http://www.ncbi.nlm.nih.gov/gene/?term=20620	Snk	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005579	20623	Snrk	http://www.ncbi.nlm.nih.gov/gene/?term=20623	"2010012F07Rik, AI448042, AW547029, E030034B15, R74830, mKIAA0096 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005580	20630	Snrpc	http://www.ncbi.nlm.nih.gov/gene/?term=20630	"Snrp1c, U1-C, U1C "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005581	206338	LVRN	http://www.ncbi.nlm.nih.gov/gene/?term=206338	"APQ, AQPEP, TAQPEP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005582	206358	SLC36A1	http://www.ncbi.nlm.nih.gov/gene/?term=206358	"Dct1, LYAAT1, PAT1, TRAMD3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005583	20639	Snrpb2	http://www.ncbi.nlm.nih.gov/gene/?term=20639	2810052G09Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005584	2063	NR2F6	http://www.ncbi.nlm.nih.gov/gene/?term=2063	"EAR-2, EAR2, ERBAL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005585	2063	NR2F6	http://www.ncbi.nlm.nih.gov/gene/?term=2063	"EAR-2, EAR2, ERBAL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005586	20643	Snrpe	http://www.ncbi.nlm.nih.gov/gene/?term=20643	"AL022645, C76690, SME "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005587	20648	Snta1	http://www.ncbi.nlm.nih.gov/gene/?term=20648	"AW228934, Snt1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005588	2064	ERBB2	http://www.ncbi.nlm.nih.gov/gene/?term=2064	"CD340, HER-2, HER-2/neu, HER2, MLN 19, NEU, NGL, TKR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005589	2064	ERBB2	http://www.ncbi.nlm.nih.gov/gene/?term=2064	"CD340, HER-2, HER-2/neu, HER2, MLN 19, NEU, NGL, TKR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005590	20650	Sntb2	http://www.ncbi.nlm.nih.gov/gene/?term=20650	Snt2	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005591	20655	Sod1	http://www.ncbi.nlm.nih.gov/gene/?term=20655	"B430204E11Rik, Cu/Zn-SOD, CuZnSOD, Ipo-1, Ipo1, SODC, Sod-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005592	20658	Son	http://www.ncbi.nlm.nih.gov/gene/?term=20658	"2900011L12Rik, AA409051, AU067731, C81487, mKIAA1019, nrebp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005593	2065	ERBB3	http://www.ncbi.nlm.nih.gov/gene/?term=2065	"ErbB-3, HER3, LCCS2, MDA-BF-1, c-erbB-3, c-erbB3, erbB3-S, p180-ErbB3, p45-sErbB3, p85-sErbB3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005594	2065	ERBB3	http://www.ncbi.nlm.nih.gov/gene/?term=2065	"ErbB-3, HER3, LCCS2, MDA-BF-1, c-erbB-3, c-erbB3, erbB3-S, p180-ErbB3, p45-sErbB3, p85-sErbB3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005595	20661	Sort1	http://www.ncbi.nlm.nih.gov/gene/?term=20661	"2900053A11Rik, AI852375, Ntr3, Ntsr3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005596	20666	Sox11	http://www.ncbi.nlm.nih.gov/gene/?term=20666	"1110038H03Rik, 6230403H02Rik, AI836553, end1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005597	20679	Sox6	http://www.ncbi.nlm.nih.gov/gene/?term=20679	"AI987981, SOX-LZ "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005598	2067	ERCC1	http://www.ncbi.nlm.nih.gov/gene/?term=2067	"COFS4, RAD10, UV20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005599	2067	ERCC1	http://www.ncbi.nlm.nih.gov/gene/?term=2067	"COFS4, RAD10, UV20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005600	20683	Sp1	http://www.ncbi.nlm.nih.gov/gene/?term=20683	"1110003E12Rik, AA450830, AI845540-1, Sp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005601	20683	Sp1	http://www.ncbi.nlm.nih.gov/gene/?term=20683	"1110003E12Rik, AA450830, AI845540-1, Sp1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005602	20687	Sp3	http://www.ncbi.nlm.nih.gov/gene/?term=20687	D130027J01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005603	2068	ERCC2	http://www.ncbi.nlm.nih.gov/gene/?term=2068	"COFS2, EM9, TFIIH, TTD, TTD1, XPD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005604	20692	Sparc	http://www.ncbi.nlm.nih.gov/gene/?term=20692	"BM-40, ON "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005605	2069	EREG	http://www.ncbi.nlm.nih.gov/gene/?term=2069	"EPR, ER, Ep "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005606	2069	EREG	http://www.ncbi.nlm.nih.gov/gene/?term=2069	"EPR, ER, Ep "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005607	2069	EREG	http://www.ncbi.nlm.nih.gov/gene/?term=2069	"EPR, ER, Ep "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005608	2069	EREG	http://www.ncbi.nlm.nih.gov/gene/?term=2069	"EPR, ER, Ep "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005609	207063	DHRSX	http://www.ncbi.nlm.nih.gov/gene/?term=207063	"CXorf11, DHRS5X, DHRS5Y, DHRSXY, DHRSY, SDR46C1, SDR7C6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005610	207063	DHRSX	http://www.ncbi.nlm.nih.gov/gene/?term=207063	"CXorf11, DHRS5X, DHRS5YY, DHRSY, SDR46C1, SDR7C6, DHRSX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005611	2070	EYA4	http://www.ncbi.nlm.nih.gov/gene/?term=2070	"CMD1J, DFNA10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005612	2070	EYA4	http://www.ncbi.nlm.nih.gov/gene/?term=2070	"CMD1J, DFNA10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005613	207165	Bptf	http://www.ncbi.nlm.nih.gov/gene/?term=207165	"9430093H17Rik, Falz "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005614	207165	Bptf	http://www.ncbi.nlm.nih.gov/gene/?term=207165	"9430093H17Rik, Falz "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005615	20717	Serpina3m	http://www.ncbi.nlm.nih.gov/gene/?term=20717	"3e46, AI195004, MMCM7, MMSPi2.4, Spi-2l, Spi-2rs1, Spi2-rs1, Spi2.4, spi2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005616	207181	Rbms3	http://www.ncbi.nlm.nih.gov/gene/?term=207181	"6720477E09Rik, 8430436O14Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005617	2071	ERCC3	http://www.ncbi.nlm.nih.gov/gene/?term=2071	"BTF2, GTF2H, RAD25, TFIIH, TTD2, XPB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005618	2071	ERCC3	http://www.ncbi.nlm.nih.gov/gene/?term=2071	"BTF2, GTF2H, RAD25, TFIIH, TTD2, XPB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005619	207212	Arhgef17	http://www.ncbi.nlm.nih.gov/gene/?term=207212	"8030463K16, AI428794, AW558066, BC035332, mKIAA0337 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005620	20724	Serpinb5	http://www.ncbi.nlm.nih.gov/gene/?term=20724	"1110036M19Rik, AI462524, AI646751, Maspin, PI-5, Spi7, ovalbumin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005621	20729	Spin1	http://www.ncbi.nlm.nih.gov/gene/?term=20729	Spin	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005622	2072	ERCC4	http://www.ncbi.nlm.nih.gov/gene/?term=2072	"ERCC11, FANCQ, RAD1, XFEPS, XPF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005623	2072	ERCC4	http://www.ncbi.nlm.nih.gov/gene/?term=2072	"ERCC11, FANCQ, RAD1, XFEPS, XPF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005624	207304	Hectd1	http://www.ncbi.nlm.nih.gov/gene/?term=207304	"A630086P08Rik, AI844876, b2b327Clo, opm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005625	207393	Elfn2	http://www.ncbi.nlm.nih.gov/gene/?term=207393	"6330514E13, AW048948, BC094219, Lrrc62, Ppp1r29 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005626	2073	ERCC5	http://www.ncbi.nlm.nih.gov/gene/?term=2073	"COFS3, ERCC5-201, ERCM2, UVDR, XPG, XPGC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005627	20740	Sptan1	http://www.ncbi.nlm.nih.gov/gene/?term=20740	"2610027H02Rik, Spna-2, Spna2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005628	207425	Wdr11	http://www.ncbi.nlm.nih.gov/gene/?term=207425	"2900055P10Rik, AW489876, Brwd2, mKIAA1351 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005629	20742	Sptbn1	http://www.ncbi.nlm.nih.gov/gene/?term=20742	"9930031C03Rik, AL033301, SPTB2, Spnb-2, Spnb2, elf1, elf3, mKIAA4049 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005630	20753	Sprr1a	http://www.ncbi.nlm.nih.gov/gene/?term=20753	"AI528815, SPR1a, mSPRR1A "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005631	20755	Sprr2a1	http://www.ncbi.nlm.nih.gov/gene/?term=20755	"Sprr2a, Sprr2a3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005632	207565	Camkk2	http://www.ncbi.nlm.nih.gov/gene/?term=207565	"6330570N16Rik, AW061083, mKIAA0787 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005633	207565	Camkk2	http://www.ncbi.nlm.nih.gov/gene/?term=207565	"6330570N16Rik, AW061083, mKIAA0787 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005634	207615	Wdr37	http://www.ncbi.nlm.nih.gov/gene/?term=207615		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005635	207667	Skor1	http://www.ncbi.nlm.nih.gov/gene/?term=207667	"AV273001, C230094B15Rik, Corl1, Lbxcor1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005636	20768	Sephs2	http://www.ncbi.nlm.nih.gov/gene/?term=20768	"Sps2, Ysg3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005637	20768	Sephs2	http://www.ncbi.nlm.nih.gov/gene/?term=20768	"Sps2, Ysg3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005638	20773	Sptlc2	http://www.ncbi.nlm.nih.gov/gene/?term=20773	"LCB2, LCB2a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005639	207740	Ubald1	http://www.ncbi.nlm.nih.gov/gene/?term=207740	"1500031H01Rik, BC013706, Fam100a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005640	20775	Sqle	http://www.ncbi.nlm.nih.gov/gene/?term=20775	AI323792	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005641	2077	ERF	http://www.ncbi.nlm.nih.gov/gene/?term=2077	"CRS4, PE-2, PE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005642	2077	ERF	http://www.ncbi.nlm.nih.gov/gene/?term=2077	"CRS4, PE-2, PE2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005643	207818	Smagp	http://www.ncbi.nlm.nih.gov/gene/?term=207818		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005644	207958	Alg11	http://www.ncbi.nlm.nih.gov/gene/?term=207958	"AI849156, AW492253, B230397C21, Mmat-4(5) "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005645	207965	Vcpkmt	http://www.ncbi.nlm.nih.gov/gene/?term=207965	"Gm71, Mettl21d, Mettl221d, VCP-KMT "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005646	2079	ERH	http://www.ncbi.nlm.nih.gov/gene/?term=2079	DROER	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005647	207	AKT1	http://www.ncbi.nlm.nih.gov/gene/?term=207	"AKT, CWS6, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005648	208043	Setd1b	http://www.ncbi.nlm.nih.gov/gene/?term=208043	"AA516740, BC035291, KMT2G, mKIAA1076 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005649	20807	Srf	http://www.ncbi.nlm.nih.gov/gene/?term=20807	"AW049942, AW240594 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005650	208092	Chmp6	http://www.ncbi.nlm.nih.gov/gene/?term=208092	2400004G01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005651	208144	Dhx37	http://www.ncbi.nlm.nih.gov/gene/?term=208144	"Gm1050, Gm451, mKIAA1517 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005652	208146	Yeats2	http://www.ncbi.nlm.nih.gov/gene/?term=208146	"BC042768, mKIAA1197 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005653	208154	Btla	http://www.ncbi.nlm.nih.gov/gene/?term=208154	A630002H24	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005654	20815	Srpk1	http://www.ncbi.nlm.nih.gov/gene/?term=20815	AU017960	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005655	20817	Srpk2	http://www.ncbi.nlm.nih.gov/gene/?term=20817	"AW226533, AW492537, AW547358, Wbp6, mSRPK2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005656	208198	Btbd2	http://www.ncbi.nlm.nih.gov/gene/?term=208198	"2610037C03Rik, 4930512K17Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005657	208228	Mob3a	http://www.ncbi.nlm.nih.gov/gene/?term=208228	"5330417K06Rik, A630029F06, AV218468, Mobkl2a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005658	20822	Trove2	http://www.ncbi.nlm.nih.gov/gene/?term=20822	"1810007I17Rik, A530054J02Rik, AI646302, SS-A/Ro, Ssa, Ssa2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005659	20823	Ssb	http://www.ncbi.nlm.nih.gov/gene/?term=20823	SS-B	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005660	20826	Nhp2l1	http://www.ncbi.nlm.nih.gov/gene/?term=20826	"FA-1, Fta1, Snu13, Ssfa1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005661	208292	Zfp871	http://www.ncbi.nlm.nih.gov/gene/?term=208292	"4732483N19, 9030612M13Rik, AI118577, AI265322, mKIAA3006 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005662	208292	Zfp871	http://www.ncbi.nlm.nih.gov/gene/?term=208292	"4732483N19, 9030612M13Rik, AI118577, AI265322, mKIAA3006 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005663	20840	Stac	http://www.ncbi.nlm.nih.gov/gene/?term=20840		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005664	20841	Zfp143	http://www.ncbi.nlm.nih.gov/gene/?term=20841	"AA959806, AU015869, D7Ertd805e, KRAB14, SBF, Staf, Zfp79, Zfp80-rs1, Znf143, pHZ-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005665	20842	Stag1	http://www.ncbi.nlm.nih.gov/gene/?term=20842	"AU045003, SA-1, Scc3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005666	20842	Stag1	http://www.ncbi.nlm.nih.gov/gene/?term=20842	"AU045003, SA-1, Scc3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005667	20842	Stag1	http://www.ncbi.nlm.nih.gov/gene/?term=20842	"AU045003, SA-1, Scc3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005668	208439	Klhl29	http://www.ncbi.nlm.nih.gov/gene/?term=208439	"A230106N14Rik, Gm68, Kbtbd9, mKIAA1921 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005669	208440	Dip2c	http://www.ncbi.nlm.nih.gov/gene/?term=208440	"2900024P20Rik, 9630044M06, mKIAA0934 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005670	208518	Cep78	http://www.ncbi.nlm.nih.gov/gene/?term=208518	"5730599I05Rik, D030027P05 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005671	208606	Rsrc2	http://www.ncbi.nlm.nih.gov/gene/?term=208606	1500011J06Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005672	208638	Slc25a38	http://www.ncbi.nlm.nih.gov/gene/?term=208638	"AV019094, BC010801 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005673	208647	Creb3l2	http://www.ncbi.nlm.nih.gov/gene/?term=208647	"BBF2H7, C530025K05Rik, SCIRR69 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005674	208650	Cblb	http://www.ncbi.nlm.nih.gov/gene/?term=208650	"AI429560, AI851073, Cbl-b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005675	208659	Fam20a	http://www.ncbi.nlm.nih.gov/gene/?term=208659	AI606893	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005676	20868	Stk10	http://www.ncbi.nlm.nih.gov/gene/?term=20868	"Gek1, Lok, mKIAA4026 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005677	208718	Dis3l2	http://www.ncbi.nlm.nih.gov/gene/?term=208718	"4930429A22Rik, 8030493P09Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005678	20873	Plk4	http://www.ncbi.nlm.nih.gov/gene/?term=20873	"1700028H20, AI385771, Sak, Stk18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005679	208748	Prrg3	http://www.ncbi.nlm.nih.gov/gene/?term=208748	Gm368	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005680	208846	Daam1	http://www.ncbi.nlm.nih.gov/gene/?term=208846		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005681	208884	Zdhhc9	http://www.ncbi.nlm.nih.gov/gene/?term=208884	"6430508G22, 9530098M12Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005682	20892	Stra13	http://www.ncbi.nlm.nih.gov/gene/?term=20892		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005683	208968	Zfp280c	http://www.ncbi.nlm.nih.gov/gene/?term=208968	"BC028839, Suhw3, Zfp633, Znf280c, mKIAA1584 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005684	20897	Stra6	http://www.ncbi.nlm.nih.gov/gene/?term=20897	AI891933	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005685	208	AKT2	http://www.ncbi.nlm.nih.gov/gene/?term=208	"HIHGHH, PKBB, PKBBETA, PRKBB, RAC-BETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005686	20901	Strap	http://www.ncbi.nlm.nih.gov/gene/?term=20901	"AW557906, C78091, C79202, Unrip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005687	209027	Pycr1	http://www.ncbi.nlm.nih.gov/gene/?term=209027		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005688	20907	Stx1a	http://www.ncbi.nlm.nih.gov/gene/?term=20907	HPC-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005689	209091	Ccnb3	http://www.ncbi.nlm.nih.gov/gene/?term=209091		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005690	20909	Stx4a	http://www.ncbi.nlm.nih.gov/gene/?term=20909	"Stx4, Syn-4, Syn4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005691	20911	Stxbp2	http://www.ncbi.nlm.nih.gov/gene/?term=20911	"C79054, Munc-18-2, Munc-18b, Munc18b, Sxtbp2, Sxtp2, Unc18-2, Unc18b, muSec1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005692	20912	Stxbp3	http://www.ncbi.nlm.nih.gov/gene/?term=20912	"Munc-18ca, Sxtbp3, Unc18-3, Stxbp3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005693	20916	Sucla2	http://www.ncbi.nlm.nih.gov/gene/?term=20916	4930547K18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005694	20918	Eif1	http://www.ncbi.nlm.nih.gov/gene/?term=20918	Sui1-rs1	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005695	2091	FBL	http://www.ncbi.nlm.nih.gov/gene/?term=2091	"FIB, FLRN, RNU3IP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005696	2091	FBL	http://www.ncbi.nlm.nih.gov/gene/?term=2091	"FIB, FLRN, RNU3IP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005697	209268	Igsf1	http://www.ncbi.nlm.nih.gov/gene/?term=209268	"5330413N23, 5530402E03, AI747649, InhBP/p120, mKIAA0364 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005698	20926	Supt6	http://www.ncbi.nlm.nih.gov/gene/?term=20926	"5131400N11Rik, AI132449, SPT6h, mKIAA0162, Supt6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005699	209318	Gps1	http://www.ncbi.nlm.nih.gov/gene/?term=209318	"Cops1, Csn1, R75577, Sgn1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005700	20933	Med22	http://www.ncbi.nlm.nih.gov/gene/?term=20933	"AW212655, AW558812, Surf-5, Surf5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005701	209416	Gpkow	http://www.ncbi.nlm.nih.gov/gene/?term=209416	"4432411B18, DXErtd697e, DXImx41e, T54 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005702	209446	Tfe3	http://www.ncbi.nlm.nih.gov/gene/?term=209446	"F830016E06Rik, Tcfe3, Tfe-3, bHLHe33 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005703	209462	Hace1	http://www.ncbi.nlm.nih.gov/gene/?term=209462	"1700042J16Rik, A730034A22Rik, BC025474 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005704	209478	Tbc1d12	http://www.ncbi.nlm.nih.gov/gene/?term=209478	BC033574	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005705	209558	Enpp3	http://www.ncbi.nlm.nih.gov/gene/?term=209558	"AI876438, CD203c "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005706	20964	Syn1	http://www.ncbi.nlm.nih.gov/gene/?term=20964	"Syn-1-S, Syn1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005707	209683	Ttc28	http://www.ncbi.nlm.nih.gov/gene/?term=209683	"2310015L07Rik, 6030435N04, AI428795, AI851761, BC002262, TPRBK "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005708	209737	Kif15	http://www.ncbi.nlm.nih.gov/gene/?term=209737	"3110023M17Rik, 3930402I10Rik, D330038N01, HKLP2, Knsl7, b2b1117.1Clo, b2b1117.1aClo "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005709	20979	Syt1	http://www.ncbi.nlm.nih.gov/gene/?term=20979	"AW124717, G630098F17Rik, SytI "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005710	20983	Syt4	http://www.ncbi.nlm.nih.gov/gene/?term=20983	SytIV	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005711	2098	ESD	http://www.ncbi.nlm.nih.gov/gene/?term=2098	FGH	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005712	20	ABCA2	http://www.ncbi.nlm.nih.gov/gene/?term=20	ABC2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005713	210106	Papd7	http://www.ncbi.nlm.nih.gov/gene/?term=210106	"LAK-1, POLK, Pols, TRF4, TRF4-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005714	210126	Lpp	http://www.ncbi.nlm.nih.gov/gene/?term=210126	"9430020K16Rik, AA959454, AU024130, B130055L10Rik, C79715, D630048H16 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005715	210126	Lpp	http://www.ncbi.nlm.nih.gov/gene/?term=210126	"9430020K16Rik, AA959454, AU024130, B130055L10Rik, C79715, D630048H16 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005716	210126	Lpp	http://www.ncbi.nlm.nih.gov/gene/?term=210126	"9430020K16Rik, AA959454, AU024130, B130055L10Rik, C79715, D630048H16 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005717	210135	Zfp180	http://www.ncbi.nlm.nih.gov/gene/?term=210135	"2310040I01Rik, AI852378, D130011P11, HHZ168 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005718	210148	Slc30a6	http://www.ncbi.nlm.nih.gov/gene/?term=210148	"9530029F08Rik, ZnT6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005719	210172	Zfp526	http://www.ncbi.nlm.nih.gov/gene/?term=210172	"D030024H03Rik, Znf526 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005720	210172	Zfp526	http://www.ncbi.nlm.nih.gov/gene/?term=210172	"D030024H03Rik, Znf526 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005721	2101	ESRRA	http://www.ncbi.nlm.nih.gov/gene/?term=2101	"ERR1, ERRa, ERRalpha, ESRL1, NR3B1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005722	2101	ESRRA	http://www.ncbi.nlm.nih.gov/gene/?term=2101	"ERR1, ERRa, ERRalpha, ESRL1, NR3B1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005723	210293	Dock10	http://www.ncbi.nlm.nih.gov/gene/?term=210293	"9330153B10Rik, A630054M16Rik, Jr4, Jr5, R75174, ZIZ3, Zizimin3, mKIAA0694 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005724	210297	Lrch2	http://www.ncbi.nlm.nih.gov/gene/?term=210297	"AI316885, mKIAA1495 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005725	210417	Thsd7b	http://www.ncbi.nlm.nih.gov/gene/?term=210417	"1700074E13Rik, B930082A18, D130067I03Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005726	2104	ESRRG	http://www.ncbi.nlm.nih.gov/gene/?term=2104	"ERR3, ERRgamma, NR3B3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005727	2104	ESRRG	http://www.ncbi.nlm.nih.gov/gene/?term=2104	"ERR3, ERRgamma, NR3B3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005728	210529	Mettl14	http://www.ncbi.nlm.nih.gov/gene/?term=210529	"G430022H21Rik, mKIAA1627 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005729	210766	Brcc3	http://www.ncbi.nlm.nih.gov/gene/?term=210766	C6.1A	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005730	2107	ETF1	http://www.ncbi.nlm.nih.gov/gene/?term=2107	"D5S1995, ERF, ERF1, RF1, SUP45L1, TB3-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005731	2107	ETF1	http://www.ncbi.nlm.nih.gov/gene/?term=2107	"D5S1995, ERF, ERF1, RF1, SUP45L1, TB3-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005732	2107	ETF1	http://www.ncbi.nlm.nih.gov/gene/?term=2107	"D5S1995, ERF, ERF1, RF1, SUP45L1, TB3-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005733	210853	Zfp947	http://www.ncbi.nlm.nih.gov/gene/?term=210853	"6720451E15, EG210853, Gm4769 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005734	2108	ETFA	http://www.ncbi.nlm.nih.gov/gene/?term=2108	"EMA, GA2, MADD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005735	2108	ETFA	http://www.ncbi.nlm.nih.gov/gene/?term=2108	"EMA, GA2, MADD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005736	210973	Kbtbd2	http://www.ncbi.nlm.nih.gov/gene/?term=210973	"BC022962, Bklhd1, mKIAA1489 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005737	210982	Gltscr1l	http://www.ncbi.nlm.nih.gov/gene/?term=210982	mKIAA0240	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005738	210992	Lpcat1	http://www.ncbi.nlm.nih.gov/gene/?term=210992	"2900035H07Rik, Aytl2, BB137372, BC005662, C87117, LPCAT, rd11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005739	210998	Fam91a1	http://www.ncbi.nlm.nih.gov/gene/?term=210998	"AV220772, BC033609, D15Ertd621e, SKIN, mKIAA0493 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005740	2109	ETFB	http://www.ncbi.nlm.nih.gov/gene/?term=2109	"FP585, MADD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005741	2109	ETFB	http://www.ncbi.nlm.nih.gov/gene/?term=2109	"FP585, MADD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005742	210	ALAD	http://www.ncbi.nlm.nih.gov/gene/?term=210	"ALADH, PBGS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005743	211006	Sepsecs	http://www.ncbi.nlm.nih.gov/gene/?term=211006	"9130208G10, AA986712, D5Ertd135e, SLA, SecS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005744	211064	Alkbh1	http://www.ncbi.nlm.nih.gov/gene/?term=211064	"2700073G19Rik, Abh, Alkbh, alkB, hABH "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005745	2110	ETFDH	http://www.ncbi.nlm.nih.gov/gene/?term=2110	"ETFQO, MADD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005746	211208	Gm382	http://www.ncbi.nlm.nih.gov/gene/?term=211208		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005747	211253	Mtrf1	http://www.ncbi.nlm.nih.gov/gene/?term=211253	"A830062K05Rik, MtRF-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005748	211286	Cln5	http://www.ncbi.nlm.nih.gov/gene/?term=211286	A730075N08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005749	211323	Nrg1	http://www.ncbi.nlm.nih.gov/gene/?term=211323	"6030402G23Rik, ARIA, D230005F13Rik, GGF, GGFII, HRG, HRGalpha, Hgl, NDF, SMDF "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005750	211389	Suox	http://www.ncbi.nlm.nih.gov/gene/?term=211389	SO	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005751	211484	Tsga10	http://www.ncbi.nlm.nih.gov/gene/?term=211484	"4933432N21Rik, AI843383, Gm217, Mtsga10 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005752	211488	Ado	http://www.ncbi.nlm.nih.gov/gene/?term=211488	Gm237	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005753	211496	4932415M13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=211496		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005754	2114	ETS2	http://www.ncbi.nlm.nih.gov/gene/?term=2114	ETS2IT1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005755	2114	ETS2	http://www.ncbi.nlm.nih.gov/gene/?term=2114	ETS2IT1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005756	211586	Tfdp2	http://www.ncbi.nlm.nih.gov/gene/?term=211586	"1110029I05Rik, A330080J22Rik, DP-3, DP3 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005757	2115	ETV1	http://www.ncbi.nlm.nih.gov/gene/?term=2115	ER81	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005758	211651	Fancd2	http://www.ncbi.nlm.nih.gov/gene/?term=211651	"2410150O07Rik, AU015151, BB137857, FA-D2, FA4, FACD, FAD, FANCD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005759	2116	ETV2	http://www.ncbi.nlm.nih.gov/gene/?term=2116	"ER71, ETSRP71 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005760	211712	Pcdh9	http://www.ncbi.nlm.nih.gov/gene/?term=211712		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005761	2117	ETV3	http://www.ncbi.nlm.nih.gov/gene/?term=2117	"METS, PE-1, PE1, bA110J1.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005762	2118	ETV4	http://www.ncbi.nlm.nih.gov/gene/?term=2118	"E1A-F, E1AF, PEA3, PEAS3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005763	211948	Pde12	http://www.ncbi.nlm.nih.gov/gene/?term=211948	"2'-PDE, E430028B21Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005764	211949	Spsb4	http://www.ncbi.nlm.nih.gov/gene/?term=211949	"D030068E18Rik, SSB-4, Ssb4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005765	2119	ETV5	http://www.ncbi.nlm.nih.gov/gene/?term=2119	ERM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005766	2119	ETV5	http://www.ncbi.nlm.nih.gov/gene/?term=2119	ERM	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005767	211	ALAS1	http://www.ncbi.nlm.nih.gov/gene/?term=211	"ALAS, ALAS-H, ALAS3, ALASH, MIG4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005768	2120	ETV6	http://www.ncbi.nlm.nih.gov/gene/?term=2120	"TEL, TEL/ABL, THC5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005769	2120	ETV6	http://www.ncbi.nlm.nih.gov/gene/?term=2120	"TEL, TEL/ABL, THC5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005770	212114	Nhlrc3	http://www.ncbi.nlm.nih.gov/gene/?term=212114	"4833441N19, 8030451K01Rik, mKIAA4083 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005771	212127	Proser1	http://www.ncbi.nlm.nih.gov/gene/?term=212127	"2810046L04Rik, 9330161F11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005772	212153	Ccdc191	http://www.ncbi.nlm.nih.gov/gene/?term=212153	"2610015P09Rik, 8430422M09Rik, AU040712 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005773	212198	Wdr25	http://www.ncbi.nlm.nih.gov/gene/?term=212198	B930090D16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005774	2121	EVC	http://www.ncbi.nlm.nih.gov/gene/?term=2121	"DWF-11, EVCL, EVC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005775	2121	EVC	http://www.ncbi.nlm.nih.gov/gene/?term=2121	"DWF-11, EVCL, EVC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005776	212281	Zfp729a	http://www.ncbi.nlm.nih.gov/gene/?term=212281	"A530054K11Rik, Rslcan3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005777	2122	MECOM	http://www.ncbi.nlm.nih.gov/gene/?term=2122	"AML1-EVI-1, EVI1, MDS1, MDS1-EVI1, PRDM3, RUSAT2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005778	212392	Ccdc110	http://www.ncbi.nlm.nih.gov/gene/?term=212392	Gm172	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005779	212448	9330159F19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=212448		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005780	212483	Fam193b	http://www.ncbi.nlm.nih.gov/gene/?term=212483	"IRIZIO, Kiaa1931 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005781	2124	EVI2B	http://www.ncbi.nlm.nih.gov/gene/?term=2124	"CD361, D17S376, EVDB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005782	212547	Nepro	http://www.ncbi.nlm.nih.gov/gene/?term=212547		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005783	212706	N4bp3	http://www.ncbi.nlm.nih.gov/gene/?term=212706	C330016O10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005784	212728	Gm17296	http://www.ncbi.nlm.nih.gov/gene/?term=212728	"Gm179, Tarbp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005785	212772	Arl14ep	http://www.ncbi.nlm.nih.gov/gene/?term=212772	"2700007P21Rik, 4930448O08Rik, ARF7EP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005786	212862	Chpt1	http://www.ncbi.nlm.nih.gov/gene/?term=212862		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005787	212880	Ddx46	http://www.ncbi.nlm.nih.gov/gene/?term=212880	"2200005K02Rik, 8430438J23Rik, AI325430, AI957095, mKIAA0801 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005788	212892	Rsph4a	http://www.ncbi.nlm.nih.gov/gene/?term=212892	"A230081C05, Rshl3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005789	212898	Dse	http://www.ncbi.nlm.nih.gov/gene/?term=212898	"6030499O08, AI480506, B130024B19Rik, DS-epi1, Sart2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005790	212919	Kctd7	http://www.ncbi.nlm.nih.gov/gene/?term=212919	"4932409E18, 9430010P06Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005791	212943	Fam46a	http://www.ncbi.nlm.nih.gov/gene/?term=212943	D930050G01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005792	212	ALAS2	http://www.ncbi.nlm.nih.gov/gene/?term=212	"ALAS-E, ALASE, ANH1, ASB, XLDPP, XLEPP, XLSA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005793	213019	Pdlim2	http://www.ncbi.nlm.nih.gov/gene/?term=213019	"4732462F18Rik, Slim "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005794	213054	Gabpb2	http://www.ncbi.nlm.nih.gov/gene/?term=213054	"1810015F01Rik, 5830427M07, 9430006E19Rik, A430024B14Rik, AV050852-1, Gabpb2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005795	213081	Wdr19	http://www.ncbi.nlm.nih.gov/gene/?term=213081	"C330027H04Rik, D330023L08Rik, DYF2, Ift144, PWDMP, mKIAA1638 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005796	2130	EWSR1	http://www.ncbi.nlm.nih.gov/gene/?term=2130	"EWS, EWS-FLI1, bK984G1.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005797	2130	EWSR1	http://www.ncbi.nlm.nih.gov/gene/?term=2130	"EWS, EWS-FLI1, bK984G1.4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005798	2130	EWSR1	http://www.ncbi.nlm.nih.gov/gene/?term=2130	"EWS, EWS-FLI1, bK984G1.4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005799	213109	Phf3	http://www.ncbi.nlm.nih.gov/gene/?term=213109	"2310061N19Rik, mKIAA0244 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005800	213119	Itga10	http://www.ncbi.nlm.nih.gov/gene/?term=213119	A630048L14	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005801	2131	EXT1	http://www.ncbi.nlm.nih.gov/gene/?term=2131	"EXT, LGCR, LGS, TRPS2, TTV "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005802	2131	EXT1	http://www.ncbi.nlm.nih.gov/gene/?term=2131	"EXT, LGCR, LGS, TRPS2, TTV "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005803	2132	EXT2	http://www.ncbi.nlm.nih.gov/gene/?term=2132	"SOTV, SSMS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005804	2132	EXT2	http://www.ncbi.nlm.nih.gov/gene/?term=2132	"SOTV, SSMS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005805	2132	EXT2	http://www.ncbi.nlm.nih.gov/gene/?term=2132	"SOTV, SSMS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005806	213311	Fbxl21	http://www.ncbi.nlm.nih.gov/gene/?term=213311	"D630045D17Rik, FBL3B, FBXL3B, Psttm "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005807	213350	Pddc1	http://www.ncbi.nlm.nih.gov/gene/?term=213350	"BC023835, D230016J19Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005808	21335	Tacc3	http://www.ncbi.nlm.nih.gov/gene/?term=21335	"Aint, C86661, Eric1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005809	21335	Tacc3	http://www.ncbi.nlm.nih.gov/gene/?term=21335	"Aint, C86661, Eric1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00005810	213402	Armc2	http://www.ncbi.nlm.nih.gov/gene/?term=213402	2610018I05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005811	213409	Lemd1	http://www.ncbi.nlm.nih.gov/gene/?term=213409	"4930540I23Rik, 6430514M23Rik, AI428128, LEMP-1 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005812	21340	Taf1b	http://www.ncbi.nlm.nih.gov/gene/?term=21340	"4930408G01Rik, A230108M10Rik, TAFI68, Tafi86, p63 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005813	21343	Taf6	http://www.ncbi.nlm.nih.gov/gene/?term=21343	"80kDa, AW549759, TAF(II)80, TAFII70, Taf2e, p80 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005814	213452	Dstyk	http://www.ncbi.nlm.nih.gov/gene/?term=213452	"A930019K20Rik, C430014H23Rik, C820013G01, Ripk5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005815	213484	Nudt18	http://www.ncbi.nlm.nih.gov/gene/?term=213484	BC036718	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005816	21353	Tank	http://www.ncbi.nlm.nih.gov/gene/?term=21353	"C86182, E430026L09Rik, I-TRAF "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005817	213556	Plekhh2	http://www.ncbi.nlm.nih.gov/gene/?term=213556	"AI256725, E030001K05, mKIAA2028 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005818	21357	Tarbp2	http://www.ncbi.nlm.nih.gov/gene/?term=21357	"Prbp, TRBP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005819	2135	EXTL2	http://www.ncbi.nlm.nih.gov/gene/?term=2135	EXTR2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005820	2135	EXTL2	http://www.ncbi.nlm.nih.gov/gene/?term=2135	EXTR2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005821	21366	Slc6a6	http://www.ncbi.nlm.nih.gov/gene/?term=21366	"AA589629, C80501, Taut "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005822	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	20833368	Nucleoplasm	Fibroblast	In situ hybridization	"Xist RNA and hnRNP U interact and upon depletion of hnRNP U, Xist RNA is detached from the Xi and diffusely localized into the nucleoplasm. "
RLID00005823	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	11891913	Nucleus	Embryo cell	qRT-PCR	"If this is the case, the extra Xist molecules may not be bound to the inactive X chromo-some and may, in fact, be located elsewhere in the nucleus or even in the cytoplasm. "
RLID00005824	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	12900552	Nucleus	Embryonic stem cell	In situ hybridization|RT-PCR	"On the active male X chromosome, the XIST and TSIX genes are transcribed in undifferentiated cells of pre-implantation embryos (undifferentiated state) and then down-regulated upon cell differentiation (differentiated state). "
RLID00005825	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	16007070	Nucleus	Oocyte	In situ hybridization	"The active and inactive X chromosomes have distinct epigenetic marks in somatic nuclei, which undergo reprogramming after transplantation into oocytes.  "
RLID00005826	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/xist/
RLID00005827	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	18625719	Nucleus	Stem cell	qRT-PCR	Xist RNA is confined to the nuclear territory of the silenced X chromosome throughout the cell cycle.
RLID00005828	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	24462204	Nucleus	Embryonic stem cell	Fluorescence in situ hybridization	"Using anti-GFP immunofluorescence (IF) combined with RNA fluorescence in situ hybridization (FISH), we observed an enrich- ment of Jarid2-EGFP on the Xist RNA-coated X chromosome by day 2-3 (D2/D3) of retinoic acid (RA) differentiation. "
RLID00005829	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	9069284	Nucleus	Embryonic stem cell	In situ hybridization	The Xist gene also maps to this region and is expressed exclusively from the inactive X chromosome. Xist is unusual in that it appears not to code for a protein but produces a nuclear RNA which colocalizes with the inactive X chromosome. 
RLID00005830	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	9660859	Nucleus	Embryonic stem cell	qRT-PCR	"Mouse Xist RNA tightly localized to an active X chromosome, demonstrating for the first time that the active X chromosome in somatic cells is competent to associate with Xist RNA.  "
RLID00005831	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	22817891	Nucleus	Bone marrow Macrophage	Next-generation sequencing	"Cluster 7, for example, contains abundant transcripts in the chromatin, with much lower transcript levels in the nucleoplasm and cytoplasm relative to the other clusters. This cluster is dominated by annotated and unannotated non-coding transcripts and miRNA precursors. (The analysis excluded transcripts shorter than 400 nucleotides and therefore excluded mature miRNAs and many miRNA precursors.) Some non-coding RNAs, such as Xist, are highly enriched in the chromatin because they function at this location (Figure S2). Examples of other non-coding RNAs in Cluster 7 are Neat1 and Malat1/Neat2 (Figure S2). Further mining of the data sets may provide insights into the subcellular locations at which many non-coding RNAs function. Cluster 7 also includes transcripts from constitutive protein-coding genes that may be highly unstable and therefore present at low levels in the cytoplasm (e.g. Leng8 in Figure S2). "
RLID00005832	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005833	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	26190105	Nucleus	Embryotem cell	Microscopy	"Figure 6: 3DSIM Showing that Xist RNA, Rbm15, Wtap, and Spen Co-localize within Perichromatin Spaces. Data are collected from Figure 6. "
RLID00005834	213742	Xist	http://www.ncbi.nlm.nih.gov/gene/?term=213742	"A430022B11, AI314753 "	lncRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"We then analyzed the abundance of several lncRNAs, namely Malat1, Meg3, Rmst, Xist and Miat. All of these lncRNAs were present in the axonal compartment.  "
RLID00005835	21374	Tbp	http://www.ncbi.nlm.nih.gov/gene/?term=21374	"GTF2D1, Gtf2d, SCA17, TFIID "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005836	213760	Prepl	http://www.ncbi.nlm.nih.gov/gene/?term=213760	"2810457N15Rik, 9530014L06Rik, D030028O16Rik, mKIAA0436 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005837	213773	Tbl3	http://www.ncbi.nlm.nih.gov/gene/?term=213773	9430070M15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005838	2137	EXTL3	http://www.ncbi.nlm.nih.gov/gene/?term=2137	"BOTV, EXTL1L, EXTR1, REGR, RPR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005839	21380	Tbx1	http://www.ncbi.nlm.nih.gov/gene/?term=21380		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005840	213819	Casd1	http://www.ncbi.nlm.nih.gov/gene/?term=213819	"Cas1, Cast1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005841	21385	Tbx2	http://www.ncbi.nlm.nih.gov/gene/?term=21385		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005842	21386	Tbx3	http://www.ncbi.nlm.nih.gov/gene/?term=21386	D5Ertd189e	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005843	213895	Bms1	http://www.ncbi.nlm.nih.gov/gene/?term=213895	"AA408648, AU020092, AU043373, BB007109, BC030906l, mKIAA0187, Bms1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005844	213948	Atg9b	http://www.ncbi.nlm.nih.gov/gene/?term=213948	"Apg912, Apg9l2, Apgdc2, Gm574, Nos3as, eONE, sONE "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005845	2139	EYA2	http://www.ncbi.nlm.nih.gov/gene/?term=2139	EAB1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005846	213	ALB	http://www.ncbi.nlm.nih.gov/gene/?term=213	"ANALBA, FDAH, PRO0883, PRO0903, PRO1341 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005847	21400	Tcea2	http://www.ncbi.nlm.nih.gov/gene/?term=21400	"AI326274, S-II-T1, SII-T1, Tceat "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005848	21402	Skp1a	http://www.ncbi.nlm.nih.gov/gene/?term=21402	"15kDa, 2610043E24Rik, 2610206H23Rik, EMC19, OCP-II, OCP2, SKP1, Tceb1l, p19A, p19Skp1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005849	214048	Larp1b	http://www.ncbi.nlm.nih.gov/gene/?term=214048	"1700108L22Rik, 4933421B21Rik, AA690246, Larp2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005850	21406	Tcf12	http://www.ncbi.nlm.nih.gov/gene/?term=21406	"A130037E08Rik, ALF1, HEB, HEBAlt, HTF-4, HTF4, ME1, REB, bHLHb20 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005851	21406	Tcf12	http://www.ncbi.nlm.nih.gov/gene/?term=21406	"A130037E08Rik, ALF1, HEB, HEBAlt, HTF-4, HTF4, ME1, REB, bHLHb20 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005852	214084	Slc18a2	http://www.ncbi.nlm.nih.gov/gene/?term=214084	"1110037L13Rik, 9330105E13, Vmat2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005853	21408	Zfp354a	http://www.ncbi.nlm.nih.gov/gene/?term=21408	"AW488485, Tcf17, Znf354a, kid1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005854	2140	EYA3	http://www.ncbi.nlm.nih.gov/gene/?term=2140		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005855	2140	EYA3	http://www.ncbi.nlm.nih.gov/gene/?term=2140		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005856	2140	EYA3	http://www.ncbi.nlm.nih.gov/gene/?term=2140		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005857	21413	Tcf4	http://www.ncbi.nlm.nih.gov/gene/?term=21413	"5730422P05Rik, ASP-I2, E2-2, E2.2, ITF-2, ITF-2b, ITF2, ME2, MITF-2A, MITF-2B, SEF-2, SEF2, SEF2-1, TFE, Tcf-4, bHLHb19 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005858	21413	Tcf4	http://www.ncbi.nlm.nih.gov/gene/?term=21413	"5730422P05Rik, ASP-I2, E2-2, E2.2, ITF-2, ITF-2b, ITF2, ME2, MITF-2A, MITF-2B, SEF-2, SEF2, SEF2-1, TFE, Tcf-4, bHLHb19 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005859	214150	Ago3	http://www.ncbi.nlm.nih.gov/gene/?term=214150	"AW048688, C130014L07Rik, Eif2c3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005860	21417	Zeb1	http://www.ncbi.nlm.nih.gov/gene/?term=21417	"3110032K11Rik, AREB6, BZP, MEB1, Nil2, TCF-8, Tcf18, Tcf8, Tw, ZEB, Zfhep, Zfhx1a, Zfx1a, Zfx1ha, [delta]EF1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005861	21417	Zeb1	http://www.ncbi.nlm.nih.gov/gene/?term=21417	"3110032K11Rik, AREB6, BZP, MEB1, Nil2, TCF-8, Tcf18, Tcf8, Tw, ZEB, Zfhep, Zfhx1a, Zfx1a, Zfx1ha, [delta]EF1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005862	21417	Zeb1	http://www.ncbi.nlm.nih.gov/gene/?term=21417	"3110032K11Rik, AREB6, BZP, MEB1, Nil2, TCF-8, Tcf18, Tcf8, Tw, ZEB, Zfhep, Zfhx1a, Zfx1a, Zfx1ha, [delta]EF1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005863	21419	Tfap2b	http://www.ncbi.nlm.nih.gov/gene/?term=21419	"AI606113, AP-2(beta), E130018K07Rik, Tcfap2b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005864	214254	Nudt15	http://www.ncbi.nlm.nih.gov/gene/?term=214254	"6530403O17, A730068G11Rik, MTH2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005865	21425	Tfeb	http://www.ncbi.nlm.nih.gov/gene/?term=21425	"Tcfeb, bHLHe35 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005866	214290	Zcchc6	http://www.ncbi.nlm.nih.gov/gene/?term=214290	"6030448M23Rik, AA420405 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005867	21429	Ubtf	http://www.ncbi.nlm.nih.gov/gene/?term=21429	"A930005G04Rik, NOR-90, Tcfubf, UBF, UBF-1, UBF1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005868	214308	Gm381	http://www.ncbi.nlm.nih.gov/gene/?term=214308		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005869	214444	Cdk5rap2	http://www.ncbi.nlm.nih.gov/gene/?term=214444	"2900018K03Rik, an, mKIAA1633 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005870	214459	Fnbp1l	http://www.ncbi.nlm.nih.gov/gene/?term=214459	"2610318I01Rik, AW548221, TOCA1, toca-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005871	214469	Fam168b	http://www.ncbi.nlm.nih.gov/gene/?term=214469	mKIAA4042	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005872	214469	Fam168b	http://www.ncbi.nlm.nih.gov/gene/?term=214469	mKIAA4042	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005873	214489	BC003965	http://www.ncbi.nlm.nih.gov/gene/?term=214489	Ccsmst1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005874	21452	Tcn2	http://www.ncbi.nlm.nih.gov/gene/?term=21452	"AW208754, Tcn-2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005875	214531	Tmprss13	http://www.ncbi.nlm.nih.gov/gene/?term=214531	"BC010843, Tpmrss13 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005876	21453	Tcof1	http://www.ncbi.nlm.nih.gov/gene/?term=21453	"AA408847, AW209012, treacle "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005877	21454	Tcp1	http://www.ncbi.nlm.nih.gov/gene/?term=21454	"AI528772, CCT, Cct1, Ccta, TRic, Tcp-1, Tp63, c-cpn, p63 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005878	214580	Pstk	http://www.ncbi.nlm.nih.gov/gene/?term=214580	"5430423O14Rik, 5730458D16Rik, Gm1099, R75284 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005879	214597	Sidt2	http://www.ncbi.nlm.nih.gov/gene/?term=214597	"B930096O19, BC023957, CGI-40 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005880	214663	Slc25a29	http://www.ncbi.nlm.nih.gov/gene/?term=214663	"C030003J19Rik, CACL, mCACL "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005881	2146	EZH2	http://www.ncbi.nlm.nih.gov/gene/?term=2146	"ENX-1, ENX1, EZH1, EZH2b, KMT6, KMT6A, WVS, WVS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005882	2146	EZH2	http://www.ncbi.nlm.nih.gov/gene/?term=2146	"ENX-1, ENX1, EZH1b, KMT6, KMT6A, WVS, WVS2, EZH2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005883	214742	Rcor3	http://www.ncbi.nlm.nih.gov/gene/?term=214742	"4921514E24Rik, C730034D20Rik, E130101E15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005884	214764	Edrf1	http://www.ncbi.nlm.nih.gov/gene/?term=214764	"2700050L05Rik, AU022667, AW558805 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005885	214804	Syde2	http://www.ncbi.nlm.nih.gov/gene/?term=214804	C430017H16Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005886	214854	Neurl3	http://www.ncbi.nlm.nih.gov/gene/?term=214854	"2010300P06Rik, Lincr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005887	214899	Kdm5a	http://www.ncbi.nlm.nih.gov/gene/?term=214899	"AA409370, C76986, Jarid1a, RBP2, Rbbp2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005888	214901	Chtf18	http://www.ncbi.nlm.nih.gov/gene/?term=214901	"6030457M03Rik, CTF18, Chl12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005889	214951	Rhbdl1	http://www.ncbi.nlm.nih.gov/gene/?term=214951	Rhbdl	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005890	2149	F2R	http://www.ncbi.nlm.nih.gov/gene/?term=2149	"CF2R, HTR, PAR-1, PAR1, TR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005891	2149	F2R	http://www.ncbi.nlm.nih.gov/gene/?term=2149	"CF2R, HTR, PAR-1, PAR1, TR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005892	2149	F2R	http://www.ncbi.nlm.nih.gov/gene/?term=2149	"CF2R, HTR, PAR-1, PAR1, TR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005893	2149	F2R	http://www.ncbi.nlm.nih.gov/gene/?term=2149	"CF2R, HTR, PAR-1, PAR1, TR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005894	214	ALCAM	http://www.ncbi.nlm.nih.gov/gene/?term=214	"CD166, MEMD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005895	214	ALCAM	http://www.ncbi.nlm.nih.gov/gene/?term=214	"CD166, MEMD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005896	215008	Vezt	http://www.ncbi.nlm.nih.gov/gene/?term=215008	"A630071D13Rik, AI848282 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005897	215031	Vgll2	http://www.ncbi.nlm.nih.gov/gene/?term=215031	"C130057C21Rik, VITO-1, Vito1, vgl-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005898	215051	Bud13	http://www.ncbi.nlm.nih.gov/gene/?term=215051	"AV305342, D030060M11Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005899	2150	F2RL1	http://www.ncbi.nlm.nih.gov/gene/?term=2150	"GPR11, PAR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005900	2150	F2RL1	http://www.ncbi.nlm.nih.gov/gene/?term=2150	"GPR11, PAR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005901	215194	Kri1	http://www.ncbi.nlm.nih.gov/gene/?term=215194		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005902	2151	F2RL2	http://www.ncbi.nlm.nih.gov/gene/?term=2151	"PAR-3, PAR3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005903	2152	F3	http://www.ncbi.nlm.nih.gov/gene/?term=2152	"CD142, TF, TFA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005904	2152	F3	http://www.ncbi.nlm.nih.gov/gene/?term=2152	"CD142, TF, TFA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00005905	215351	Senp6	http://www.ncbi.nlm.nih.gov/gene/?term=215351	"2810017C20Rik, E130319N12Rik, Susp1, mKIAA0797 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005906	215418	Csrnp1	http://www.ncbi.nlm.nih.gov/gene/?term=215418	"4931429D10Rik, Axud1, CSRNP-1, URAX1, taip-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005907	215446	Entpd3	http://www.ncbi.nlm.nih.gov/gene/?term=215446	"Cd39l3, HB6, NTPDase-3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005908	215476	Prr14l	http://www.ncbi.nlm.nih.gov/gene/?term=215476	"6030436E02Rik, C330019G07Rik, Prl14l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005909	215476	Prr14l	http://www.ncbi.nlm.nih.gov/gene/?term=215476	"6030436E02Rik, C330019G07Rik, Prl14l "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005910	215641	Mageb18	http://www.ncbi.nlm.nih.gov/gene/?term=215641	B430216B18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005911	215690	Nav1	http://www.ncbi.nlm.nih.gov/gene/?term=215690	"9530089B19, 9930003A20Rik, C230080M11Rik, Pomfil3, Unc53h1, mKIAA1151, steerin-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005912	215693	Zmat1	http://www.ncbi.nlm.nih.gov/gene/?term=215693	"A230096A06, AW990744, B930008K04Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005913	215728	9230019H11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=215728		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005914	215751	Ginm1	http://www.ncbi.nlm.nih.gov/gene/?term=215751	AA589616	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005915	215789	Phactr2	http://www.ncbi.nlm.nih.gov/gene/?term=215789	"AV158170, BC012871 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005916	215798	Adgrg6	http://www.ncbi.nlm.nih.gov/gene/?term=215798	"1190004A11Rik, AI449247, AW045736, DREG, Gm222, Gpr126 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005917	2157	F8	http://www.ncbi.nlm.nih.gov/gene/?term=2157	"AHF, DXS1253E, F8B, F8C, FVIII, HEMA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005918	215866	Gm29673	http://www.ncbi.nlm.nih.gov/gene/?term=215866		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005919	216028	Lrrtm3	http://www.ncbi.nlm.nih.gov/gene/?term=216028	9630044H04Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005920	216119	Ybey	http://www.ncbi.nlm.nih.gov/gene/?term=216119	"1110068N23Rik, A130042E20Rik, C21orf57, ORF57, ORF66 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005921	216154	Med16	http://www.ncbi.nlm.nih.gov/gene/?term=216154	"95kDa, A630083L04, Thrap5, Trap95 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005922	216156	Wdr18	http://www.ncbi.nlm.nih.gov/gene/?term=216156	"2310012I10Rik, AU044733, AW122032 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005923	216188	Aldh1l2	http://www.ncbi.nlm.nih.gov/gene/?term=216188	"D330038I09Rik, mtFDH "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005924	216190	Appl2	http://www.ncbi.nlm.nih.gov/gene/?term=216190	Dip3b	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005925	216197	Ckap4	http://www.ncbi.nlm.nih.gov/gene/?term=216197	"5630400A09Rik, CLIMP-63, P63 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005926	2161	F12	http://www.ncbi.nlm.nih.gov/gene/?term=2161	"HAE3, HAEX, HAF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005927	216274	Cep290	http://www.ncbi.nlm.nih.gov/gene/?term=216274	"BC004690, Nphp6, b2b1454Clo, b2b1752Clo "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005928	216292	Mettl25	http://www.ncbi.nlm.nih.gov/gene/?term=216292		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005929	2162	F13A1	http://www.ncbi.nlm.nih.gov/gene/?term=2162	F13A	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005930	216345	Zfc3h1	http://www.ncbi.nlm.nih.gov/gene/?term=216345	"BC033596, Ccdc131, Psrc2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005931	216395	Tmem5	http://www.ncbi.nlm.nih.gov/gene/?term=216395	6330415D21Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005932	216438	March9	http://www.ncbi.nlm.nih.gov/gene/?term=216438	"AI608492, BC019560 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005933	216459	Myl6b	http://www.ncbi.nlm.nih.gov/gene/?term=216459	"5730437E04Rik, BC037527, MLC1SA "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005934	216527	Ccm2	http://www.ncbi.nlm.nih.gov/gene/?term=216527	BC029157	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005935	216543	Cep68	http://www.ncbi.nlm.nih.gov/gene/?term=216543	"6030463E10Rik, AI481761, BC027174, Kiaa0582 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005936	216549	Aftph	http://www.ncbi.nlm.nih.gov/gene/?term=216549		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005937	216558	Ugp2	http://www.ncbi.nlm.nih.gov/gene/?term=216558	"UDPGP, UGPase "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005938	21665	Tdg	http://www.ncbi.nlm.nih.gov/gene/?term=21665	"E130317C12Rik, JZA-3, Jza1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005939	2166	FAAH	http://www.ncbi.nlm.nih.gov/gene/?term=2166	"FAAH-1, PSAB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005940	216739	Acsl6	http://www.ncbi.nlm.nih.gov/gene/?term=216739	"A330035H04Rik, AW050338, Facl6, LACS, Lacsl, mKIAA0837 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005941	216742	Fnip1	http://www.ncbi.nlm.nih.gov/gene/?term=216742	"A730024A03Rik, AI838773, AW557298 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005942	216760	Mfap3	http://www.ncbi.nlm.nih.gov/gene/?term=216760	"2610509F16Rik, 2700079M14Rik, AW536327 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005943	21676	Tead1	http://www.ncbi.nlm.nih.gov/gene/?term=21676	"2610024B07Rik, B230114H05Rik, Gtrgeo5, TEAD-1, TEF-1, Tcf13, mTEF-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005944	2167	FABP4	http://www.ncbi.nlm.nih.gov/gene/?term=2167	"A-FABP, AFABP, ALBP, HEL-S-104, aP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005945	216835	Usp43	http://www.ncbi.nlm.nih.gov/gene/?term=216835		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005946	21683	Tecta	http://www.ncbi.nlm.nih.gov/gene/?term=21683	Tctna	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005947	216848	Chd3	http://www.ncbi.nlm.nih.gov/gene/?term=216848	"2600010P09Rik, AF020312, Chd7, Prp7, Prp9-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005948	216853	Wrap53	http://www.ncbi.nlm.nih.gov/gene/?term=216853	"BC021790, Wdr79 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005949	216856	Nlgn2	http://www.ncbi.nlm.nih.gov/gene/?term=216856	NL2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005950	21685	Tef	http://www.ncbi.nlm.nih.gov/gene/?term=21685	2310028D20Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005951	21685	Tef	http://www.ncbi.nlm.nih.gov/gene/?term=21685	2310028D20Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005952	216965	Taok1	http://www.ncbi.nlm.nih.gov/gene/?term=216965	"2810468K05Rik, AU020252, D130018F14Rik, Map3k16, Markk, Psk2, mKIAA1361 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005953	216976	BC030499	http://www.ncbi.nlm.nih.gov/gene/?term=216976	"BC037104, Sgk494 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005954	216	ALDH1A1	http://www.ncbi.nlm.nih.gov/gene/?term=216	"ALDC, ALDH-E1, ALDH1, ALDH11, HEL-9, HEL-S-53e, HEL12, PUMB1, RALDH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005955	217011	Nle1	http://www.ncbi.nlm.nih.gov/gene/?term=217011	"AL022765, BC018399, Nle, l11Jus1, l11Jus4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005956	217031	Tada2a	http://www.ncbi.nlm.nih.gov/gene/?term=217031	"AV319371, D030022J10Rik, Tada2l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005957	217109	Utp18	http://www.ncbi.nlm.nih.gov/gene/?term=217109	"6230425C22Rik, 6430513M13, Wdr50 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005958	217124	Ppp1r9b	http://www.ncbi.nlm.nih.gov/gene/?term=217124	"SPL, Spn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005959	217124	Ppp1r9b	http://www.ncbi.nlm.nih.gov/gene/?term=217124	"SPL, Spn "	mRNA	Mus musculus	22215810	Dendrite	Hippocampus	Fluorescence in situ hybridization	"In order to confirm the functional consequence of the interaction between ZBP1 and its predicted target mRNAs that was observed in vivo, we investigated the dendritic localization of spinophilin (PPP1R9B) mRNA in developing hippocampal neurons using fluorescence in situ hybridization (FISH). "
RLID00005960	217125	Samd14	http://www.ncbi.nlm.nih.gov/gene/?term=217125	"AI839049, AI854782, BC034054 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005961	217125	Samd14	http://www.ncbi.nlm.nih.gov/gene/?term=217125	"AI839049, AI854782, BC034054 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005962	217140	Scrn2	http://www.ncbi.nlm.nih.gov/gene/?term=217140	"AV001119, D11Moh48, SES2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005963	217166	Nr1d1	http://www.ncbi.nlm.nih.gov/gene/?term=217166	"A530070C09Rik, R75201 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005964	2171	FABP5	http://www.ncbi.nlm.nih.gov/gene/?term=2171	"E-FABP, EFABP, KFABP, PA-FABP, PAFABP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005965	2171	FABP5	http://www.ncbi.nlm.nih.gov/gene/?term=2171	"E-FABP, EFABP, KFABP, PA-FABP, PAFABP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005966	2171	FABP5	http://www.ncbi.nlm.nih.gov/gene/?term=2171	"E-FABP, EFABP, KFABP, PA-FABP, PAFABP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005967	217216	BC030867	http://www.ncbi.nlm.nih.gov/gene/?term=217216		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005968	217217	Asb16	http://www.ncbi.nlm.nih.gov/gene/?term=217217		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005969	217218	Atxn7l3	http://www.ncbi.nlm.nih.gov/gene/?term=217218	E030022H21Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005970	217232	Cdc27	http://www.ncbi.nlm.nih.gov/gene/?term=217232	"AI452358, APC3, BC023187 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005971	2172	FABP6	http://www.ncbi.nlm.nih.gov/gene/?term=2172	"I-15P, I-BABP, I-BALB, I-BAP, ILBP, ILBP3, ILLBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005972	217333	Trim47	http://www.ncbi.nlm.nih.gov/gene/?term=217333	2210023F24Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005973	217366	Lrrc45	http://www.ncbi.nlm.nih.gov/gene/?term=217366	BC023296	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005974	217410	Trib2	http://www.ncbi.nlm.nih.gov/gene/?term=217410	"AW319517, TRB-2, TRB2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005975	217430	Pqlc3	http://www.ncbi.nlm.nih.gov/gene/?term=217430	"C78076, E030024M05Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005976	217480	Dgkb	http://www.ncbi.nlm.nih.gov/gene/?term=217480	"6430574F24, 90kda, C630029D13Rik, DAGK2, DGK, DGK-beta, mKIAA0718 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005977	217578	Baz1a	http://www.ncbi.nlm.nih.gov/gene/?term=217578	"Acf1, B930060C03, BC065123, Gtl5, Wcrf180, cbp146 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005978	217588	Mbip	http://www.ncbi.nlm.nih.gov/gene/?term=217588	4933408E06Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005979	2175	FANCA	http://www.ncbi.nlm.nih.gov/gene/?term=2175	"FA, FA-H, FA1, FAA, FACA, FAH, FANCH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005980	2175	FANCA	http://www.ncbi.nlm.nih.gov/gene/?term=2175	"FA, FA-H, FA1, FAA, FACA, FAH, FANCH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00005981	217601	BC042761	http://www.ncbi.nlm.nih.gov/gene/?term=217601		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005982	21761	Morf4l1	http://www.ncbi.nlm.nih.gov/gene/?term=21761	"MORFRG15, MRG15, TEG-189, Tex189, mKIAA4002 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005983	21761	Morf4l1	http://www.ncbi.nlm.nih.gov/gene/21761		mRNA	Mus musculus	11985882	Dendrite	pyramidal cell	In situ hybridization	"The findings indicate that CPER9 was actually localized at the apical dendrites of a portion of cerebral cortex layer V pyramidal cells, as well as at the proximal dendrites of some of the cerebellar Purkinje cells. CPER9 was found to encode a mouse homolog of MRG15, a nuclear protein which contains a chromodomain identified in several proteins that act as regulators of transcription.  "
RLID00005984	217664	Mgat2	http://www.ncbi.nlm.nih.gov/gene/?term=217664	"AA407964, CDGS2, GLCNACTII, GNT-II, GNT2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005985	21766	Tex261	http://www.ncbi.nlm.nih.gov/gene/?term=21766	"3110001O07Rik, AA409339, AI480706, AL033351, TEG-261 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005986	217692	Sipa1l1	http://www.ncbi.nlm.nih.gov/gene/?term=217692	"4931426N11Rik, AW213287, Spar, mKIAA0440 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005987	21769	Zfand3	http://www.ncbi.nlm.nih.gov/gene/?term=21769	"AW539211, TEG-27, Tex27 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005988	217718	Nek9	http://www.ncbi.nlm.nih.gov/gene/?term=217718	C130021H08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005989	217732	Cipc	http://www.ncbi.nlm.nih.gov/gene/?term=217732	"2310044G17Rik, AI842544, AI853744, Kiaa1737, mKIAA1737 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005990	217734	Pomt2	http://www.ncbi.nlm.nih.gov/gene/?term=217734		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005991	2177	FANCD2	http://www.ncbi.nlm.nih.gov/gene/?term=2177	"FA-D2, FA4, FACD, FAD, FAD2, FANCD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00005992	2177	FANCD2	http://www.ncbi.nlm.nih.gov/gene/?term=2177	"FA-D2, FA4, FACD, FAD, FAD2, FANCD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00005993	21780	Tfam	http://www.ncbi.nlm.nih.gov/gene/?term=21780	"AI661103, Hmgts, mtTFA, tsHMG "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005994	217843	Unc79	http://www.ncbi.nlm.nih.gov/gene/?term=217843	"9030205A07Rik, Mlca3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005995	217864	Rcor1	http://www.ncbi.nlm.nih.gov/gene/?term=217864	"5730409O11, 6720480E22Rik, AU042633, D12Wsu95e, Rocr1, mKIAA0071 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005996	217869	Eif5	http://www.ncbi.nlm.nih.gov/gene/?term=217869	"2810011H21Rik, D12Ertd549e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005997	217869	Eif5	http://www.ncbi.nlm.nih.gov/gene/?term=217869	"2810011H21Rik, D12Ertd549e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00005998	21788	Tfpi	http://www.ncbi.nlm.nih.gov/gene/?term=21788	"A630013F22Rik, AW552122, EPI, LACI "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00005999	2178	FANCE	http://www.ncbi.nlm.nih.gov/gene/?term=2178	"FACE, FAE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006000	217944	Rapgef5	http://www.ncbi.nlm.nih.gov/gene/?term=217944	"4932413M22, C86120, D030051B22Rik, GFR, Mrgef, mKIAA0277, mmr-gef "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006001	217946	Cdca7l	http://www.ncbi.nlm.nih.gov/gene/?term=217946	"BC006933, JPO2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006002	217980	Larp4b	http://www.ncbi.nlm.nih.gov/gene/?term=217980	"A630096F19, AI256361, D13Wsu64e, Larp5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006003	217980	Larp4b	http://www.ncbi.nlm.nih.gov/gene/?term=217980	"A630096F19, AI256361, D13Wsu64e, Larp5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006004	217995	Heatr1	http://www.ncbi.nlm.nih.gov/gene/?term=217995	"AA517551, B130016L12Rik, BC019693 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006005	218035	Vps41	http://www.ncbi.nlm.nih.gov/gene/?term=218035	"AI317346, Vam2, mVam2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006006	21803	Tgfb1	http://www.ncbi.nlm.nih.gov/gene/?term=21803	"TGF-beta1, TGFbeta1, Tgfb, Tgfb-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006007	21804	Tgfb1i1	http://www.ncbi.nlm.nih.gov/gene/?term=21804	"ARA55, Hic5, TSC-5, hic-5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006008	21808	Tgfb2	http://www.ncbi.nlm.nih.gov/gene/?term=21808	"BB105277, Tgf-beta2, Tgfb-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006009	2180	ACSL1	http://www.ncbi.nlm.nih.gov/gene/?term=2180	"ACS1, FACL1, FACL2, LACS, LACS1, LACS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006010	2180	ACSL1	http://www.ncbi.nlm.nih.gov/gene/?term=2180	"ACS1, FACL1, FACL2, LACS, LACS1, LACS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006011	2180	ACSL1	http://www.ncbi.nlm.nih.gov/gene/?term=2180	"ACS1, FACL1, FACL2, LACS, LACS1, LACS2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006012	218100	Zfp322a	http://www.ncbi.nlm.nih.gov/gene/?term=218100	"Znf322, Znf322a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006013	21812	Tgfbr1	http://www.ncbi.nlm.nih.gov/gene/?term=21812	"ALK5, AU017191, Alk-5, ESK2, TGFR-1, TbetaR-I, TbetaRI "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006014	2181	ACSL3	http://www.ncbi.nlm.nih.gov/gene/?term=2181	"ACS3, FACL3, PRO2194 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006015	2181	ACSL3	http://www.ncbi.nlm.nih.gov/gene/?term=2181	"ACS3, FACL3, PRO2194 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006016	2181	ACSL3	http://www.ncbi.nlm.nih.gov/gene/?term=2181	"ACS3, FACL3, PRO2194 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006017	218210	Nup153	http://www.ncbi.nlm.nih.gov/gene/?term=218210	"B130015D15Rik, C88147 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006018	218214	Kdm1b	http://www.ncbi.nlm.nih.gov/gene/?term=218214	"4632428N09Rik, AI482520, Aof1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006019	21821	Ift88	http://www.ncbi.nlm.nih.gov/gene/?term=21821	"AW552028, Tg737, Tg737Rpw, TgN737Rpw, Ttc10, flexo, fxo, orpk, polaris "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006020	21822	Tgtp1	http://www.ncbi.nlm.nih.gov/gene/?term=21822	"Gtp2, Irgb6, Mg21, Tgtp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006021	218236	Fam120a	http://www.ncbi.nlm.nih.gov/gene/?term=218236	"C9orf10, Ossa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006022	21823	Th	http://www.ncbi.nlm.nih.gov/gene/?term=21823		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006023	21827	Thbs3	http://www.ncbi.nlm.nih.gov/gene/?term=21827	"TSP3, Thbs-3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006024	218294	Cdc14b	http://www.ncbi.nlm.nih.gov/gene/?term=218294	"2810432N10Rik, A530086E13Rik, AA472821, CDC14B3, Cdc14B1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006025	218294	Cdc14b	http://www.ncbi.nlm.nih.gov/gene/?term=218294	"2810432N10Rik, A530086E13Rik, AA472821, CDC14B3, Cdc14B1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006026	2182	ACSL4	http://www.ncbi.nlm.nih.gov/gene/?term=2182	"ACS4, FACL4, LACS4, MRX63, MRX68 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006027	218311	Zfp455	http://www.ncbi.nlm.nih.gov/gene/?term=218311	"3732412P20Rik, Rslcan-10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006028	218314	Zfp595	http://www.ncbi.nlm.nih.gov/gene/?term=218314	"A230042K10Rik, Rslcan23 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006029	218333	Ice1	http://www.ncbi.nlm.nih.gov/gene/?term=218333	"C77245, mKIAA0947 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006030	21833	Thra	http://www.ncbi.nlm.nih.gov/gene/?term=21833	"6430529J03Rik, AW259572, Erba, Nr1a1, Rvr, T3R[a], T3Ralpha1, Thra2, c-erbA-1, c-erbA-alpha, c-erbAalpha, Thra "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006031	218341	Rfesd	http://www.ncbi.nlm.nih.gov/gene/?term=218341	"AI256775, D030068K09 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006032	218397	Rasa1	http://www.ncbi.nlm.nih.gov/gene/?term=218397	"Gap, RasGAP, Rasa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006033	218397	Rasa1	http://www.ncbi.nlm.nih.gov/gene/?term=218397	"Gap, RasGAP, Rasa "	mRNA	Mus musculus	24381269	Axon	Dorsal root ganglia	qRT-PCR	"Using qRT-PCR, we confirmed the presence of Rasa1 mRNA in isolated DRG axons. "
RLID00006034	21841	Tia1	http://www.ncbi.nlm.nih.gov/gene/?term=21841	"2310050N03Rik, AI256674, TIA-1, mTIA-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006035	21843	Tial1	http://www.ncbi.nlm.nih.gov/gene/?term=21843	"5330433G13Rik, AL033329, TIAR, mTIAR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006036	21844	Tiam1	http://www.ncbi.nlm.nih.gov/gene/?term=21844	"AI847750, D16Ium10, D16Ium10e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006037	21848	Trim24	http://www.ncbi.nlm.nih.gov/gene/?term=21848	"A130082H20Rik, AI447469, D430004I05Rik, TIF1, TIF1-alpha, TIF1alpha, Tif1a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006038	21849	Trim28	http://www.ncbi.nlm.nih.gov/gene/?term=21849	"AA408787, KAP-1, KRIP-1, MommeD9, Tif1b, Tif1beta "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006039	2184	FAH	http://www.ncbi.nlm.nih.gov/gene/?term=2184		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006040	218518	Marveld2	http://www.ncbi.nlm.nih.gov/gene/?term=218518	"BC003296, MARVD2, Mrvldc2, Tric, Trica, Tricb, Tricc "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006041	218543	Srek1	http://www.ncbi.nlm.nih.gov/gene/?term=218543	"8430401B01, AI450757, AI462342, SRrp508, SRrp86, Sfrs12, Srsf12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006042	218544	Sgtb	http://www.ncbi.nlm.nih.gov/gene/?term=218544	C630001O05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006043	21855	Timm17b	http://www.ncbi.nlm.nih.gov/gene/?term=21855	"17kDa, Sfc3, mTim17b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006044	218581	Depdc1b	http://www.ncbi.nlm.nih.gov/gene/?term=218581	"9830132O03, AW260467, XTP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006045	218629	Dhx29	http://www.ncbi.nlm.nih.gov/gene/?term=218629	"3732415M03, AU043276, Ddxx, E130202M19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006046	218693	Paip1	http://www.ncbi.nlm.nih.gov/gene/?term=218693	PAIP-1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006047	2186	BPTF	http://www.ncbi.nlm.nih.gov/gene/?term=2186	"FAC1, FALZ, NURF301 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006048	2186	BPTF	http://www.ncbi.nlm.nih.gov/gene/?term=2186	"FAC1, FALZ, NURF301 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006049	2186	BPTF	http://www.ncbi.nlm.nih.gov/gene/?term=2186	"FAC1, FALZ, NURF301 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006050	218756	Slc4a7	http://www.ncbi.nlm.nih.gov/gene/?term=218756	"E430014N10Rik, NBC3, NBCn1, NBCn1-G "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006051	21885	Tle1	http://www.ncbi.nlm.nih.gov/gene/?term=21885	"C230057C06Rik, Estm14, Grg-1, Grg1, Tle4l "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006052	21888	Tle4	http://www.ncbi.nlm.nih.gov/gene/?term=21888	"5730411M05Rik, AA792082, Bce-1, Bce1, ESTM13, ESTM14, Grg4, X83332, X83333, grg-4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006053	2188	FANCF	http://www.ncbi.nlm.nih.gov/gene/?term=2188	FAF	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006054	2188	FANCF	http://www.ncbi.nlm.nih.gov/gene/?term=2188	FAF	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006055	218914	Wapl	http://www.ncbi.nlm.nih.gov/gene/?term=218914	"A530089A20Rik, BC037674, DIF-2, FOE, Wapal "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006056	2189	FANCG	http://www.ncbi.nlm.nih.gov/gene/?term=2189	"FAG, XRCC9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006057	2189	FANCG	http://www.ncbi.nlm.nih.gov/gene/?term=2189	"FAG, XRCC9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006058	2189	FANCG	http://www.ncbi.nlm.nih.gov/gene/?term=2189	"FAG, XRCC9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006059	218	ALDH3A1	http://www.ncbi.nlm.nih.gov/gene/?term=218	"ALDH3, ALDHIII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006060	219103	Cenpj	http://www.ncbi.nlm.nih.gov/gene/?term=219103	"4932437H03Rik, CPAP, Gm81, LAP, LIP1, Sas4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006061	219131	Phf11a	http://www.ncbi.nlm.nih.gov/gene/?term=219131	"4933417L10Rik, Phf11, Phf11l "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006062	219144	Arl11	http://www.ncbi.nlm.nih.gov/gene/?term=219144	"ARLTS1, C730007L20Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006063	2191	FAP	http://www.ncbi.nlm.nih.gov/gene/?term=2191	"DPPIV, FAPA, SIMP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006064	219228	Pcdh17	http://www.ncbi.nlm.nih.gov/gene/?term=219228	"C030033F14Rik, Gm78 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006065	219249	Tdrd3	http://www.ncbi.nlm.nih.gov/gene/?term=219249	"4732418C03Rik, 6720468N18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006066	219257	Pcdh20	http://www.ncbi.nlm.nih.gov/gene/?term=219257	"C630015B17Rik, Pcdh13 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006067	219293	ATAD3C	http://www.ncbi.nlm.nih.gov/gene/?term=219293		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006068	219293	ATAD3C	http://www.ncbi.nlm.nih.gov/gene/?term=219293		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006069	219333	USP12	http://www.ncbi.nlm.nih.gov/gene/?term=219333	"UBH1, USP12L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006070	21934	Tnfrsf11a	http://www.ncbi.nlm.nih.gov/gene/?term=21934	"Ly109, ODFR, OFE, Rank, TRANCE-R, mRANK "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006071	21938	Tnfrsf1b	http://www.ncbi.nlm.nih.gov/gene/?term=21938	"CD120b, TNF-R-II, TNF-R2, TNF-R75, TNF-alphaR2, TNFBR, TNFR80, TNFRII, TNFalpha-R2, Tnfr-1, Tnfr2, p75 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006072	2193	FARSA	http://www.ncbi.nlm.nih.gov/gene/?term=2193	"CML33, FARSL, FARSLA, FRSA, PheHA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006073	2193	FARSA	http://www.ncbi.nlm.nih.gov/gene/?term=2193	"CML33, FARSL, FARSLA, FRSA, PheHA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006074	2193	FARSA	http://www.ncbi.nlm.nih.gov/gene/?term=2193	"CML33, FARSL, FARSLA, FRSA, PheHA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006075	219402	MTIF3	http://www.ncbi.nlm.nih.gov/gene/?term=219402	IF3mt	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006076	219402	MTIF3	http://www.ncbi.nlm.nih.gov/gene/?term=219402	IF3mt	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006077	21940	Cd27	http://www.ncbi.nlm.nih.gov/gene/?term=21940	"S152, Tnfrsf7, Tp55 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006078	2194	FASN	http://www.ncbi.nlm.nih.gov/gene/?term=2194	"FAS, OA-519, SDR27X1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006079	2194	FASN	http://www.ncbi.nlm.nih.gov/gene/?term=2194	"FAS, OA-519, SDR27X1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006080	219539	YPEL4	http://www.ncbi.nlm.nih.gov/gene/?term=219539		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006081	219557	C7orf62	http://www.ncbi.nlm.nih.gov/gene/?term=219557		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006082	2195	FAT1	http://www.ncbi.nlm.nih.gov/gene/?term=2195	"CDHF7, CDHR8, FAT, ME5, hFat1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006083	2195	FAT1	http://www.ncbi.nlm.nih.gov/gene/?term=2195	"CDHF7, CDHR8, FAT, ME5, hFat1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006084	21969	Top1	http://www.ncbi.nlm.nih.gov/gene/?term=21969	"AI467334, D130064I21Rik, Top-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006085	2196	FAT2	http://www.ncbi.nlm.nih.gov/gene/?term=2196	"CDHF8, CDHR9, HFAT2, MEGF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006086	219736	STOX1	http://www.ncbi.nlm.nih.gov/gene/?term=219736	"C10orf24, PEE4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006087	21973	Top2a	http://www.ncbi.nlm.nih.gov/gene/?term=21973	Top-2	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006088	219743	TYSND1	http://www.ncbi.nlm.nih.gov/gene/?term=219743	NET41	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006089	219743	TYSND1	http://www.ncbi.nlm.nih.gov/gene/?term=219743	NET41	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006090	219743	TYSND1	http://www.ncbi.nlm.nih.gov/gene/?term=219743	NET41	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006091	21974	Top2b	http://www.ncbi.nlm.nih.gov/gene/?term=21974	"D230016L12Rik, Top-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006092	219771	CCNY	http://www.ncbi.nlm.nih.gov/gene/?term=219771	"C10orf9, CBCP1, CCNX, CFP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006093	219771	CCNY	http://www.ncbi.nlm.nih.gov/gene/?term=219771	"C10orf9, CBCP1, CCNX, CFP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006094	219790	RTKN2	http://www.ncbi.nlm.nih.gov/gene/?term=219790	"PLEKHK1, bA531F24.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006095	2197	FAU	http://www.ncbi.nlm.nih.gov/gene/?term=2197	"FAU1, Fub1, Fubi, MNSFbeta, RPS30, S30, asr1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006096	2197	FAU	http://www.ncbi.nlm.nih.gov/gene/?term=2197	"FAU1, Fub1, Fubi, MNSFbeta, RPS30, S30, asr1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006097	2197	FAU	http://www.ncbi.nlm.nih.gov/gene/?term=2197	"FAU1, Fub1, Fubi, MNSFbeta, RPS30, S30, asr1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006098	21982	Tmem165	http://www.ncbi.nlm.nih.gov/gene/?term=21982	"AV026557, Tpardl, Tparl, pFT27 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006099	219854	TMEM218	http://www.ncbi.nlm.nih.gov/gene/?term=219854		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006100	219899	TBCEL	http://www.ncbi.nlm.nih.gov/gene/?term=219899	"El, LRRC35 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006101	219902	TMEM136	http://www.ncbi.nlm.nih.gov/gene/?term=219902		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006102	21990	Tph1	http://www.ncbi.nlm.nih.gov/gene/?term=21990	Tph	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006103	219927	MRPL21	http://www.ncbi.nlm.nih.gov/gene/?term=219927	"L21mt, MRP-L21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006104	219927	MRPL21	http://www.ncbi.nlm.nih.gov/gene/?term=219927	"L21mt, MRP-L21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006105	219988	PATL1	http://www.ncbi.nlm.nih.gov/gene/?term=219988	"Pat1b, hPat1b "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006106	219988	PATL1	http://www.ncbi.nlm.nih.gov/gene/?term=219988	"Pat1b, hPat1b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006107	219988	PATL1	http://www.ncbi.nlm.nih.gov/gene/?term=219988	"Pat1b, hPat1b "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006108	2199	FBLN2	http://www.ncbi.nlm.nih.gov/gene/?term=2199		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006109	219	ALDH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=219	"ALDH5, ALDHX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006110	219	ALDH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=219	"ALDH5, ALDHX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006111	219	ALDH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=219	"ALDH5, ALDHX "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006112	219	ALDH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=219	"ALDH5, ALDHX "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006113	21	ABCA3	http://www.ncbi.nlm.nih.gov/gene/?term=21	"ABC-C, ABC3, EST111653, LBM180, SMDP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006114	220002	CYB561A3	http://www.ncbi.nlm.nih.gov/gene/?term=220002	"CYBASC3, LCYTB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006115	22003	Tpm1	http://www.ncbi.nlm.nih.gov/gene/?term=22003	"AA986836, AI854628, TM2, Tm3, Tmpa, Tpm-1, alpha-TM "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00006116	220064	ORAOV1	http://www.ncbi.nlm.nih.gov/gene/?term=220064	TAOS1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006117	220064	ORAOV1	http://www.ncbi.nlm.nih.gov/gene/?term=220064	TAOS1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006118	220074	LRTOMT	http://www.ncbi.nlm.nih.gov/gene/?term=220074	"CFAP111, DFNB63, LRRC51 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006119	220074	LRTOMT	http://www.ncbi.nlm.nih.gov/gene/?term=220074	"CFAP111, DFNB63, LRRC51 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006120	220074	LRTOMT	http://www.ncbi.nlm.nih.gov/gene/?term=220074	"CFAP111, DFNB63, LRRC51 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006121	220074	LRTOMT	http://www.ncbi.nlm.nih.gov/gene/?term=220074	"CFAP111, DFNB63, LRRC51 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006122	2200	FBN1	http://www.ncbi.nlm.nih.gov/gene/?term=2200	"ACMICD, ECTOL1, FBN, GPHYSD2, MASS, MFS1, OCTD, SGS, SSKS, WMS, WMS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006123	220134	SKA1	http://www.ncbi.nlm.nih.gov/gene/?term=220134	C18orf24	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006124	220134	SKA1	http://www.ncbi.nlm.nih.gov/gene/?term=220134	C18orf24	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006125	220134	SKA1	http://www.ncbi.nlm.nih.gov/gene/?term=220134	C18orf24	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006126	220134	SKA1	http://www.ncbi.nlm.nih.gov/gene/?term=220134	C18orf24	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006127	220164	DOK6	http://www.ncbi.nlm.nih.gov/gene/?term=220164	"DOK5L, HsT3226 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006128	22019	Tpp2	http://www.ncbi.nlm.nih.gov/gene/?term=22019	"TPP-2, TppII "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006129	2201	FBN2	http://www.ncbi.nlm.nih.gov/gene/?term=2201	"CCA, DA9, EOMD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006130	220213	OTUD1	http://www.ncbi.nlm.nih.gov/gene/?term=220213	"DUBA7, OTDC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006131	22021	Tpst1	http://www.ncbi.nlm.nih.gov/gene/?term=22021	"R75054, Tango13a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006132	22026	Nr2c2	http://www.ncbi.nlm.nih.gov/gene/?term=22026	"TAK1, Tr4, mKIAA4145 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006133	22026	Nr2c2	http://www.ncbi.nlm.nih.gov/gene/?term=22026	"TAK1, Tr4, mKIAA4145 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006134	22027	Hsp90b1	http://www.ncbi.nlm.nih.gov/gene/?term=22027	"TA-3, Tra1, gp96, ERp99, GRP94, Targ2, Tra-1, endoplasmin "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00006135	22027	Hsp90b1	http://www.ncbi.nlm.nih.gov/gene/?term=22027	"ERp99, GRP94, TA-3, Targ2, Tra-1, Tra1, endoplasmin, gp96 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006136	22027	Hsp90b1	http://www.ncbi.nlm.nih.gov/gene/?term=22027	"ERp99, GRP94, TA-3, Targ2, Tra-1, Tra1, endoplasmin, gp96 "	mRNA	Mus musculus	12923260	Endoplasmic reticulum	B cell	Northern blot	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61α and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00006137	22027	Hsp90b1	http://www.ncbi.nlm.nih.gov/gene/?term=22027	"ERp99, GRP94, TA-3, Targ2, Tra-1, Tra1, endoplasmin, gp96 "	mRNA	Mus musculus	12923260	Endoplasmic reticulum	NIH-3T3 Fibroblast	In situ hybridization	"For these experiments, three mRNAs were examined: that encoding GRP94, which is highly enriched in the ER membrane fraction of fractionated cells; GAPDH, which displays a predominately (but not uniquely) soluble enrichment; and Hsp90, which displays noncanonical partitioning on the ER. Experiments were performed using NIH-3T3 fibroblasts and digoxygenin-labeled antisense RNA probes, with optical sections obtained by widefield microscopy.As expected, mRNAs encoding GRP94 display a typical, perinuclear and reticular ER pattern (Fig. 6A), with the ImageJ rendering providing a graphical display of the perinuclear, ER partitioning of this mRNA species (Fig. 6A, far right panel). "
RLID00006138	22027	Hsp90b1	http://www.ncbi.nlm.nih.gov/gene/?term=22027	"ERp99, GRP94, TA-3, Targ2, Tra-1, Tra1, endoplasmin, gp96 "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. mRNAs for resident proteins of the ER lumen, including BiP, calreticulin, and GRP94, were also highly enriched on membrane-bound polysomes. "
RLID00006139	2202	EFEMP1	http://www.ncbi.nlm.nih.gov/gene/?term=2202	"DHRD, DRAD, FBLN3, FBNL, FIBL-3, MLVT, MTLV, S1-5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006140	22031	Traf3	http://www.ncbi.nlm.nih.gov/gene/?term=22031	"AI528849, CAP-1, CD40bp, CRAF1, LAP1, T-BAM, amn "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006141	220323	OAF	http://www.ncbi.nlm.nih.gov/gene/?term=220323	NS5ATP13TP2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006142	220323	OAF	http://www.ncbi.nlm.nih.gov/gene/?term=220323	NS5ATP13TP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006143	22032	Traf4	http://www.ncbi.nlm.nih.gov/gene/?term=22032	"A530032M13Rik, CART1, msp2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006144	22034	Traf6	http://www.ncbi.nlm.nih.gov/gene/?term=22034	"2310003F17Rik, AI851288, C630032O20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006145	220359	TIGD3	http://www.ncbi.nlm.nih.gov/gene/?term=220359		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006146	22042	Tfrc	http://www.ncbi.nlm.nih.gov/gene/?term=22042	"2610028K12Rik, CD71, E430033M20Rik, Mtvr1, TFR, TFR1, TR, Trfr, p90 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006147	22042	Tfrc	http://www.ncbi.nlm.nih.gov/gene/?term=22042	"2610028K12Rik, CD71, E430033M20Rik, Mtvr1, TFR, TFR1, TR, Trfr, p90 "	mRNA	Mus musculus	7493976	Endoplasmic reticulum	Fibroblast	Northern blot	Here we demonstrate that part of the active IRP co-localizes with TfR mRNA to the rough endoplasmic reticulum.
RLID00006148	22042	Tfrc	http://www.ncbi.nlm.nih.gov/gene/?term=22042	"2610028K12Rik, CD71, E430033M20Rik, Mtvr1, TFR, TFR1, TR, Trfr, p90 "	mRNA	Mus musculus	9367630	Nucleus	Muscle cell	In situ hybridization	In situ hybridization of myotubes of the mouse muscle cell line C2 shows that TfR mRNA is concentrated in the core of the myotubes. Its distribution around the nuclei is often asymmetric and its concentration changes abruptly.
RLID00006149	2204	FCAR	http://www.ncbi.nlm.nih.gov/gene/?term=2204	"CD89, CTB-61M7.2, FcalphaRI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006150	2204	FCAR	http://www.ncbi.nlm.nih.gov/gene/?term=2204	"CD89, CTB-61M7.2, FcalphaRI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006151	22051	Trip6	http://www.ncbi.nlm.nih.gov/gene/?term=22051		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006152	22067	Trpc5	http://www.ncbi.nlm.nih.gov/gene/?term=22067	"CCE2, TRP-5, TRP5, Trrp5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006153	2207	FCER1G	http://www.ncbi.nlm.nih.gov/gene/?term=2207	FCRG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006154	22083	Ctr9	http://www.ncbi.nlm.nih.gov/gene/?term=22083	"AA409336, Sh2bp1, Tsbp, Tsp, mKIAA0155 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006155	220869	CBWD5	http://www.ncbi.nlm.nih.gov/gene/?term=220869	DC36	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006156	220869	CBWD5	http://www.ncbi.nlm.nih.gov/gene/?term=220869	DC36	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006157	220963	SLC16A9	http://www.ncbi.nlm.nih.gov/gene/?term=220963	"C10orf36, MCT9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006158	220965	FAM13C	http://www.ncbi.nlm.nih.gov/gene/?term=220965	FAM13C1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006159	220972	MARCH8	http://www.ncbi.nlm.nih.gov/gene/?term=220972	"CMIR, MARCH-VIII, MIR, RNF178, c-MIR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006160	22097	Tsix	http://www.ncbi.nlm.nih.gov/gene/?term=22097		lncRNA	Mus musculus	12900552	Nucleus	Embryonic stem cell	In situ hybridization|RT-PCR	"On the active male X chromosome, the XIST and TSIX genes are transcribed in undifferentiated cells of pre-implantation embryos (undifferentiated state) and then down-regulated upon cell differentiation (differentiated state). "
RLID00006161	220988	HNRNPA3	http://www.ncbi.nlm.nih.gov/gene/?term=220988	"2610510D13Rik, D10S102, FBRNP, HNRPA3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006162	220988	HNRNPA3	http://www.ncbi.nlm.nih.gov/gene/?term=220988	"2610510D13Rik, D10S102, FBRNP, HNRPA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006163	22099	Tsn	http://www.ncbi.nlm.nih.gov/gene/?term=22099	"2610034C24Rik, AU040286, C3PO, TB-RBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006164	221002	RASGEF1A	http://www.ncbi.nlm.nih.gov/gene/?term=221002	CG4853	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006165	221035	REEP3	http://www.ncbi.nlm.nih.gov/gene/?term=221035	"C10orf74, Yip2b "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006166	221035	REEP3	http://www.ncbi.nlm.nih.gov/gene/?term=221035	"C10orf74, Yip2b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006167	221037	JMJD1C	http://www.ncbi.nlm.nih.gov/gene/?term=221037	"TRIP-8, TRIP8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006168	221037	JMJD1C	http://www.ncbi.nlm.nih.gov/gene/?term=221037	"TRIP-8, TRIP8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006169	221079	ARL5B	http://www.ncbi.nlm.nih.gov/gene/?term=221079	ARL8	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006170	221120	ALKBH3	http://www.ncbi.nlm.nih.gov/gene/?term=221120	"ABH3, DEPC-1, DEPC1, PCA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006171	221150	SKA3	http://www.ncbi.nlm.nih.gov/gene/?term=221150	"C13orf3, RAMA1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006172	22115	Tssk2	http://www.ncbi.nlm.nih.gov/gene/?term=22115	"DGS-G, SPOGA2, Stk22b, Tsk2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006173	22116	Tsks	http://www.ncbi.nlm.nih.gov/gene/?term=22116	"Stk22s1, Tssks1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006174	221178	SPATA13	http://www.ncbi.nlm.nih.gov/gene/?term=221178	"ARHGEF29, ASEF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006175	22117	Tst	http://www.ncbi.nlm.nih.gov/gene/?term=22117	Rhodanese	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006176	221188	ADGRG5	http://www.ncbi.nlm.nih.gov/gene/?term=221188	"GPR114, PGR27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006177	22121	Rpl13a	http://www.ncbi.nlm.nih.gov/gene/?term=22121	"1810026N22Rik, Tstap198-7, tum-antigen "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006178	221294	NT5DC1	http://www.ncbi.nlm.nih.gov/gene/?term=221294	"C6orf200, LP2642, NT5C2L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006179	221294	NT5DC1	http://www.ncbi.nlm.nih.gov/gene/?term=221294	"C6orf200, LP2642, NT5C2L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006180	2212	FCGR2A	http://www.ncbi.nlm.nih.gov/gene/?term=2212	"CD32, CD32A, CDw32, FCG2, FCGR2, FCGR2A1, FcGR, IGFR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006181	2212	FCGR2A	http://www.ncbi.nlm.nih.gov/gene/?term=2212	"CD32, CD32A, CDw32, FCG2, FCGR21, FcGR, IGFR2, FCGR2A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006182	2212	FCGR2A	http://www.ncbi.nlm.nih.gov/gene/?term=2212	"CD32, CD32A, CDw32, FCG2, FCGR21, FcGR, IGFR2, FCGR2A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006183	221302	ZUFSP	http://www.ncbi.nlm.nih.gov/gene/?term=221302	"C6orf113, dJ412I7.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006184	22130	Ttf1	http://www.ncbi.nlm.nih.gov/gene/?term=22130	"AV245725, TTF-1, TTF-I "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006185	22135	Tgoln2	http://www.ncbi.nlm.nih.gov/gene/?term=22135	"TGN38B, TGN41, TGN46, Ttgn2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006186	22137	Ttk	http://www.ncbi.nlm.nih.gov/gene/?term=22137	"AL022661, Esk1, Mps1, PYT, esk "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006187	221395	ADGRF5	http://www.ncbi.nlm.nih.gov/gene/?term=221395	"GPR116, KPG_001 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006188	2213	FCGR2B	http://www.ncbi.nlm.nih.gov/gene/?term=2213	"CD32, CD32B, FCG2, FCGR2, IGFR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006189	221400	TDRD6	http://www.ncbi.nlm.nih.gov/gene/?term=221400	"CT41.2, NY-CO-45, SPATA36, TDR2, bA446F17.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006190	22143	Tuba1b	http://www.ncbi.nlm.nih.gov/gene/?term=22143	Tuba2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006191	221443	OARD1	http://www.ncbi.nlm.nih.gov/gene/?term=221443	"C6orf130, TARG1, dJ34B21.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006192	22145	Tuba4a	http://www.ncbi.nlm.nih.gov/gene/?term=22145	"M[a]4, Tuba4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006193	22145	Tuba4a	http://www.ncbi.nlm.nih.gov/gene/?term=22145	"M[a]4, Tuba4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006194	221472	FGD2	http://www.ncbi.nlm.nih.gov/gene/?term=221472	ZFYVE4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006195	221472	FGD2	http://www.ncbi.nlm.nih.gov/gene/?term=221472	ZFYVE4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006196	221472	FGD2	http://www.ncbi.nlm.nih.gov/gene/?term=221472	ZFYVE4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006197	221477	C6orf89	http://www.ncbi.nlm.nih.gov/gene/?term=221477	BRAP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006198	221477	C6orf89	http://www.ncbi.nlm.nih.gov/gene/?term=221477	BRAP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006199	221491	C6orf1	http://www.ncbi.nlm.nih.gov/gene/?term=221491	LBH	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006200	221496	LEMD2	http://www.ncbi.nlm.nih.gov/gene/?term=221496	"NET25, dJ482C21.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006201	2214	FCGR3A	http://www.ncbi.nlm.nih.gov/gene/?term=2214	"CD16, CD16A, FCG3, FCGR3, FCGRIII, FCR-10, FCRIII, FCRIIIA, IGFR3, IMD20 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006202	221545	C6orf136	http://www.ncbi.nlm.nih.gov/gene/?term=221545		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006203	22160	Twist1	http://www.ncbi.nlm.nih.gov/gene/?term=22160	"M-Twist, Pde, Ska10, Ska<m10Jus>, Twist, bHLHa38, pdt "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006204	221656	KDM1B	http://www.ncbi.nlm.nih.gov/gene/?term=221656	"AOF1, C6orf193, LSD2, bA204B7.3, dJ298J15.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006205	221656	KDM1B	http://www.ncbi.nlm.nih.gov/gene/?term=221656	"AOF1, C6orf193, LSD2, bA204B7.3, dJ298J15.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006206	221785	ZSCAN25	http://www.ncbi.nlm.nih.gov/gene/?term=221785	ZNF498	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006207	2217	FCGRT	http://www.ncbi.nlm.nih.gov/gene/?term=2217	"FCRN, alpha-chain "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006208	2217	FCGRT	http://www.ncbi.nlm.nih.gov/gene/?term=2217	"FCRN, alpha-chain "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006209	221830	TWISTNB	http://www.ncbi.nlm.nih.gov/gene/?term=221830		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006210	221830	TWISTNB	http://www.ncbi.nlm.nih.gov/gene/?term=221830		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006211	22183	Zrsr1	http://www.ncbi.nlm.nih.gov/gene/?term=22183	"D11Ncvs75, Irlgs2, SP2, U2af1-rs1, U2afbp-rs "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006212	22186	Uba52	http://www.ncbi.nlm.nih.gov/gene/?term=22186	"D8Ertd21e, Gm1863, Rps27a, Ubb, Ubc "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006213	22186	Uba52	http://www.ncbi.nlm.nih.gov/gene/?term=22186	"D8Ertd21e, Gm1863, Rps27a, Ubb, Ubc "	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00006214	22187	Ubb	http://www.ncbi.nlm.nih.gov/gene/?term=22187	"AL033289, Rps27a, Uba522, Ubc, Ubb "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006215	22187	Ubb	http://www.ncbi.nlm.nih.gov/gene/?term=22187	"AL033289, Rps27a, Uba522, Ubc, Ubb "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00006216	2218	FKTN	http://www.ncbi.nlm.nih.gov/gene/?term=2218	"CMD1X, FCMD, LGMD2M, MDDGA4, MDDGB4, MDDGC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006217	2218	FKTN	http://www.ncbi.nlm.nih.gov/gene/?term=2218	"CMD1X, FCMD, LGMD2M, MDDGA4, MDDGB4, MDDGC4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006218	2218	FKTN	http://www.ncbi.nlm.nih.gov/gene/?term=2218	"CMD1X, FCMD, LGMD2M, MDDGA4, MDDGB4, MDDGC4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006219	221908	PPP1R35	http://www.ncbi.nlm.nih.gov/gene/?term=221908	C7orf47	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006220	221908	PPP1R35	http://www.ncbi.nlm.nih.gov/gene/?term=221908	C7orf47	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006221	221927	BRAT1	http://www.ncbi.nlm.nih.gov/gene/?term=221927	"BAAT1, C7orf27, RMFSL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006222	221937	FOXK1	http://www.ncbi.nlm.nih.gov/gene/?term=221937	FOXK1L	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006223	221937	FOXK1	http://www.ncbi.nlm.nih.gov/gene/?term=221937	FOXK1L	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006224	221937	FOXK1	http://www.ncbi.nlm.nih.gov/gene/?term=221937	FOXK1L	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006225	221937	FOXK1	http://www.ncbi.nlm.nih.gov/gene/?term=221937	FOXK1L	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006226	221955	DAGLB	http://www.ncbi.nlm.nih.gov/gene/?term=221955	"DAGLBETA, KCCR13L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006227	22195	Ube2l3	http://www.ncbi.nlm.nih.gov/gene/?term=22195	"C79827, UbcM4, Ubce7 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006228	221960	CCZ1B	http://www.ncbi.nlm.nih.gov/gene/?term=221960	"C7orf28B, H_NH0577018.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006229	22196	Ube2i	http://www.ncbi.nlm.nih.gov/gene/?term=22196	"5830467E05Rik, F830028O17Rik, UBC9, Ubce2i, Ubce9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006230	221981	THSD7A	http://www.ncbi.nlm.nih.gov/gene/?term=221981		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006231	221	ALDH3B1	http://www.ncbi.nlm.nih.gov/gene/?term=221	"ALDH4, ALDH7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006232	22200	Uba3	http://www.ncbi.nlm.nih.gov/gene/?term=22200	"A830034N06Rik, AI256736, AI848246, AW546539, Ube1c "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006233	222068	TMED4	http://www.ncbi.nlm.nih.gov/gene/?term=222068	"ERS25, GMP25iso, HNLF, p24a3, p24alpha3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006234	222068	TMED4	http://www.ncbi.nlm.nih.gov/gene/?term=222068	"ERS25, GMP25iso, HNLF, p24a3, p24alpha3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006235	22210	Ube2b	http://www.ncbi.nlm.nih.gov/gene/?term=22210	"2610301N02Rik, E2-14k, HR6B, Rad6b, mHR6B "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006236	22213	Ube2g2	http://www.ncbi.nlm.nih.gov/gene/?term=22213	"1110003O05Rik, D10Xrf369, UBC7, Ubc7p "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006237	22215	Ube3a	http://www.ncbi.nlm.nih.gov/gene/?term=22215	"4732496B02, 5830462N02Rik, A130086L21Rik, Hpve6a, mKIAA4216 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006238	222166	MTURN	http://www.ncbi.nlm.nih.gov/gene/?term=222166	"C7orf41, Ells1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006239	222171	PRR15	http://www.ncbi.nlm.nih.gov/gene/?term=222171		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006240	222194	RSBN1L	http://www.ncbi.nlm.nih.gov/gene/?term=222194		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006241	222194	RSBN1L	http://www.ncbi.nlm.nih.gov/gene/?term=222194		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006242	222194	RSBN1L	http://www.ncbi.nlm.nih.gov/gene/?term=222194		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006243	222229	LRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=222229	"CENP-33, ORCA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006244	22222	Ubr1	http://www.ncbi.nlm.nih.gov/gene/?term=22222	AI504731	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006245	222236	NAPEPLD	http://www.ncbi.nlm.nih.gov/gene/?term=222236	"FMP30, NAPE-PLD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006246	22223	Uchl1	http://www.ncbi.nlm.nih.gov/gene/?term=22223	"AW822034, C88048, PGP 9.5, PGP9.5, R75593, UCH-L1, UCHL-1, gad "	lncRNA	Mus musculus	23064229	Cytoplasm	MN9D cell	qRT-PCR|In situ hybridizationq|Northern blot	"Antisense Uchl1 function is under the control of stress signalling pathways, as mTORC1 inhibition by rapamycin causes an increase in UCHL1 protein that is associated to the shuttling of antisense Uchl1 RNA from the nucleus to the cytoplasm.  "
RLID00006247	22223	Uchl1	http://www.ncbi.nlm.nih.gov/gene/?term=22223	"AW822034, C88048, PGP 9.5, PGP9.5, R75593, UCH-L1, UCHL-1, gad "	lncRNA	Mus musculus	23064229	Nucleus	MN9D cell	qRT-PCR|In situ hybridizationq|Northern blot	"Antisense Uchl1 function is under the control of stress signalling pathways, as mTORC1 inhibition by rapamycin causes an increase in UCHL1 protein that is associated to the shuttling of antisense Uchl1 RNA from the nucleus to the cytoplasm.  "
RLID00006248	222255	ATXN7L1	http://www.ncbi.nlm.nih.gov/gene/?term=222255	ATXN7L4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006249	22225	Usp5	http://www.ncbi.nlm.nih.gov/gene/?term=22225	"AA407472, ISOT, ISOT-1, Ucht "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006250	2222	FDFT1	http://www.ncbi.nlm.nih.gov/gene/?term=2222	"DGPT, ERG9, SQS, SS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006251	2222	FDFT1	http://www.ncbi.nlm.nih.gov/gene/?term=2222	"DGPT, ERG9, SQS, SS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006252	22230	Ufd1l	http://www.ncbi.nlm.nih.gov/gene/?term=22230	Ufd1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006253	22234	Ugcg	http://www.ncbi.nlm.nih.gov/gene/?term=22234	"AU043821, C80537, Epcs21, GlcT-1l, Ugcg "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006254	22235	Ugdh	http://www.ncbi.nlm.nih.gov/gene/?term=22235	Udpgdh	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006255	22240	Dpysl3	http://www.ncbi.nlm.nih.gov/gene/?term=22240	"CRMP-4, DRP-3, TUC4, ULIP-1, Ulip, Ulip1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006256	22240	Dpysl3	http://www.ncbi.nlm.nih.gov/gene/?term=22240	"CRMP-4, DRP-3, TUC4, ULIP-1, Ulip, Ulip1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006257	222484	LNX2	http://www.ncbi.nlm.nih.gov/gene/?term=222484	PDZRN1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006258	222484	LNX2	http://www.ncbi.nlm.nih.gov/gene/?term=222484	PDZRN1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006259	22248	Unc119	http://www.ncbi.nlm.nih.gov/gene/?term=22248	"D11Bhm52, HRG4, MRG4, Rg4, Rtg4h, Unc119 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006260	2224	FDPS	http://www.ncbi.nlm.nih.gov/gene/?term=2224	"FPPS, FPS, POROK9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006261	2224	FDPS	http://www.ncbi.nlm.nih.gov/gene/?term=2224	"FPPS, FPS, POROK9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006262	2224	FDPS	http://www.ncbi.nlm.nih.gov/gene/?term=2224	"FPPS, FPS, POROK9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006263	22253	Unc5c	http://www.ncbi.nlm.nih.gov/gene/?term=22253	"B130051O18Rik, Unc5h3, rcm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006264	222553	SLC35F1	http://www.ncbi.nlm.nih.gov/gene/?term=222553	"C6orf169, dJ230I3.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006265	222553	SLC35F1	http://www.ncbi.nlm.nih.gov/gene/?term=222553	"C6orf169, dJ230I3.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006266	22259	Nr1h3	http://www.ncbi.nlm.nih.gov/gene/?term=22259	"AU018371, LXR, RLD1, Unr1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006267	222643	UNC5CL	http://www.ncbi.nlm.nih.gov/gene/?term=222643	"MUXA, ZUD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006268	222658	KCTD20	http://www.ncbi.nlm.nih.gov/gene/?term=222658	"C6orf69, dJ108K11.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006269	222658	KCTD20	http://www.ncbi.nlm.nih.gov/gene/?term=222658	"C6orf69, dJ108K11.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006270	22271	Upp1	http://www.ncbi.nlm.nih.gov/gene/?term=22271	"AI325217, UPase, UdRPase, Up, Upp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006271	22275	Urod	http://www.ncbi.nlm.nih.gov/gene/?term=22275	"AI323803, UPD, Uro-d "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006272	22284	Usp9x	http://www.ncbi.nlm.nih.gov/gene/?term=22284	"5730589N07Rik, AA407302, AA407699, AL022658, AL022749, Dffrx, FAF-X, Fafl "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006273	222865	TMEM130	http://www.ncbi.nlm.nih.gov/gene/?term=222865		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006274	22288	Utrn	http://www.ncbi.nlm.nih.gov/gene/?term=22288	"AA589569, DRP, Dmdl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006275	222962	SLC29A4	http://www.ncbi.nlm.nih.gov/gene/?term=222962	"ENT4, PMAT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006276	22297	Vmn1r45	http://www.ncbi.nlm.nih.gov/gene/?term=22297	"V1RA9, V1r2, V1ra11, V1ra2, mV1R2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006277	223082	ZNRF2	http://www.ncbi.nlm.nih.gov/gene/?term=223082	RNF202	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006278	2230	FDX1	http://www.ncbi.nlm.nih.gov/gene/?term=2230	"ADX, FDX, LOH11CR1D "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006279	2230	FDX1	http://www.ncbi.nlm.nih.gov/gene/?term=2230	"ADX, FDX, LOH11CR1D "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006280	22310	Vmn2r42	http://www.ncbi.nlm.nih.gov/gene/?term=22310	V2r4	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006281	223117	SEMA3D	http://www.ncbi.nlm.nih.gov/gene/?term=223117	"Sema-Z2, coll-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006282	223117	SEMA3D	http://www.ncbi.nlm.nih.gov/gene/?term=223117	"Sema-Z2, coll-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006283	22311	Vmn2r32	http://www.ncbi.nlm.nih.gov/gene/?term=22311	V2r5	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006284	22317	Vamp1	http://www.ncbi.nlm.nih.gov/gene/?term=22317	"Syb-1, Syb1, VAMP-1, lew "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006285	22318	Vamp2	http://www.ncbi.nlm.nih.gov/gene/?term=22318	"Syb-2, Syb2, sybII "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006286	22320	Vamp8	http://www.ncbi.nlm.nih.gov/gene/?term=22320	"AU041171, Edb, endobrevin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006287	2232	FDXR	http://www.ncbi.nlm.nih.gov/gene/?term=2232	ADXR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006288	22330	Vcl	http://www.ncbi.nlm.nih.gov/gene/?term=22330	"9430097D22, AA571387, AI462105, AW545629 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006289	223337	Ugt3a2	http://www.ncbi.nlm.nih.gov/gene/?term=223337	AI313915	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006290	22339	Vegfa	http://www.ncbi.nlm.nih.gov/gene/?term=22339	"Vegf, Vpf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006291	22341	Vegfc	http://www.ncbi.nlm.nih.gov/gene/?term=22341	"AW228853, VEGF-C "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006292	22344	Vezf1	http://www.ncbi.nlm.nih.gov/gene/?term=22344	"AI848691, AW046909, db1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006293	223455	March6	http://www.ncbi.nlm.nih.gov/gene/?term=223455	"3830408G03, F830029L24Rik, mKIAA0597 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006294	223499	Dcaf13	http://www.ncbi.nlm.nih.gov/gene/?term=223499	"Gm83, Wdsof1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006295	223499	Dcaf13	http://www.ncbi.nlm.nih.gov/gene/?term=223499	"Gm83, Wdsof1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006296	22349	Vil1	http://www.ncbi.nlm.nih.gov/gene/?term=22349	Vil	mRNA	Mus musculus	8026647	Apical	Enterocytes	In situ hybridization	"In adult tissues, however, each mRNA species was associated with a specific compartment (Fig. 6B). In the apical cytoplasm, mRNAs coding for brush-border NEP were concentrated closer to the nucleus than those encoding for villin, which were localized in a more apical region of the cytoplasm. "
RLID00006297	223593	E430025E21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=223593	"AL022848, C76463, Kiaa0196, mKIAA0196, strumpellin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006298	2235	FECH	http://www.ncbi.nlm.nih.gov/gene/?term=2235	"EPP, FCE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006299	2235	FECH	http://www.ncbi.nlm.nih.gov/gene/?term=2235	"EPP, FCE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006300	2235	FECH	http://www.ncbi.nlm.nih.gov/gene/?term=2235	"EPP, FCE "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006301	2235	FECH	http://www.ncbi.nlm.nih.gov/gene/?term=2235	"EPP, FCE "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006302	223601	Fam49b	http://www.ncbi.nlm.nih.gov/gene/?term=223601	"0910001A06Rik, AW122079 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006303	22360	Nrsn1	http://www.ncbi.nlm.nih.gov/gene/?term=22360	"Neurensin-1, Neuro-p24, Vmp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006304	223626	Them6	http://www.ncbi.nlm.nih.gov/gene/?term=223626	4930572J05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006305	223646	Naprt	http://www.ncbi.nlm.nih.gov/gene/?term=223646	"9130210N20Rik1, Naprt "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006306	223664	Lrrc14	http://www.ncbi.nlm.nih.gov/gene/?term=223664	"E130306I01Rik, mKIAA0014 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006307	223690	Ankrd54	http://www.ncbi.nlm.nih.gov/gene/?term=223690	"C730048E16Rik, EST1068184, EST475269, Liar "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006308	223723	Ttll12	http://www.ncbi.nlm.nih.gov/gene/?term=223723	"BC055368, D430005B17 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006309	223739	5031439G07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=223739	"AW554572, mKIAA0930 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006310	223752	Gramd4	http://www.ncbi.nlm.nih.gov/gene/?term=223752	9930016O13	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006311	22375	Wars	http://www.ncbi.nlm.nih.gov/gene/?term=22375	"TrpRS, WRS "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006312	223775	Pim3	http://www.ncbi.nlm.nih.gov/gene/?term=223775	"BC026639, Kid1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006313	22378	Wbp2	http://www.ncbi.nlm.nih.gov/gene/?term=22378		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006314	2237	FEN1	http://www.ncbi.nlm.nih.gov/gene/?term=2237	"FEN-1, MF1, RAD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006315	2237	FEN1	http://www.ncbi.nlm.nih.gov/gene/?term=2237	"FEN-1, MF1, RAD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006316	22380	Wbp4	http://www.ncbi.nlm.nih.gov/gene/?term=22380	"AW545037, BB101031, FBP21 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006317	22385	Baz1b	http://www.ncbi.nlm.nih.gov/gene/?term=22385	"C87820, WSTF, Wbscr9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006318	223864	Rapgef3	http://www.ncbi.nlm.nih.gov/gene/?term=223864	"2310016P22Rik, 9330170P05Rik, Epac, Epac1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006319	223869	A130012F09	http://www.ncbi.nlm.nih.gov/gene/?term=223869		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006320	223870	Senp1	http://www.ncbi.nlm.nih.gov/gene/?term=223870	"2310046A20Rik, D15Ertd528e, E330036L07Rik, suPr-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006321	223922	Atf7	http://www.ncbi.nlm.nih.gov/gene/?term=223922	"1110012F10Rik, 9430065F09Rik, AI549878, C130020M04Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006322	2239	GPC4	http://www.ncbi.nlm.nih.gov/gene/?term=2239	K-glypican	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006323	223	ALDH9A1	http://www.ncbi.nlm.nih.gov/gene/?term=223	"ALDH4, ALDH7, ALDH9, E3, TMABADH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006324	223	ALDH9A1	http://www.ncbi.nlm.nih.gov/gene/?term=223	"ALDH4, ALDH7, ALDH9, E3, TMABADH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006325	223	ALDH9A1	http://www.ncbi.nlm.nih.gov/gene/?term=223	"ALDH4, ALDH7, ALDH9, E3, TMABADH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006326	224014	Fgd4	http://www.ncbi.nlm.nih.gov/gene/?term=224014	"9030023J02Rik, 9330209B17Rik, Frabp, ZFYVE6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006327	224019	Tmem191c	http://www.ncbi.nlm.nih.gov/gene/?term=224019	"4933405M22Rik, D16Bwg1494e, MNCb-4137 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006328	22401	Zmat3	http://www.ncbi.nlm.nih.gov/gene/?term=22401	Wig1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006329	22402	Wisp1	http://www.ncbi.nlm.nih.gov/gene/?term=22402	"AW146261, CCN4, Elm1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006330	224044	Cyp2ab1	http://www.ncbi.nlm.nih.gov/gene/?term=224044	"EG224044, F730023N20 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006331	22404	Wiz	http://www.ncbi.nlm.nih.gov/gene/?term=22404		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006332	224088	Atp13a3	http://www.ncbi.nlm.nih.gov/gene/?term=224088	"AU022875, Gm1745, Gm541, Gm542 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006333	224092	Lsg1	http://www.ncbi.nlm.nih.gov/gene/?term=224092	"5830465I20, AA409273, D16Bwg1547e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006334	224111	Ubxn7	http://www.ncbi.nlm.nih.gov/gene/?term=224111	"A630090P18, AI196514, Ubxd7, mKIAA0794 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006335	224116	Muc20	http://www.ncbi.nlm.nih.gov/gene/?term=224116	BC026367	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006336	22411	Wnt11	http://www.ncbi.nlm.nih.gov/gene/?term=22411		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006337	224139	Golgb1	http://www.ncbi.nlm.nih.gov/gene/?term=224139	"4930428L02Rik, 628101, 6330407A06Rik, AU042952, C130074L01Rik, F730017E11Rik, Gm6840, mKIAA4151 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006338	224143	Poglut1	http://www.ncbi.nlm.nih.gov/gene/?term=224143	"9630046K23Rik, Clp46, Ktelc1, Rumi "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006339	22415	Wnt3	http://www.ncbi.nlm.nih.gov/gene/?term=22415	"Int-4, Wnt-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006340	224170	Dzip3	http://www.ncbi.nlm.nih.gov/gene/?term=224170	"2310047C04Rik, 2A-HUB, 6430549P11Rik, A230104G20 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006341	224250	Cldnd1	http://www.ncbi.nlm.nih.gov/gene/?term=224250	"1110019C08Rik, AA407103, AI849195, AW489850, Cldn25 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006342	22427	Wrn	http://www.ncbi.nlm.nih.gov/gene/?term=22427	AI846146	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006343	22428	Dctn6	http://www.ncbi.nlm.nih.gov/gene/?term=22428	"AU044699, WS-3, p27 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006344	22431	Wt1	http://www.ncbi.nlm.nih.gov/gene/?term=22431	"D630046I19Rik, Wt-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006345	22431	Wt1	http://www.ncbi.nlm.nih.gov/gene/?term=22431	"D630046I19Rik, Wt-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006346	22433	Xbp1	http://www.ncbi.nlm.nih.gov/gene/?term=22433	"D11Ertd39e, TREB-5, TREB5, XBP-1 "	mRNA	Mus musculus	26068456	Nucleus	MCF-7|293T|T47D |3T3 cell	RT-PCR	"Our results reveal the presence of basal unconventional splicing of XBP1 mRNA in the nucleus that also requires inositol-requiring transmembrane kinase and endonuclease 1a (IRE1a) and can occur independently of acute ER stress. Furthermore, we confirm that acute ER stress induces the splicing of XBP1 mRNA predominantly occurring in the cytoplasm, but it also promotes the splicing in the nucleus. "
RLID00006347	22433	Xbp1	http://www.ncbi.nlm.nih.gov/gene/?term=22433	"D11Ertd39e, TREB-5, TREB5, XBP-1 "	mRNA	Mus musculus	26068456	Cytoplasm	MCF-7|293T|T47D |3T3 cell	RT-PCR	"Our results reveal the presence of basal unconventional splicing of XBP1 mRNA in the nucleus that also requires inositol-requiring transmembrane kinase and endonuclease 1a (IRE1a) and can occur independently of acute ER stress. Furthermore, we confirm that acute ER stress induces the splicing of XBP1 mRNA predominantly occurring in the cytoplasm, but it also promotes the splicing in the nucleus. "
RLID00006348	22437	Xirp1	http://www.ncbi.nlm.nih.gov/gene/?term=22437	"AI415219, Cmya1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006349	2243	FGA	http://www.ncbi.nlm.nih.gov/gene/?term=2243	Fib2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006350	2244	FGB	http://www.ncbi.nlm.nih.gov/gene/?term=2244	HEL-S-78p	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006351	224613	Flywch1	http://www.ncbi.nlm.nih.gov/gene/?term=224613	"E030034P13Rik, mKIAA1552 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006352	224647	D17Wsu92e	http://www.ncbi.nlm.nih.gov/gene/?term=224647	"AU020189, C030010A15, C80239 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006353	224694	Zfp81	http://www.ncbi.nlm.nih.gov/gene/?term=224694	"AA409460, AA409461, C330034P10Rik, D330034E10Rik, Hszfp36, KRAB13, Zfp78 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006354	2246	FGF1	http://www.ncbi.nlm.nih.gov/gene/?term=2246	"AFGF, ECGF, ECGF-beta, ECGFA, ECGFB, FGF-1, FGF-alpha, FGFA, GLIO703, HBGF-1, HBGF1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006355	224703	March2	http://www.ncbi.nlm.nih.gov/gene/?term=224703	"9530046H09Rik, MARCH-II "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006356	224742	Abcf1	http://www.ncbi.nlm.nih.gov/gene/?term=224742	"AU041969, Abc50, D17Wsu166e, GCN20 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006357	224794	Enpp4	http://www.ncbi.nlm.nih.gov/gene/?term=224794	"4933413N07Rik, AA986363, AI195364, E-NPP 4, Gm90, mKIAA0879 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006358	2247	FGF2	http://www.ncbi.nlm.nih.gov/gene/?term=2247	"BFGF, FGF-2, FGFB, HBGF-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006359	2247	FGF2	http://www.ncbi.nlm.nih.gov/gene/?term=2247	"BFGF, FGF-2, FGFB, HBGF-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006360	224813	Lrrc73	http://www.ncbi.nlm.nih.gov/gene/?term=224813	Gm88	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006361	224824	Pex6	http://www.ncbi.nlm.nih.gov/gene/?term=224824	"AI132582, D130055I09Rik, mKIAA4177 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006362	224826	Ubr2	http://www.ncbi.nlm.nih.gov/gene/?term=224826	"9930021A08Rik, AI462103, AW540746, E130209G04Rik, mKIAA0349 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006363	224826	Ubr2	http://www.ncbi.nlm.nih.gov/gene/?term=224826	"9930021A08Rik, AI462103, AW540746, E130209G04Rik, mKIAA0349 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006364	224860	Plcl2	http://www.ncbi.nlm.nih.gov/gene/?term=224860	"PLC-L2, PRIP-2, Plce2, mKIAA1092 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006365	224902	Safb2	http://www.ncbi.nlm.nih.gov/gene/?term=224902	"AA389433, AI255170, mKIAA0138 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006366	224903	Safb	http://www.ncbi.nlm.nih.gov/gene/?term=224903	"3110021E02Rik, 5330423C17Rik, AU018122, D18386, E130307D12, HAP, HET, SAF-B1, SAFB1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006367	224938	Pja2	http://www.ncbi.nlm.nih.gov/gene/?term=224938	"AI447901, AL022700, Neurodap1, mKIAA0438 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006368	224	ALDH3A2	http://www.ncbi.nlm.nih.gov/gene/?term=224	"ALDH10, FALDH, SLS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006369	224	ALDH3A2	http://www.ncbi.nlm.nih.gov/gene/?term=224	"ALDH10, FALDH, SLS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006370	225028	Map4k3	http://www.ncbi.nlm.nih.gov/gene/?term=225028	"4833416M01Rik, 4833416M07Rik, 9530052P13Rik, Glk, MAPKKKK3, MEKKK 3, MEKKK3, RAB8IPL1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006371	2250	FGF5	http://www.ncbi.nlm.nih.gov/gene/?term=2250	"HBGF-5, Smag-82, TCMGLY "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006372	2250	FGF5	http://www.ncbi.nlm.nih.gov/gene/?term=2250	"HBGF-5, Smag-82, TCMGLY "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006373	225131	Wac	http://www.ncbi.nlm.nih.gov/gene/?term=225131	"1110067P07Rik, A230035H12Rik, AI256735, AI256776, Wwp4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006374	225164	Mib1	http://www.ncbi.nlm.nih.gov/gene/?term=225164	"DIP-1, E430019M12Rik, Mib, mKIAA1323 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006375	225182	Rbbp8	http://www.ncbi.nlm.nih.gov/gene/?term=225182	"9930104E21Rik, CtIP, RBBP-8, RIM, SAE2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006376	225207	Zfp521	http://www.ncbi.nlm.nih.gov/gene/?term=225207	"B930086A16Rik, Evi3, Znf521 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006377	225228	Gm4835	http://www.ncbi.nlm.nih.gov/gene/?term=225228	EG225228	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006378	225283	Rprd1a	http://www.ncbi.nlm.nih.gov/gene/?term=225283	"C77387, mKIAA4077 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006379	225339	Ammecr1l	http://www.ncbi.nlm.nih.gov/gene/?term=225339	"5430429D03Rik, AU022236, AU040755, AW111353, E230022H04Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006380	225339	Ammecr1l	http://www.ncbi.nlm.nih.gov/gene/?term=225339	"5430429D03Rik, AU022236, AU040755, AW111353, E230022H04Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006381	225341	Lims2	http://www.ncbi.nlm.nih.gov/gene/?term=225341	PINCH2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006382	225348	Wdr36	http://www.ncbi.nlm.nih.gov/gene/?term=225348	"5730444A13Rik, Ta-wdrp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006383	225363	Etf1	http://www.ncbi.nlm.nih.gov/gene/?term=225363	"AI463371, D6Ertd109e, ERF, ERF1, SUP45L1, TB3-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006384	225432	Rbm27	http://www.ncbi.nlm.nih.gov/gene/?term=225432	"A730010I06, AI043120, Psc1, mKIAA1311 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006385	225467	Pggt1b	http://www.ncbi.nlm.nih.gov/gene/?term=225467	"2010207C17Rik, 2610100E13, AI451237, AI551093, BGG1, GGT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006386	225471	Ticam2	http://www.ncbi.nlm.nih.gov/gene/?term=225471	"B430113A10, TICAM-2, TRAM, Tirp, Trif "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006387	225497	Fam170a	http://www.ncbi.nlm.nih.gov/gene/?term=225497	"Gm93, Znfd "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006388	225523	Cep120	http://www.ncbi.nlm.nih.gov/gene/?term=225523	"A230075C01, AU016693, Ccdc100 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006389	225608	Sh3tc2	http://www.ncbi.nlm.nih.gov/gene/?term=225608	D430044G18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006390	225631	Onecut2	http://www.ncbi.nlm.nih.gov/gene/?term=225631	"C730009D12, OC-2, Oc2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006391	225638	Alpk2	http://www.ncbi.nlm.nih.gov/gene/?term=225638	"Gm549, Hak "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006392	225745	Haus1	http://www.ncbi.nlm.nih.gov/gene/?term=225745	"BC024400, Ccdc5, HEI-C "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006393	225791	Zadh2	http://www.ncbi.nlm.nih.gov/gene/?term=225791	"C530046K17Rik, Pthr3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006394	2257	FGF12	http://www.ncbi.nlm.nih.gov/gene/?term=2257	"FGF12B, FHF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006395	225849	Ppp2r5b	http://www.ncbi.nlm.nih.gov/gene/?term=225849	"B'beta, BC026670 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006396	225870	Rin1	http://www.ncbi.nlm.nih.gov/gene/?term=225870		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006397	225876	Kdm2a	http://www.ncbi.nlm.nih.gov/gene/?term=225876	"100043628, 5530401A10Rik, AA589516, AW536790, Cxxc8, Fbl11, Fbl7, Fbxl11, Gm4560, Jhdm1, Jhdm1a, lalina "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006398	225887	Ndufs8	http://www.ncbi.nlm.nih.gov/gene/?term=225887	"BC021616, CI-23kD, TYKY "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006399	225895	Taf6l	http://www.ncbi.nlm.nih.gov/gene/?term=225895	"2810417N14Rik, BB223262, C530024J06Rik, Paf65a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006400	22589	Atrx	http://www.ncbi.nlm.nih.gov/gene/?term=22589	"4833408C14Rik, AI447451, ATR2, DXHXS6677E, HP1-BP38, Hp1bp2, Hp1bp38, MRXS3, RAD54L, Rad54, XH2, Xnp, ZNF-HX "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006401	22590	Xpa	http://www.ncbi.nlm.nih.gov/gene/?term=22590	"AI573865c, Xpa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006402	22592	Ercc5	http://www.ncbi.nlm.nih.gov/gene/?term=22592	Xpg	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006403	22594	Xrcc1	http://www.ncbi.nlm.nih.gov/gene/?term=22594	Xrcc-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006404	2259	FGF14	http://www.ncbi.nlm.nih.gov/gene/?term=2259	"FGF-14, FHF-4, FHF4, SCA27 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006405	226049	Dmrt2	http://www.ncbi.nlm.nih.gov/gene/?term=226049	Terra	mRNA	Mus musculus	17916692	Nucleus	Renal cancer cell	In situ hybridization|Northern blot	"TERRA molecules are heterogeneous in length, are transcribed from several subtelomeric loci toward chromosome ends, and localize to telomeres. "
RLID00006406	226049	Dmrt2	http://www.ncbi.nlm.nih.gov/gene/?term=226049	Terra	lncRNA	Mus musculus	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/terra/
RLID00006407	226089	Ric1	http://www.ncbi.nlm.nih.gov/gene/?term=226089	"C030046E11Rik, C130057E09Rik, Kiaa1432 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006408	2260	FGFR1	http://www.ncbi.nlm.nih.gov/gene/?term=2260	"BFGFR, CD331, CEK, FGFBR, FGFR-1, FLG, FLT-2, FLT2, HBGFR, HH2, HRTFDS, KAL2, N-SAM, OGD, bFGF-R-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006409	226122	Ubtd1	http://www.ncbi.nlm.nih.gov/gene/?term=226122	BC016129	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006410	22612	Yes1	http://www.ncbi.nlm.nih.gov/gene/?term=22612	"Yes, p61-Yes "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006411	226144	Erlin1	http://www.ncbi.nlm.nih.gov/gene/?term=226144	"2810439N09Rik, C80197, Keo4, Spfh1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006412	226151	Fam178a	http://www.ncbi.nlm.nih.gov/gene/?term=226151	"3632432H19, 6030443O07Rik, AU014917, Slf2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006413	226162	Dpcd	http://www.ncbi.nlm.nih.gov/gene/?term=226162	"5330431N19Rik, Ndac "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006414	2261	FGFR3	http://www.ncbi.nlm.nih.gov/gene/?term=2261	"ACH, CD333, CEK2, HSFGFR3EX, JTK4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006415	226252	Fam160b1	http://www.ncbi.nlm.nih.gov/gene/?term=226252	"AI450540, mKIAA1600 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006416	226255	Atrnl1	http://www.ncbi.nlm.nih.gov/gene/?term=226255	"AI504415, AW555641, Alp, Atrnl, Atrnlp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006417	22630	Ywhaq	http://www.ncbi.nlm.nih.gov/gene/?term=22630	"2700028P07Rik, AA409740, AU021156, R74690 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006418	22631	Ywhaz	http://www.ncbi.nlm.nih.gov/gene/?term=22631	"1110013I11Rik, 14-3-3zeta, AI596267, AL022924, AU020854 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006419	22632	Yy1	http://www.ncbi.nlm.nih.gov/gene/?term=22632	"AW488674, NF-E1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006420	22632	Yy1	http://www.ncbi.nlm.nih.gov/gene/?term=22632	"AW488674, NF-E1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006421	22632	Yy1	http://www.ncbi.nlm.nih.gov/gene/?term=22632	"AW488674, NF-E1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006422	226351	Tmem185b	http://www.ncbi.nlm.nih.gov/gene/?term=226351	2500001K11Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006423	226352	Epb41l5	http://www.ncbi.nlm.nih.gov/gene/?term=226352	"1700030C16Rik, AL022914, BE37, E230025E14Rik, Epb4.1l5, Lulu1, NBL5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006424	2263	FGFR2	http://www.ncbi.nlm.nih.gov/gene/?term=2263	"BBDS, BEK, BFR-1, CD332, CEK3, CFD1, ECT1, JWS, K-SAM, KGFR, TK14, TK25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006425	2263	FGFR2	http://www.ncbi.nlm.nih.gov/gene/?term=2263	"BBDS, BEK, BFR-1, CD332, CEK3, CFD1, ECT1, JWS, K-SAM, KGFR, TK14, TK25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006426	226412	R3hdm1	http://www.ncbi.nlm.nih.gov/gene/?term=226412	R3hdm	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006427	226414	Dars	http://www.ncbi.nlm.nih.gov/gene/?term=226414	5730439G15Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006428	226422	Rab29	http://www.ncbi.nlm.nih.gov/gene/?term=226422	Rab7l1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006429	226442	Zfp281	http://www.ncbi.nlm.nih.gov/gene/?term=226442	Znf281	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006430	226442	Zfp281	http://www.ncbi.nlm.nih.gov/gene/?term=226442	Znf281	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006431	22644	Rnf103	http://www.ncbi.nlm.nih.gov/gene/?term=22644	"AW146237, AW212918, Zfp103, kf-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006432	22646	Zfp105	http://www.ncbi.nlm.nih.gov/gene/?term=22646	AW557864	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006433	2264	FGFR4	http://www.ncbi.nlm.nih.gov/gene/?term=2264	"CD334, JTK2, TKF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006434	226517	Smg7	http://www.ncbi.nlm.nih.gov/gene/?term=226517	"9430023P16Rik, mKIAA0250 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006435	226519	Lamc1	http://www.ncbi.nlm.nih.gov/gene/?term=226519	Lamb2	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006436	22651	Zfp125	http://www.ncbi.nlm.nih.gov/gene/?term=22651	ZT2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006437	226548	Aph1a	http://www.ncbi.nlm.nih.gov/gene/?term=226548	"6530402N02Rik, APH-1a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006438	22654	Zfp13	http://www.ncbi.nlm.nih.gov/gene/?term=22654	"4933429B21, AI835008, Krox-8, Rhit, Zfp-13 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006439	226562	Prrc2c	http://www.ncbi.nlm.nih.gov/gene/?term=226562	"1810043M20Rik, 9630039I18Rik, A630006J20, Bat2d, Bat2d1, Bat2l2, E130112L15Rik, Prrc3, mKIAA1096 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006440	226562	Prrc2c	http://www.ncbi.nlm.nih.gov/gene/?term=226562	"1810043M20Rik, 9630039I18Rik, A630006J20, Bat2d, Bat2d1, Bat2l2, E130112L15Rik, Prrc3, mKIAA1096 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006441	22658	Pcgf2	http://www.ncbi.nlm.nih.gov/gene/?term=22658	"Mel18, Rnf110, Zfp144, mel-18 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006442	226591	Tiprl	http://www.ncbi.nlm.nih.gov/gene/?term=226591	1810011K17Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006443	226610	Fam78b	http://www.ncbi.nlm.nih.gov/gene/?term=226610	"C030014K22Rik, C030020L09Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006444	22661	Zfp148	http://www.ncbi.nlm.nih.gov/gene/?term=22661	"2210405J08Rik, AI480666, AW045217, BERF-1, BFCOL1, ZBP-89, Znf148 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006445	226641	Atf6	http://www.ncbi.nlm.nih.gov/gene/?term=226641	"9130025P16Rik, 9630036G24, AA789574alpha, ESTM49, Atf6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006446	226641	Atf6	http://www.ncbi.nlm.nih.gov/gene/?term=226641	"9130025P16Rik, 9630036G24, AA789574alpha, ESTM49, Atf6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006447	226654	Tstd1	http://www.ncbi.nlm.nih.gov/gene/?term=226654	"AV065366, EG226654, Gm4848, KAT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006448	22668	Sf1	http://www.ncbi.nlm.nih.gov/gene/?term=22668	"BBP, MZFM, WBP4, Zfp162 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006449	22668	Sf1	http://www.ncbi.nlm.nih.gov/gene/?term=22668	"BBP, MZFM, WBP4, Zfp162 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006450	226691	AI607873	http://www.ncbi.nlm.nih.gov/gene/?term=226691		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006451	226744	Cnst	http://www.ncbi.nlm.nih.gov/gene/?term=226744	9630058J23Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006452	226747	Ahctf1	http://www.ncbi.nlm.nih.gov/gene/?term=226747	"6230412P20Rik, AV011447, Elys "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006453	226751	Cdc42bpa	http://www.ncbi.nlm.nih.gov/gene/?term=226751	"A930014J19Rik, DMPK-like "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006454	226757	Wdr26	http://www.ncbi.nlm.nih.gov/gene/?term=226757	"1600024A01Rik, AA693241, AI447817, AU044014, C77982, Gid7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006455	22680	Zfp207	http://www.ncbi.nlm.nih.gov/gene/?term=22680	"8430401D15Rik, BuGZ, Zep, Znf207 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006456	22682	Zfand5	http://www.ncbi.nlm.nih.gov/gene/?term=22682	"2310057A04Rik, 5830475F03Rik, AA415485, Za20d2, Zfp216 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006457	226844	Mfsd7b	http://www.ncbi.nlm.nih.gov/gene/?term=226844	"9630055N22Rik, FLVCR, Flvcr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006458	226849	Ppp2r5a	http://www.ncbi.nlm.nih.gov/gene/?term=226849	PR61alpha	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006459	226849	Ppp2r5a	http://www.ncbi.nlm.nih.gov/gene/?term=226849	PR61alpha	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006460	226856	Lpgat1	http://www.ncbi.nlm.nih.gov/gene/?term=226856	"AI649174, AW112037, BC013667 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006461	22688	Zfp26	http://www.ncbi.nlm.nih.gov/gene/?term=22688	"5033428C05Rik, KRAB15, Zfp-26, Zfp70, Zfp81-rs1, mKIAA4196, mkr-3, mszf14, mszf52 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006462	22690	Zfp28	http://www.ncbi.nlm.nih.gov/gene/?term=22690	"2810438M17Rik, Zfp-28, mkr-5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006463	22695	Zfp36	http://www.ncbi.nlm.nih.gov/gene/?term=22695	"Gos24, Nup475, TIS11D, TISII, Tis11, Ttp, Zfp-36 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006464	226976	Kansl3	http://www.ncbi.nlm.nih.gov/gene/?term=226976	"4632411B12Rik, 4932435K23, AI431067, AI647574, C85723, Kiaa1310, mKIAA1310 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006465	226	ALDOA	http://www.ncbi.nlm.nih.gov/gene/?term=226	"ALDA, GSD12, HEL-S-87p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006466	226	ALDOA	http://www.ncbi.nlm.nih.gov/gene/?term=226	"ALDA, GSD12, HEL-S-87p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006467	226	ALDOA	http://www.ncbi.nlm.nih.gov/gene/?term=226	"ALDA, GSD12, HEL-S-87p "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006468	227095	Hibch	http://www.ncbi.nlm.nih.gov/gene/?term=227095	"2610509I15Rik, HIBYL-COA-H "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006469	22709	Zfp51	http://www.ncbi.nlm.nih.gov/gene/?term=22709	"Zfp-51, zfec12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006470	22712	Zfp54	http://www.ncbi.nlm.nih.gov/gene/?term=22712	"2810034D10Rik, KRAB10, Zfp-54, Zfp76, mszf83 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006471	22717	Zfp59	http://www.ncbi.nlm.nih.gov/gene/?term=22717	"Mfg-2, Mfg2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006472	22718	Zfp60	http://www.ncbi.nlm.nih.gov/gene/?term=22718	"6330516O17Rik, AI426106, AI449354, Mfg-3, Mfg3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006473	227197	Ndufs1	http://www.ncbi.nlm.nih.gov/gene/?term=227197	"5830412M15Rik, 9930026A05Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006474	22719	Zfp61	http://www.ncbi.nlm.nih.gov/gene/?term=22719		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006475	2271	FH	http://www.ncbi.nlm.nih.gov/gene/?term=2271	"FMRD, HLRCC, LRCC, MCL, MCUL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006476	2271	FH	http://www.ncbi.nlm.nih.gov/gene/?term=2271	"FMRD, HLRCC, LRCC, MCL, MCUL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006477	2271	FH	http://www.ncbi.nlm.nih.gov/gene/?term=2271	"FMRD, HLRCC, LRCC, MCL, MCUL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006478	227210	Ccnyl1	http://www.ncbi.nlm.nih.gov/gene/?term=227210	"9630037P07Rik, AW554339 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006479	22722	Zfp64	http://www.ncbi.nlm.nih.gov/gene/?term=22722		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006480	22724	Zbtb7b	http://www.ncbi.nlm.nih.gov/gene/?term=22724	"Thpok, Zfp67, c-Krox "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006481	227292	Ctdsp1	http://www.ncbi.nlm.nih.gov/gene/?term=227292	"GIP, NLIIF, Nif3, SCP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006482	2272	FHIT	http://www.ncbi.nlm.nih.gov/gene/?term=2272	"AP3Aase, FRA3B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006483	227331	Gigyf2	http://www.ncbi.nlm.nih.gov/gene/?term=227331	"2610016F01Rik, A830080H02Rik, AI852361, AW259676, BC006835, Tnrc15, mKIAA0642 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006484	227334	Usp40	http://www.ncbi.nlm.nih.gov/gene/?term=227334	"B230215L03Rik, C730029K03 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006485	227399	Ppip5k2	http://www.ncbi.nlm.nih.gov/gene/?term=227399	"AW555814, Cfap160, D330021B20, Hisppd1, Vip2, mKIAA0433 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006486	227446	2310035C23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=227446	"6430401N10, Kiaa1468, mKIAA1468 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006487	227449	Zcchc2	http://www.ncbi.nlm.nih.gov/gene/?term=227449	"9930114B20Rik, AW212015 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006488	2274	FHL2	http://www.ncbi.nlm.nih.gov/gene/?term=2274	"AAG11, DRAL, FHL-2, SLIM-3, SLIM3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006489	2274	FHL2	http://www.ncbi.nlm.nih.gov/gene/?term=2274	"AAG11, DRAL, FHL-2, SLIM-3, SLIM3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006490	2274	FHL2	http://www.ncbi.nlm.nih.gov/gene/?term=2274	"AAG11, DRAL, FHL-2, SLIM-3, SLIM3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006491	22758	Zscan12	http://www.ncbi.nlm.nih.gov/gene/?term=22758	"2510038J07Rik, FPM315, Zfp96, mKIAA0426, zfp-96 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006492	22759	Zfp97	http://www.ncbi.nlm.nih.gov/gene/?term=22759	NGD16-4	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006493	2275	FHL3	http://www.ncbi.nlm.nih.gov/gene/?term=2275	SLIM2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006494	227619	Man1b1	http://www.ncbi.nlm.nih.gov/gene/?term=227619	"E430019H13Rik, ERMan1, Gm108, MANA-ER "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006495	227622	BC029214	http://www.ncbi.nlm.nih.gov/gene/?term=227622	"D930050G13Rik, Paxx "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006496	22763	Zfr	http://www.ncbi.nlm.nih.gov/gene/?term=22763	C920030H05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006497	227644	Snapc4	http://www.ncbi.nlm.nih.gov/gene/?term=227644	5730436L13Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006498	22764	Zfx	http://www.ncbi.nlm.nih.gov/gene/?term=22764	"Zfx55, 6, Zfx6, Zfx "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006499	227700	Sh3glb2	http://www.ncbi.nlm.nih.gov/gene/?term=227700	SPAS-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006500	22771	Zic1	http://www.ncbi.nlm.nih.gov/gene/?term=22771	"ZIC, ZNF201 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006501	227721	Plpp7	http://www.ncbi.nlm.nih.gov/gene/?term=227721	"D830019K17Rik, NET39, Ppapdc3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006502	227723	Prrc2b	http://www.ncbi.nlm.nih.gov/gene/?term=227723	"5830434P21Rik, AI173903, Bat2l, Bat2l1, D430039P21, mKIAA0515 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006503	22772	Zic2	http://www.ncbi.nlm.nih.gov/gene/?term=22772	"HPE5, Ku "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006504	227731	Slc25a25	http://www.ncbi.nlm.nih.gov/gene/?term=227731	"1110030N17Rik, MCSC, mKIAA1896 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006505	227737	Fam129b	http://www.ncbi.nlm.nih.gov/gene/?term=227737	9130404D14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006506	227746	Rabepk	http://www.ncbi.nlm.nih.gov/gene/?term=227746	"8430412M01Rik, 9530020D24Rik, AV073337, C87311, Rab9p40 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006507	227746	Rabepk	http://www.ncbi.nlm.nih.gov/gene/?term=227746	"8430412M01Rik, 9530020D24Rik, AV073337, C87311, Rab9p40 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006508	227753	Gsn	http://www.ncbi.nlm.nih.gov/gene/?term=227753	ADF	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006509	227800	Rabgap1	http://www.ncbi.nlm.nih.gov/gene/?term=227800	"Gapcena, mKIAA4104 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006510	22782	Slc30a1	http://www.ncbi.nlm.nih.gov/gene/?term=22782	"AI839647, C130040I11Rik, Znt1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006511	227835	Gtdc1	http://www.ncbi.nlm.nih.gov/gene/?term=227835	E330008O22Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006512	22785	Slc30a4	http://www.ncbi.nlm.nih.gov/gene/?term=22785	"Znt4, lm, znT-4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006513	22785	Slc30a4	http://www.ncbi.nlm.nih.gov/gene/?term=22785	"Znt4, lm, znT-4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006514	227929	Cytip	http://www.ncbi.nlm.nih.gov/gene/?term=227929	"A130053M09Rik, AI462064, C80816, Cbp, Cybr, Pscdbp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006515	227937	Pkp4	http://www.ncbi.nlm.nih.gov/gene/?term=227937	"5031422I09Rik, 9430019K17Rik, Armrp, p0071 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00006516	22793	Zyx	http://www.ncbi.nlm.nih.gov/gene/?term=22793	"9530098H06Rik, R75157 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006517	22794	CASC3	http://www.ncbi.nlm.nih.gov/gene/?term=22794	"BTZ, MLN51 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006518	22796	COG2	http://www.ncbi.nlm.nih.gov/gene/?term=22796	LDLC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006519	22796	COG2	http://www.ncbi.nlm.nih.gov/gene/?term=22796	LDLC	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006520	228003	Klhl41	http://www.ncbi.nlm.nih.gov/gene/?term=228003	"Gm112, Kbtbd10, SARCOSIN "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006521	228005	Ppig	http://www.ncbi.nlm.nih.gov/gene/?term=228005	"AU019516, AU022200, B230312B02Rik, CYP, SRCyp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006522	22800	RRAS2	http://www.ncbi.nlm.nih.gov/gene/?term=22800	TC21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006523	22800	RRAS2	http://www.ncbi.nlm.nih.gov/gene/?term=22800	TC21	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006524	228012	Tlk1	http://www.ncbi.nlm.nih.gov/gene/?term=228012	4930545J15Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006525	228026	Pdk1	http://www.ncbi.nlm.nih.gov/gene/?term=228026	"B830012B01, D530020C15Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006526	22803	XRN2	http://www.ncbi.nlm.nih.gov/gene/?term=22803		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006527	22803	XRN2	http://www.ncbi.nlm.nih.gov/gene/?term=22803		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006528	22808	MRAS	http://www.ncbi.nlm.nih.gov/gene/?term=22808	"M-RAs, R-RAS3, RRAS3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006529	22808	MRAS	http://www.ncbi.nlm.nih.gov/gene/?term=22808	"M-RAs, R-RAS3, RRAS3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006530	22809	ATF5	http://www.ncbi.nlm.nih.gov/gene/?term=22809	"ATFX, HMFN0395 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006531	22809	ATF5	http://www.ncbi.nlm.nih.gov/gene/?term=22809	"ATFX, HMFN0395 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006532	22809	ATF5	http://www.ncbi.nlm.nih.gov/gene/?term=22809	"ATFX, HMFN0395 "	mRNA	Homo sapiens	26131922	Axon	Brain	In situ hybridization	"Finally, Atf4 mRNA is found in adult axons of mice and human brains in the context of Abeta-induced neurodegeneration. "
RLID00006533	2280	FKBP1A	http://www.ncbi.nlm.nih.gov/gene/?term=2280	"FKBP-12, FKBP-1A, FKBP1, FKBP12, PKC12, PKCI2, PPIASE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006534	2280	FKBP1A	http://www.ncbi.nlm.nih.gov/gene/?term=2280	"FKBP-12, FKBP-1A, FKBP1, FKBP12, PKC12, PKCI2, PPIASE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006535	2280	FKBP1A	http://www.ncbi.nlm.nih.gov/gene/?term=2280	"FKBP-12, FKBP-1A, FKBP1, FKBP12, PKC12, PKCI2, PPIASE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006536	22818	COPZ1	http://www.ncbi.nlm.nih.gov/gene/?term=22818	"CGI-120, COPZ, HSPC181, zeta-COP, zeta1-COP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006537	22818	COPZ1	http://www.ncbi.nlm.nih.gov/gene/?term=22818	"CGI-120, COPZ, HSPC181, zeta-COP, zeta1-COP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006538	22818	COPZ1	http://www.ncbi.nlm.nih.gov/gene/?term=22818	"CGI-120, COPZ, HSPC181, zeta-COP, zeta1-COP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006539	22820	COPG1	http://www.ncbi.nlm.nih.gov/gene/?term=22820	COPG	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006540	22822	PHLDA1	http://www.ncbi.nlm.nih.gov/gene/?term=22822	"DT1P1B11, PHRIP, TDAG51 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006541	22822	PHLDA1	http://www.ncbi.nlm.nih.gov/gene/?term=22822	"DT1P1B11, PHRIP, TDAG51 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006542	22822	PHLDA1	http://www.ncbi.nlm.nih.gov/gene/?term=22822	"DT1P1B11, PHRIP, TDAG51 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006543	22823	MTF2	http://www.ncbi.nlm.nih.gov/gene/?term=22823	"M96, PCL2, TDRD19A, dJ976O13.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006544	22823	MTF2	http://www.ncbi.nlm.nih.gov/gene/?term=22823	"M96, PCL2, TDRD19A, dJ976O13.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006545	22824	HSPA4L	http://www.ncbi.nlm.nih.gov/gene/?term=22824	"APG-1, HSPH3, Osp94 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006546	22824	HSPA4L	http://www.ncbi.nlm.nih.gov/gene/?term=22824	"APG-1, HSPH3, Osp94 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006547	22824	HSPA4L	http://www.ncbi.nlm.nih.gov/gene/?term=22824	"APG-1, HSPH3, Osp94 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006548	22826	DNAJC8	http://www.ncbi.nlm.nih.gov/gene/?term=22826	"HSPC331, SPF31 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006549	22826	DNAJC8	http://www.ncbi.nlm.nih.gov/gene/?term=22826	"HSPC331, SPF31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006550	22827	PUF60	http://www.ncbi.nlm.nih.gov/gene/?term=22827	"FIR, RoBPI, SIAHBP1, VRJS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006551	22827	PUF60	http://www.ncbi.nlm.nih.gov/gene/?term=22827	"FIR, RoBPI, SIAHBP1, VRJS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006552	22828	SCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=22828	RBM16	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006553	22834	ZNF652	http://www.ncbi.nlm.nih.gov/gene/?term=22834		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006554	22834	ZNF652	http://www.ncbi.nlm.nih.gov/gene/?term=22834		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006555	22834	ZNF652	http://www.ncbi.nlm.nih.gov/gene/?term=22834		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006556	228356	1110051M20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=228356	AI586322	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006557	228361	Ambra1	http://www.ncbi.nlm.nih.gov/gene/?term=228361	"2310079H06Rik, A130023A14, AA474864, AV021921, D030051N19Rik, mKIAA1736 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006558	22836	RHOBTB3	http://www.ncbi.nlm.nih.gov/gene/?term=22836		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006559	22836	RHOBTB3	http://www.ncbi.nlm.nih.gov/gene/?term=22836		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006560	22837	COBLL1	http://www.ncbi.nlm.nih.gov/gene/?term=22837	COBLR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006561	22839	DLGAP4	http://www.ncbi.nlm.nih.gov/gene/?term=22839	"DAP-4, DAP4, DLP4, SAPAP-4, SAPAP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006562	228410	Cstf3	http://www.ncbi.nlm.nih.gov/gene/?term=228410	"4732468G05Rik, C79532, CstF-77 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006563	228421	Kif18a	http://www.ncbi.nlm.nih.gov/gene/?term=228421	"AU024633, B130001M12Rik, gcd2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006564	22843	PPM1E	http://www.ncbi.nlm.nih.gov/gene/?term=22843	"CaMKP-N, POPX1, PP2CH, caMKN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006565	22843	PPM1E	http://www.ncbi.nlm.nih.gov/gene/?term=22843	"CaMKP-N, POPX1, PP2CH, caMKN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006566	22845	DOLK	http://www.ncbi.nlm.nih.gov/gene/?term=22845	"CDG1M, DK, DK1, SEC59, TMEM15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006567	22846	VASH1	http://www.ncbi.nlm.nih.gov/gene/?term=22846	KIAA1036	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006568	22847	ZNF507	http://www.ncbi.nlm.nih.gov/gene/?term=22847		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006569	22847	ZNF507	http://www.ncbi.nlm.nih.gov/gene/?term=22847		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006570	22848	AAK1	http://www.ncbi.nlm.nih.gov/gene/?term=22848		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006571	22848	AAK1	http://www.ncbi.nlm.nih.gov/gene/?term=22848		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006572	22848	AAK1	http://www.ncbi.nlm.nih.gov/gene/?term=22848		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006573	22850	ADNP2	http://www.ncbi.nlm.nih.gov/gene/?term=22850	ZNF508	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006574	22850	ADNP2	http://www.ncbi.nlm.nih.gov/gene/?term=22850	ZNF508	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006575	22850	ADNP2	http://www.ncbi.nlm.nih.gov/gene/?term=22850	ZNF508	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006576	22853	LMTK2	http://www.ncbi.nlm.nih.gov/gene/?term=22853	"AATYK2, BREK, KPI-2, KPI2, LMR2, PPP1R100, cprk, hBREK "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006577	228545	Vps18	http://www.ncbi.nlm.nih.gov/gene/?term=228545	9930024E13Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006578	22858	ICK	http://www.ncbi.nlm.nih.gov/gene/?term=22858	"ECO, LCK2, MRK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006579	22858	ICK	http://www.ncbi.nlm.nih.gov/gene/?term=22858	"ECO, LCK2, MRK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006580	22858	ICK	http://www.ncbi.nlm.nih.gov/gene/?term=22858	"ECO, LCK2, MRK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006581	22858	ICK	http://www.ncbi.nlm.nih.gov/gene/?term=22858	"ECO, LCK2, MRK "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006582	22859	ADGRL1	http://www.ncbi.nlm.nih.gov/gene/?term=22859	"CIRL1, CL1, LEC2, LPHN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006583	228608	Smox	http://www.ncbi.nlm.nih.gov/gene/?term=228608	"B130066H01Rik, PAO, PAOh1, SMO "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006584	22861	NLRP1	http://www.ncbi.nlm.nih.gov/gene/?term=22861	"CARD7, CIDED, CLR17.1, DEFCAP, DEFCAP-L/S, NAC, NALP1, PP1044, SLEV1, VAMAS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006585	22862	FNDC3A	http://www.ncbi.nlm.nih.gov/gene/?term=22862	"FNDC3, HUGO, bA203I16.1, bA203I16.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006586	22862	FNDC3A	http://www.ncbi.nlm.nih.gov/gene/?term=22862	"FNDC3, HUGO, bA203I16.1, bA203I16.5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006587	22864	R3HDM2	http://www.ncbi.nlm.nih.gov/gene/?term=22864	"CAG6, PR01365 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006588	228684	Sel1l2	http://www.ncbi.nlm.nih.gov/gene/?term=228684	Gm118	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006589	22868	FASTKD2	http://www.ncbi.nlm.nih.gov/gene/?term=22868	KIAA0971	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006590	22869	ZNF510	http://www.ncbi.nlm.nih.gov/gene/?term=22869		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006591	2286	FKBP2	http://www.ncbi.nlm.nih.gov/gene/?term=2286	"FKBP-13, PPIase "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006592	2286	FKBP2	http://www.ncbi.nlm.nih.gov/gene/?term=2286	"FKBP-13, PPIase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006593	22870	PPP6R1	http://www.ncbi.nlm.nih.gov/gene/?term=22870	"KIAA1115, PP6R1, SAP190, SAPS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006594	22872	SEC31A	http://www.ncbi.nlm.nih.gov/gene/?term=22872	"ABP125, ABP130, HSPC275, HSPC334, SEC31L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006595	22872	SEC31A	http://www.ncbi.nlm.nih.gov/gene/?term=22872	"ABP125, ABP130, HSPC275, HSPC334, SEC31L1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006596	22872	SEC31A	http://www.ncbi.nlm.nih.gov/gene/?term=22872	"ABP125, ABP130, HSPC275, HSPC334, SEC31L1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006597	22873	DZIP1	http://www.ncbi.nlm.nih.gov/gene/?term=22873	"DZIP, DZIPt1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006598	22873	DZIP1	http://www.ncbi.nlm.nih.gov/gene/?term=22873	"DZIP, DZIPt1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006599	22874	PLEKHA6	http://www.ncbi.nlm.nih.gov/gene/?term=22874	"PEPP-3, PEPP3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006600	228756	Cstl1	http://www.ncbi.nlm.nih.gov/gene/?term=228756	"RCET1, RCET2, RCET3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006601	228765	Sdcbp2	http://www.ncbi.nlm.nih.gov/gene/?term=228765		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006602	228769	Psmf1	http://www.ncbi.nlm.nih.gov/gene/?term=228769	"AW048666, BC012260, PI31 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006603	22876	INPP5F	http://www.ncbi.nlm.nih.gov/gene/?term=22876	"MSTP007, MSTPO47, SAC2, hSAC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006604	228775	Trib3	http://www.ncbi.nlm.nih.gov/gene/?term=228775	"Ifld2, Nipk, SINK, SKIP3, TRB-3, Trb3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006605	228785	Mylk2	http://www.ncbi.nlm.nih.gov/gene/?term=228785	"9830004H17Rik, BB138278 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006606	22878	TRAPPC8	http://www.ncbi.nlm.nih.gov/gene/?term=22878	"GSG1, HsT2706, KIAA1012, TRS85 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006607	22878	TRAPPC8	http://www.ncbi.nlm.nih.gov/gene/?term=22878	"GSG1, HsT2706, KIAA1012, TRS85 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006608	228790	Asxl1	http://www.ncbi.nlm.nih.gov/gene/?term=228790	mKIAA0978	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006609	22879	MON1B	http://www.ncbi.nlm.nih.gov/gene/?term=22879	"HSRG1, SAND2, SRG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006610	2287	FKBP3	http://www.ncbi.nlm.nih.gov/gene/?term=2287	"FKBP-25, FKBP-3, FKBP25, PPIase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006611	22880	MORC2	http://www.ncbi.nlm.nih.gov/gene/?term=22880	"CMT2Z, ZCW3, ZCWCC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006612	22880	MORC2	http://www.ncbi.nlm.nih.gov/gene/?term=22880	"CMT2Z, ZCW3, ZCWCC1 "	mRNA	Homo sapiens	25630241	Cytoplasm	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00006613	22880	MORC2	http://www.ncbi.nlm.nih.gov/gene/?term=22880	"CMT2Z, ZCW3, ZCWCC1 "	mRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00006614	228836	Dlgap4	http://www.ncbi.nlm.nih.gov/gene/?term=228836	"AI225853, BC024558, DAP-4, DAP4, SAPAP-4, Sapap4, WBP16 "	mRNA	Mus musculus	18539120	Dendrite	Neuron	Fluorescence in situ hybridization	Figure 5d: Dendritic SAPAP4 mRNA localization in response to DHPG (11DIV).
RLID00006615	228836	Dlgap4	http://www.ncbi.nlm.nih.gov/gene/?term=228836	"AI225853, BC024558, DAP-4, DAP4, SAPAP-4, Sapap4, WBP16 "	mRNA	Mus musculus	18539120	Synapse	Brain	qRT-PCR	"The mRNA targets reduced in Kif5 association included genes involved in actin remodeling at synapses (cofilin phosphatase (PP2Ac); p116-RIP), synapse-associated signaling (DAG1;RGS5) and synapse structure (SAPAP4; CaMKIIa; MAP1b). Not all mRNAs were significantly reduced in Kif5 IPs, as OCRL1 mRNA was similar in KO brain (P>0.05, n=8). "
RLID00006616	228839	Tgif2	http://www.ncbi.nlm.nih.gov/gene/?term=228839	"4921501K24, 5730599O09Rik, C80753, C81206 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006617	22883	CLSTN1	http://www.ncbi.nlm.nih.gov/gene/?term=22883	"ALC-ALPHA, CDHR12, CST-1, CSTN1, PIK3CD, XB31alpha, alcalpha1, alcalpha2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006618	22883	CLSTN1	http://www.ncbi.nlm.nih.gov/gene/?term=22883	"ALC-ALPHA, CDHR12, CST-1, CSTN1, PIK3CD, XB31alpha, alcalpha1, alcalpha2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006619	22883	CLSTN1	http://www.ncbi.nlm.nih.gov/gene/?term=22883	"ALC-ALPHA, CDHR12, CST-1, CSTN1, PIK3CD, XB31alpha, alcalpha1, alcalpha2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006620	22884	WDR37	http://www.ncbi.nlm.nih.gov/gene/?term=22884		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006621	228858	Gdap1l1	http://www.ncbi.nlm.nih.gov/gene/?term=228858	Gdap1l	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006622	228866	Pcif1	http://www.ncbi.nlm.nih.gov/gene/?term=228866	"2310022K11Rik, C20orf67, F730014I05Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006623	22887	FOXJ3	http://www.ncbi.nlm.nih.gov/gene/?term=22887		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006624	22887	FOXJ3	http://www.ncbi.nlm.nih.gov/gene/?term=22887		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006625	228880	Zmynd8	http://www.ncbi.nlm.nih.gov/gene/?term=228880	"1110013E22Rik, 2010005I16Rik, 3632413B07Rik, AI316811, AL024039, Prkcbp1, RACK7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006626	22888	UBOX5	http://www.ncbi.nlm.nih.gov/gene/?term=22888	"RNF37, UBCE7IP5, UIP5, hUIP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006627	22889	KIAA0907	http://www.ncbi.nlm.nih.gov/gene/?term=22889	BLOM7	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006628	2288	FKBP4	http://www.ncbi.nlm.nih.gov/gene/?term=2288	"FKBP51, FKBP52, FKBP59, HBI, Hsp56, PPIase, p52 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006629	22890	ZBTB1	http://www.ncbi.nlm.nih.gov/gene/?term=22890	ZNF909	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006630	228911	Tshz2	http://www.ncbi.nlm.nih.gov/gene/?term=228911	"2900073F20Rik, B830045G17, Mtsh2, Sdccag33l, Tsh2, Zfp218, mKIAA4248, teashirt2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006631	22894	DIS3	http://www.ncbi.nlm.nih.gov/gene/?term=22894	"2810028N01Rik, EXOSC11, KIAA1008, RRP44, dis3p "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006632	228960	Stx16	http://www.ncbi.nlm.nih.gov/gene/?term=228960	"4930401D03, 5430410K23Rik, 6330500A18Rik, AI648908, AW553605, Syn16 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006633	22897	CEP164	http://www.ncbi.nlm.nih.gov/gene/?term=22897	NPHP15	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006634	228983	Osbpl2	http://www.ncbi.nlm.nih.gov/gene/?term=228983	"C130070J12Rik, ORP-2, Orp2, mKIAA0772 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006635	2289	FKBP5	http://www.ncbi.nlm.nih.gov/gene/?term=2289	"AIG6, FKBP51, FKBP54, P54, PPIase, Ptg-10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006636	2289	FKBP5	http://www.ncbi.nlm.nih.gov/gene/?term=2289	"AIG61, FKBP54, P54, PPIase, Ptg-10, FKBP5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006637	22900	CARD8	http://www.ncbi.nlm.nih.gov/gene/?term=22900	"CARDINAL, DACAR, DAKAR, NDPP, NDPP1, TUCAN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006638	22900	CARD8	http://www.ncbi.nlm.nih.gov/gene/?term=22900	"CARDINAL, DACAR, DAKAR, NDPP, NDPP1, TUCAN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006639	22902	RUFY3	http://www.ncbi.nlm.nih.gov/gene/?term=22902	"RIPX, SINGAR1, ZFYVE30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006640	22903	BTBD3	http://www.ncbi.nlm.nih.gov/gene/?term=22903	dJ742J24.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006641	22904	SBNO2	http://www.ncbi.nlm.nih.gov/gene/?term=22904	"KIAA0963, SNO, STNO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006642	22906	TRAK1	http://www.ncbi.nlm.nih.gov/gene/?term=22906	"MILT1, OIP106 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006643	22907	DHX30	http://www.ncbi.nlm.nih.gov/gene/?term=22907	"DDX30, RETCOR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006644	22907	DHX30	http://www.ncbi.nlm.nih.gov/gene/?term=22907	"DDX30, RETCOR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006645	22907	DHX30	http://www.ncbi.nlm.nih.gov/gene/?term=22907	"DDX30, RETCOR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006646	22908	SACM1L	http://www.ncbi.nlm.nih.gov/gene/?term=22908	SAC1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006647	22908	SACM1L	http://www.ncbi.nlm.nih.gov/gene/?term=22908	SAC1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006648	22908	SACM1L	http://www.ncbi.nlm.nih.gov/gene/?term=22908	SAC1	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00006649	22908	SACM1L	http://www.ncbi.nlm.nih.gov/gene/?term=22908	SAC1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006650	22909	FAN1	http://www.ncbi.nlm.nih.gov/gene/?term=22909	"KIAA1018, KMIN, MTMR15, hFAN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006651	22909	FAN1	http://www.ncbi.nlm.nih.gov/gene/?term=22909	"KIAA1018, KMIN, MTMR15, hFAN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006652	2290	FOXG1	http://www.ncbi.nlm.nih.gov/gene/?term=2290	"BF1, BF2, FHKL3, FKH2, FKHL1, FKHL2, FKHL3, FKHL4, FOXG1A, FOXG1B, FOXG1C, HBF-1, HBF-2, HBF-3, HBF-G2, HBF2, HFK1, HFK2, HFK3, KHL2, QIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006653	22913	RALY	http://www.ncbi.nlm.nih.gov/gene/?term=22913	"HNRPCL2, P542 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006654	22913	RALY	http://www.ncbi.nlm.nih.gov/gene/?term=22913	"HNRPCL2, P542 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006655	22914	KLRK1	http://www.ncbi.nlm.nih.gov/gene/?term=22914	"CD314, D12S2489E, KLR, NKG2-D, NKG2D "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006656	22916	NCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=22916	"CBC2, CBP20, NIP1, PIG55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006657	22916	NCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=22916	"CBC2, CBP20, NIP1, PIG55 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006658	22919	MAPRE1	http://www.ncbi.nlm.nih.gov/gene/?term=22919	EB1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006659	22919	MAPRE1	http://www.ncbi.nlm.nih.gov/gene/?term=22919	EB1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006660	22919	MAPRE1	http://www.ncbi.nlm.nih.gov/gene/?term=22919	EB1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006661	22920	KIFAP3	http://www.ncbi.nlm.nih.gov/gene/?term=22920	"FLA3, KAP-1, KAP-3, KAP3, SMAP, Smg-GDS, dJ190I16.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006662	22921	MSRB2	http://www.ncbi.nlm.nih.gov/gene/?term=22921	"CBS-1, CBS1, CGI-131, MSRB, PILB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006663	22921	MSRB2	http://www.ncbi.nlm.nih.gov/gene/?term=22921	"CBS-1, CBS1, CGI-131, MSRB, PILB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006664	229227	4932438A13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=229227	"4732443H21, B830039D19Rik, D630029K19Rik, FSA, Kiaa1109, Tweek "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006665	22924	MAPRE3	http://www.ncbi.nlm.nih.gov/gene/?term=22924	"EB3, EBF3, EBF3-S, RP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006666	22924	MAPRE3	http://www.ncbi.nlm.nih.gov/gene/?term=22924	"EB3, EBF3, EBF3-S, RP3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006667	22925	PLA2R1	http://www.ncbi.nlm.nih.gov/gene/?term=22925	"CLEC13C, PLA2-R, PLA2G1R, PLA2IR, PLA2R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006668	22926	ATF6	http://www.ncbi.nlm.nih.gov/gene/?term=22926	"ACHM7, ATF6A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006669	22926	ATF6	http://www.ncbi.nlm.nih.gov/gene/?term=22926	"ACHM7A, ATF6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006670	229279	Hnrnpa3	http://www.ncbi.nlm.nih.gov/gene/?term=229279	"2410013L13Rik, 2610209F03Rik, 2610510D13Rik, Hnrpa3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006671	229279	Hnrnpa3	http://www.ncbi.nlm.nih.gov/gene/?term=229279	"2410013L13Rik, 2610209F03Rik, 2610510D13Rik, Hnrpa3 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00006672	22929	SEPHS1	http://www.ncbi.nlm.nih.gov/gene/?term=22929	"SELD, SPS, SPS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006673	22930	RAB3GAP1	http://www.ncbi.nlm.nih.gov/gene/?term=22930	"P130, RAB3GAP, RAB3GAP130, WARBM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006674	22930	RAB3GAP1	http://www.ncbi.nlm.nih.gov/gene/?term=22930	"P130, RAB3GAP30, WARBM1, RAB3GAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006675	229317	Eif2a	http://www.ncbi.nlm.nih.gov/gene/?term=229317	"D030048D22, D3Ertd194e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006676	22931	RAB18	http://www.ncbi.nlm.nih.gov/gene/?term=22931	"RAB18LI1, WARBM3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006677	22931	RAB18	http://www.ncbi.nlm.nih.gov/gene/?term=22931	"RAB18LI1, WARBM3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006678	22932	POMZP3	http://www.ncbi.nlm.nih.gov/gene/?term=22932	"POM-ZP3, POM121 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006679	22933	SIRT2	http://www.ncbi.nlm.nih.gov/gene/?term=22933	"SIR2, SIR2L, SIR2L2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006680	22934	RPIA	http://www.ncbi.nlm.nih.gov/gene/?term=22934	"RPI, RPIAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006681	22934	RPIA	http://www.ncbi.nlm.nih.gov/gene/?term=22934	"RPID, RPIA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006682	229357	Gpr149	http://www.ncbi.nlm.nih.gov/gene/?term=229357	"9630018L10Rik, Ieda, PGR10, R35 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006683	229363	Gmps	http://www.ncbi.nlm.nih.gov/gene/?term=229363	"AA591640, AI047208 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006684	22936	ELL2	http://www.ncbi.nlm.nih.gov/gene/?term=22936		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006685	22937	SCAP	http://www.ncbi.nlm.nih.gov/gene/?term=22937		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006686	22937	SCAP	http://www.ncbi.nlm.nih.gov/gene/?term=22937		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006687	22938	SNW1	http://www.ncbi.nlm.nih.gov/gene/?term=22938	"Bx42, NCOA-62, PRPF45, Prp45, SKIIP, SKIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006688	22938	SNW1	http://www.ncbi.nlm.nih.gov/gene/?term=22938	"Bx42, NCOA-62, PRPF45, Prp45, SKIIP, SKIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006689	229473	D930015E06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=229473	"Kiaa0922, mKIAA0922 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006690	229474	Fhdc1	http://www.ncbi.nlm.nih.gov/gene/?term=229474	"6330505N24Rik, Gm126 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006691	229488	Fam160a1	http://www.ncbi.nlm.nih.gov/gene/?term=229488	9930021J17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006692	22948	CCT5	http://www.ncbi.nlm.nih.gov/gene/?term=22948	"CCT-epsilon, CCTE, HEL-S-69, PNAS-102, TCP-1-epsilon "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006693	22948	CCT5	http://www.ncbi.nlm.nih.gov/gene/?term=22948	"CCT-epsilon, CCTE, HEL-S-69, PNAS-102, TCP-1-epsilon "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006694	22948	CCT5	http://www.ncbi.nlm.nih.gov/gene/?term=22948	"CCT-epsilon, CCTE, HEL-S-69, PNAS-102, TCP-1-epsilon "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006695	2294	FOXF1	http://www.ncbi.nlm.nih.gov/gene/?term=2294	"ACDMPV, FKHL5, FREAC1 "	mRNA	Homo sapiens	25630241	Cytoplasm	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00006696	2294	FOXF1	http://www.ncbi.nlm.nih.gov/gene/?term=2294	"ACDMPV, FKHL5, FREAC1 "	mRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00006697	229517	Slc25a44	http://www.ncbi.nlm.nih.gov/gene/?term=229517	"6720482A19, B430110G05Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006698	229521	Syt11	http://www.ncbi.nlm.nih.gov/gene/?term=229521	"1500004A13Rik, 3632445O20Rik, 5430404N14Rik, 6530420C11Rik, AI851970 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006699	229521	Syt11	http://www.ncbi.nlm.nih.gov/gene/?term=229521	"1500004A13Rik, 3632445O20Rik, 5430404N14Rik, 6530420C11Rik, AI851970 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006700	229524	Msto1	http://www.ncbi.nlm.nih.gov/gene/?term=229524	"BC008103, mst "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006701	22955	SCMH1	http://www.ncbi.nlm.nih.gov/gene/?term=22955	Scml3	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006702	229562	Sprr4	http://www.ncbi.nlm.nih.gov/gene/?term=229562		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006703	229574	Flg2	http://www.ncbi.nlm.nih.gov/gene/?term=229574	EG229574	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006704	229663	Csde1	http://www.ncbi.nlm.nih.gov/gene/?term=229663	"AA960392, BC016898, D3Jfr1, mKIAA0885, unr "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006705	229663	Csde1	http://www.ncbi.nlm.nih.gov/gene/?term=229663	"AA960392, BC016898, D3Jfr1, mKIAA0885, unr "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006706	2296	FOXC1	http://www.ncbi.nlm.nih.gov/gene/?term=2296	"ARA, FKHL7, FREAC-3, FREAC3, IGDA, IHG1, IRID1, RIEG3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006707	229700	Rbm15	http://www.ncbi.nlm.nih.gov/gene/?term=229700	"C230088J01Rik, mKIAA1438 "	mRNA	Mus musculus	26190105	Nucleus	Embryotem cell	Microscopy	"Figure 6: 3DSIM Showing that Xist RNA, Rbm15, Wtap, and Spen Co-localize within Perichromatin Spaces. Data are collected from Figure 6. "
RLID00006708	229709	Ahcyl1	http://www.ncbi.nlm.nih.gov/gene/?term=229709	"1110034F20Rik, AA409031, AA414901, Ahcy-rs3, DCAL, Irbit "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006709	229722	5330417C22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=229722	"BB183350, mKIAA1324 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006710	229731	Slc25a24	http://www.ncbi.nlm.nih.gov/gene/?term=229731	2610016M12Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006711	22974	TPX2	http://www.ncbi.nlm.nih.gov/gene/?term=22974	"C20orf1, C20orf2, DIL-2, DIL2, FLS353, GD:C20orf1, HCA519, HCTP4, REPP86, p100 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006712	22974	TPX2	http://www.ncbi.nlm.nih.gov/gene/?term=22974	"C20orf1, C20orf2, DIL-2, DIL2, FLS353, GD:C20orf1, HCA519, HCTP4, REPP86, p100 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006713	22976	PAXIP1	http://www.ncbi.nlm.nih.gov/gene/?term=22976	"CAGF28, CAGF29, PACIP1, PAXIP1L, PTIP, TNRC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006714	22976	PAXIP1	http://www.ncbi.nlm.nih.gov/gene/?term=22976	"CAGF28, CAGF29, PACIP1L, PTIP, TNRC2, PAXIP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006715	22977	AKR7A3	http://www.ncbi.nlm.nih.gov/gene/?term=22977	AFAR2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006716	229780	Trmt13	http://www.ncbi.nlm.nih.gov/gene/?term=229780	"4631408H19Rik, A330067P21, A930028L21Rik, Ccdc76 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006717	229782	Slc35a3	http://www.ncbi.nlm.nih.gov/gene/?term=229782	2310050P13Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006718	22978	NT5C2	http://www.ncbi.nlm.nih.gov/gene/?term=22978	"GMP, NT5B, PNT5, SPG45, SPG65, cN-II "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006719	22978	NT5C2	http://www.ncbi.nlm.nih.gov/gene/?term=22978	"GMP, NT5B, PNT5, SPG45, SPG65, cN-II "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006720	229791	Plppr4	http://www.ncbi.nlm.nih.gov/gene/?term=229791	"A330086D10, D3Bwg0562e, Lppr4, PRG-1, mKIAA0455 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006721	22979	EFR3B	http://www.ncbi.nlm.nih.gov/gene/?term=22979	KIAA0953	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006722	22979	EFR3B	http://www.ncbi.nlm.nih.gov/gene/?term=22979	KIAA0953	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006723	2297	FOXD1	http://www.ncbi.nlm.nih.gov/gene/?term=2297	"FKHL8, FREAC-4, FREAC4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006724	2297	FOXD1	http://www.ncbi.nlm.nih.gov/gene/?term=2297	"FKHL8, FREAC-4, FREAC4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006725	2297	FOXD1	http://www.ncbi.nlm.nih.gov/gene/?term=2297	"FKHL8, FREAC-4, FREAC4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006726	22980	TCF25	http://www.ncbi.nlm.nih.gov/gene/?term=22980	"FKSG26, Hulp1, NULP1, PRO2620, hKIAA1049 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006727	22980	TCF25	http://www.ncbi.nlm.nih.gov/gene/?term=22980	"FKSG26, Hulp1, NULP1, PRO2620, hKIAA1049 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006728	22983	MAST1	http://www.ncbi.nlm.nih.gov/gene/?term=22983	"SAST, SAST170 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006729	22984	PDCD11	http://www.ncbi.nlm.nih.gov/gene/?term=22984	"ALG-4, ALG4, NFBP, RRP5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006730	22985	ACIN1	http://www.ncbi.nlm.nih.gov/gene/?term=22985	"ACINUS, ACN, fSAP152 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006731	22985	ACIN1	http://www.ncbi.nlm.nih.gov/gene/?term=22985	"ACINUS, ACN, fSAP152 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006732	22985	ACIN1	http://www.ncbi.nlm.nih.gov/gene/?term=22985	"ACINUS, ACN, fSAP152 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006733	229905	Ccbl2	http://www.ncbi.nlm.nih.gov/gene/?term=229905	"KATIII, Kat3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006734	22990	PCNX1	http://www.ncbi.nlm.nih.gov/gene/?term=22990	"PCNX, PCNXL1, pecanex "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006735	22990	PCNX1	http://www.ncbi.nlm.nih.gov/gene/?term=22990	"PCNX, PCNXL1, pecanex "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006736	22992	KDM2A	http://www.ncbi.nlm.nih.gov/gene/?term=22992	"CXXC8, FBL11, FBL7, FBXL11, JHDM1A, LILINA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006737	22992	KDM2A	http://www.ncbi.nlm.nih.gov/gene/?term=22992	"CXXC8, FBL11, FBL7, FBXL11, JHDM1A, LILINA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006738	22993	HMGXB3	http://www.ncbi.nlm.nih.gov/gene/?term=22993	"HMGX3, SMF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006739	22995	CEP152	http://www.ncbi.nlm.nih.gov/gene/?term=22995	"MCPH4, MCPH9, SCKL5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006740	22999	RIMS1	http://www.ncbi.nlm.nih.gov/gene/?term=22999	"CORD7, RAB3IP2, RIM, RIM1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006741	229	ALDOB	http://www.ncbi.nlm.nih.gov/gene/?term=229	"ALDB, ALDO2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006742	23001	WDFY3	http://www.ncbi.nlm.nih.gov/gene/?term=23001	"ALFY, ZFYVE25 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006743	23002	DAAM1	http://www.ncbi.nlm.nih.gov/gene/?term=23002		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006744	23002	DAAM1	http://www.ncbi.nlm.nih.gov/gene/?term=23002		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006745	23005	MAPKBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23005	"JNKBP-1, JNKBP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006746	23008	KLHDC10	http://www.ncbi.nlm.nih.gov/gene/?term=23008	slim	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006747	23008	KLHDC10	http://www.ncbi.nlm.nih.gov/gene/?term=23008	slim	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006748	23011	RAB21	http://www.ncbi.nlm.nih.gov/gene/?term=23011		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006749	23011	RAB21	http://www.ncbi.nlm.nih.gov/gene/?term=23011		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006750	23011	RAB21	http://www.ncbi.nlm.nih.gov/gene/?term=23011		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006751	230125	Slc25a51	http://www.ncbi.nlm.nih.gov/gene/?term=230125	"9130208E07Rik, D130005A03Rik, Gm138, Mcart1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006752	230126	Shb	http://www.ncbi.nlm.nih.gov/gene/?term=230126	BC028832	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006753	23012	STK38L	http://www.ncbi.nlm.nih.gov/gene/?term=23012	NDR2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006754	23012	STK38L	http://www.ncbi.nlm.nih.gov/gene/?term=23012	NDR2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006755	23013	SPEN	http://www.ncbi.nlm.nih.gov/gene/?term=23013	"HIAA0929, MINT, RBM15C, SHARP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006756	23013	SPEN	http://www.ncbi.nlm.nih.gov/gene/?term=23013	"HIAA0929, MINT, RBM15C, SHARP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006757	23014	FBXO21	http://www.ncbi.nlm.nih.gov/gene/?term=23014	FBX21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006758	23014	FBXO21	http://www.ncbi.nlm.nih.gov/gene/?term=23014	FBX21	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006759	230157	Tmeff1	http://www.ncbi.nlm.nih.gov/gene/?term=230157	"A830033E11, M7365, Tr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006760	23015	GOLGA8A	http://www.ncbi.nlm.nih.gov/gene/?term=23015	GM88	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006761	230161	Acnat1	http://www.ncbi.nlm.nih.gov/gene/?term=230161	AI132189	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006762	23016	EXOSC7	http://www.ncbi.nlm.nih.gov/gene/?term=23016	"EAP1, RRP42, Rrp42p, hRrp42p, p8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006763	23019	CNOT1	http://www.ncbi.nlm.nih.gov/gene/?term=23019	"AD-005, CDC39, NOT1, NOT1H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006764	23019	CNOT1	http://www.ncbi.nlm.nih.gov/gene/?term=23019	"AD-005, CDC39, NOT1, NOT1H "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006765	23020	SNRNP200	http://www.ncbi.nlm.nih.gov/gene/?term=23020	"ASCC3L1, BRR2, HELIC2, RP33, U5-200KD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006766	23022	PALLD	http://www.ncbi.nlm.nih.gov/gene/?term=23022	"CGI-151, CGI151, MYN, PNCA1, SIH002 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006767	230233	Ikbkap	http://www.ncbi.nlm.nih.gov/gene/?term=230233	"3110040G09Rik, 6030413P05, C78473, Elp1, IKAP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006768	23023	TMCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23023		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006769	230257	Ptbp3	http://www.ncbi.nlm.nih.gov/gene/?term=230257	"5830471K22Rik, AA407443, AI462022, AW107884, C86549, Rod1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006770	230259	E130308A19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=230259		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006771	230259	E130308A19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=230259		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006772	23028	KDM1A	http://www.ncbi.nlm.nih.gov/gene/?term=23028	"AOF2, BHC110, CPRF, KDM1, LSD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006773	23028	KDM1A	http://www.ncbi.nlm.nih.gov/gene/?term=23028	"AOF2, BHC110, CPRF, KDM1, LSD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006774	23029	RBM34	http://www.ncbi.nlm.nih.gov/gene/?term=23029		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006775	23030	KDM4B	http://www.ncbi.nlm.nih.gov/gene/?term=23030	"JMJD2B, TDRD14B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006776	23031	MAST3	http://www.ncbi.nlm.nih.gov/gene/?term=23031		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006777	23031	MAST3	http://www.ncbi.nlm.nih.gov/gene/?term=23031		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006778	23031	MAST3	http://www.ncbi.nlm.nih.gov/gene/?term=23031		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006779	23032	USP33	http://www.ncbi.nlm.nih.gov/gene/?term=23032	VDU1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006780	23032	USP33	http://www.ncbi.nlm.nih.gov/gene/?term=23032	VDU1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006781	23032	USP33	http://www.ncbi.nlm.nih.gov/gene/?term=23032	VDU1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006782	23033	DOPEY1	http://www.ncbi.nlm.nih.gov/gene/?term=23033	"DOP1, KIAA1117, dJ202D23.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006783	23036	ZNF292	http://www.ncbi.nlm.nih.gov/gene/?term=23036	"Nbla00365, ZFP292, ZN-16, Zn-15, bA393I2.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006784	23036	ZNF292	http://www.ncbi.nlm.nih.gov/gene/?term=23036	"Nbla00365, ZFP292, ZN-16, Zn-15, bA393I2.3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006785	230376	Haus6	http://www.ncbi.nlm.nih.gov/gene/?term=230376	"6230416J20Rik, 9830144E06, D4Ertd27e, mKIAA1574 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006786	23038	WDTC1	http://www.ncbi.nlm.nih.gov/gene/?term=23038	"ADP, DCAF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006787	23039	XPO7	http://www.ncbi.nlm.nih.gov/gene/?term=23039	"EXP7, RANBP16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006788	23039	XPO7	http://www.ncbi.nlm.nih.gov/gene/?term=23039	"EXP7, RANBP16 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006789	23039	XPO7	http://www.ncbi.nlm.nih.gov/gene/?term=23039	"EXP7, RANBP16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006790	23041	MON2	http://www.ncbi.nlm.nih.gov/gene/?term=23041		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006791	23041	MON2	http://www.ncbi.nlm.nih.gov/gene/?term=23041		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006792	23042	PDXDC1	http://www.ncbi.nlm.nih.gov/gene/?term=23042	LP8165	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006793	23042	PDXDC1	http://www.ncbi.nlm.nih.gov/gene/?term=23042	LP8165	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006794	23043	TNIK	http://www.ncbi.nlm.nih.gov/gene/?term=23043		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006795	23043	TNIK	http://www.ncbi.nlm.nih.gov/gene/?term=23043		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006796	23046	KIF21B	http://www.ncbi.nlm.nih.gov/gene/?term=23046		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006797	23048	FNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23048	FBP17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006798	23048	FNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23048	FBP17	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006799	23048	FNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23048	FBP17	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006800	23048	FNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23048	FBP17	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006801	23049	SMG1	http://www.ncbi.nlm.nih.gov/gene/?term=23049	"61E3.4, ATX, LIP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006802	23049	SMG1	http://www.ncbi.nlm.nih.gov/gene/?term=23049	"61E3.4, ATX, LIP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006803	23049	SMG1	http://www.ncbi.nlm.nih.gov/gene/?term=23049	"61E3.4, ATX, LIP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006804	23051	ZHX3	http://www.ncbi.nlm.nih.gov/gene/?term=23051	TIX1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006805	23052	ENDOD1	http://www.ncbi.nlm.nih.gov/gene/?term=23052		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006806	23052	ENDOD1	http://www.ncbi.nlm.nih.gov/gene/?term=23052		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006807	23053	ZSWIM8	http://www.ncbi.nlm.nih.gov/gene/?term=23053	KIAA0913	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006808	23054	NCOA6	http://www.ncbi.nlm.nih.gov/gene/?term=23054	"AIB3, ASC2, NRC, PRIP, RAP250, TRBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006809	230558	C8a	http://www.ncbi.nlm.nih.gov/gene/?term=230558		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006810	230594	Zcchc11	http://www.ncbi.nlm.nih.gov/gene/?term=230594	"6030404K05Rik, 9230115F04Rik, PPAPD3, mKIAA0191 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006811	230598	Nrd1	http://www.ncbi.nlm.nih.gov/gene/?term=230598	"2600011I06Rik, AI875733, NRD-C, Nrdc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006812	2305	FOXM1	http://www.ncbi.nlm.nih.gov/gene/?term=2305	"FKHL16, FOXM1B, HFH-11, HFH11, HNF-3, INS-1, MPHOSPH2, MPP-2, MPP2, PIG29, TRIDENT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006813	2305	FOXM1	http://www.ncbi.nlm.nih.gov/gene/?term=2305	"FKHL16B, HFH-11, HFH11, HNF-3, INS-1, MPHOSPH2, MPP-2, MPP2, PIG29, TRIDENT, FOXM1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006814	230603	Ttc39a	http://www.ncbi.nlm.nih.gov/gene/?term=230603	4922503N01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006815	23060	ZNF609	http://www.ncbi.nlm.nih.gov/gene/?term=23060		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006816	23061	TBC1D9B	http://www.ncbi.nlm.nih.gov/gene/?term=23061	GRAMD9B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006817	23061	TBC1D9B	http://www.ncbi.nlm.nih.gov/gene/?term=23061	GRAMD9B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006818	23062	GGA2	http://www.ncbi.nlm.nih.gov/gene/?term=23062	VEAR	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006819	23062	GGA2	http://www.ncbi.nlm.nih.gov/gene/?term=23062	VEAR	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006820	23062	GGA2	http://www.ncbi.nlm.nih.gov/gene/?term=23062	VEAR	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006821	23063	WAPL	http://www.ncbi.nlm.nih.gov/gene/?term=23063	"FOE, KIAA0261, WAPAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006822	23064	SETX	http://www.ncbi.nlm.nih.gov/gene/?term=23064	"ALS4, AOA2, SCAR1, bA479K20.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006823	23064	SETX	http://www.ncbi.nlm.nih.gov/gene/?term=23064	"ALS4, AOA2, SCAR1, bA479K20.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006824	23064	SETX	http://www.ncbi.nlm.nih.gov/gene/?term=23064	"ALS4, AOA2, SCAR1, bA479K20.2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006825	230654	Lrrc41	http://www.ncbi.nlm.nih.gov/gene/?term=230654	"AA409966, AW555107, D630045E04Rik, D730026A16Rik, MUF1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006826	230657	Tmem69	http://www.ncbi.nlm.nih.gov/gene/?term=230657	A630048M13Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006827	23065	EMC1	http://www.ncbi.nlm.nih.gov/gene/?term=23065	KIAA0090	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006828	23065	EMC1	http://www.ncbi.nlm.nih.gov/gene/?term=23065	"CAVIPMR, KIAA0090 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006829	23070	CMTR1	http://www.ncbi.nlm.nih.gov/gene/?term=23070	"FTSJD2, KIAA0082, MTr1, hMTr1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006830	23070	CMTR1	http://www.ncbi.nlm.nih.gov/gene/?term=23070	"FTSJD2, KIAA0082, MTr1, hMTr1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006831	23071	ERP44	http://www.ncbi.nlm.nih.gov/gene/?term=23071	"PDIA10, TXNDC4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006832	230721	Pabpc4	http://www.ncbi.nlm.nih.gov/gene/?term=230721		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006833	23072	HECW1	http://www.ncbi.nlm.nih.gov/gene/?term=23072	NEDL1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006834	230734	Yrdc	http://www.ncbi.nlm.nih.gov/gene/?term=230734	"AV303379, BC023823, IRIP, ITIP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006835	230737	Gnl2	http://www.ncbi.nlm.nih.gov/gene/?term=230737	"BC003262, HUMAUANTIG, Ngp-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006836	23074	UHRF1BP1L	http://www.ncbi.nlm.nih.gov/gene/?term=23074	SHIP164	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006837	23074	UHRF1BP1L	http://www.ncbi.nlm.nih.gov/gene/?term=23074	SHIP164	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006838	230752	Eva1b	http://www.ncbi.nlm.nih.gov/gene/?term=230752	"2610027C15Rik, Fam176b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006839	230753	Thrap3	http://www.ncbi.nlm.nih.gov/gene/?term=230753	"9330151F09Rik, B230333E16Rik, Trap150 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006840	230757	5730409E04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=230757	"7530403E16Rik, AI849033 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006841	23076	RRP1B	http://www.ncbi.nlm.nih.gov/gene/?term=23076	"KIAA0179, NNP1L, Nnp1, PPP1R136, RRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006842	23076	RRP1B	http://www.ncbi.nlm.nih.gov/gene/?term=23076	"KIAA0179, NNP1L, Nnp1, PPP1R136, RRP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006843	23077	MYCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23077	"Myc-bp2, PAM, Phr "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006844	23077	MYCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23077	"Myc-bp2, PAM, Phr "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006845	230784	Sesn2	http://www.ncbi.nlm.nih.gov/gene/?term=230784	"HI95, SEST2, Ses2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006846	23078	VWA8	http://www.ncbi.nlm.nih.gov/gene/?term=23078	KIAA0564	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006847	23078	VWA8	http://www.ncbi.nlm.nih.gov/gene/?term=23078	KIAA0564	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006848	230796	Wdtc1	http://www.ncbi.nlm.nih.gov/gene/?term=230796	"Gm695, adipose, adp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006849	23080	AVL9	http://www.ncbi.nlm.nih.gov/gene/?term=23080	KIAA0241	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006850	23081	KDM4C	http://www.ncbi.nlm.nih.gov/gene/?term=23081	"GASC1, JHDM3C, JMJD2C, TDRD14C "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006851	23082	PPRC1	http://www.ncbi.nlm.nih.gov/gene/?term=23082	PRC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006852	23082	PPRC1	http://www.ncbi.nlm.nih.gov/gene/?term=23082	PRC	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006853	230868	Igsf21	http://www.ncbi.nlm.nih.gov/gene/?term=230868	"BC055811, Gm141 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006854	23086	EXPH5	http://www.ncbi.nlm.nih.gov/gene/?term=23086	"SLAC2-B, SLAC2B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006855	23086	EXPH5	http://www.ncbi.nlm.nih.gov/gene/?term=23086	"SLAC2-B, SLAC2B "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006856	23087	TRIM35	http://www.ncbi.nlm.nih.gov/gene/?term=23087	"HLS5, MAIR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006857	23087	TRIM35	http://www.ncbi.nlm.nih.gov/gene/?term=23087	"HLS5, MAIR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006858	23087	TRIM35	http://www.ncbi.nlm.nih.gov/gene/?term=23087	"HLS5, MAIR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006859	230895	Vps13d	http://www.ncbi.nlm.nih.gov/gene/?term=230895		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006860	23089	PEG10	http://www.ncbi.nlm.nih.gov/gene/?term=23089	"EDR, HB-1, MEF3L, Mar2, Mart2, RGAG3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006861	23089	PEG10	http://www.ncbi.nlm.nih.gov/gene/?term=23089	"EDR, HB-1, MEF3L, Mar2, Mart2, RGAG3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006862	2308	FOXO1	http://www.ncbi.nlm.nih.gov/gene/?term=2308	"FKH1, FKHR, FOXO1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006863	2308	FOXO1	http://www.ncbi.nlm.nih.gov/gene/?term=2308	"FKH1, FKHRA, FOXO1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006864	230903	Fbxo44	http://www.ncbi.nlm.nih.gov/gene/?term=230903	"5730411K09, AV001623, FBG3, FBX30, Fbx6a, Fbxo6a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006865	230903	Fbxo44	http://www.ncbi.nlm.nih.gov/gene/?term=230903	"5730411K09, AV001623, FBG3, FBX30, Fbx6a, Fbxo6a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006866	23091	ZC3H13	http://www.ncbi.nlm.nih.gov/gene/?term=23091	KIAA0853	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006867	23092	ARHGAP26	http://www.ncbi.nlm.nih.gov/gene/?term=23092	"GRAF, GRAF1, OPHN1L, OPHN1L1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006868	23092	ARHGAP26	http://www.ncbi.nlm.nih.gov/gene/?term=23092	"GRAF, GRAF1, OPHN1L, OPHN1L1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006869	23093	TTLL5	http://www.ncbi.nlm.nih.gov/gene/?term=23093	"CORD19, KIAA0998, STAMP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006870	23093	TTLL5	http://www.ncbi.nlm.nih.gov/gene/?term=23093	"CORD19, KIAA0998, STAMP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006871	23094	SIPA1L3	http://www.ncbi.nlm.nih.gov/gene/?term=23094	"CTRCT45, SPAL3, SPAR3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006872	230959	Ajap1	http://www.ncbi.nlm.nih.gov/gene/?term=230959	Gm573	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006873	23095	KIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=23095	"CMT2, CMT2A, CMT2A1, HMSNII, KLP, NBLST1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006874	23095	KIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=23095	"CMT2, CMT2A, CMT2A1, HMSNII, KLP, NBLST1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006875	23097	CDK19	http://www.ncbi.nlm.nih.gov/gene/?term=23097	"CDC2L6, CDK11, bA346C16.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006876	23099	ZBTB43	http://www.ncbi.nlm.nih.gov/gene/?term=23099	"ZBTB22B, ZNF-X, ZNF297B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006877	2309	FOXO3	http://www.ncbi.nlm.nih.gov/gene/?term=2309	"AF6q21, FKHRL1, FKHRL1P2, FOXO2, FOXO3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006878	2309	FOXO3	http://www.ncbi.nlm.nih.gov/gene/?term=2309	"AF6q21, FKHRL1, FKHRL1P2, FOXO2A, FOXO3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006879	230	ALDOC	http://www.ncbi.nlm.nih.gov/gene/?term=230	ALDC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006880	230	ALDOC	http://www.ncbi.nlm.nih.gov/gene/?term=230	ALDC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006881	230	ALDOC	http://www.ncbi.nlm.nih.gov/gene/?term=230	ALDC	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00006882	23101	MCF2L2	http://www.ncbi.nlm.nih.gov/gene/?term=23101	ARHGEF22	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006883	23101	MCF2L2	http://www.ncbi.nlm.nih.gov/gene/?term=23101	ARHGEF22	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006884	231050	Galnt11	http://www.ncbi.nlm.nih.gov/gene/?term=231050	"A430075I06Rik, AI648252, E430002F06Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006885	231051	Kmt2c	http://www.ncbi.nlm.nih.gov/gene/?term=231051	"E330008K23Rik, HALR, Mll3, mKIAA1506 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006886	231051	Kmt2c	http://www.ncbi.nlm.nih.gov/gene/?term=231051	"E330008K23Rik, HALR, Mll3, mKIAA1506 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006887	23107	MRPS27	http://www.ncbi.nlm.nih.gov/gene/?term=23107	"MRP-S27, S27mt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006888	23107	MRPS27	http://www.ncbi.nlm.nih.gov/gene/?term=23107	"MRP-S27, S27mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006889	23107	MRPS27	http://www.ncbi.nlm.nih.gov/gene/?term=23107	"MRP-S27, S27mt "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006890	23107	MRPS27	http://www.ncbi.nlm.nih.gov/gene/?term=23107	"MRP-S27, S27mt "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006891	231086	Hadhb	http://www.ncbi.nlm.nih.gov/gene/?term=231086	"4930479F15Rik, Mtpb, TP-beta "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006892	23108	RAP1GAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23108	"GARNL4, RAP1GA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006893	23111	SPG20	http://www.ncbi.nlm.nih.gov/gene/?term=23111	"SPARTIN, TAHCCP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006894	23112	TNRC6B	http://www.ncbi.nlm.nih.gov/gene/?term=23112		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006895	23112	TNRC6B	http://www.ncbi.nlm.nih.gov/gene/?term=23112		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006896	23112	TNRC6B	http://www.ncbi.nlm.nih.gov/gene/?term=23112		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006897	23116	FAM179B	http://www.ncbi.nlm.nih.gov/gene/?term=23116	KIAA0423	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006898	23117	NPIPB3	http://www.ncbi.nlm.nih.gov/gene/?term=23117	"KIAA0220L, NPIP, NPIPB, NPIPB5, NPIPL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006899	23118	TAB2	http://www.ncbi.nlm.nih.gov/gene/?term=23118	"CHTD2, MAP3K7IP2, TAB-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006900	23118	TAB2	http://www.ncbi.nlm.nih.gov/gene/?term=23118	"CHTD2, MAP3K7IP2, TAB-2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006901	23120	ATP10B	http://www.ncbi.nlm.nih.gov/gene/?term=23120	ATPVB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006902	23122	CLASP2	http://www.ncbi.nlm.nih.gov/gene/?term=23122		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006903	23122	CLASP2	http://www.ncbi.nlm.nih.gov/gene/?term=23122		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006904	23122	CLASP2	http://www.ncbi.nlm.nih.gov/gene/?term=23122		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006905	231238	Sel1l3	http://www.ncbi.nlm.nih.gov/gene/?term=231238	"2310045A20Rik, AI429585, mKIAA0746 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006906	231252	Chrna9	http://www.ncbi.nlm.nih.gov/gene/?term=231252	"2410015I05Rik, Acra9, EG666827, Gm8311 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006907	23125	CAMTA2	http://www.ncbi.nlm.nih.gov/gene/?term=23125		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006908	23127	COLGALT2	http://www.ncbi.nlm.nih.gov/gene/?term=23127	"C1orf17, GLT25D2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006909	23129	PLXND1	http://www.ncbi.nlm.nih.gov/gene/?term=23129	PLEXD1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006910	23130	ATG2A	http://www.ncbi.nlm.nih.gov/gene/?term=23130		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006911	23131	GPATCH8	http://www.ncbi.nlm.nih.gov/gene/?term=23131	"GPATC8, KIAA0553 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006912	23131	GPATCH8	http://www.ncbi.nlm.nih.gov/gene/?term=23131	"GPATC8, KIAA0553 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006913	23131	GPATCH8	http://www.ncbi.nlm.nih.gov/gene/?term=23131	"GPATC8, KIAA0553 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006914	231326	Aasdh	http://www.ncbi.nlm.nih.gov/gene/?term=231326	"A230062G08Rik, A830035E16, Acsf4, U26 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006915	231329	Polr2b	http://www.ncbi.nlm.nih.gov/gene/?term=231329	"Pol2rb, Rpb140, Rpb2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006916	23133	PHF8	http://www.ncbi.nlm.nih.gov/gene/?term=23133	"JHDM1F, MRXSSD, ZNF422 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006917	23135	KDM6B	http://www.ncbi.nlm.nih.gov/gene/?term=23135	JMJD3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006918	23137	SMC5	http://www.ncbi.nlm.nih.gov/gene/?term=23137	SMC5L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006919	23137	SMC5	http://www.ncbi.nlm.nih.gov/gene/?term=23137	SMC5L1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006920	23137	SMC5	http://www.ncbi.nlm.nih.gov/gene/?term=23137	SMC5L1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006921	231380	Uba6	http://www.ncbi.nlm.nih.gov/gene/?term=231380	"4930542H01, 5730469D23Rik, AU021846, AW124799, E1-L2, Ube1l2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006922	231386	Ythdc1	http://www.ncbi.nlm.nih.gov/gene/?term=231386	"A730098D12Rik, C80342, mKIAA1966 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006923	231386	Ythdc1	http://www.ncbi.nlm.nih.gov/gene/?term=231386	"A730098D12Rik, C80342, mKIAA1966 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006924	23139	MAST2	http://www.ncbi.nlm.nih.gov/gene/?term=23139	"MAST205, MTSSK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006925	2313	FLI1	http://www.ncbi.nlm.nih.gov/gene/?term=2313	"EWSR2, SIC-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006926	23140	ZZEF1	http://www.ncbi.nlm.nih.gov/gene/?term=23140	ZZZ4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006927	23140	ZZEF1	http://www.ncbi.nlm.nih.gov/gene/?term=23140	ZZZ4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006928	23140	ZZEF1	http://www.ncbi.nlm.nih.gov/gene/?term=23140	ZZZ4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006929	231413	Grsf1	http://www.ncbi.nlm.nih.gov/gene/?term=231413	"BB232551, C80280, D5Wsu31e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006930	23141	ANKLE2	http://www.ncbi.nlm.nih.gov/gene/?term=23141	"KIAA0692, LEMD7, Lem4, MCPH16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006931	23142	DCUN1D4	http://www.ncbi.nlm.nih.gov/gene/?term=23142		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006932	23143	LRCH1	http://www.ncbi.nlm.nih.gov/gene/?term=23143	"CHDC1, NP81 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006933	231452	Sdad1	http://www.ncbi.nlm.nih.gov/gene/?term=231452	"4931421J16, AA591032, AW538460 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006934	231474	Paqr3	http://www.ncbi.nlm.nih.gov/gene/?term=231474	"6330415A20Rik, AY424292, RKTG "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006935	23149	FCHO1	http://www.ncbi.nlm.nih.gov/gene/?term=23149		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006936	2314	FLII	http://www.ncbi.nlm.nih.gov/gene/?term=2314	"FLI, FLIL, Fli1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006937	2314	FLII	http://www.ncbi.nlm.nih.gov/gene/?term=2314	"FLI, FLIL, Fli1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006938	2314	FLII	http://www.ncbi.nlm.nih.gov/gene/?term=2314	"FLI, FLIL, Fli1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006939	231503	Tmem150c	http://www.ncbi.nlm.nih.gov/gene/?term=231503		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006940	23151	GRAMD4	http://www.ncbi.nlm.nih.gov/gene/?term=23151	"DIP, dA59H18.1, dJ439F8.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006941	23152	CIC	http://www.ncbi.nlm.nih.gov/gene/?term=23152		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006942	23154	NCDN	http://www.ncbi.nlm.nih.gov/gene/?term=23154		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006943	23155	CLCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23155	MCLC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006944	23155	CLCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23155	MCLC	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006945	23155	CLCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23155	MCLC	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006946	2315	MLANA	http://www.ncbi.nlm.nih.gov/gene/?term=2315	"MART-1, MART1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006947	231600	Chfr	http://www.ncbi.nlm.nih.gov/gene/?term=231600	"5730484M20Rik, C230082M18, RNF116 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006948	23160	WDR43	http://www.ncbi.nlm.nih.gov/gene/?term=23160	"NET12, UTP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006949	23161	SNX13	http://www.ncbi.nlm.nih.gov/gene/?term=23161	RGS-PX1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006950	231637	Ssh1	http://www.ncbi.nlm.nih.gov/gene/?term=231637	"AW551225, Gm1394, Gm1395, SSH-1, mSSH-1L "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006951	231637	Ssh1	http://www.ncbi.nlm.nih.gov/gene/?term=231637	"AW551225, Gm1394, Gm1395, SSH-1, mSSH-1L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006952	23163	GGA3	http://www.ncbi.nlm.nih.gov/gene/?term=23163		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006953	231646	Myo1h	http://www.ncbi.nlm.nih.gov/gene/?term=231646	4631401O15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006954	23164	MPRIP	http://www.ncbi.nlm.nih.gov/gene/?term=23164	"M-RIP, MRIP, RHOIP3, RIP3, p116Rip "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006955	23164	MPRIP	http://www.ncbi.nlm.nih.gov/gene/?term=23164	"M-RIP, MRIP, RHOIP3, RIP3, p116Rip "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006956	23164	MPRIP	http://www.ncbi.nlm.nih.gov/gene/?term=23164	"M-RIP, MRIP, RHOIP3, RIP3, p116Rip "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006957	231659	Gcn1l1	http://www.ncbi.nlm.nih.gov/gene/?term=231659	"4932409G22, AL022764, G431004K08Rik, GCN1L, Gcn1, mKIAA0219 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006958	23165	NUP205	http://www.ncbi.nlm.nih.gov/gene/?term=23165	C7orf14	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006959	23165	NUP205	http://www.ncbi.nlm.nih.gov/gene/?term=23165	"C7orf14, NPHS13 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006960	231670	Fbxo21	http://www.ncbi.nlm.nih.gov/gene/?term=231670	"2810425J22Rik, AU016673, mKIAA0875 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006961	231672	Fbxw8	http://www.ncbi.nlm.nih.gov/gene/?term=231672	"4930438M06Rik, FBW6, FBW8, FBXO29, Fbx29 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006962	23167	EFR3A	http://www.ncbi.nlm.nih.gov/gene/?term=23167		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006963	23167	EFR3A	http://www.ncbi.nlm.nih.gov/gene/?term=23167		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006964	23168	RTF1	http://www.ncbi.nlm.nih.gov/gene/?term=23168	"GTL7, KIAA0252 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006965	23168	RTF1	http://www.ncbi.nlm.nih.gov/gene/?term=23168	"GTL7, KIAA0252 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006966	23169	SLC35D1	http://www.ncbi.nlm.nih.gov/gene/?term=23169	UGTREL7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006967	23169	SLC35D1	http://www.ncbi.nlm.nih.gov/gene/?term=23169	UGTREL7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006968	23169	SLC35D1	http://www.ncbi.nlm.nih.gov/gene/?term=23169	UGTREL7	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006969	2316	FLNA	http://www.ncbi.nlm.nih.gov/gene/?term=2316	"ABP-280, ABPX, CSBS, CVD1, FLN, FLN-A, FLN1, FMD, MNS, NHBP, OPD, OPD1, OPD2, XLVD, XMVD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006970	2316	FLNA	http://www.ncbi.nlm.nih.gov/gene/?term=2316	"ABP-280, ABPX, CSBS, CVD1, FLN, FLN-A, FLN1, FMD, MNS, NHBP, OPD, OPD1, OPD2, XLVD, XMVD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006971	2316	FLNA	http://www.ncbi.nlm.nih.gov/gene/?term=2316	"ABP-280, ABPX, CSBS, CVD1, FLN, FLN-A, FLN1, FMD, MNS, NHBP, OPD, OPD1, OPD2, XLVD, XMVD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006972	23170	TTLL12	http://www.ncbi.nlm.nih.gov/gene/?term=23170	dJ526I14.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006973	23170	TTLL12	http://www.ncbi.nlm.nih.gov/gene/?term=23170	dJ526I14.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006974	231713	Naa25	http://www.ncbi.nlm.nih.gov/gene/?term=231713	"4833422K13Rik, A630046C11, AI450868, C330023M02Rik, Mdm20 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006975	231717	Fam109a	http://www.ncbi.nlm.nih.gov/gene/?term=231717	"A230106M15Rik, AU017694, IPIP27A, Ses1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006976	23171	GPD1L	http://www.ncbi.nlm.nih.gov/gene/?term=23171	GPD1-L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006977	23171	GPD1L	http://www.ncbi.nlm.nih.gov/gene/?term=23171	GPD1-L	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006978	23171	GPD1L	http://www.ncbi.nlm.nih.gov/gene/?term=23171	GPD1-L	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006979	23172	FAM175B	http://www.ncbi.nlm.nih.gov/gene/?term=23172	"ABRO1, KIAA0157 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006980	23173	METAP1	http://www.ncbi.nlm.nih.gov/gene/?term=23173	"MAP1A, MetAP1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006981	23173	METAP1	http://www.ncbi.nlm.nih.gov/gene/?term=23173	"MAP1A, MetAP1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006982	23173	METAP1	http://www.ncbi.nlm.nih.gov/gene/?term=23173	"MAP1A, MetAP1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00006983	23174	ZCCHC14	http://www.ncbi.nlm.nih.gov/gene/?term=23174	"BDG-29, BDG29 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006984	23175	LPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=23175	PAP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006985	23175	LPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=23175	PAP1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006986	231769	Sfswap	http://www.ncbi.nlm.nih.gov/gene/?term=231769	"1190005N23Rik, 6330437E22Rik, AI197402, AW212079, SWAP, Sfrs8, Srsf8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006987	23176	SEPT8	http://www.ncbi.nlm.nih.gov/gene/?term=23176	42615	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006988	23177	CEP68	http://www.ncbi.nlm.nih.gov/gene/?term=23177	KIAA0582	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006989	23177	CEP68	http://www.ncbi.nlm.nih.gov/gene/?term=23177	KIAA0582	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006990	23177	CEP68	http://www.ncbi.nlm.nih.gov/gene/?term=23177	KIAA0582	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006991	2317	FLNB	http://www.ncbi.nlm.nih.gov/gene/?term=2317	"ABP-278, ABP-280, AOI, FH1, FLN-B, FLN1L, LRS1, SCT, TABP, TAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006992	2317	FLNB	http://www.ncbi.nlm.nih.gov/gene/?term=2317	"ABP-278, ABP-280, AOI, FH1, FLN-B, FLN1L, LRS1, SCT, TABP, TAP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00006993	231801	Agfg2	http://www.ncbi.nlm.nih.gov/gene/?term=231801	"A630095P14Rik, Hrbl, RAB-R, RABR "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00006994	231805	Pilra	http://www.ncbi.nlm.nih.gov/gene/?term=231805	"AV021745, FDF03 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006995	23181	DIP2A	http://www.ncbi.nlm.nih.gov/gene/?term=23181	"C21orf106, DIP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00006996	23181	DIP2A	http://www.ncbi.nlm.nih.gov/gene/?term=23181	"C21orf106, DIP2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006997	23181	DIP2A	http://www.ncbi.nlm.nih.gov/gene/?term=23181	"C21orf106, DIP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00006998	231821	Adap1	http://www.ncbi.nlm.nih.gov/gene/?term=231821	"4930431P11Rik, Centa1, GC1L, p42IP4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00006999	231830	Micall2	http://www.ncbi.nlm.nih.gov/gene/?term=231830	"A930021H16Rik, JRAB, MICAL-L2, mFLJ00139 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007000	231842	Amz1	http://www.ncbi.nlm.nih.gov/gene/?term=231842	"5330426I05, 6530401C20Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007001	23184	MESDC2	http://www.ncbi.nlm.nih.gov/gene/?term=23184	"BOCA, MESD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007002	23184	MESDC2	http://www.ncbi.nlm.nih.gov/gene/?term=23184	"BOCA, MESD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007003	23185	LARP4B	http://www.ncbi.nlm.nih.gov/gene/?term=23185	"KIAA0217, LARP5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007004	23185	LARP4B	http://www.ncbi.nlm.nih.gov/gene/?term=23185	"KIAA0217, LARP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007005	231866	Zfp12	http://www.ncbi.nlm.nih.gov/gene/?term=231866	"C530015C18, Krox-7, Zfp-12, Znf12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007006	231868	E130309D02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=231868	A630028N22	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007007	23186	RCOR1	http://www.ncbi.nlm.nih.gov/gene/?term=23186	"COREST, RCOR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007008	231874	Ccz1	http://www.ncbi.nlm.nih.gov/gene/?term=231874	AU022870	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007009	23187	PHLDB1	http://www.ncbi.nlm.nih.gov/gene/?term=23187	LL5A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007010	231887	Pdap1	http://www.ncbi.nlm.nih.gov/gene/?term=231887	"HASPP28, PAP, PAP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007011	231889	Bud31	http://www.ncbi.nlm.nih.gov/gene/?term=231889	"C77604, EDG-2, EDG2, G10 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007012	23189	KANK1	http://www.ncbi.nlm.nih.gov/gene/?term=23189	"ANKRD15, CPSQ2, KANK "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007013	23190	UBXN4	http://www.ncbi.nlm.nih.gov/gene/?term=23190	"UBXD2, UBXDC1, erasin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007014	23190	UBXN4	http://www.ncbi.nlm.nih.gov/gene/?term=23190	"UBXD2, UBXDC1, erasin "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007015	23190	UBXN4	http://www.ncbi.nlm.nih.gov/gene/?term=23190	"UBXD2, UBXDC1, erasin "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007016	23190	UBXN4	http://www.ncbi.nlm.nih.gov/gene/?term=23190	"UBXD2, UBXDC1, erasin "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007017	23191	CYFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=23191	"P140SRA-1, SHYC, SRA-1, SRA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007018	23191	CYFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=23191	"P140SRA-1, SHYC, SRA-1, SRA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007019	23192	ATG4B	http://www.ncbi.nlm.nih.gov/gene/?term=23192	"APG4B, AUTL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007020	231931	Gimap6	http://www.ncbi.nlm.nih.gov/gene/?term=231931	"4833419H03Rik, Ian6, mFLJ00102 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007021	23193	GANAB	http://www.ncbi.nlm.nih.gov/gene/?term=23193	"G2AN, GIIA, GLUII "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007022	23195	MDN1	http://www.ncbi.nlm.nih.gov/gene/?term=23195	Rea1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007023	23195	MDN1	http://www.ncbi.nlm.nih.gov/gene/?term=23195	Rea1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007024	23196	FAM120A	http://www.ncbi.nlm.nih.gov/gene/?term=23196	"C9orf10, DNAPTP1, DNAPTP5, OSSA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007025	23196	FAM120A	http://www.ncbi.nlm.nih.gov/gene/?term=23196	"C9orf10, DNAPTP1, DNAPTP5, OSSA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007026	23196	FAM120A	http://www.ncbi.nlm.nih.gov/gene/?term=23196	"C9orf10, DNAPTP1, DNAPTP5, OSSA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007027	23197	FAF2	http://www.ncbi.nlm.nih.gov/gene/?term=23197	"ETEA, UBXD8, UBXN3B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007028	23197	FAF2	http://www.ncbi.nlm.nih.gov/gene/?term=23197	"ETEA, UBXD8, UBXN3B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007029	231986	Jazf1	http://www.ncbi.nlm.nih.gov/gene/?term=231986	"AI591476, C820002C15, Jaz1, Tip27 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007030	23198	PSME4	http://www.ncbi.nlm.nih.gov/gene/?term=23198	PA200	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007031	23198	PSME4	http://www.ncbi.nlm.nih.gov/gene/?term=23198	PA200	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007032	23199	GSE1	http://www.ncbi.nlm.nih.gov/gene/?term=23199	KIAA0182	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007033	2319	FLOT2	http://www.ncbi.nlm.nih.gov/gene/?term=2319	"ECS-1, ECS1, ESA, ESA1, M17S1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007034	2319	FLOT2	http://www.ncbi.nlm.nih.gov/gene/?term=2319	"ECS-1, ECS1, ESA, ESA1, M17S1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007035	231	AKR1B1	http://www.ncbi.nlm.nih.gov/gene/?term=231	"ADR, ALDR1, ALR2, AR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007036	23200	ATP11B	http://www.ncbi.nlm.nih.gov/gene/?term=23200	"ATPIF, ATPIR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007037	23200	ATP11B	http://www.ncbi.nlm.nih.gov/gene/?term=23200	"ATPIF, ATPIR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007038	23203	PMPCA	http://www.ncbi.nlm.nih.gov/gene/?term=23203	"Alpha-MPP, INPP5E, P-55, SCAR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007039	23203	PMPCA	http://www.ncbi.nlm.nih.gov/gene/?term=23203	"Alpha-MPP, INPP5E, P-55, SCAR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007040	23204	ARL6IP1	http://www.ncbi.nlm.nih.gov/gene/?term=23204	"AIP1, ARL6IP, ARMER, SPG61 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007041	23204	ARL6IP1	http://www.ncbi.nlm.nih.gov/gene/?term=23204	"AIP1, ARL6IP, ARMER, SPG61 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007042	232087	Mat2a	http://www.ncbi.nlm.nih.gov/gene/?term=232087	D630045P18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007043	23208	SYT11	http://www.ncbi.nlm.nih.gov/gene/?term=23208	"SYT12, sytXI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007044	23208	SYT11	http://www.ncbi.nlm.nih.gov/gene/?term=23208	"SYT12, sytXI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007045	23210	JMJD6	http://www.ncbi.nlm.nih.gov/gene/?term=23210	"PSR, PTDSR, PTDSR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007046	23211	ZC3H4	http://www.ncbi.nlm.nih.gov/gene/?term=23211	C19orf7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007047	23214	XPO6	http://www.ncbi.nlm.nih.gov/gene/?term=23214	"EXP6, RANBP20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007048	23214	XPO6	http://www.ncbi.nlm.nih.gov/gene/?term=23214	"EXP6, RANBP20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007049	232157	Mob1a	http://www.ncbi.nlm.nih.gov/gene/?term=232157	"4022402H07Rik, MOB1, MOB4B, Mobk1b, Mobkl1b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007050	23215	PRRC2C	http://www.ncbi.nlm.nih.gov/gene/?term=23215	"BAT2-iso, BAT2D1, BAT2L2, XTP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007051	23215	PRRC2C	http://www.ncbi.nlm.nih.gov/gene/?term=23215	"BAT2-iso, BAT2D1, BAT2L2, XTP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007052	232187	Smyd5	http://www.ncbi.nlm.nih.gov/gene/?term=232187	"AW536703, NN8-4AG, Rai15, Rrg1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007053	23218	NBEAL2	http://www.ncbi.nlm.nih.gov/gene/?term=23218	"BDPLT4, GPS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007054	232196	C87436	http://www.ncbi.nlm.nih.gov/gene/?term=232196		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007055	23219	FBXO28	http://www.ncbi.nlm.nih.gov/gene/?term=23219	"CENP-30, Fbx28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007056	23219	FBXO28	http://www.ncbi.nlm.nih.gov/gene/?term=23219	"CENP-30, Fbx28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007057	2321	FLT1	http://www.ncbi.nlm.nih.gov/gene/?term=2321	"FLT, FLT-1, VEGFR-1, VEGFR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007058	23220	DTX4	http://www.ncbi.nlm.nih.gov/gene/?term=23220	RNF155	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007059	23220	DTX4	http://www.ncbi.nlm.nih.gov/gene/?term=23220	RNF155	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007060	232236	Ccdc174	http://www.ncbi.nlm.nih.gov/gene/?term=232236	C130022K22Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007061	23224	SYNE2	http://www.ncbi.nlm.nih.gov/gene/?term=23224	"EDMD5, NUA, NUANCE, Nesp2, Nesprin-2, SYNE-2, TROPH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007062	23224	SYNE2	http://www.ncbi.nlm.nih.gov/gene/?term=23224	"EDMD5, NUA, NUANCE, Nesp2, Nesprin-2, SYNE-2, TROPH "	mRNA	Homo sapiens	26272916	Endoplasmic reticulum	U2OS cell	Fluorescence in situ hybridization	"Next, we monitored the localization of nesprin-2 (SYNE2) mRNA, which encodes a giant tail-anchored protein (796 kDa) that is present on the outer nuclear envelope and is involved in nuclear positioning (Luxton et al., 2010). After extraction, about two thirds of the foci remained, indicating that some of this mRNA was anchored to the ER (Fig. 1A,B). To ensure that the FISH signal was specific, we also probed cells that were depleted of the endogenous nesprin-2 mRNA using RNA interference (RNAi). Indeed, small hairpin RNA (shRNA)-treated cells lost 90% of their signal (supplementary material Fig. S1), indicating that our nesprin-2 probes detected the intended target. Like Sec61b, nesprin-2 mRNA largely remained associated with the ER in cells treated with HHT, or puromycin and EDTA. Thus nesprin-2, like Sec61b, can associate with the ER membrane, and this activity is mostly independent of translation. "
RLID00007063	23225	NUP210	http://www.ncbi.nlm.nih.gov/gene/?term=23225	"GP210, POM210 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007064	23225	NUP210	http://www.ncbi.nlm.nih.gov/gene/?term=23225	"GP210, POM210 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007065	23225	NUP210	http://www.ncbi.nlm.nih.gov/gene/?term=23225	"GP210, POM210 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007066	232286	Tmf1	http://www.ncbi.nlm.nih.gov/gene/?term=232286	"7030402D04Rik, Gm153`, Tmf1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007067	23230	VPS13A	http://www.ncbi.nlm.nih.gov/gene/?term=23230	"CHAC, CHOREIN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007068	23231	SEL1L3	http://www.ncbi.nlm.nih.gov/gene/?term=23231	Sel-1L3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007069	232339	Ankrd26	http://www.ncbi.nlm.nih.gov/gene/?term=232339	"5730521P14Rik, BC008111, mKIAA1074 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007070	232341	Wnk1	http://www.ncbi.nlm.nih.gov/gene/?term=232341	"6430573H23Rik, EG406236, Hsn2, Prkwnk1, mKIAA0344 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007071	232341	Wnk1	http://www.ncbi.nlm.nih.gov/gene/?term=232341	"6430573H23Rik, EG406236, Hsn2, Prkwnk1, mKIAA0344 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007072	23234	DNAJC9	http://www.ncbi.nlm.nih.gov/gene/?term=23234	"HDJC9, JDD1, SB73 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007073	23235	SIK2	http://www.ncbi.nlm.nih.gov/gene/?term=23235	"LOH11CR1I, QIK, SIK-2, SNF1LK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007074	23237	ARC	http://www.ncbi.nlm.nih.gov/gene/?term=23237	Arg3.1	mRNA	Homo sapiens	11466419	Dendrite	NIH3T3 cell|Neuro2a cell	In situ hybridization|Northern blot	"More recently, arg3.1/arc became of interest, because after synaptic stimulation, arg3.1/arc mRNA is rapidly induced and distributed to dendritic processes and may be locally translated there to facilitate synapse-specific modifications. "
RLID00007075	23239	PHLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=23239	"PHLPP, PLEKHE1, PPM3A, SCOP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007076	23239	PHLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=23239	"PHLPP, PLEKHE1, PPM3A, SCOP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007077	2323	FLT3LG	http://www.ncbi.nlm.nih.gov/gene/?term=2323	"FL, FLT3L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007078	232409	Clec2e	http://www.ncbi.nlm.nih.gov/gene/?term=232409	"Clra, clr-a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007079	23241	PACS2	http://www.ncbi.nlm.nih.gov/gene/?term=23241	"PACS-2, PACS1L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007080	23241	PACS2	http://www.ncbi.nlm.nih.gov/gene/?term=23241	"PACS-2, PACS1L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007081	23241	PACS2	http://www.ncbi.nlm.nih.gov/gene/?term=23241	"PACS-2, PACS1L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007082	23243	ANKRD28	http://www.ncbi.nlm.nih.gov/gene/?term=23243	"PITK, PPP1R65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007083	23243	ANKRD28	http://www.ncbi.nlm.nih.gov/gene/?term=23243	"PITK, PPP1R65 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007084	23244	PDS5A	http://www.ncbi.nlm.nih.gov/gene/?term=23244	"PIG54, SCC-112, SCC112 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007085	23244	PDS5A	http://www.ncbi.nlm.nih.gov/gene/?term=23244	"PIG54, SCC-112, SCC112 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007086	23248	RPRD2	http://www.ncbi.nlm.nih.gov/gene/?term=23248	"HSPC099, KIAA0460 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007087	23250	ATP11A	http://www.ncbi.nlm.nih.gov/gene/?term=23250	"ATPIH, ATPIS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007088	23250	ATP11A	http://www.ncbi.nlm.nih.gov/gene/?term=23250	"ATPIH, ATPIS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007089	23252	OTUD3	http://www.ncbi.nlm.nih.gov/gene/?term=23252	DUBA4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007090	23252	OTUD3	http://www.ncbi.nlm.nih.gov/gene/?term=23252	DUBA4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007091	23252	OTUD3	http://www.ncbi.nlm.nih.gov/gene/?term=23252	DUBA4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007092	23253	ANKRD12	http://www.ncbi.nlm.nih.gov/gene/?term=23253	"ANCO-2, ANCO1, GAC-1, Nbla00144 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007093	23253	ANKRD12	http://www.ncbi.nlm.nih.gov/gene/?term=23253	"ANCO-2, ANCO1, GAC-1, Nbla00144 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007094	23253	ANKRD12	http://www.ncbi.nlm.nih.gov/gene/?term=23253	"ANCO-2, ANCO1, GAC-1, Nbla00144 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007095	232560	Caprin2	http://www.ncbi.nlm.nih.gov/gene/?term=232560	"C1qdc1, Eeg1, rng140 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007096	232566	Amn1	http://www.ncbi.nlm.nih.gov/gene/?term=232566	"5830467E07Rik, A230083D09, C730024G19Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007097	232566	Amn1	http://www.ncbi.nlm.nih.gov/gene/?term=232566	"5830467E07Rik, A230083D09, C730024G19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007098	23256	SCFD1	http://www.ncbi.nlm.nih.gov/gene/?term=23256	"C14orf163, RA410, SLY1, SLY1P, STXBP1L2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007099	23256	SCFD1	http://www.ncbi.nlm.nih.gov/gene/?term=23256	"C14orf163, RA410, SLY1, SLY1P, STXBP1L2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007100	23258	DENND5A	http://www.ncbi.nlm.nih.gov/gene/?term=23258	RAB6IP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007101	232599	Gm4876	http://www.ncbi.nlm.nih.gov/gene/?term=232599	"B930018B01, EG232599 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007102	23261	CAMTA1	http://www.ncbi.nlm.nih.gov/gene/?term=23261	CANPMR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007103	23261	CAMTA1	http://www.ncbi.nlm.nih.gov/gene/?term=23261	CANPMR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007104	23261	CAMTA1	http://www.ncbi.nlm.nih.gov/gene/?term=23261	CANPMR	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007105	23262	PPIP5K2	http://www.ncbi.nlm.nih.gov/gene/?term=23262	"CFAP160, HISPPD1, IP7K2, VIP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007106	23262	PPIP5K2	http://www.ncbi.nlm.nih.gov/gene/?term=23262	"CFAP160, HISPPD1, IP7K2, VIP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007107	23263	MCF2L	http://www.ncbi.nlm.nih.gov/gene/?term=23263	"ARHGEF14, DBS, OST "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007108	23263	MCF2L	http://www.ncbi.nlm.nih.gov/gene/?term=23263	"ARHGEF14, DBS, OST "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007109	23264	ZC3H7B	http://www.ncbi.nlm.nih.gov/gene/?term=23264	RoXaN	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007110	23265	EXOC7	http://www.ncbi.nlm.nih.gov/gene/?term=23265	"2-5-3p, EX070, EXO70, EXOC1, Exo70p, YJL085W "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007111	23265	EXOC7	http://www.ncbi.nlm.nih.gov/gene/?term=23265	"2-5-3p, EX070, EXO70, EXOC1, Exo70p, YJL085W "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007112	232680	Cpa2	http://www.ncbi.nlm.nih.gov/gene/?term=232680		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007113	232685	Lncpint	http://www.ncbi.nlm.nih.gov/gene/?term=232685	"Lincpint, MNCb-1768, Pint, linc-Pint "	lncRNA	Mus musculus	24070194	Nucleus	Lung tumor cell	qRT-PCR	"Pint is a nuclear lincRNA that directly interacts with the Polycomb repressive complex 2 (PRC2), and is required for PRC2 targeting of specific genes for H3K27 tri-methylation and repression.  "
RLID00007114	23268	DNMBP	http://www.ncbi.nlm.nih.gov/gene/?term=23268	"ARHGEF36, TUBA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007115	23269	MGA	http://www.ncbi.nlm.nih.gov/gene/?term=23269	"MAD5, MXD5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007116	23269	MGA	http://www.ncbi.nlm.nih.gov/gene/?term=23269	"MAD5, MXD5 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007117	2326	FMO1	http://www.ncbi.nlm.nih.gov/gene/?term=2326		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007118	23270	TSPYL4	http://www.ncbi.nlm.nih.gov/gene/?term=23270	dJ486I3.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007119	23272	FAM208A	http://www.ncbi.nlm.nih.gov/gene/?term=23272	"C3orf63, RAP140, se89-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007120	23274	CLEC16A	http://www.ncbi.nlm.nih.gov/gene/?term=23274	"Gop-1, KIAA0350 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007121	23275	POFUT2	http://www.ncbi.nlm.nih.gov/gene/?term=23275	"C21orf80, FUT13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007122	23276	KLHL18	http://www.ncbi.nlm.nih.gov/gene/?term=23276		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007123	23276	KLHL18	http://www.ncbi.nlm.nih.gov/gene/?term=23276		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007124	23277	CLUH	http://www.ncbi.nlm.nih.gov/gene/?term=23277	"CLU1, KIAA0664 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007125	232798	Leng8	http://www.ncbi.nlm.nih.gov/gene/?term=232798	AW049671	mRNA	Mus musculus	22817891	Nucleus	Bone marrow Macrophage	Next-generation sequencing	"Cluster 7, for example, contains abundant transcripts in the chromatin, with much lower transcript levels in the nucleoplasm and cytoplasm relative to the other clusters. This cluster is dominated by annotated and unannotated non-coding transcripts and miRNA precursors. (The analysis excluded transcripts shorter than 400 nucleotides and therefore excluded mature miRNAs and many miRNA precursors.) Some non-coding RNAs, such as Xist, are highly enriched in the chromatin because they function at this location (Figure S2). Examples of other non-coding RNAs in Cluster 7 are Neat1 and Malat1/Neat2 (Figure S2). Further mining of the data sets may provide insights into the subcellular locations at which many non-coding RNAs function. Cluster 7 also includes transcripts from constitutive protein-coding genes that may be highly unstable and therefore present at low levels in the cytoplasm (e.g. Leng8 in Figure S2). "
RLID00007126	23279	NUP160	http://www.ncbi.nlm.nih.gov/gene/?term=23279		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007127	23279	NUP160	http://www.ncbi.nlm.nih.gov/gene/?term=23279		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007128	232801	Lilra5	http://www.ncbi.nlm.nih.gov/gene/?term=232801	"E030017K20, EG232801, Gm4878, Lilrc1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007129	232807	Ppp1r12c	http://www.ncbi.nlm.nih.gov/gene/?term=232807	"2410197A17Rik, AI839747, B430101M08, Mbs85 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007130	232821	Ccdc106	http://www.ncbi.nlm.nih.gov/gene/?term=232821	BC018462	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007131	23283	CSTF2T	http://www.ncbi.nlm.nih.gov/gene/?term=23283	CstF-64T	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007132	23286	WWC1	http://www.ncbi.nlm.nih.gov/gene/?term=23286	"HBEBP3, HBEBP36, KIBRA, MEMRYQTL, PPP1R168 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007133	232875	Zscan18	http://www.ncbi.nlm.nih.gov/gene/?term=232875	EG232875	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007134	23287	AGTPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23287	"CCP1, NNA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007135	23287	AGTPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23287	"CCP1, NNA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007136	23291	FBXW11	http://www.ncbi.nlm.nih.gov/gene/?term=23291	"BTRC2, BTRCP2, FBW1B, FBXW1B, Fbw11, Hos "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007137	23291	FBXW11	http://www.ncbi.nlm.nih.gov/gene/?term=23291	"BTRC2, BTRCP2, FBW1B, FBXW1B, Fbw11, Hos "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007138	232934	Mypop	http://www.ncbi.nlm.nih.gov/gene/?term=232934	"Myodysa, P42pop "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007139	23293	SMG6	http://www.ncbi.nlm.nih.gov/gene/?term=23293	"C17orf31, EST1A, SMG-6, hSMG5/7a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007140	232943	Klc3	http://www.ncbi.nlm.nih.gov/gene/?term=232943	"BC017147, Klct "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007141	232947	Ppp1r37	http://www.ncbi.nlm.nih.gov/gene/?term=232947	"Gm158, Lrrc68 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007142	23294	ANKS1A	http://www.ncbi.nlm.nih.gov/gene/?term=23294	ANKS1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007143	23294	ANKS1A	http://www.ncbi.nlm.nih.gov/gene/?term=23294	ANKS1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007144	23295	MGRN1	http://www.ncbi.nlm.nih.gov/gene/?term=23295	RNF156	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007145	23295	MGRN1	http://www.ncbi.nlm.nih.gov/gene/?term=23295	RNF156	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007146	23295	MGRN1	http://www.ncbi.nlm.nih.gov/gene/?term=23295	RNF156	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007147	23295	MGRN1	http://www.ncbi.nlm.nih.gov/gene/?term=23295	RNF156	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007148	232969	Zfp428	http://www.ncbi.nlm.nih.gov/gene/?term=232969	"2410005H09Rik, AV271806, AW047854, Znf428 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007149	232987	B9d2	http://www.ncbi.nlm.nih.gov/gene/?term=232987	stumpy	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007150	232989	Hnrnpul1	http://www.ncbi.nlm.nih.gov/gene/?term=232989	"E130317O14Rik, E1B-AP5, E1BAP5, Hnrnpul, Hnrpul1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007151	23299	BICD2	http://www.ncbi.nlm.nih.gov/gene/?term=23299	"SMALED2, bA526D8.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007152	23300	ATMIN	http://www.ncbi.nlm.nih.gov/gene/?term=23300	"ASCIZ, ZNF822 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007153	23300	ATMIN	http://www.ncbi.nlm.nih.gov/gene/?term=23300	"ASCIZ, ZNF822 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007154	233016	Blvrb	http://www.ncbi.nlm.nih.gov/gene/?term=233016		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007155	23303	KIF13B	http://www.ncbi.nlm.nih.gov/gene/?term=23303	GAKIN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007156	23304	UBR2	http://www.ncbi.nlm.nih.gov/gene/?term=23304	"C6orf133, bA49A4.1, dJ242G1.1, dJ392M17.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007157	23304	UBR2	http://www.ncbi.nlm.nih.gov/gene/?term=23304	"C6orf133, bA49A4.1, dJ242G1.1, dJ392M17.3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007158	233056	Zfp790	http://www.ncbi.nlm.nih.gov/gene/?term=233056	6330581L23Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007159	233058	Zfp420	http://www.ncbi.nlm.nih.gov/gene/?term=233058	"B230119D13, B230312I18Rik, mszf59-1, mszf70 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007160	233065	Alkbh6	http://www.ncbi.nlm.nih.gov/gene/?term=233065	"AI839550, Abh6, C130099A02 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007161	23306	NEMP1	http://www.ncbi.nlm.nih.gov/gene/?term=23306	"TMEM194, TMEM194A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007162	23306	NEMP1	http://www.ncbi.nlm.nih.gov/gene/?term=23306	"TMEM194, TMEM194A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007163	233079	Ffar2	http://www.ncbi.nlm.nih.gov/gene/?term=233079	"GPCR43, Gpr43 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007164	23308	ICOSLG	http://www.ncbi.nlm.nih.gov/gene/?term=23308	"B7-H2, B7H2, B7RP-1, B7RP1, CD275, GL50, ICOS-L, ICOSL, LICOS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007165	23309	SIN3B	http://www.ncbi.nlm.nih.gov/gene/?term=23309		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007166	23309	SIN3B	http://www.ncbi.nlm.nih.gov/gene/?term=23309		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007167	2330	FMO5	http://www.ncbi.nlm.nih.gov/gene/?term=2330		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007168	23310	NCAPD3	http://www.ncbi.nlm.nih.gov/gene/?term=23310	"CAP-D3, CAPD3, hCAP-D3, hHCP-6, hcp-6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007169	23313	KIAA0930	http://www.ncbi.nlm.nih.gov/gene/?term=23313	"C22orf9, LSC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007170	23314	SATB2	http://www.ncbi.nlm.nih.gov/gene/?term=23314	GLSS	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007171	23317	DNAJC13	http://www.ncbi.nlm.nih.gov/gene/?term=23317	"PARK21, RME8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007172	233189	Ctu1	http://www.ncbi.nlm.nih.gov/gene/?term=233189	"Atpbd3, BC005752 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007173	23318	ZCCHC11	http://www.ncbi.nlm.nih.gov/gene/?term=23318	"PAPD3, TUT4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007174	23318	ZCCHC11	http://www.ncbi.nlm.nih.gov/gene/?term=23318	"PAPD3, TUT4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007175	2331	FMOD	http://www.ncbi.nlm.nih.gov/gene/?term=2331	"FM, SLRR2E "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007176	23321	TRIM2	http://www.ncbi.nlm.nih.gov/gene/?term=23321	"CMT2R, RNF86 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007177	23322	RPGRIP1L	http://www.ncbi.nlm.nih.gov/gene/?term=23322	"CORS3, FTM, JBTS7, MKS5, NPHP8, PPP1R134 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007178	23322	RPGRIP1L	http://www.ncbi.nlm.nih.gov/gene/?term=23322	"CORS3, FTM, JBTS7, MKS5, NPHP8, PPP1R134 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007179	23324	MAN2B2	http://www.ncbi.nlm.nih.gov/gene/?term=23324		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007180	23324	MAN2B2	http://www.ncbi.nlm.nih.gov/gene/?term=23324		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007181	23326	USP22	http://www.ncbi.nlm.nih.gov/gene/?term=23326	USP3L	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007182	23326	USP22	http://www.ncbi.nlm.nih.gov/gene/?term=23326	USP3L	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007183	23326	USP22	http://www.ncbi.nlm.nih.gov/gene/?term=23326	USP3L	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007184	233276	Tubgcp5	http://www.ncbi.nlm.nih.gov/gene/?term=233276	"B130010C12Rik, GCP5, mKIAA1899 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007185	23327	NEDD4L	http://www.ncbi.nlm.nih.gov/gene/?term=23327	"NEDD4-2, NEDD4.2, RSP5, hNEDD4-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007186	23327	NEDD4L	http://www.ncbi.nlm.nih.gov/gene/?term=23327	"NEDD4-2, NEDD4.2, RSP5, hNEDD4-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007187	233280	Nipa1	http://www.ncbi.nlm.nih.gov/gene/?term=233280	"1110027G09Rik, A830014A18Rik, FSP3, Spg6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007188	23328	SASH1	http://www.ncbi.nlm.nih.gov/gene/?term=23328	"SH3D6A, dJ323M4, dJ323M4.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007189	23328	SASH1	http://www.ncbi.nlm.nih.gov/gene/?term=23328	"SH3D6A, dJ323M4, dJ323M4.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007190	23328	SASH1	http://www.ncbi.nlm.nih.gov/gene/?term=23328	"SH3D6A, dJ323M4, dJ323M4.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007191	2332	FMR1	http://www.ncbi.nlm.nih.gov/gene/?term=2332	"FMRP, FRAXA, POF, POF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007192	2332	FMR1	http://www.ncbi.nlm.nih.gov/gene/?term=2332	"FMRP, FRAXA, POF, POF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007193	2332	FMR1	http://www.ncbi.nlm.nih.gov/gene/?term=2332	"FMRP, FRAXA, POF, POF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007194	23331	TTC28	http://www.ncbi.nlm.nih.gov/gene/?term=23331	TPRBK	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007195	23332	CLASP1	http://www.ncbi.nlm.nih.gov/gene/?term=23332	MAST1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007196	23333	DPY19L1	http://www.ncbi.nlm.nih.gov/gene/?term=23333		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007197	23333	DPY19L1	http://www.ncbi.nlm.nih.gov/gene/?term=23333		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007198	23334	SZT2	http://www.ncbi.nlm.nih.gov/gene/?term=23334	"C1orf84, EIEE18, KIAA0467, SZT2A, SZT2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007199	23338	JADE2	http://www.ncbi.nlm.nih.gov/gene/?term=23338	"JADE-2, PHF15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007200	23338	JADE2	http://www.ncbi.nlm.nih.gov/gene/?term=23338	"JADE-2, PHF15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007201	23339	VPS39	http://www.ncbi.nlm.nih.gov/gene/?term=23339	"TLP, VAM6, hVam6p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007202	23339	VPS39	http://www.ncbi.nlm.nih.gov/gene/?term=23339	"TLP, VAM6, hVam6p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007203	23339	VPS39	http://www.ncbi.nlm.nih.gov/gene/?term=23339	"TLP, VAM6, hVam6p "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007204	23339	VPS39	http://www.ncbi.nlm.nih.gov/gene/?term=23339	"TLP, VAM6, hVam6p "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007205	23339	VPS39	http://www.ncbi.nlm.nih.gov/gene/?term=23339	"TLP, VAM6, hVam6p "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007206	233405	Vps33b	http://www.ncbi.nlm.nih.gov/gene/?term=233405		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007207	233406	Prc1	http://www.ncbi.nlm.nih.gov/gene/?term=233406	D7Ertd348e	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007208	23341	DNAJC16	http://www.ncbi.nlm.nih.gov/gene/?term=23341		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007209	23344	ESYT1	http://www.ncbi.nlm.nih.gov/gene/?term=23344	"FAM62A, MBC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007210	23344	ESYT1	http://www.ncbi.nlm.nih.gov/gene/?term=23344	"FAM62A, MBC2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007211	23347	SMCHD1	http://www.ncbi.nlm.nih.gov/gene/?term=23347		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007212	233489	Picalm	http://www.ncbi.nlm.nih.gov/gene/?term=233489	"CALM, CLTH, PAP180, fit-1, fit1, mKIAA4114 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007213	23348	DOCK9	http://www.ncbi.nlm.nih.gov/gene/?term=23348	"ZIZ1, ZIZIMIN1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007214	23350	U2SURP	http://www.ncbi.nlm.nih.gov/gene/?term=23350	"SR140, fSAPa "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007215	23350	U2SURP	http://www.ncbi.nlm.nih.gov/gene/?term=23350	"SR140, fSAPa "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007216	23350	U2SURP	http://www.ncbi.nlm.nih.gov/gene/?term=23350	"SR140, fSAPa "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007217	23351	KHNYN	http://www.ncbi.nlm.nih.gov/gene/?term=23351	KIAA0323	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007218	23351	KHNYN	http://www.ncbi.nlm.nih.gov/gene/?term=23351	KIAA0323	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007219	23352	UBR4	http://www.ncbi.nlm.nih.gov/gene/?term=23352	"RBAF600, ZUBR1, p600 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007220	23352	UBR4	http://www.ncbi.nlm.nih.gov/gene/?term=23352	"RBAF600, ZUBR1, p600 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007221	23352	UBR4	http://www.ncbi.nlm.nih.gov/gene/?term=23352	"RBAF600, ZUBR1, p600 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007222	23353	SUN1	http://www.ncbi.nlm.nih.gov/gene/?term=23353	UNC84A	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007223	23353	SUN1	http://www.ncbi.nlm.nih.gov/gene/?term=23353	UNC84A	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007224	23357	ANGEL1	http://www.ncbi.nlm.nih.gov/gene/?term=23357	"Ccr4e, KIAA0759 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007225	23357	ANGEL1	http://www.ncbi.nlm.nih.gov/gene/?term=23357	"Ccr4e, KIAA0759 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007226	23358	USP24	http://www.ncbi.nlm.nih.gov/gene/?term=23358		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007227	23358	USP24	http://www.ncbi.nlm.nih.gov/gene/?term=23358		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007228	23359	FAM189A1	http://www.ncbi.nlm.nih.gov/gene/?term=23359	TMEM228	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007229	2335	FN1	http://www.ncbi.nlm.nih.gov/gene/?term=2335	"CIG, ED-B, FINC, FN, FNZ, GFND, GFND2, LETS, MSF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007230	2335	FN1	http://www.ncbi.nlm.nih.gov/gene/?term=2335	"CIG, ED-B, FINC, FN, FNZ, GFND, GFND2, LETS, MSF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007231	23360	FNBP4	http://www.ncbi.nlm.nih.gov/gene/?term=23360	FBP30	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007232	23361	ZNF629	http://www.ncbi.nlm.nih.gov/gene/?term=23361	"ZNF, ZNF65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007233	23362	PSD3	http://www.ncbi.nlm.nih.gov/gene/?term=23362	"EFA6D, EFA6R, HCA67 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007234	23362	PSD3	http://www.ncbi.nlm.nih.gov/gene/?term=23362	"EFA6D, EFA6R, HCA67 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007235	23363	OBSL1	http://www.ncbi.nlm.nih.gov/gene/?term=23363		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007236	23365	ARHGEF12	http://www.ncbi.nlm.nih.gov/gene/?term=23365	"LARG, PRO2792 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007237	23365	ARHGEF12	http://www.ncbi.nlm.nih.gov/gene/?term=23365	"LARG, PRO2792 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007238	23365	ARHGEF12	http://www.ncbi.nlm.nih.gov/gene/?term=23365	"LARG, PRO2792 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007239	23367	LARP1	http://www.ncbi.nlm.nih.gov/gene/?term=23367	LARP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007240	23367	LARP1	http://www.ncbi.nlm.nih.gov/gene/?term=23367	LARP	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007241	23369	PUM2	http://www.ncbi.nlm.nih.gov/gene/?term=23369	"PUMH2, PUML2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007242	23369	PUM2	http://www.ncbi.nlm.nih.gov/gene/?term=23369	"PUMH2, PUML2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007243	23369	PUM2	http://www.ncbi.nlm.nih.gov/gene/?term=23369	"PUMH2, PUML2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007244	23370	ARHGEF18	http://www.ncbi.nlm.nih.gov/gene/?term=23370	P114-RhoGEF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007245	233726	Ipo7	http://www.ncbi.nlm.nih.gov/gene/?term=233726	"A330055O14Rik, C330016G14, Imp7, Ranbp7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007246	233733	Galnt18	http://www.ncbi.nlm.nih.gov/gene/?term=233733	"2900011G21Rik, BC024988, Galntl4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007247	23373	CRTC1	http://www.ncbi.nlm.nih.gov/gene/?term=23373	"MECT1, TORC-1, TORC1, WAMTP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007248	233744	Spon1	http://www.ncbi.nlm.nih.gov/gene/?term=233744	"AI666765, AW455831, BC020531, D330035F22Rik, FSP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007249	23376	UFL1	http://www.ncbi.nlm.nih.gov/gene/?term=23376	"KIAA0776, Maxer, NLBP, RCAD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007250	23376	UFL1	http://www.ncbi.nlm.nih.gov/gene/?term=23376	"KIAA0776, Maxer, NLBP, RCAD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007251	23378	RRP8	http://www.ncbi.nlm.nih.gov/gene/?term=23378	"KIAA0409, NML "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007252	23378	RRP8	http://www.ncbi.nlm.nih.gov/gene/?term=23378	"KIAA0409, NML "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007253	23379	ICE1	http://www.ncbi.nlm.nih.gov/gene/?term=23379	KIAA0947	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007254	233802	Thumpd1	http://www.ncbi.nlm.nih.gov/gene/?term=233802	6330575P11Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007255	23381	SMG5	http://www.ncbi.nlm.nih.gov/gene/?term=23381	"EST1B, LPTS-RP1, LPTSRP1, SMG-5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007256	233833	Tnrc6a	http://www.ncbi.nlm.nih.gov/gene/?term=233833	"2010321I05Rik, 3110054G10Rik, AW557223, CAGH26, D130023A07Rik, GW182, Tnrc6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007257	233833	Tnrc6a	http://www.ncbi.nlm.nih.gov/gene/?term=233833	"2010321I05Rik, 3110054G10Rik, AW557223, CAGH26, D130023A07Rik, GW182, Tnrc6 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007258	23383	MAU2	http://www.ncbi.nlm.nih.gov/gene/?term=23383	"KIAA0892L, SCC4, mau-2, MAU2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007259	23384	SPECC1L	http://www.ncbi.nlm.nih.gov/gene/?term=23384	"CYTSA, GBBB2, OBLFC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007260	23385	NCSTN	http://www.ncbi.nlm.nih.gov/gene/?term=23385	ATAG1874	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007261	23385	NCSTN	http://www.ncbi.nlm.nih.gov/gene/?term=23385	ATAG1874	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007262	23386	NUDCD3	http://www.ncbi.nlm.nih.gov/gene/?term=23386	NudCL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007263	233877	Kctd13	http://www.ncbi.nlm.nih.gov/gene/?term=233877	"1500003N18Rik, AV259508, PDIP1alpha, Pdip1, Poldip1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007264	23387	SIK3	http://www.ncbi.nlm.nih.gov/gene/?term=23387	"L19, QSK, SIK-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007265	23387	SIK3	http://www.ncbi.nlm.nih.gov/gene/?term=23387	"L19, QSK, SIK-3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007266	23389	MED13L	http://www.ncbi.nlm.nih.gov/gene/?term=23389	"MRFACD, PROSIT240, THRAP2, TRAP240L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007267	23389	MED13L	http://www.ncbi.nlm.nih.gov/gene/?term=23389	"MRFACD, PROSIT240, THRAP2, TRAP240L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007268	233905	Zfp646	http://www.ncbi.nlm.nih.gov/gene/?term=233905	6820429M01	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007269	233908	Fus	http://www.ncbi.nlm.nih.gov/gene/?term=233908	"D430004D17Rik, D930039C12Rik1, Tls, Fus "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007270	23390	ZDHHC17	http://www.ncbi.nlm.nih.gov/gene/?term=23390	"HIP14, HIP3, HSPC294, HYPH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007271	23390	ZDHHC17	http://www.ncbi.nlm.nih.gov/gene/?term=23390	"HIP14, HIP3, HSPC294, HYPH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007272	233918	4933402N03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=233918	4930412O05	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007273	23392	KIAA0368	http://www.ncbi.nlm.nih.gov/gene/?term=23392	ECM29	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007274	23394	ADNP	http://www.ncbi.nlm.nih.gov/gene/?term=23394	"ADNP1, HVDAS, MRD28 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007275	23394	ADNP	http://www.ncbi.nlm.nih.gov/gene/?term=23394	"ADNP1, HVDAS, MRD28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007276	23395	LARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23395	"LEURS, PRLTS4, mtLeuRS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007277	23395	LARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23395	"LEURS, PRLTS4, mtLeuRS "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00007278	23395	LARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23395	"LEURS, PRLTS4, mtLeuRS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007279	23396	PIP5K1C	http://www.ncbi.nlm.nih.gov/gene/?term=23396	"LCCS3, PIP5K-GAMMA, PIP5K1-gamma, PIP5Kgamma "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007280	23397	NCAPH	http://www.ncbi.nlm.nih.gov/gene/?term=23397	"BRRN1, CAP-H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007281	23397	NCAPH	http://www.ncbi.nlm.nih.gov/gene/?term=23397	"BRRN1, CAP-H "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007282	23397	NCAPH	http://www.ncbi.nlm.nih.gov/gene/?term=23397	"BRRN1, CAP-H "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007283	233987	Zfp958	http://www.ncbi.nlm.nih.gov/gene/?term=233987		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007284	23399	CTDNEP1	http://www.ncbi.nlm.nih.gov/gene/?term=23399	"DULLARD, HSA011916, NET56 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007285	2339	FNTA	http://www.ncbi.nlm.nih.gov/gene/?term=2339	"FPTA, PGGT1A, PTAR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007286	2339	FNTA	http://www.ncbi.nlm.nih.gov/gene/?term=2339	"FPTA, PGGT1A, PTAR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007287	23400	ATP13A2	http://www.ncbi.nlm.nih.gov/gene/?term=23400	"CLN12, HSA9947, KRPPD, PARK9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007288	23401	FRAT2	http://www.ncbi.nlm.nih.gov/gene/?term=23401		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007289	234023	Arglu1	http://www.ncbi.nlm.nih.gov/gene/?term=234023	"9430010O03Rik, C130008N12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007290	23403	FBXO46	http://www.ncbi.nlm.nih.gov/gene/?term=23403	"20D7-FC4, FBXO34L, Fbx46 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007291	23404	EXOSC2	http://www.ncbi.nlm.nih.gov/gene/?term=23404	"RRP4, Rrp4p, hRrp4p, p7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007292	23405	DICER1	http://www.ncbi.nlm.nih.gov/gene/?term=23405	"DCR1, Dicer, Dicer1e, HERNA, K12H4.8-LIKE, MNG1, RMSE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007293	23405	DICER1	http://www.ncbi.nlm.nih.gov/gene/?term=23405	"DCR1, Dicer, Dicer1e, HERNA, K12H4.8-LIKE, MNG1, RMSE2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007294	23405	DICER1	http://www.ncbi.nlm.nih.gov/gene/?term=23405	"DCR1, Dicer, Dicer1e, HERNA, K12H4.8-LIKE, MNG1, RMSE2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007295	23406	COTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23406	CLP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007296	23406	COTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23406	CLP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007297	23406	COTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23406	CLP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007298	234076	Tmco3	http://www.ncbi.nlm.nih.gov/gene/?term=234076	"B230339H12Rik, C87304 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007299	23408	SIRT5	http://www.ncbi.nlm.nih.gov/gene/?term=23408	SIR2L5	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007300	23408	SIRT5	http://www.ncbi.nlm.nih.gov/gene/?term=23408	SIR2L5	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007301	23409	SIRT4	http://www.ncbi.nlm.nih.gov/gene/?term=23409	SIR2L4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007302	23410	SIRT3	http://www.ncbi.nlm.nih.gov/gene/?term=23410	SIR2L3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007303	23410	SIRT3	http://www.ncbi.nlm.nih.gov/gene/?term=23410	SIR2L3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007304	23411	SIRT1	http://www.ncbi.nlm.nih.gov/gene/?term=23411	"SIR2, SIR2L1, SIR2alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007305	23411	SIRT1	http://www.ncbi.nlm.nih.gov/gene/?term=23411	"SIR2, SIR2L1, SIR2alpha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007306	23412	COMMD3	http://www.ncbi.nlm.nih.gov/gene/?term=23412	"BUP, C10orf8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007307	23413	NCS1	http://www.ncbi.nlm.nih.gov/gene/?term=23413	"FLUP, FREQ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007308	23413	NCS1	http://www.ncbi.nlm.nih.gov/gene/?term=23413	"FLUP, FREQ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007309	234199	Fgl1	http://www.ncbi.nlm.nih.gov/gene/?term=234199	Mfire1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007310	234203	Zfp353-ps	http://www.ncbi.nlm.nih.gov/gene/?term=234203	Zfp353	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007311	23420	NOMO1	http://www.ncbi.nlm.nih.gov/gene/?term=23420	"Nomo, PM5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007312	23421	ITGB3BP	http://www.ncbi.nlm.nih.gov/gene/?term=23421	"CENP-R, CENPR, HSU37139, NRIF3, TAP20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007313	23421	ITGB3BP	http://www.ncbi.nlm.nih.gov/gene/?term=23421	"CENP-R, CENPR, HSU37139, NRIF3, TAP20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007314	23423	TMED3	http://www.ncbi.nlm.nih.gov/gene/?term=23423	"C15orf22, P24B, p24g4, p26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007315	23424	TDRD7	http://www.ncbi.nlm.nih.gov/gene/?term=23424	"CATC4, PCTAIRE2BP, TRAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007316	23428	SLC7A8	http://www.ncbi.nlm.nih.gov/gene/?term=23428	"LAT2, LPI-PC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007317	23429	RYBP	http://www.ncbi.nlm.nih.gov/gene/?term=23429	"AAP1, APAP-1, DEDAF, YEAF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007318	23429	RYBP	http://www.ncbi.nlm.nih.gov/gene/?term=23429	"AAP1, APAP-1, DEDAF, YEAF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007319	2342	FNTB	http://www.ncbi.nlm.nih.gov/gene/?term=2342	FPTB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007320	234309	Cbr4	http://www.ncbi.nlm.nih.gov/gene/?term=234309	"A730083J17Rik, BC009118 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007321	23431	AP4E1	http://www.ncbi.nlm.nih.gov/gene/?term=23431	"CPSQ4, SPG51, STUT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007322	23431	AP4E1	http://www.ncbi.nlm.nih.gov/gene/?term=23431	"CPSQ4, SPG51, STUT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007323	23434	LINC01565	http://www.ncbi.nlm.nih.gov/gene/?term=23434	"C3orf27, GR6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007324	23434	LINC01565	http://www.ncbi.nlm.nih.gov/gene/?term=23434	"C3orf27, GR6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007325	23435	TARDBP	http://www.ncbi.nlm.nih.gov/gene/?term=23435	"ALS10, TDP-43 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007326	23435	TARDBP	http://www.ncbi.nlm.nih.gov/gene/?term=23435	"ALS10, TDP-43 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007327	234366	Gatad2a	http://www.ncbi.nlm.nih.gov/gene/?term=234366	"1110066C11Rik, BC031407, C80248 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007328	234374	Ddx49	http://www.ncbi.nlm.nih.gov/gene/?term=234374	R27090_2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007329	234384	Mpv17l2	http://www.ncbi.nlm.nih.gov/gene/?term=234384	Fksg24	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007330	23438	HARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23438	"HARSL, HARSR, HO3, PRLTS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007331	23438	HARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23438	"HARSL, HARSR, HO3, PRLTS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007332	23438	HARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23438	"HARSL, HARSR, HO3, PRLTS2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007333	23439	ATP1B4	http://www.ncbi.nlm.nih.gov/gene/?term=23439		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007334	23439	ATP1B4	http://www.ncbi.nlm.nih.gov/gene/?term=23439		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007335	234404	Nxnl1	http://www.ncbi.nlm.nih.gov/gene/?term=234404	"A930031O08Rik, RdCVF, Txnl6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007336	234413	Zfp961	http://www.ncbi.nlm.nih.gov/gene/?term=234413	"A230105L22Rik, BC065788, mszf37, mszf55-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007337	23443	SLC35A3	http://www.ncbi.nlm.nih.gov/gene/?term=23443	AMRS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007338	23443	SLC35A3	http://www.ncbi.nlm.nih.gov/gene/?term=23443	AMRS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007339	234463	Tmem184c	http://www.ncbi.nlm.nih.gov/gene/?term=234463	"8430433H16Rik, AI645453, AL033298, BC004056, Tmem34 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007340	23446	SLC44A1	http://www.ncbi.nlm.nih.gov/gene/?term=23446	"CD92, CDW92, CHTL1, CTL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007341	23446	SLC44A1	http://www.ncbi.nlm.nih.gov/gene/?term=23446	"CD92, CDW92, CHTL1, CTL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007342	23450	SF3B3	http://www.ncbi.nlm.nih.gov/gene/?term=23450	"RSE1, SAP130, SF3b130, STAF130 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007343	23450	SF3B3	http://www.ncbi.nlm.nih.gov/gene/?term=23450	"RSE1, SAP130, SF3b130, STAF130 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007344	23451	SF3B1	http://www.ncbi.nlm.nih.gov/gene/?term=23451	"Hsh155, MDS, PRP10, PRPF10, SAP155, SF3b155 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007345	23456	ABCB10	http://www.ncbi.nlm.nih.gov/gene/?term=23456	"EST20237, M-ABC2, MTABC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007346	23456	ABCB10	http://www.ncbi.nlm.nih.gov/gene/?term=23456	"EST20237, M-ABC2, MTABC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007347	234594	Cnot1	http://www.ncbi.nlm.nih.gov/gene/?term=234594	"6030411K04Rik, AA815922, D830048B13 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007348	23461	ABCA5	http://www.ncbi.nlm.nih.gov/gene/?term=23461	"ABC13, EST90625 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007349	23461	ABCA5	http://www.ncbi.nlm.nih.gov/gene/?term=23461	"ABC13, EST90625 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007350	23461	ABCA5	http://www.ncbi.nlm.nih.gov/gene/?term=23461	"ABC13, EST90625 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007351	23461	ABCA5	http://www.ncbi.nlm.nih.gov/gene/?term=23461	"ABC13, EST90625 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007352	234624	A330008L17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=234624		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007353	23462	HEY1	http://www.ncbi.nlm.nih.gov/gene/?term=23462	"BHLHb31, CHF2, HERP2, HESR1, HRT-1, OAF1, hHRT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007354	23463	ICMT	http://www.ncbi.nlm.nih.gov/gene/?term=23463	"HSTE14, MST098, MSTP098, PCCMT, PCMT, PPMT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007355	23463	ICMT	http://www.ncbi.nlm.nih.gov/gene/?term=23463	"HSTE14, MST098, MSTP098, PCCMT, PCMT, PPMT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007356	23463	ICMT	http://www.ncbi.nlm.nih.gov/gene/?term=23463	"HSTE14, MST098, MSTP098, PCCMT, PCMT, PPMT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007357	23463	ICMT	http://www.ncbi.nlm.nih.gov/gene/?term=23463	"HSTE14, MST098, MSTP098, PCCMT, PCMT, PPMT "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007358	23463	ICMT	http://www.ncbi.nlm.nih.gov/gene/?term=23463	"HSTE14, MST098, MSTP098, PCCMT, PCMT, PPMT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007359	23464	GCAT	http://www.ncbi.nlm.nih.gov/gene/?term=23464	KBL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007360	23464	GCAT	http://www.ncbi.nlm.nih.gov/gene/?term=23464	KBL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007361	234663	Dync1li2	http://www.ncbi.nlm.nih.gov/gene/?term=234663	"AA409702, C920003I06, Dncli2, Dnclic2, LIC2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007362	23466	CBX6	http://www.ncbi.nlm.nih.gov/gene/?term=23466		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007363	23466	CBX6	http://www.ncbi.nlm.nih.gov/gene/?term=23466		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007364	23468	CBX5	http://www.ncbi.nlm.nih.gov/gene/?term=23468	"HEL25, HP1, HP1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007365	23468	CBX5	http://www.ncbi.nlm.nih.gov/gene/?term=23468	"HEL25, HP1, HP1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007366	23468	CBX5	http://www.ncbi.nlm.nih.gov/gene/?term=23468	"HEL25, HP1, HP1A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007367	23468	CBX5	http://www.ncbi.nlm.nih.gov/gene/?term=23468	"HEL25, HP1, HP1A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007368	234695	Rltpr	http://www.ncbi.nlm.nih.gov/gene/?term=234695	"CARMIL2, CG1399-PB, D130029J02Rik, Gm585 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007369	23469	PHF3	http://www.ncbi.nlm.nih.gov/gene/?term=23469		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007370	23469	PHF3	http://www.ncbi.nlm.nih.gov/gene/?term=23469		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007371	234703	Rpl10-ps2	http://www.ncbi.nlm.nih.gov/gene/?term=234703	"EG234703, Gm4892 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007372	23471	TRAM1	http://www.ncbi.nlm.nih.gov/gene/?term=23471	"PNAS8, TRAM, TRAMP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007373	23471	TRAM1	http://www.ncbi.nlm.nih.gov/gene/?term=23471	"PNAS8, TRAM, TRAMP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007374	23471	TRAM1	http://www.ncbi.nlm.nih.gov/gene/?term=23471	"PNAS8, TRAM, TRAMP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007375	234723	Txnl4b	http://www.ncbi.nlm.nih.gov/gene/?term=234723	"AI595343, D530025J19Rik, DLP, Dim2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007376	234725	Zfp612	http://www.ncbi.nlm.nih.gov/gene/?term=234725	B230354B21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007377	23473	CAPN7	http://www.ncbi.nlm.nih.gov/gene/?term=23473	"CALPAIN7, PALBH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007378	23473	CAPN7	http://www.ncbi.nlm.nih.gov/gene/?term=23473	"CALPAIN7, PALBH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007379	23474	ETHE1	http://www.ncbi.nlm.nih.gov/gene/?term=23474	"HSCO, YF13H12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007380	23475	QPRT	http://www.ncbi.nlm.nih.gov/gene/?term=23475	"HEL-S-90n, QPRTase "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007381	23475	QPRT	http://www.ncbi.nlm.nih.gov/gene/?term=23475	"HEL-S-90nase, QPRT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007382	23476	BRD4	http://www.ncbi.nlm.nih.gov/gene/?term=23476	"CAP, HUNK1, HUNKI, MCAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007383	234797	6430548M08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=234797	"AW049007, Kiaa0513, mKIAA0513 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007384	23479	ISCU	http://www.ncbi.nlm.nih.gov/gene/?term=23479	"2310020H20Rik, HML, ISU2, NIFU, NIFUN, hnifU "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007385	23479	ISCU	http://www.ncbi.nlm.nih.gov/gene/?term=23479	"2310020H20Rik, HML, ISU2, NIFU, NIFUN, hnifU "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007386	23479	ISCU	http://www.ncbi.nlm.nih.gov/gene/?term=23479	"2310020H20Rik, HML, ISU2, NIFU, NIFUN, hnifU "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007387	23480	SEC61G	http://www.ncbi.nlm.nih.gov/gene/?term=23480	SSS1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007388	23480	SEC61G	http://www.ncbi.nlm.nih.gov/gene/?term=23480	SSS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007389	23480	SEC61G	http://www.ncbi.nlm.nih.gov/gene/?term=23480	SSS1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007390	23481	PES1	http://www.ncbi.nlm.nih.gov/gene/?term=23481	PES	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007391	23481	PES1	http://www.ncbi.nlm.nih.gov/gene/?term=23481	PES	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007392	234847	Spg7	http://www.ncbi.nlm.nih.gov/gene/?term=234847	"AI452278, AU015315, Cmar, PGN "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007393	234847	Spg7	http://www.ncbi.nlm.nih.gov/gene/?term=234847	"AI452278, AU015315, Cmar, PGN "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007394	23484	LEPROTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23484	"HSPC112, Vps55, my047 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007395	23484	LEPROTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23484	"HSPC112, Vps55, my047 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007396	234852	Chmp1a	http://www.ncbi.nlm.nih.gov/gene/?term=234852	"2900018H07Rik, Pcoln3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007397	234857	Spire2	http://www.ncbi.nlm.nih.gov/gene/?term=234857	"BC026502, Spir-2, Spir2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007398	234875	Ttc13	http://www.ncbi.nlm.nih.gov/gene/?term=234875	BC017545	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007399	2348	FOLR1	http://www.ncbi.nlm.nih.gov/gene/?term=2348	"FBP, FOLR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007400	234967	Slc36a4	http://www.ncbi.nlm.nih.gov/gene/?term=234967	"6330573I15Rik, PAT4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007401	23498	HAAO	http://www.ncbi.nlm.nih.gov/gene/?term=23498	"3-HAO, HAO "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007402	23499	MACF1	http://www.ncbi.nlm.nih.gov/gene/?term=23499	"ABP620, ACF7, MACF, OFC4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007403	23499	MACF1	http://www.ncbi.nlm.nih.gov/gene/?term=23499	"ABP620, ACF7, MACF, OFC4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007404	23499	MACF1	http://www.ncbi.nlm.nih.gov/gene/?term=23499	"ABP620, ACF7, MACF, OFC4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007405	235040	Atg4d	http://www.ncbi.nlm.nih.gov/gene/?term=235040	"9830134P12Rik, APG4-D, Apg4dl, Autl4, Atg4d "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007406	235047	Zfp809	http://www.ncbi.nlm.nih.gov/gene/?term=235047	"BB114266, C330026E23 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007407	23505	TMEM131	http://www.ncbi.nlm.nih.gov/gene/?term=23505	"CC28, PRO1048, RW1, YR-23 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007408	23506	GLTSCR1L	http://www.ncbi.nlm.nih.gov/gene/?term=23506	KIAA0240	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007409	235072	Sept7	http://www.ncbi.nlm.nih.gov/gene/?term=235072	"Cdc10, E430034N22 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00007410	23507	LRRC8B	http://www.ncbi.nlm.nih.gov/gene/?term=23507	"TA-LRRP, TALRRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007411	23509	POFUT1	http://www.ncbi.nlm.nih.gov/gene/?term=23509	"DDD2, FUT12, O-FUT, O-Fuc-T, O-FucT-1, OFUCT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007412	23509	POFUT1	http://www.ncbi.nlm.nih.gov/gene/?term=23509	"DDD2, FUT12, O-FUT, O-Fuc-T, O-FucT-1, OFUCT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007413	23509	POFUT1	http://www.ncbi.nlm.nih.gov/gene/?term=23509	"DDD2, FUT12, O-FUT, O-Fuc-T, O-FucT-1, OFUCT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007414	23509	POFUT1	http://www.ncbi.nlm.nih.gov/gene/?term=23509	"DDD2, FUT12, O-FUT, O-Fuc-T, O-FucT-1, OFUCT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007415	2350	FOLR2	http://www.ncbi.nlm.nih.gov/gene/?term=2350	"BETA-HFR, FBP, FBP/PL-1, FR-BETA, FR-P3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007416	235106	Ntm	http://www.ncbi.nlm.nih.gov/gene/?term=235106	"6230410L23Rik, B230210G24Rik, Hnt, Igdcc2, R75390 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007417	23510	KCTD2	http://www.ncbi.nlm.nih.gov/gene/?term=23510		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007418	23510	KCTD2	http://www.ncbi.nlm.nih.gov/gene/?term=23510		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007419	23511	NUP188	http://www.ncbi.nlm.nih.gov/gene/?term=23511	"KIAA0169, hNup188 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007420	23512	SUZ12	http://www.ncbi.nlm.nih.gov/gene/?term=23512	"CHET9, JJAZ1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007421	235132	Zbtb44	http://www.ncbi.nlm.nih.gov/gene/?term=235132	"6030404E16Rik, Btbd15, E230011F09 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007422	23513	SCRIB	http://www.ncbi.nlm.nih.gov/gene/?term=23513	"CRIB1, SCRB11, Vartul, SCRIB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007423	23514	SPIDR	http://www.ncbi.nlm.nih.gov/gene/?term=23514	KIAA0146	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007424	23515	MORC3	http://www.ncbi.nlm.nih.gov/gene/?term=23515	"NXP2, ZCW5, ZCWCC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007425	23515	MORC3	http://www.ncbi.nlm.nih.gov/gene/?term=23515	"NXP2, ZCW5, ZCWCC3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007426	23516	SLC39A14	http://www.ncbi.nlm.nih.gov/gene/?term=23516	"LZT-Hs4, NET34, ZIP14, cig19 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007427	23516	SLC39A14	http://www.ncbi.nlm.nih.gov/gene/?term=23516	"LZT-Hs4, NET34, ZIP14, cig19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007428	235184	Msantd2	http://www.ncbi.nlm.nih.gov/gene/?term=235184	"2810450G17Rik, 9530092B10Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007429	23518	R3HDM1	http://www.ncbi.nlm.nih.gov/gene/?term=23518	R3HDM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007430	23518	R3HDM1	http://www.ncbi.nlm.nih.gov/gene/?term=23518	R3HDM	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007431	23521	RPL13A	http://www.ncbi.nlm.nih.gov/gene/?term=23521	"L13A, TSTA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007432	23521	RPL13A	http://www.ncbi.nlm.nih.gov/gene/?term=23521	"L13A, TSTA1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007433	23521	RPL13A	http://www.ncbi.nlm.nih.gov/gene/?term=23521	"L13A, TSTA1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007434	23521	RPL13A	http://www.ncbi.nlm.nih.gov/gene/?term=23521	"L13A, TSTA1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007435	23523	CABIN1	http://www.ncbi.nlm.nih.gov/gene/?term=23523	"CAIN, KB-318B8.7, PPP3IN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007436	23524	SRRM2	http://www.ncbi.nlm.nih.gov/gene/?term=23524	"300-KD, CWF21, Cwc21, HSPC075, SRL300, SRm300 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007437	23526	HMHA1	http://www.ncbi.nlm.nih.gov/gene/?term=23526	"ARHGAP45, HA-1, HLA-HA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007438	23527	ACAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23527	"CENTB2, CNT-B2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007439	23527	ACAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23527	"CENTB2, CNT-B2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007440	23527	ACAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23527	"CENTB2, CNT-B2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007441	235283	Gramd1b	http://www.ncbi.nlm.nih.gov/gene/?term=235283	"3222402H23, A930008A22Rik, AI593249, mKIAA1201 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007442	23528	ZNF281	http://www.ncbi.nlm.nih.gov/gene/?term=23528	"ZBP-99, ZNP-99 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007443	2352	FOLR3	http://www.ncbi.nlm.nih.gov/gene/?term=2352	"FR-G, FR-gamma, gamma-hFR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007444	23530	NNT	http://www.ncbi.nlm.nih.gov/gene/?term=23530	GCCD4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007445	23530	NNT	http://www.ncbi.nlm.nih.gov/gene/?term=23530	GCCD4	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007446	23531	MMD	http://www.ncbi.nlm.nih.gov/gene/?term=23531	"MMA, MMD1, PAQR11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007447	23531	MMD	http://www.ncbi.nlm.nih.gov/gene/?term=23531	"MMA1, PAQR11, MMD "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007448	23531	MMD	http://www.ncbi.nlm.nih.gov/gene/?term=23531	"MMA1, PAQR11, MMD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007449	23532	PRAME	http://www.ncbi.nlm.nih.gov/gene/?term=23532	"CT130, MAPE, OIP-4, OIP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007450	23534	TNPO3	http://www.ncbi.nlm.nih.gov/gene/?term=23534	"IPO12, LGMD1F, MTR10A, TRN-SR, TRN-SR2, TRNSR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007451	23536	ADAT1	http://www.ncbi.nlm.nih.gov/gene/?term=23536	HADAT1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007452	235379	Gldn	http://www.ncbi.nlm.nih.gov/gene/?term=235379	"CRG-L2, Clom, Colm, Crgl2, Crlg2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007453	235380	Dmxl2	http://www.ncbi.nlm.nih.gov/gene/?term=235380	"6330586A12, 6430411K14Rik, E130119P06Rik, mKIAA0856 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007454	2353	FOS	http://www.ncbi.nlm.nih.gov/gene/?term=2353	"AP-1, C-FOS, p55 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007455	2353	FOS	http://www.ncbi.nlm.nih.gov/gene/?term=2353	"AP-1, C-FOS, p55 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007456	235431	Coro2b	http://www.ncbi.nlm.nih.gov/gene/?term=235431	"CLIPINC, E130012P22Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007457	235435	Lctl	http://www.ncbi.nlm.nih.gov/gene/?term=235435	"E130104I05Rik, KLPH "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007458	235439	Herc1	http://www.ncbi.nlm.nih.gov/gene/?term=235439	"2810449H11Rik, B230218H07, D130015N03Rik, tbl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007459	23543	RBFOX2	http://www.ncbi.nlm.nih.gov/gene/?term=23543	"FOX2, Fox-2, HNRBP2, HRNBP2, RBM9, RTA, dJ106I20.3, fxh "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007460	23543	RBFOX2	http://www.ncbi.nlm.nih.gov/gene/?term=23543	"FOX2, Fox-2, HNRBP2, HRNBP2, RBM9, RTA, dJ106I20.3, fxh "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007461	235459	Gtf2a2	http://www.ncbi.nlm.nih.gov/gene/?term=235459	"TFIIA-gamma, TfIIg, Tfiia2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007462	23545	ATP6V0A2	http://www.ncbi.nlm.nih.gov/gene/?term=23545	"A2, ARCL, ARCL2A, ATP6A2, ATP6N1D, J6B7, RTF, STV1, TJ6, TJ6M, TJ6S, VPH1, WSS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007463	23545	ATP6V0A2	http://www.ncbi.nlm.nih.gov/gene/?term=23545	"A2, ARCL, ARCL2A, ATP6A2, ATP6N1D, J6B7, RTF, STV1, TJ6, TJ6M, TJ6S, VPH1, WSS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007464	23545	ATP6V0A2	http://www.ncbi.nlm.nih.gov/gene/?term=23545	"A2, ARCL, ARCL2A, ATP6A2, ATP6N1D, J6B7, RTF, STV1, TJ6, TJ6M, TJ6S, VPH1, WSS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007465	235469	Zfp280d	http://www.ncbi.nlm.nih.gov/gene/?term=235469	"A930005F02Rik, BC027163, Suhw4, ZNF634, Znf280d "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007466	23547	LILRA4	http://www.ncbi.nlm.nih.gov/gene/?term=23547	"CD85g, ILT7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007467	23548	TTC33	http://www.ncbi.nlm.nih.gov/gene/?term=23548	OSRF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007468	235497	Leo1	http://www.ncbi.nlm.nih.gov/gene/?term=235497	Gm185	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007469	23549	DNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=23549	"ASPEP, DAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007470	2354	FOSB	http://www.ncbi.nlm.nih.gov/gene/?term=2354	"AP-1, G0S3, GOS3, GOSB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007471	235504	Slc17a5	http://www.ncbi.nlm.nih.gov/gene/?term=235504	"4631416G20Rik, 4732491M05, AST, ISSD, NSD, SD, SIALIN, SIASD, SLD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007472	23553	HYAL4	http://www.ncbi.nlm.nih.gov/gene/?term=23553	CSHY	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007473	235542	Ppp2r3a	http://www.ncbi.nlm.nih.gov/gene/?term=235542	"3222402P14Rik, A730042E07 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007474	23554	TSPAN12	http://www.ncbi.nlm.nih.gov/gene/?term=23554	"EVR5, NET-2, NET2, TM4SF12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007475	23554	TSPAN12	http://www.ncbi.nlm.nih.gov/gene/?term=23554	"EVR5, NET-2, NET2, TM4SF12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007476	235559	Topbp1	http://www.ncbi.nlm.nih.gov/gene/?term=235559	"1110031N14Rik, 2810429C13Rik, AI256758, D430026L04Rik, mKIAA0259 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007477	23555	TSPAN15	http://www.ncbi.nlm.nih.gov/gene/?term=23555	"2700063A19Rik, NET-7, NET7, TM4SF15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007478	23555	TSPAN15	http://www.ncbi.nlm.nih.gov/gene/?term=23555	"2700063A19Rik, NET-7, NET7, TM4SF15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007479	23555	TSPAN15	http://www.ncbi.nlm.nih.gov/gene/?term=23555	"2700063A19Rik, NET-7, NET7, TM4SF15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007480	235567	Dnajc13	http://www.ncbi.nlm.nih.gov/gene/?term=235567	"D030002L11Rik, Gm1124, RME-8, Rme8, mKIAA0678 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007481	23556	PIGN	http://www.ncbi.nlm.nih.gov/gene/?term=23556	"MCAHS, MCAHS1, MCD4, MDC4, PIG-N "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007482	23556	PIGN	http://www.ncbi.nlm.nih.gov/gene/?term=23556	"MCAHS, MCAHS1, MCD4, MDC4, PIG-N "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007483	23556	PIGN	http://www.ncbi.nlm.nih.gov/gene/?term=23556	"MCAHS, MCAHS1, MCD4, MDC4, PIG-N "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007484	235574	Atp2c1	http://www.ncbi.nlm.nih.gov/gene/?term=235574	"1700121J11Rik, ATP2C1A, AW061228, BCPM, D930003G21Rik, HHD, SPCA, pmr1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007485	23557	SNAPIN	http://www.ncbi.nlm.nih.gov/gene/?term=23557	"BLOC1S7, BLOS7, BORCS3, SNAPAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007486	23557	SNAPIN	http://www.ncbi.nlm.nih.gov/gene/?term=23557	"BLOC1S7, BLOS7, BORCS3, SNAPAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007487	23557	SNAPIN	http://www.ncbi.nlm.nih.gov/gene/?term=23557	"BLOC1S7, BLOS7, BORCS3, SNAPAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007488	23558	WBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23558	"GRAMD6, WBP-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007489	23558	WBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23558	"GRAMD6, WBP-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007490	2355	FOSL2	http://www.ncbi.nlm.nih.gov/gene/?term=2355	FRA2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007491	2355	FOSL2	http://www.ncbi.nlm.nih.gov/gene/?term=2355	FRA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007492	23560	GTPBP4	http://www.ncbi.nlm.nih.gov/gene/?term=23560	"CRFG, NGB, NOG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007493	23560	GTPBP4	http://www.ncbi.nlm.nih.gov/gene/?term=23560	"CRFG, NGB, NOG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007494	23560	GTPBP4	http://www.ncbi.nlm.nih.gov/gene/?term=23560	"CRFG, NGB, NOG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007495	235626	Setd2	http://www.ncbi.nlm.nih.gov/gene/?term=235626	"4921524K10Rik, BC031601, KMT3A "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007496	23563	CHST5	http://www.ncbi.nlm.nih.gov/gene/?term=23563	"I-GlcNAc-6-ST, I-GlcNAc6ST, glcNAc6ST-3, gn6st-3, hIGn6ST "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007497	23563	CHST5	http://www.ncbi.nlm.nih.gov/gene/?term=23563	"I-GlcNAc-6-ST, I-GlcNAc6ST, glcNAc6ST-3, gn6st-3, hIGn6ST "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007498	235661	Dync1li1	http://www.ncbi.nlm.nih.gov/gene/?term=235661	"1110053F02Rik, Dnclic1, LIC-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007499	235682	Zfp445	http://www.ncbi.nlm.nih.gov/gene/?term=235682	"AW610627, ZNF168, Znf445, mszf29, mszf50 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007500	23568	ARL2BP	http://www.ncbi.nlm.nih.gov/gene/?term=23568	"BART, BART1, RP66 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007501	23568	ARL2BP	http://www.ncbi.nlm.nih.gov/gene/?term=23568	"BART, BART1, RP66 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007502	23568	ARL2BP	http://www.ncbi.nlm.nih.gov/gene/?term=23568	"BART, BART1, RP66 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007503	2356	FPGS	http://www.ncbi.nlm.nih.gov/gene/?term=2356		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007504	2356	FPGS	http://www.ncbi.nlm.nih.gov/gene/?term=2356		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007505	23576	DDAH1	http://www.ncbi.nlm.nih.gov/gene/?term=23576	"DDAH, HEL-S-16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007506	23580	CDC42EP4	http://www.ncbi.nlm.nih.gov/gene/?term=23580	"BORG4, CEP4, KAIA1777 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007507	23580	CDC42EP4	http://www.ncbi.nlm.nih.gov/gene/?term=23580	"BORG4, CEP4, KAIA1777 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007508	23580	CDC42EP4	http://www.ncbi.nlm.nih.gov/gene/?term=23580	"BORG4, CEP4, KAIA1777 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007509	23582	CCNDBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23582	"DIP1, GCIP, HHM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007510	23582	CCNDBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23582	"DIP1, GCIP, HHM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007511	23582	CCNDBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23582	"DIP1, GCIP, HHM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007512	23583	SMUG1	http://www.ncbi.nlm.nih.gov/gene/?term=23583	"FDG, HMUDG, UNG3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007513	23585	TMEM50A	http://www.ncbi.nlm.nih.gov/gene/?term=23585	"IFNRC, SMP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007514	23586	DDX58	http://www.ncbi.nlm.nih.gov/gene/?term=23586	"RIG-I, RIGI, RLR-1, SGMRT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007515	23586	DDX58	http://www.ncbi.nlm.nih.gov/gene/?term=23586	"RIG-I, RIGI, RLR-1, SGMRT2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007516	23587	ELP5	http://www.ncbi.nlm.nih.gov/gene/?term=23587	"C17orf81, DERP6, HSPC002, MST071, MSTP071 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007517	23588	KLHDC2	http://www.ncbi.nlm.nih.gov/gene/?term=23588	"HCLP-1, HCLP1, LCP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007518	23588	KLHDC2	http://www.ncbi.nlm.nih.gov/gene/?term=23588	"HCLP-1, HCLP1, LCP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007519	23589	CARHSP1	http://www.ncbi.nlm.nih.gov/gene/?term=23589	"CRHSP-24, CSDC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007520	23589	CARHSP1	http://www.ncbi.nlm.nih.gov/gene/?term=23589	"CRHSP-24, CRHSP24, CSDC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007521	23589	CARHSP1	http://www.ncbi.nlm.nih.gov/gene/?term=23589	"CRHSP-24, CRHSP24, CSDC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007522	23589	CARHSP1	http://www.ncbi.nlm.nih.gov/gene/?term=23589	"CRHSP-24, CRHSP24, CSDC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007523	23589	CARHSP1	http://www.ncbi.nlm.nih.gov/gene/?term=23589	"CRHSP-24, CRHSP24, CSDC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007524	23590	PDSS1	http://www.ncbi.nlm.nih.gov/gene/?term=23590	"COQ1, COQ10D2, DPS, SPS, TPRT, TPT, TPT 1, hDPS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007525	23592	LEMD3	http://www.ncbi.nlm.nih.gov/gene/?term=23592	MAN1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007526	23592	LEMD3	http://www.ncbi.nlm.nih.gov/gene/?term=23592	MAN1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007527	23593	HEBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23593	"C6ORF34B, C6orf34, PP23, SOUL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007528	23593	HEBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23593	"C6ORF34B, C6orf34, PP23, SOUL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007529	23593	HEBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23593	"C6ORF34B, C6orf34, PP23, SOUL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007530	23594	ORC6	http://www.ncbi.nlm.nih.gov/gene/?term=23594	ORC6L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007531	23594	ORC6	http://www.ncbi.nlm.nih.gov/gene/?term=23594	ORC6L	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007532	23595	ORC3	http://www.ncbi.nlm.nih.gov/gene/?term=23595	"LAT, LATHEO, ORC3L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007533	23595	ORC3	http://www.ncbi.nlm.nih.gov/gene/?term=23595	"LAT, LATHEOL, ORC3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007534	23596	OPN3	http://www.ncbi.nlm.nih.gov/gene/?term=23596	"ECPN, PPP1R116 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007535	23597	ACOT9	http://www.ncbi.nlm.nih.gov/gene/?term=23597	"ACATE2, CGI-16, MT-ACT48, MTACT48 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007536	23598	PATZ1	http://www.ncbi.nlm.nih.gov/gene/?term=23598	"MAZR, PATZ, RIAZ, ZBTB19, ZNF278, ZSG, dJ400N23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007537	23600	AMACR	http://www.ncbi.nlm.nih.gov/gene/?term=23600	"AMACRD, CBAS4, RACE, RM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007538	23603	CORO1C	http://www.ncbi.nlm.nih.gov/gene/?term=23603	HCRNN4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007539	23603	CORO1C	http://www.ncbi.nlm.nih.gov/gene/?term=23603	HCRNN4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007540	23607	CD2AP	http://www.ncbi.nlm.nih.gov/gene/?term=23607	CMS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007541	23607	CD2AP	http://www.ncbi.nlm.nih.gov/gene/?term=23607	CMS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007542	23607	CD2AP	http://www.ncbi.nlm.nih.gov/gene/?term=23607	CMS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007543	23608	MKRN1	http://www.ncbi.nlm.nih.gov/gene/?term=23608	RNF61	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007544	23609	MKRN2	http://www.ncbi.nlm.nih.gov/gene/?term=23609	"HSPC070, RNF62 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007545	23612	PHLDA3	http://www.ncbi.nlm.nih.gov/gene/?term=23612	TIH1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007546	23613	ZMYND8	http://www.ncbi.nlm.nih.gov/gene/?term=23613	"PRKCBP1, PRO2893, RACK7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007547	23614	PPY2P	http://www.ncbi.nlm.nih.gov/gene/?term=23614	PPY2	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007548	23614	PPY2P	http://www.ncbi.nlm.nih.gov/gene/?term=23614	PPY2	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00007549	23623	RUSC1	http://www.ncbi.nlm.nih.gov/gene/?term=23623	NESCA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007550	23624	CBLC	http://www.ncbi.nlm.nih.gov/gene/?term=23624	"CBL-3, CBL-SL, RNF57 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007551	23625	FAM89B	http://www.ncbi.nlm.nih.gov/gene/?term=23625	"LRAP25, MTVR, MTVR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007552	236266	Alms1	http://www.ncbi.nlm.nih.gov/gene/?term=236266	bbb	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007553	23627	PRND	http://www.ncbi.nlm.nih.gov/gene/?term=23627	"DOPPEL, DPL, PrPLP, dJ1068H6.4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007554	23627	PRND	http://www.ncbi.nlm.nih.gov/gene/?term=23627	"DOPPEL, DPL, PrPLP, dJ1068H6.4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007555	23633	KPNA6	http://www.ncbi.nlm.nih.gov/gene/?term=23633	"IPOA7, KPNA7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007556	23633	KPNA6	http://www.ncbi.nlm.nih.gov/gene/?term=23633	"IPOA7, KPNA7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007557	23633	KPNA6	http://www.ncbi.nlm.nih.gov/gene/?term=23633	"IPOA7, KPNA7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007558	23635	SSBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23635	"HSPC116, SOSS-B2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007559	23635	SSBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23635	"HSPC116, SOSS-B2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007560	236366	5730507C01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=236366		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007561	23636	NUP62	http://www.ncbi.nlm.nih.gov/gene/?term=23636	"IBSN, SNDI, p62 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007562	23637	RABGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=23637	"GAPCENA, TBC1D11 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007563	23640	HSPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23640	FES1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007564	23640	HSPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23640	FES1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007565	23642	SNHG1	http://www.ncbi.nlm.nih.gov/gene/?term=23642	"LINC00057, NCRNA00057, U22HG, UHG "	lncRNA	Homo sapiens	9671460	Cytoplasm	HeLa cell 	Northern blot	"We investigated the cellular localization of the U17HG RNA. Cell fractionation experiments indicated that U17HG RNA is enriched in the cytoplasm (Fig.5A), similar to UHG RNA, another noncoding snoRNA host having no protein-coding potential (Fig.5B). As expected, U17 snoRNA, used as a control, was found mainly in the nuclear fraction (Fig.5C). "
RLID00007566	23642	SNHG1	http://www.ncbi.nlm.nih.gov/gene/?term=23642	"LINC00057, NCRNA00057, U22HG, UHG "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007567	23644	EDC4	http://www.ncbi.nlm.nih.gov/gene/?term=23644	"GE1, Ge-1, HEDL5, HEDLS, RCD-8, RCD8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007568	23644	EDC4	http://www.ncbi.nlm.nih.gov/gene/?term=23644	"GE1, Ge-1, HEDL5, HEDLS, RCD-8, RCD8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007569	23645	PPP1R15A	http://www.ncbi.nlm.nih.gov/gene/?term=23645	GADD34	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007570	23646	PLD3	http://www.ncbi.nlm.nih.gov/gene/?term=23646	"AD19, HU-K4, HUK4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007571	23647	ARFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=23647	POR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007572	23647	ARFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=23647	POR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007573	23647	ARFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=23647	POR1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007574	23648	SSBP3	http://www.ncbi.nlm.nih.gov/gene/?term=23648	"CSDP, SSDP, SSDP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007575	23649	POLA2	http://www.ncbi.nlm.nih.gov/gene/?term=23649		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007576	23650	TRIM29	http://www.ncbi.nlm.nih.gov/gene/?term=23650	ATDC	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007577	23650	TRIM29	http://www.ncbi.nlm.nih.gov/gene/?term=23650	ATDC	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007578	236537	Zfp352	http://www.ncbi.nlm.nih.gov/gene/?term=236537	2czf48	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007579	236537	Zfp352	http://www.ncbi.nlm.nih.gov/gene/?term=236537	2czf48	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007580	236539	Phgdh	http://www.ncbi.nlm.nih.gov/gene/?term=236539	"3-PGDH, 3PGDH, 4930479N23, A10, PGAD, PGD, PGDH, SERA "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007581	23654	PLXNB2	http://www.ncbi.nlm.nih.gov/gene/?term=23654	"MM1, Nbla00445, PLEXB2, dJ402G11.3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007582	23657	SLC7A11	http://www.ncbi.nlm.nih.gov/gene/?term=23657	"CCBR1, xCT "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007583	23657	SLC7A11	http://www.ncbi.nlm.nih.gov/gene/?term=23657	"CCBR1, xCT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007584	23658	LSM5	http://www.ncbi.nlm.nih.gov/gene/?term=23658	YER146W	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007585	23658	LSM5	http://www.ncbi.nlm.nih.gov/gene/?term=23658	YER146W	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007586	236598	Rn28s1	http://www.ncbi.nlm.nih.gov/gene/?term=236598	28s	rRNA	Mus musculus	25847616	Mitochondrion	Liver	Next-generation sequencing|qRT-PCR	"Both the 28S rRNA and RNase P RNAs were found in the mitochondrial pellet, even at the highest digitonin concentration, where the pellet likely consisted primarily of ruptured inner mitochondrial membranes, suggesting a potential association with the inner mitochondrial membrane. "
RLID00007587	23659	PLA2G15	http://www.ncbi.nlm.nih.gov/gene/?term=23659	"ACS, GXVPLA2, LLPL, LPLA2, LYPLA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007588	23660	ZKSCAN5	http://www.ncbi.nlm.nih.gov/gene/?term=23660	"ZFP-95, ZFP95, ZNF914, ZSCAN37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007589	236643	Sytl5	http://www.ncbi.nlm.nih.gov/gene/?term=236643	"ENSMUSG00000054453, slp5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007590	23666	UBBP4	http://www.ncbi.nlm.nih.gov/gene/?term=23666		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007591	23670	TMEM2	http://www.ncbi.nlm.nih.gov/gene/?term=23670		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007592	23670	TMEM2	http://www.ncbi.nlm.nih.gov/gene/?term=23670		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007593	236732	Rbm10	http://www.ncbi.nlm.nih.gov/gene/?term=236732	E430039K10Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007594	23673	STX12	http://www.ncbi.nlm.nih.gov/gene/?term=23673	"STX13, STX14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007595	236790	Ddx26b	http://www.ncbi.nlm.nih.gov/gene/?term=236790	"4930535D10Rik, 6330505F04Rik, D130066O12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007596	23682	RAB38	http://www.ncbi.nlm.nih.gov/gene/?term=23682	"NY-MEL-1, rrGTPbp "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007597	23682	RAB38	http://www.ncbi.nlm.nih.gov/gene/?term=23682	"NY-MEL-1, rrGTPbp "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007598	23682	RAB38	http://www.ncbi.nlm.nih.gov/gene/?term=23682	"NY-MEL-1, rrGTPbp "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007599	23683	PRKD3	http://www.ncbi.nlm.nih.gov/gene/?term=23683	"EPK2, PKC-NU, PKD3, PRKCN, nPKC-NU "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007600	236930	Ercc6l	http://www.ncbi.nlm.nih.gov/gene/?term=236930	"BC004701, D330021P09Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007601	23704	KCNE4	http://www.ncbi.nlm.nih.gov/gene/?term=23704	MIRP3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007602	23704	KCNE4	http://www.ncbi.nlm.nih.gov/gene/?term=23704	MIRP3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007603	23708	GSPT2	http://www.ncbi.nlm.nih.gov/gene/?term=23708	"ERF3B, GST2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007604	23708	GSPT2	http://www.ncbi.nlm.nih.gov/gene/?term=23708	"ERF3B, GST2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007605	23710	GABARAPL1	http://www.ncbi.nlm.nih.gov/gene/?term=23710	"APG8-LIKE, APG8L, ATG8, ATG8B, ATG8L, GEC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007606	23710	GABARAPL1	http://www.ncbi.nlm.nih.gov/gene/?term=23710	"APG8-LIKE, APG8L, ATG8, ATG8B, ATG8L, GEC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007607	237253	Lrp11	http://www.ncbi.nlm.nih.gov/gene/?term=237253	"1700034J19Rik, 6330533B21, 9830160H19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007608	237300	Gm4922	http://www.ncbi.nlm.nih.gov/gene/?term=237300	"4933423E17, EG237300 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007609	237310	Il22ra2	http://www.ncbi.nlm.nih.gov/gene/?term=237310	"CRF2-10, CRF2-s1, CRF2X, Il-22bp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007610	23731	TMEM245	http://www.ncbi.nlm.nih.gov/gene/?term=23731	"C9orf5, CG-2, CG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007611	23731	TMEM245	http://www.ncbi.nlm.nih.gov/gene/?term=23731	"C9orf5, CG-2, CG2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007612	237336	Tbpl1	http://www.ncbi.nlm.nih.gov/gene/?term=237336	"4732475G08, AW011832, AW491032, D18347, STD, TLF, TRF2, TRP, Tlp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007613	23741	EID1	http://www.ncbi.nlm.nih.gov/gene/?term=23741	"C15orf3, CRI1, EID-1, IRO45620, PNAS-22, PTD014, RBP21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007614	237422	Ric8b	http://www.ncbi.nlm.nih.gov/gene/?term=237422	"BC051080, Ric-8, Ric-8b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007615	23742	NPAP1	http://www.ncbi.nlm.nih.gov/gene/?term=23742	C15orf2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007616	23742	NPAP1	http://www.ncbi.nlm.nih.gov/gene/?term=23742	C15orf2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007617	237436	Gas2l3	http://www.ncbi.nlm.nih.gov/gene/?term=237436	"8430435B07Rik, Gm240 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007618	237459	Cdk17	http://www.ncbi.nlm.nih.gov/gene/?term=237459	"6430598J10Rik, Pctk2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007619	237465	Ccdc38	http://www.ncbi.nlm.nih.gov/gene/?term=237465	4933417K05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007620	237500	Tmtc3	http://www.ncbi.nlm.nih.gov/gene/?term=237500	"9130014E20Rik, B130008E12Rik, mSmile "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007621	23753	SDF2L1	http://www.ncbi.nlm.nih.gov/gene/?term=23753		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007622	23753	SDF2L1	http://www.ncbi.nlm.nih.gov/gene/?term=23753		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007623	237542	Osbpl8	http://www.ncbi.nlm.nih.gov/gene/?term=237542	"AA536976, AA536995, C730029P18Rik, D330025H14Rik, ORP-8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007624	237553	Trhde	http://www.ncbi.nlm.nih.gov/gene/?term=237553	9330155P21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007625	237560	Lrrc10	http://www.ncbi.nlm.nih.gov/gene/?term=237560	"D330003I11Rik, Hrlrrp, Serdin1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007626	23759	PPIL2	http://www.ncbi.nlm.nih.gov/gene/?term=23759	"CYC4, CYP60, Cyp-60, UBOX7, hCyP-60 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007627	23759	PPIL2	http://www.ncbi.nlm.nih.gov/gene/?term=23759	"CYC4, CYP60, Cyp-60, UBOX7, hCyP-60 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007628	23760	PITPNB	http://www.ncbi.nlm.nih.gov/gene/?term=23760	"PI-TP-beta, PtdInsTP, VIB1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007629	237611	Stac3	http://www.ncbi.nlm.nih.gov/gene/?term=237611	9.83E+24	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007630	23761	PISD	http://www.ncbi.nlm.nih.gov/gene/?term=23761	"DJ858B16, PSD, PSDC, PSSC, dJ858B16.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007631	23762	OSBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23762	"HLM, ORP-4, ORP4, OSBPL1, OSBPL4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007632	23764	MAFF	http://www.ncbi.nlm.nih.gov/gene/?term=23764	"U-MAF, hMafF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007633	23764	MAFF	http://www.ncbi.nlm.nih.gov/gene/?term=23764	"U-MAF, hMafF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007634	23764	MAFF	http://www.ncbi.nlm.nih.gov/gene/?term=23764	"U-MAF, hMafF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007635	23765	IL17RA	http://www.ncbi.nlm.nih.gov/gene/?term=23765	"CANDF5, CD217, CDw217, IL-17RA, IL17R, hIL-17R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007636	23768	FLRT2	http://www.ncbi.nlm.nih.gov/gene/?term=23768		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007637	23770	FKBP8	http://www.ncbi.nlm.nih.gov/gene/?term=23770	"FKBP38, FKBPr38 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007638	23770	FKBP8	http://www.ncbi.nlm.nih.gov/gene/?term=23770	"FKBP38, FKBPr38 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007639	237711	Eml6	http://www.ncbi.nlm.nih.gov/gene/?term=237711	"2900083P10Rik, C230094A16Rik, EMAP-6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007640	237730	Fbll1	http://www.ncbi.nlm.nih.gov/gene/?term=237730	AI595406	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007641	237782	Smcr8	http://www.ncbi.nlm.nih.gov/gene/?term=237782	"2310076G09Rik, AI642055, D030073L15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007642	23780	APOL2	http://www.ncbi.nlm.nih.gov/gene/?term=23780	"APOL-II, APOL3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007643	23780	APOL2	http://www.ncbi.nlm.nih.gov/gene/?term=23780	"APOL-II, APOL3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007644	237823	Pfas	http://www.ncbi.nlm.nih.gov/gene/?term=237823	"4432409B16Rik, FGAMS, FGAR-AT, FGARAT, Gm18, PURL, Sofa "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007645	23784	POTEH	http://www.ncbi.nlm.nih.gov/gene/?term=23784	"A26C3, ACTBL1, CT104.7, POTE22 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007646	23784	POTEH	http://www.ncbi.nlm.nih.gov/gene/?term=23784	"A26C3, ACTBL1, CT104.7, POTE22 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007647	237860	Ssh2	http://www.ncbi.nlm.nih.gov/gene/?term=237860	"SSH-2, SSH-2L, mSSH-2L "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007648	23786	BCL2L13	http://www.ncbi.nlm.nih.gov/gene/?term=23786	"BCL-RAMBO, Bcl2-L-13, MIL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007649	23787	MTCH1	http://www.ncbi.nlm.nih.gov/gene/?term=23787	"CGI-64, PIG60, PSAP, SLC25A49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007650	23788	MTCH2	http://www.ncbi.nlm.nih.gov/gene/?term=23788	"HSPC032, MIMP, SLC25A50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007651	23788	MTCH2	http://www.ncbi.nlm.nih.gov/gene/?term=23788	"HSPC032, MIMP, SLC25A50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007652	23790	Coro1c	http://www.ncbi.nlm.nih.gov/gene/?term=23790	"AL022675, AW455561, AW548837 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007653	23792	Adam23	http://www.ncbi.nlm.nih.gov/gene/?term=23792	"AW046396, MDC3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007654	237940	Aoc2	http://www.ncbi.nlm.nih.gov/gene/?term=237940	RAO	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007655	237943	Gpatch8	http://www.ncbi.nlm.nih.gov/gene/?term=237943	"5430405G24Rik, AU018890, ENSMUSG00000075516, Fbm1, Gpatc8, mKIAA0553 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007656	23794	Adamts5	http://www.ncbi.nlm.nih.gov/gene/?term=23794	"9530092O11Rik, ADAM-TS5, ADAMTS1, ADAMTS11, AI481094, ASMP-2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007657	23796	Aplnr	http://www.ncbi.nlm.nih.gov/gene/?term=23796	"APJ, Agtrl1, msr/apj "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007658	238023	Hexdc	http://www.ncbi.nlm.nih.gov/gene/?term=238023	BC069960	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007659	238037	BC068281	http://www.ncbi.nlm.nih.gov/gene/?term=238037	A430092C04	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007660	23806	Arih1	http://www.ncbi.nlm.nih.gov/gene/?term=23806	"AU021774, Ari, Ari1, Hari, Hhari, Ubch7bp, Uip77 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007661	23808	Ash2l	http://www.ncbi.nlm.nih.gov/gene/?term=23808		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007662	238130	Dock4	http://www.ncbi.nlm.nih.gov/gene/?term=238130	"5330406C03, 6330411N01Rik, AF263288, C030023J22, mKIAA0716 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007663	238130	Dock4	http://www.ncbi.nlm.nih.gov/gene/?term=238130	"5330406C03, 6330411N01Rik, AF263288, C030023J22, mKIAA0716 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007664	238252	Gpr135	http://www.ncbi.nlm.nih.gov/gene/?term=238252	PAFR	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007665	23825	Banf1	http://www.ncbi.nlm.nih.gov/gene/?term=23825	"Baf, Bcrp1, L2bp1/Baf "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007666	23830	Capn10	http://www.ncbi.nlm.nih.gov/gene/?term=23830	"AW049679, Capn8, mKIAA1845 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007667	23834	Cdc6	http://www.ncbi.nlm.nih.gov/gene/?term=23834	CDC18L	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007668	23837	Cfdp1	http://www.ncbi.nlm.nih.gov/gene/?term=23837	"AA408409, Bcnt, Bucentaur, Cfdp, cp27 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007669	238386	Btbd7	http://www.ncbi.nlm.nih.gov/gene/?term=238386	"5730507E09Rik, 8030448M07, E130118E17Rik, FUP1, mKIAA1525 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007670	23849	Klf6	http://www.ncbi.nlm.nih.gov/gene/?term=23849	"AI448727, BCD1, C86813, CPBP, Copeb, FM2, FM6, Ierepo1, Ierepo3, R75280, Zf9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007671	23853	Def6	http://www.ncbi.nlm.nih.gov/gene/?term=23853	"2410003F05Rik, 6430538D02Rik, AV094905, Ibp, Slat, Slat2, Slat6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007672	23854	Def8	http://www.ncbi.nlm.nih.gov/gene/?term=23854	"AI449518, D8Ertd713e, DEF-8 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007673	23856	Dido1	http://www.ncbi.nlm.nih.gov/gene/?term=23856	"6720461J16Rik, D130048F08Rik, DATF-1, DIO-1, Datf1, dido "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007674	23857	Dmtf1	http://www.ncbi.nlm.nih.gov/gene/?term=23857	"Dimp, Dmp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007675	23859	Dlg2	http://www.ncbi.nlm.nih.gov/gene/?term=23859	"A330103J02Rik, B230218P12Rik, B330007M19Rik, Dlgh2, Gm1197, PSD93 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007676	23859	Dlg2	http://www.ncbi.nlm.nih.gov/gene/?term=23859	"A330103J02Rik, B230218P12Rik, B330007M19Rik, Dlgh2, Gm1197, PSD93 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007677	238662	Spata31d1b	http://www.ncbi.nlm.nih.gov/gene/?term=238662	"EG238662, Fam75d1b, Gm4934 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007678	238692	Zfp874a	http://www.ncbi.nlm.nih.gov/gene/?term=238692	"C330011K17Rik, Rslcan15, Zfp874 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007679	238693	Zfp58	http://www.ncbi.nlm.nih.gov/gene/?term=238693	"A530094I17Rik, Mfg-1, Mfg1, Rslcan5, Zfp817 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007680	23877	Fiz1	http://www.ncbi.nlm.nih.gov/gene/?term=23877	"AI790204, mFLJ00416 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007681	23881	G3bp2	http://www.ncbi.nlm.nih.gov/gene/?term=23881	"AA409541, E430034L04Rik, G3BP, mKIAA0660 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007682	23885	Gmcl1	http://www.ncbi.nlm.nih.gov/gene/?term=23885	"2810049L19Rik, Gcl, mglc-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007683	238880	Actbl2	http://www.ncbi.nlm.nih.gov/gene/?term=238880	4732495G21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007684	23894	Gtf2h2	http://www.ncbi.nlm.nih.gov/gene/?term=23894	"44kDa, BTF2 p44, BTF2-p44, Btf2p44, p44 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007685	238988	Erc2	http://www.ncbi.nlm.nih.gov/gene/?term=238988	"6430531D06, CAST, CAST1/ERC2, D14Ertd171e, ELKS2alpha "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007686	239037	Lrit1	http://www.ncbi.nlm.nih.gov/gene/?term=239037	"BC032270, Lrrc21 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007687	23918	Impdh2	http://www.ncbi.nlm.nih.gov/gene/?term=23918	IMPD	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00007688	23921	Sh2b2	http://www.ncbi.nlm.nih.gov/gene/?term=23921	Aps	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007689	23922	Jtb	http://www.ncbi.nlm.nih.gov/gene/?term=23922	Gm622	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007690	23927	Krtap14	http://www.ncbi.nlm.nih.gov/gene/?term=23927	"AA589630, Pmg1, mKAP13 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007691	239318	Plcxd3	http://www.ncbi.nlm.nih.gov/gene/?term=239318	B130016O10Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007692	239393	Lrp12	http://www.ncbi.nlm.nih.gov/gene/?term=239393	"AI848829, C820005L12Rik, LRP-12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007693	239408	Tmem74	http://www.ncbi.nlm.nih.gov/gene/?term=239408	"AA549547, B230382K22Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007694	23945	Mgll	http://www.ncbi.nlm.nih.gov/gene/?term=23945	"AA589436, Magl, Mgl "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007695	23950	Dnajb6	http://www.ncbi.nlm.nih.gov/gene/?term=23950	"Mrj, mDj4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007696	239510	Phf20l1	http://www.ncbi.nlm.nih.gov/gene/?term=239510	"CGI-72, E130113K22Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007697	239528	Ago2	http://www.ncbi.nlm.nih.gov/gene/?term=239528	"1110029L17Rik, 2310051F07Rik, AI225898, AL022874, AW546247, ENSMUSG00000072493, Eif2c2, Gerp95, Gm10365, mKIAA4215 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007698	239528	Ago2	http://www.ncbi.nlm.nih.gov/gene/?term=239528	"1110029L17Rik, 2310051F07Rik, AI225898, AL022874, AW546247, ENSMUSG00000072493, Eif2c2, Gerp95, Gm10365, mKIAA4215 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007699	23955	Nek4	http://www.ncbi.nlm.nih.gov/gene/?term=23955	Stk2	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007700	2395	FXN	http://www.ncbi.nlm.nih.gov/gene/?term=2395	"CyaY, FA, FARR, FRDA, X25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007701	2395	FXN	http://www.ncbi.nlm.nih.gov/gene/?term=2395	"CyaY, FA, FARR, FRDA, X25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007702	23964	Tenm2	http://www.ncbi.nlm.nih.gov/gene/?term=23964	"Odz2, Odz3, Ten-2, Ten-m2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007703	23965	Tenm3	http://www.ncbi.nlm.nih.gov/gene/?term=23965	"2610100B16Rik, Odz1, Odz3, Ten-m3, mKIAA1455 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007704	23966	Tenm4	http://www.ncbi.nlm.nih.gov/gene/?term=23966	"Doc4, ELM2, Odz4, R75022, Ten-m4, l(7)-3Rn, l7Rn3, mKIAA1302 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007705	23966	Tenm4	http://www.ncbi.nlm.nih.gov/gene/?term=23966	"Doc4, ELM2, Odz4, R75022, Ten-m4, l(7)-3Rn, l7Rn3, mKIAA1302 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007706	23967	Osr1	http://www.ncbi.nlm.nih.gov/gene/?term=23967	"Odd1, Osr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007707	239706	Mettl22	http://www.ncbi.nlm.nih.gov/gene/?term=239706		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007708	23970	Pacsin2	http://www.ncbi.nlm.nih.gov/gene/?term=23970	AI197433	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007709	239766	Rtp1	http://www.ncbi.nlm.nih.gov/gene/?term=239766	"Gm1766, Gm604 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007710	239833	Lmln	http://www.ncbi.nlm.nih.gov/gene/?term=239833	"5330415H22Rik, AI465495 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007711	239857	Cadm2	http://www.ncbi.nlm.nih.gov/gene/?term=239857	"2900078E11Rik, 9330131D06, A830029E02Rik, Igdf4d, Igsf4d, NECL3, SynCAM 2, SynCAM2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007712	23985	Slc26a4	http://www.ncbi.nlm.nih.gov/gene/?term=23985	"Pds, pendrin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007713	23999	Twf2	http://www.ncbi.nlm.nih.gov/gene/?term=23999	"A6-related, AU014993, Ptk9l, Ptk9r "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007714	239	ALOX12	http://www.ncbi.nlm.nih.gov/gene/?term=239	"12-LOX, 12S-LOX, LOG12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007715	23	ABCF1	http://www.ncbi.nlm.nih.gov/gene/?term=23	"ABC27, ABC50 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007716	23	ABCF1	http://www.ncbi.nlm.nih.gov/gene/?term=23	"ABC27, ABC50 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007717	24001	Tiam2	http://www.ncbi.nlm.nih.gov/gene/?term=24001	"3000002F19Rik, STEF, mKIAA2016 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007718	240028	Lnpep	http://www.ncbi.nlm.nih.gov/gene/?term=240028	"2010309L07Rik, 4732490P18Rik, CAP, IRAP, PLAP, gp160, vp165 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007719	240058	Cpne5	http://www.ncbi.nlm.nih.gov/gene/?term=240058	A830083G22Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007720	240064	Zfp799	http://www.ncbi.nlm.nih.gov/gene/?term=240064	6030490I01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007721	240068	Zfp563	http://www.ncbi.nlm.nih.gov/gene/?term=240068	"D10628, D130054H01, NTfin7, Zfp413 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007722	24014	Rnasel	http://www.ncbi.nlm.nih.gov/gene/?term=24014	E230029I04Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007723	24015	Abce1	http://www.ncbi.nlm.nih.gov/gene/?term=24015	"C79080, Oabp, RLI, RNS41, Rnaseli "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007724	24017	Rnf13	http://www.ncbi.nlm.nih.gov/gene/?term=24017	"2010001H16Rik, Rzf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007725	24018	Rngtt	http://www.ncbi.nlm.nih.gov/gene/?term=24018	"AU020997, HCE, MCE1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007726	240289	Gm4950	http://www.ncbi.nlm.nih.gov/gene/?term=240289	EG240289	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007727	24030	Mrps12	http://www.ncbi.nlm.nih.gov/gene/?term=24030	"AI327385, Rpms12, rps12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007728	240427	Setbp1	http://www.ncbi.nlm.nih.gov/gene/?term=240427	"C130092E12, Seb, mKIAA0437 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007729	24050	Sept3	http://www.ncbi.nlm.nih.gov/gene/?term=24050	"3110018K01Rik, AV154067, B530002E20Rik, Sep3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007730	240514	Ccdc85b	http://www.ncbi.nlm.nih.gov/gene/?term=240514	"AI842788, BB115872 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007731	24051	Sgcb	http://www.ncbi.nlm.nih.gov/gene/?term=24051	"43kDa, AI747103, AI844814, beta-SG "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007732	24058	Sigirr	http://www.ncbi.nlm.nih.gov/gene/?term=24058	"AI256711, TIR8 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007733	240590	Dmrt3	http://www.ncbi.nlm.nih.gov/gene/?term=240590		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007734	24060	Slc35a1	http://www.ncbi.nlm.nih.gov/gene/?term=24060	"AA408150, AI314851 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007735	24061	Smc1a	http://www.ncbi.nlm.nih.gov/gene/?term=24061	"5830426I24Rik, SMC-1A, Sb1.8, Smc1lpha, Smc1l1, Smcb, mKIAA0178, Smc1a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007736	24068	Sra1	http://www.ncbi.nlm.nih.gov/gene/?term=24068	"AA959952, Sra, Srap, Straa1, Strra1 "	lncRNA	Mus musculus	14517287	Nucleus	HeLa cell	In situ hybridization|qRT-PCR	"In addition, in situ analysis traced SRA transcripts to the nuclei of the luminal epithelial cells of the mammary ducts (Fig. 2E, micrographs a to c) and the nuclei of the epithelial cells of the male accessory sex glands (micrographs d to f), showing an almost uniform expression pattern in the mammary glands and seminal vesicles. "
RLID00007737	24068	Sra1	http://www.ncbi.nlm.nih.gov/gene/?term=24068	"AA959952, Sra, Srap, Straa1, Strra1 "	lncRNA	Mus musculus	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/sra/
RLID00007738	24068	Sra1	http://www.ncbi.nlm.nih.gov/gene/?term=24068	"AA959952, Sra, Srap, Straa1, Strra1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00007739	24074	Taf7	http://www.ncbi.nlm.nih.gov/gene/?term=24074	"55kDa, AI607308, BB007175, TAFII55, Taf2f "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007740	240752	Pik3c2b	http://www.ncbi.nlm.nih.gov/gene/?term=240752	"C330011J12Rik, Gm199, PI3K-C2beta, PI3KC2beta "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007741	240776	Kcnt2	http://www.ncbi.nlm.nih.gov/gene/?term=240776	"E330038N15Rik, Slick "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007742	240869	Zbtb37	http://www.ncbi.nlm.nih.gov/gene/?term=240869	D430004I08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007743	24086	Tlk2	http://www.ncbi.nlm.nih.gov/gene/?term=24086	"4933403M19Rik, PKU-alpha, PKUalpha, Tlk "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007744	240899	Lrrc52	http://www.ncbi.nlm.nih.gov/gene/?term=240899	4930413P14Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007745	240899	Lrrc52	http://www.ncbi.nlm.nih.gov/gene/?term=240899	4930413P14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007746	24099	Tnfsf13b	http://www.ncbi.nlm.nih.gov/gene/?term=24099	"BAFF, BLyS, D8Ertd387e, TALL-1, TALL1, THANK, TNFSF20, Tnlg7a, zTNF4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007747	240	ALOX5	http://www.ncbi.nlm.nih.gov/gene/?term=240	"5-LO, 5-LOX, 5LPG, LOG5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007748	24105	Rbck1	http://www.ncbi.nlm.nih.gov/gene/?term=24105	"AL033326, HOIL-1, HOIL-1L, UIP28, Ubce7ip3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007749	241128	Fam124b	http://www.ncbi.nlm.nih.gov/gene/?term=241128	A830043J08Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007750	24113	Vax2	http://www.ncbi.nlm.nih.gov/gene/?term=24113	Dres93	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007751	241263	Gpr158	http://www.ncbi.nlm.nih.gov/gene/?term=241263	"5330427M13Rik, mKIAA1136 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007752	24127	Xrn1	http://www.ncbi.nlm.nih.gov/gene/?term=24127	"Dhm2, exo, mXrn1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007753	24128	Xrn2	http://www.ncbi.nlm.nih.gov/gene/?term=24128		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007754	24135	Zfp68	http://www.ncbi.nlm.nih.gov/gene/?term=24135	"KRAB3, KRAZ2, Zfp70, mszf22, mszf49 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007755	24136	Zeb2	http://www.ncbi.nlm.nih.gov/gene/?term=24136	"9130203F04Rik, D130016B08Rik, SIP1, Zfhx1b, Zfx1b, Zfxh1b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007756	241391	Galnt5	http://www.ncbi.nlm.nih.gov/gene/?term=241391	4832424J23	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007757	24139	EML2	http://www.ncbi.nlm.nih.gov/gene/?term=24139	"ELP70, EMAP-2, EMAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007758	24140	FTSJ1	http://www.ncbi.nlm.nih.gov/gene/?term=24140	"CDLIV, JM23, MRX44, MRX9, SPB1, TRMT7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007759	241431	Xirp2	http://www.ncbi.nlm.nih.gov/gene/?term=241431	"2310003D02Rik, 2310008C07Rik, A530024P18Rik, AI452089, Cmya3, Gm352, Xin2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007760	24144	TFIP11	http://www.ncbi.nlm.nih.gov/gene/?term=24144	"NTR1, Spp382, TIP39, bK445C9.6, hNtr1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007761	24144	TFIP11	http://www.ncbi.nlm.nih.gov/gene/?term=24144	"NTR1, Spp382, TIP39, bK445C9.6, hNtr1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007762	24145	PANX1	http://www.ncbi.nlm.nih.gov/gene/?term=24145	"MRS1, PX1, UNQ2529 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007763	24145	PANX1	http://www.ncbi.nlm.nih.gov/gene/?term=24145	"MRS1, PX1, UNQ2529 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007764	24147	FJX1	http://www.ncbi.nlm.nih.gov/gene/?term=24147		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007765	24148	PRPF6	http://www.ncbi.nlm.nih.gov/gene/?term=24148	"ANT-1, ANT1, C20orf14, Prp6, RP60, SNRNP102, TOM, U5-102K, hPrp6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007766	24148	PRPF6	http://www.ncbi.nlm.nih.gov/gene/?term=24148	"ANT-1, ANT1, C20orf14, Prp6, RP60, SNRNP102, TOM, U5-102K, hPrp6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007767	241490	Rbm45	http://www.ncbi.nlm.nih.gov/gene/?term=241490	"Drb1, Drbp1, G430095G15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007768	24149	ZNF318	http://www.ncbi.nlm.nih.gov/gene/?term=24149	"HRIHFB2436, TZF, ZFP318 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007769	241514	Zfp804a	http://www.ncbi.nlm.nih.gov/gene/?term=241514	"C630007C17Rik, Znf804a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007770	241547	Harbi1	http://www.ncbi.nlm.nih.gov/gene/?term=241547	D230010M03Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007771	241556	Tspan18	http://www.ncbi.nlm.nih.gov/gene/?term=241556	"2610042G18Rik, 6720430O15, BB226562 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007772	241627	Wdr76	http://www.ncbi.nlm.nih.gov/gene/?term=241627	"5830411K18Rik, 6030457D09, AA517836 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007773	24186	Alb	http://www.ncbi.nlm.nih.gov/gene/?term=24186	"Alb1za, Alb "	mRNA	Rattus norvegicus	3301049	Endoplasmic reticulum	Liver	In situ hybridization	"When examined at the ultrastructural level, albumin was localized in the rough endoplasmic reticulum as well as in Golgi complexes located near the nucleus in nearly all these hepatocytes. "
RLID00007774	24186	Alb	http://www.ncbi.nlm.nih.gov/gene/?term=24186	"Alb1za, Alb "	mRNA	Rattus norvegicus	3301049	Golgi apparatus	Liver	In situ hybridization	"When examined at the ultrastructural level, albumin was localized in the rough endoplasmic reticulum as well as in Golgi complexes located near the nucleus in nearly all these hepatocytes. "
RLID00007775	24186	Alb	http://www.ncbi.nlm.nih.gov/gene/?term=24186	"Alb1za, Alb "	mRNA	Rattus norvegicus	2405055	Cytoplasm	Liver	In situ hybridization	"In normal rat liver, alb mRNA was expressed in all hepatocytes and was localized to discrete subcellular structures distributed as aggregates in the cytoplasm and in specific structures encircling the nucleus; these subcellular structures most likely represent the endoplasmic reticulum and nuclear envelope. "
RLID00007776	24186	Alb	http://www.ncbi.nlm.nih.gov/gene/?term=24186	"Alb1za, Alb "	mRNA	Rattus norvegicus	2405055	Endoplasmic reticulum	Liver	In situ hybridization	"In normal rat liver, alb mRNA was expressed in all hepatocytes and was localized to discrete subcellular structures distributed as aggregates in the cytoplasm and in specific structures encircling the nucleus; these subcellular structures most likely represent the endoplasmic reticulum and nuclear envelope. "
RLID00007777	24186	Alb	http://www.ncbi.nlm.nih.gov/gene/?term=24186	"Alb1za, Alb "	mRNA	Rattus norvegicus	2405055	Nucleus	Liver	In situ hybridization	"In normal rat liver, alb mRNA was expressed in all hepatocytes and was localized to discrete subcellular structures distributed as aggregates in the cytoplasm and in specific structures encircling the nucleus; these subcellular structures most likely represent the endoplasmic reticulum and nuclear envelope. Figure 3. In situ hybridization for albumin mRNA using aldehyde-fixed non-frozen sactions of rat liver, biotin-1 1-UTP anti-sense albumin RNA (riboprobe), and streptavidin-alkaline phosphatase detection system. (a, b) Biotinylated anti-sense alb RNA (riboprobe);(c)sense alb ANYcontrol probe. PT, portal triad; CV, central vein; N, nucleus. Albumin mANA is seen only in hepatocytes (a, b) and is shown as a diffuse cytoplasmic stain (arrows). "
RLID00007778	24191	Aldoc	http://www.ncbi.nlm.nih.gov/gene/?term=24191	"ALDCAA, F16dip7, RATALDCAA "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007779	241944	D3Ertd254e	http://www.ncbi.nlm.nih.gov/gene/?term=241944		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007780	242083	Ppm1l	http://www.ncbi.nlm.nih.gov/gene/?term=242083	"3222401G13, 5930404J21Rik, AI481720, AW045850, PP2C, PP2Cepsilon, Pp2ce, Ppp2ce, mKIAA4175 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007781	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	7753814	Axon	Hypothalamus	In situ hybridization	"In contrast, wild-type and mutant AVP mRNAs are present in dendrites. It will be demonstrated that in heterozygous BB rats, which express both alleles of the AVP gene, only the wild-type mRNA is subject to axonal compartmentation, whereas wild-type and mutant mRNAs are directed to dendrites of Hypothalamic magnocellular Neurons. "
RLID00007782	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	7753814	Dendrite	Hypothalamus	In situ hybridization	"In contrast, wild-type and mutant AVP mRNAs are present in dendrites. It will be demonstrated that in heterozygous BB rats, which express both alleles of the AVP gene, only the wild-type mRNA is subject to axonal compartmentation, whereas wild-type and mutant mRNAs are directed to dendrites of Hypothalamic magnocellular Neurons. "
RLID00007783	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	8283246	Dendrite	Neuron	In situ hybridization	"When vasopressin mRNA was detected in medium-size dendrites, it was always associated with the rough endoplasmic reticulum (RER). "
RLID00007784	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	8283246	Endoplasmic reticulum	Neuron	In situ hybridization	"Within the labeled magnocellular perikarya, the abundant vasopressin mRNA was mainly associated with discrete areas of the RER. These data suggest that vasopressin mRNA translation is restricted to certain segments within the RER, and that axonal transport of vasopressin mRNA does not involve the classical neurosecretory pathway, via the Golgi apparatus and the neurosecretory granules, as has been proposed. "
RLID00007785	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	8812056	Endoplasmic reticulum	Hypothalamus	In situ hybridization	"Altogether, these ultrastructural studies strongly suggested that the Gas and AVP mRNAs might be associated with distinct domains of the RER. "
RLID00007786	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	9104594	Dendrite	Hypothalamus	In situ hybridization	"As revealed by in situ hybridization at the electron microscopic level, the mRNA is located in proximal and distal dendritic segments and is exclusively confined to regions containing rough endoplasmic reticulum.  The data reported here confirm the presence of VP mRNA in proximal and distal segments of dendrites. Sections taken from the ventral glial lamina revealed the dendritic compartmentalization of VP mRNA. "
RLID00007787	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	12106310	Cytoplasm	Neuron	Northern blot	"Most likely, vasopressin transcripts are absent from the nerve terminals as a consequence of the impaired precursor biosynthesis in the cytoplasm of the mutant rat. "
RLID00007788	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	12814355	Cytoplasm	Neuron	In situ hybridization	"Furthermore, galanin and vasopressin messenger RNAs were detected at different domains of the endoplasmic reticulum, suggesting that translation might also occur at different locations, thus leading to partial segregation of galanin and vasopressin cargoes between two populations of secretory granules. In contrast, galanin mRNA was detected in a perinuclear area and in patches scattered in peripheral cytoplasm. In processes, vasopressin mRNA signal was clearly detected(Fig.1B) but labelling remained weak for galanin mRNA. "
RLID00007789	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	12814355	Endoplasmic reticulum	Neuron	In situ hybridization	"Furthermore, galanin and vasopressin messenger RNAs were detected at different domains of the endoplasmic reticulum, suggesting that translation might also occur at different locations, thus leading to partial segregation of galanin and vasopressin cargoes between two populations of secretory granules. In contrast, galanin mRNA was detected in a perinuclear area and in patches scattered in peripheral cytoplasm. In processes, vasopressin mRNA signal was clearly detected(Fig.1B) but labelling remained weak for galanin mRNA. "
RLID00007790	24221	Avp	http://www.ncbi.nlm.nih.gov/gene/?term=24221	"DI, VP, Vas "	mRNA	Rattus norvegicus	8283246	Axon	Neuron	In situ hybridization	"Within the magnocellular neuron axons, vasopressin mRNA could be detected only in a subset of axonal swellings, all of which were confined to the internal layer of the ME and the PP. vasopressin mRNA could be detected only in a subset of axonal swellings, "
RLID00007791	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Nonstimulated rats: BDNF, TrkB, and CaMKII-β mRNAs localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of dentate gyrus (DG) granule cells; CaMKII-α mRNA localized throughout the dendritic length in neurons of all hippocampal subfields.  In contrast, CaMKII-α (Figs. 1C and 2D), BDNF (Figs. 1E and 2G), and TrkB mRNAs (Figs.1G and 2J) were localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of DG granule cells. "
RLID00007792	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Pilocarpine seizures: increased staining levels of CaMKII-β mRNA throughout the whole dendritic length in all hippocampal subfields; induction of CaMKII-α, BDNF, and TrkB mRNAs dendritic targeting in CA1, CA3, and DG neurons.  Data provide evidence that BDNF, TrkB, and CaMKII-α and -β mRNAs are accumulated in the dendrites of specific hippocampal neurons during pilocarpine seizures and kindling development. "
RLID00007793	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	15282290	Dendrite	Hippocampus	In situ hybridization	"In untreated rats (n = 10) (Fig. 1, control), BDNF mRNA was present in the soma and the proximal dendritic compartment of CA1 and CA3 pyramidal neurons (up to ?50-70 ?m from the cell body) (Fig. 2A, arrowheads), whereas in dentate gyrus granule cells, labeling was present in the soma only. "
RLID00007794	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	16388108	Dendrite	Neuron	In situ hybridization	"Strong depolarizing stimuli, both in vitro and in vivo, elicit accumulation of BDNF mRNA and protein in the distal dendrites through a signaling pathway involving the activation of the N-methyl-D-aspartate and tyrosine kinase B receptors and an intracellular increase in Ca2+ concentration "
RLID00007795	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	18497100	Dendrite	Hippocampus	In situ hybridization	"The first clear evidence that BDNF and TrkB mRNAs are located in dendrites was found in primary cultures of rat hippocampal neurons where, under basal conditions, these two mRNAs are localized in the initial dendritic compartment (an average of 31.5m from the cell soma considering all types of dendrites and within a range of 30-100m from the cell soma, when considering apical dendrites only).  "
RLID00007796	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	26578876	Dendrite	Hippocampus	RNAi Interference|Clip	"We found that dendritic localization of BDNF mRNAs with short 3' UTR was induced by depolarization and NT3 in vitro or by seizures in vivo and required CPEB-1, -2 and ELAV-2, -4. "
RLID00007797	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	26700412	Dendrite	Hippocampus	RT-PCR	"BDNF mRNA is transported to dendritic and axons,where it is expressed locally. BDNF mRNA is not only translated in the cell body but is also transported to dendrites.  "
RLID00007798	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	26700412	Axon	Hippocampus	RT-PCR	"BDNF mRNA is transported to dendritic and axons,where it is expressed locally. BDNF mRNA is not only translated in the cell body but is also transported to dendrites.  "
RLID00007799	24225	Bdnf	http://www.ncbi.nlm.nih.gov/gene/?term=24225		mRNA	Rattus norvegicus	26700412	Cell body	Hippocampus	RT-PCR	"BDNF mRNA is transported to dendritic and axons,where it is expressed locally. BDNF mRNA is not only translated in the cell body but is also transported to dendrites.  "
RLID00007800	242291	Impad1	http://www.ncbi.nlm.nih.gov/gene/?term=242291	"1110001C20Rik, AA408880, AI451589, AL022796, B230207P20, Jaws, gPAPP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007801	242291	Impad1	http://www.ncbi.nlm.nih.gov/gene/?term=242291	"1110001C20Rik, AA408880, AI451589, AL022796, B230207P20, Jaws, gPAPP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007802	24241	Calca	http://www.ncbi.nlm.nih.gov/gene/?term=24241	"CAL6, CGRP, Cal1, Calc, RATCAL6, calcitonin "	mRNA	Rattus norvegicus	19225405	Axon	Peripheral nerve	RT-PCR|Fluorescence in situ hybridization	"Intense peptide expression accompanied local rises in alphaCGRP mRNA in the nerve trunk, and there was evidence of transport of alphaCGRP mRNA into regenerating axons, indicating intra-axonal peptide synthesis. "
RLID00007803	242466	Zfp462	http://www.ncbi.nlm.nih.gov/gene/?term=242466	"6030417H05, 9430078C22Rik, Gt4-2, Zfpip "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007804	242474	Tmem245	http://www.ncbi.nlm.nih.gov/gene/?term=242474	"A630051L19Rik, AI957324, D730040F13Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007805	242509	Bnc2	http://www.ncbi.nlm.nih.gov/gene/?term=242509	"5031434M05Rik, 8430420F16Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007806	242585	Slc35d1	http://www.ncbi.nlm.nih.gov/gene/?term=242585	"AI834976, C330011J09, UGTREL7, mKIAA0260 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007807	242608	Podn	http://www.ncbi.nlm.nih.gov/gene/?term=242608	"9430070G18, Pcan, SLRR5A "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007808	242662	Rims3	http://www.ncbi.nlm.nih.gov/gene/?term=242662	"A730060M23Rik, Nim3, Rim3, mKIAA0237 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007809	242669	Azin2	http://www.ncbi.nlm.nih.gov/gene/?term=242669	"4933429I20Rik, Adc, Azi2, B930082O19, ODC-p, Odcp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007810	242726	Padi6	http://www.ncbi.nlm.nih.gov/gene/?term=242726	"Pad6, Padi5, ePAD "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007811	242860	Rsbn1l	http://www.ncbi.nlm.nih.gov/gene/?term=242860	"8430412F05Rik, AI447441, C330002G24Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007812	242915	Gareml	http://www.ncbi.nlm.nih.gov/gene/?term=242915	"Fam59b, Garem2, Gm444 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007813	24316	Drd1	http://www.ncbi.nlm.nih.gov/gene/?term=24316	"D1a, Drd-1a, Drd1 "	mRNA	Rattus norvegicus	9541476	Perinuclear	Brain	In situ hybridization	D1 mRNA was localized to perikarya but not to dendrites or axons.
RLID00007814	243219	2900026A02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=243219	"8430408O14Rik, A530094D01, AW539426, Gm449, Kiaa1671, mKIAA1671 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007815	243308	A430033K04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=243308	C86988	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007816	24333	Eno1	http://www.ncbi.nlm.nih.gov/gene/?term=24333	Nne	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007817	24334	Eno2	http://www.ncbi.nlm.nih.gov/gene/?term=24334	"NSE, RNEN3 "	mRNA	Rattus norvegicus	12106310	Axon	Neuron	Northern blot	"To determine whether NSE mRNA, detected in the stalk region, is present in axons, RNAs were subsequently analysed for primary gene transcripts by amplifying an intronic sequence. This could clearly be detected in the neural stalk (Fig. lc), indicating NSE gene expression in cells of the hypophyseal stalk. The presence of NSE primary transcripts in the neural lobe (Fig. lc) is most likely due to the expression of this gene in intermediate lobe cells. "
RLID00007818	24334	Eno2	http://www.ncbi.nlm.nih.gov/gene/?term=24334	"NSE, RNEN3 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007819	243499	Lrrtm4	http://www.ncbi.nlm.nih.gov/gene/?term=243499	"7530419J18Rik, A230052N11 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007820	243548	Prickle2	http://www.ncbi.nlm.nih.gov/gene/?term=243548	"6230400G14Rik, 6720451F06Rik, mpk2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007821	243653	Clec1a	http://www.ncbi.nlm.nih.gov/gene/?term=243653	5930406N14Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007822	243822	Fam71e2	http://www.ncbi.nlm.nih.gov/gene/?term=243822	4930401F20Rik	mRNA	Mus musculus	26071953	Nucleus	Sperm	RT-PCR	"Within this set of RNAs, the Prm1 transcript, as well as Erich2 and Fam71e2 (formerly 4933404M02Rik and 4930401F20Rik, respectively), were previously identified within the mouse sperm nucleus by RT-PCR though their preferential localization within the gamete could not be inferred from that study (15).  "
RLID00007823	24383	Gapdh	http://www.ncbi.nlm.nih.gov/gene/?term=24383	"BARS-38, Gapd "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007824	243846	Ccdc9	http://www.ncbi.nlm.nih.gov/gene/?term=243846	2600011L02Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007825	243874	Nlrp9b	http://www.ncbi.nlm.nih.gov/gene/?term=243874	"Nalp-delta, Nalp9b, Nlrp9 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007826	243905	Zfp568	http://www.ncbi.nlm.nih.gov/gene/?term=243905	"C80731, Gm1691, chato "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007827	243912	Hspb6	http://www.ncbi.nlm.nih.gov/gene/?term=243912	"AA387366, Gm479, Hsp20 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007828	24391	Gh1	http://www.ncbi.nlm.nih.gov/gene/?term=24391	"Gh, Ghb1, RNGHGP "	mRNA	Rattus norvegicus	16691013	Axon	Retina	In situ hybridization	"Fig. 5. In situ hybridization of GH mRNA in the neural retina of newborn rats. (A) Specific hybridization with a 693- bp DIG-labeled BamH1 antisense probe for GH mRNA is shown throughout the neural retina, particularly in large, rounded cells in the RGC layer of the inner retina. Magnification,x40. (B) Magnification, x100. (C) Magnification, x400. (D) Magnification, x1000. Labeling to a large ganglion cell and its axon (green arrow) is shown. (E) The neural retina is not labeled in the presence of a Not1 DIG-labeled sense probe. Magnification, x40. Representative of similar data from at least three rats. "
RLID00007829	24391	Gh1	http://www.ncbi.nlm.nih.gov/gene/?term=24391	"Gh, Ghb1, RNGHGP "	mRNA	Rattus norvegicus	1607645	Endoplasmic reticulum	Pituitary gland	In situ hybridization	"With the purpose of comparing the sensitivity, resolution, and ultrastructural preservation of these three methods, we examined the expression of the growth hormone (GH) gene in anterior pituitary cells by in situ hybridization at the ultrastructural level, using a synthetic oligonucleotide complementary to the codons of the mRNA from Gln 45 to Ser 54 labeled at the 3' end of biotin-21dUTP. All these methods gave similar results: mRNA was located on the lamellar endoplasmic reticulum of somatotrophs. "
RLID00007830	24391	Gh1	http://www.ncbi.nlm.nih.gov/gene/?term=24391	"Gh, Ghb1, RNGHGP "	mRNA	Rattus norvegicus	7843989	Ribosome	Pituitary cell	In situ hybridization	"Preembedding electron microscopic ISH localized rat growth hormone and prolactin mRNAs on the polysomes of the rough endoplasmic reticulum (RER). Rat growth hormone mRNA was distributed diffusely on the RER, whereas rat prolactin mRNA was scattered and distributed focally. Thus there might be a specific translational site for prolactin mRNA on the RER. Rat growth hormone mRNA signals were also recognized on the polysomes of the RER, using the postembedding method with streptavidin gold conjugate. "
RLID00007831	24391	Gh1	http://www.ncbi.nlm.nih.gov/gene/?term=24391	"Gh, Ghb1, RNGHGP "	mRNA	Rattus norvegicus	7843989	Endoplasmic reticulum	Pituitary cell	In situ hybridization	"Preembedding electron microscopic ISH localized rat growth hormone and prolactin mRNAs on the polysomes of the rough endoplasmic reticulum (RER). Rat growth hormone mRNA was distributed diffusely on the RER, whereas rat prolactin mRNA was scattered and distributed focally. Thus there might be a specific translational site for prolactin mRNA on the RER. Rat growth hormone mRNA signals were also recognized on the polysomes of the RER, using the postembedding method with streptavidin gold conjugate. "
RLID00007832	243937	Zfp536	http://www.ncbi.nlm.nih.gov/gene/?term=243937	"9630010P11Rik, Znf536, mKIAA0390 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007833	243983	Zdhhc13	http://www.ncbi.nlm.nih.gov/gene/?term=243983	"2410004E01Rik, C530010M18, HIP3RP, Hip14l, kojak, skc4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007834	244049	Mctp2	http://www.ncbi.nlm.nih.gov/gene/?term=244049	Gm489	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007835	244059	Chd2	http://www.ncbi.nlm.nih.gov/gene/?term=244059	"2810013C04Rik, 2810040A01Rik, 5630401D06Rik, AI851092, BC029703, CHD-2 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007836	244059	Chd2	http://www.ncbi.nlm.nih.gov/gene/?term=244059	"2810013C04Rik, 2810040A01Rik, 5630401D06Rik, AI851092, BC029703, CHD-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007837	24409	Grin2a	http://www.ncbi.nlm.nih.gov/gene/?term=24409	"GluN2A, NMDAR2A, NR2A "	mRNA	Rattus norvegicus	23678131	Dendrite	Hippocampus	Fluorescence in situ hybridization	Dendra2 fluorescence levels were significantly increased at 25 min after glycine application and reached a plateau by 40 min. These data suggest that glycine treatment induces the local translation of GluN2A mRNA in dendrites.Dendra2 fluorescence levels were significantly increased at 25 min after glycine application and reached a plateau by 40 min. These data suggest that glycine treatment induces the local translation of GluN2A mRNA in dendrites.
RLID00007838	244141	Nars2	http://www.ncbi.nlm.nih.gov/gene/?term=244141	AI875199	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007839	244141	Nars2	http://www.ncbi.nlm.nih.gov/gene/?term=244141	AI875199	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007840	244216	Zfp771	http://www.ncbi.nlm.nih.gov/gene/?term=244216	"G630024C07Rik, Znf771 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007841	244219	Zfp668	http://www.ncbi.nlm.nih.gov/gene/?term=244219	"BC030314, E130018B19Rik, Znf668 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007842	244329	Mcph1	http://www.ncbi.nlm.nih.gov/gene/?term=244329	"5430437K10Rik, BRIT1, D030046N04Rik, MCT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007843	244334	Defb8	http://www.ncbi.nlm.nih.gov/gene/?term=244334	"BD-8, Defr1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007844	244373	Erlin2	http://www.ncbi.nlm.nih.gov/gene/?term=244373	"BC036333, C87251, Spfh2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007845	244418	D8Ertd82e	http://www.ncbi.nlm.nih.gov/gene/?term=244418	"9830148H23, NACK, Sgk223, mFLJ00269 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007846	244421	Lonrf1	http://www.ncbi.nlm.nih.gov/gene/?term=244421		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007847	244448	Triml1	http://www.ncbi.nlm.nih.gov/gene/?term=244448	"4933403D14, BC050188 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007848	244654	Mtss1l	http://www.ncbi.nlm.nih.gov/gene/?term=244654	ABBA	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007849	244667	Disc1	http://www.ncbi.nlm.nih.gov/gene/?term=244667		mRNA	Mus musculus	25821909	Dendrite	Neuron	Fluorescence in situ hybridization	"DISC1 colocalizes with HZF and ITPR1 mRNA in hippocampal dendrites and directly associates with neuronal mRNAs, including ITPR1 mRNA.  DISC1 colocalized with HZF and Itpr1 mRNA in hippocampal dendrites. "
RLID00007850	244713	Zfp317	http://www.ncbi.nlm.nih.gov/gene/?term=244713	"4932416G03, D230022C05Rik, KRAB9, Zfp67, Zfp75, mszf40 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007851	24471	Hspb1	http://www.ncbi.nlm.nih.gov/gene/?term=24471	"Hsp25, Hsp27 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007852	24471	Hspb1	http://www.ncbi.nlm.nih.gov/gene/?term=24471	"Hsp25, Hsp27 "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00007853	244864	Layn	http://www.ncbi.nlm.nih.gov/gene/?term=244864	"E030012M19Rik, Gm511 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007854	244879	Npat	http://www.ncbi.nlm.nih.gov/gene/?term=244879	"6820401K01, AI427561, BB112559 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007855	244891	Scaper	http://www.ncbi.nlm.nih.gov/gene/?term=244891	"C430017I08, D530014O03Rik, Zfp291 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007856	244962	Snx14	http://www.ncbi.nlm.nih.gov/gene/?term=244962	"B830022K16, C330035N22Rik, YR-14 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007857	245000	Atr	http://www.ncbi.nlm.nih.gov/gene/?term=245000		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007858	245109	Zscan4c	http://www.ncbi.nlm.nih.gov/gene/?term=245109	"Gm397, XM_142517, Zscan4d "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007859	245381	Sowahd	http://www.ncbi.nlm.nih.gov/gene/?term=245381	"A630014H24Rik, Ankrd58 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007860	245474	Dkc1	http://www.ncbi.nlm.nih.gov/gene/?term=245474	BC068171	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007861	24547	Mbp	http://www.ncbi.nlm.nih.gov/gene/?term=24547	Mbps	mRNA	Rattus norvegicus	7877439	Cytoplasm	Oligodendrocytes	In situ hybridization	MBP mRNA was confined to the perinuclear cytoplasm of immature oligodendrocytes and was then transported into the myelin sheath at a developmental stage corresponding to myelination. 
RLID00007862	245509	4932429P05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=245509		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007863	245555	C77370	http://www.ncbi.nlm.nih.gov/gene/?term=245555	"A230051P11, C77386, Kiaa2022, Xpn, mKIAA2022 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007864	245598	4921511C20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=245598	Gm383	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007865	245610	Nxf3	http://www.ncbi.nlm.nih.gov/gene/?term=245610	Gm384	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007866	24564	Mpz	http://www.ncbi.nlm.nih.gov/gene/?term=24564	"MPP, P0 "	mRNA	Rattus norvegicus	1706417	Endoplasmic reticulum	Schwann cell	In situ hybridization	"In sections of ganglia from 2-day-old rats, studied by light and electron microscopy, peroxidase reaction product localizing hybridized P0 mRNA was found on profiles of granular (rough) endoplasmic reticulum (RER) in perinuclear regions of Schwann cells which had formed two to three compact myelin lamellae. "
RLID00007867	245666	Iqsec2	http://www.ncbi.nlm.nih.gov/gene/?term=245666	Brag1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007868	245812	CNPY4	http://www.ncbi.nlm.nih.gov/gene/?term=245812	PRAT4B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007869	245828	Trappc1	http://www.ncbi.nlm.nih.gov/gene/?term=245828	"BET5, D11Ertd172e, MUM2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007870	245847	Amdhd2	http://www.ncbi.nlm.nih.gov/gene/?term=245847	5730457F11Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007871	24586	Ncam1	http://www.ncbi.nlm.nih.gov/gene/?term=24586	"Cd56, N-CAM, N-CAM-1, NCAM-1, NCAM-C, NCAMC, Ncam "	mRNA	Rattus norvegicus	7599960	Synapse	Muscle fibers	In situ hybridization	"N-CAM, 43K-rapsyn, and S-laminin mRNAs are concentrated at synaptic sites in muscle fibers "
RLID00007872	24591	Neu1	http://www.ncbi.nlm.nih.gov/gene/?term=24591		mRNA	Rattus norvegicus	12213446	Dendrite	Brain	In situ hybridization	The most interesting observation regarding neu1 mRNA localization in the adult brain was the clear dendritic localization of the transcripts in the hippocampus.
RLID00007873	24596	Ngfr	http://www.ncbi.nlm.nih.gov/gene/?term=24596	"LNGFR, RNNGFRR, Tnfrsf16, p75, p75NTR "	mRNA	Rattus norvegicus	11043561	Dendrite	ForeBrain	In situ hybridization	"We find that TrkA, TrkC and p75 mRNAs are restricted to the cell soma but in addition, p75 mRNA labelling extends in average for 8 um within the proximal dendrites of 34% of the labelled neurons.  The in situ staining for p75 mRNA, was generally restricted to the cell soma but in some neurons the staining was present in the proximal portion of the dendrites of the septum (Fig. 1h, arrows) and diagonal band (not shown) but not of the caudateputamen (Fig. 1i). "
RLID00007874	245972	ATP6V0D2	http://www.ncbi.nlm.nih.gov/gene/?term=245972	"ATP6D2, VMA6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007875	245972	ATP6V0D2	http://www.ncbi.nlm.nih.gov/gene/?term=245972	"ATP6D2, VMA6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007876	245972	ATP6V0D2	http://www.ncbi.nlm.nih.gov/gene/?term=245972	"ATP6D2, VMA6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007877	245973	ATP6V1C2	http://www.ncbi.nlm.nih.gov/gene/?term=245973	"ATP6C2, VMA5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007878	24598	Nos1	http://www.ncbi.nlm.nih.gov/gene/?term=24598	bNOS	mRNA	Rattus norvegicus	9351678	Cell body	Neuron	In situ hybridization	Here we show mRNA expression of NOS type-1 (neuronal or brain NOS) transcripts in cell bodies of sympathetic preganglionic neurons (SPNs) of the intermediolateral (IML) cell column by non-radioactive in situ hybridization using NOS-I riboprobes.
RLID00007879	24599	Nos2	http://www.ncbi.nlm.nih.gov/gene/?term=24599	"Nos2a, iNos "	mRNA	Rattus norvegicus	9290578	Cytoplasm	Vascular endothelial cell	In situ hybridization	"After endotoxin administration, iNOS mRNA was localized in the cytoplasm of vascular endothelial cells, vascular smooth muscle cells and cardiomyocytes (Figure 4). "
RLID00007880	246048	Chodl	http://www.ncbi.nlm.nih.gov/gene/?term=246048	"3110074E07Rik, MT75, PRED12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007881	246118	Tubb3	http://www.ncbi.nlm.nih.gov/gene/?term=246118		mRNA	Rattus norvegicus	21098654	Axon	Embryo	RT-PCR	"Tubulin-beta3 (Tubb3) mRNA is present only in embryonic axons, with Tubb3 locally synthesized in axons of embryonic, but not adult neurons where it is transported "
RLID00007882	246175	CNOT6L	http://www.ncbi.nlm.nih.gov/gene/?term=246175	CCR4b	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007883	246184	CDC26	http://www.ncbi.nlm.nih.gov/gene/?term=246184	"ANAPC12, APC12, C9orf17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007884	246184	CDC26	http://www.ncbi.nlm.nih.gov/gene/?term=246184	"ANAPC12, APC12, C9orf17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007885	246221	Mpst	http://www.ncbi.nlm.nih.gov/gene/?term=246221	Mst	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007886	246243	RNASEH1	http://www.ncbi.nlm.nih.gov/gene/?term=246243	"H1RNA, PEOB2, RNH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007887	246243	RNASEH1	http://www.ncbi.nlm.nih.gov/gene/?term=246243	"H1RNA, PEOB2, RNH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007888	246243	RNASEH1	http://www.ncbi.nlm.nih.gov/gene/?term=246243	"H1RNA, PEOB2, RNH1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007889	246274	Faim2	http://www.ncbi.nlm.nih.gov/gene/?term=246274	"Lfg, NMP35 "	mRNA	Rattus norvegicus	23966695	Axon	Sensory neuron	RT-PCR	We recently reported that neural membrane protein 35 (NMP35) mRNA is transported into axons through its 3'UTR
RLID00007890	246274	Faim2	http://www.ncbi.nlm.nih.gov/gene/?term=246274	"Lfg, NMP35 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007891	246313	Prokr2	http://www.ncbi.nlm.nih.gov/gene/?term=246313	"B830005M06Rik, EG-VEGRF2, Gpcr73l1, Gpr73l1, PKR2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007892	246330	PELI3	http://www.ncbi.nlm.nih.gov/gene/?term=246330		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007893	24644	Pgk1	http://www.ncbi.nlm.nih.gov/gene/?term=24644	Pgk	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007894	246534	CG30291	http://www.ncbi.nlm.nih.gov/gene/?term=246534	"Dmel_ CG3282, Dmel\CG30291 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00007895	246596	Tango11	http://www.ncbi.nlm.nih.gov/gene/?term=246596	"Dmel_CG30404, BEST:LD33633, BcDNA:LD22567, CG30404, Dmel\CG30404, TANGO11, anon-EST:fe1F11, tango11 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00007896	246627	CG30463	http://www.ncbi.nlm.nih.gov/gene/?term=246627	"Dmel_ CG15713, CG8456, CG8463, Dmel\CG30463, dppGalNAcT9 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00007897	246715	CKS1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=246715		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007898	246721	POLR2J2	http://www.ncbi.nlm.nih.gov/gene/?term=246721	"HRPB11B, RPB11b1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007899	246721	POLR2J2	http://www.ncbi.nlm.nih.gov/gene/?term=246721	"HRPB11B, RPB11b1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007900	246721	POLR2J2	http://www.ncbi.nlm.nih.gov/gene/?term=246721	"HRPB11B, RPB11b1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007901	246728	Oas2	http://www.ncbi.nlm.nih.gov/gene/?term=246728	Oasl11	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007902	24683	Prl	http://www.ncbi.nlm.nih.gov/gene/?term=24683	"Gha1, PRLB, PRLSD11a1, Prol, RATPRLSD1, RNPROL, Prl "	mRNA	Rattus norvegicus	2703695	Nucleus	Pituitary	In situ hybridization	"Figure 4. Electron microscopic autoradiography showing labeling of typical PRL cell. Silver grains are found over the rough endoplasmic reticulum (RER) and nucleus (N). SG, secretory granules; GO, golgi apparatus. Exposure time 14 days. "
RLID00007903	24683	Prl	http://www.ncbi.nlm.nih.gov/gene/?term=24683	"Gha1, PRLB, PRLSD11a1, Prol, RATPRLSD1, RNPROL, Prl "	mRNA	Rattus norvegicus	7843989	Ribosome	Pituitary cell	In situ hybridization	"Preembedding electron microscopic ISH localized rat growth hormone and prolactin mRNAs on the polysomes of the rough endoplasmic reticulum (RER). Rat growth hormone mRNA was distributed diffusely on the RER, whereas rat prolactin mRNA was scattered and distributed focally. Thus there might be a specific translational site for prolactin mRNA on the RER. Rat growth hormone mRNA signals were also recognized on the polysomes of the RER, using the postembedding method with streptavidin gold conjugate. "
RLID00007904	24683	Prl	http://www.ncbi.nlm.nih.gov/gene/?term=24683	"Gha1, PRLB, PRLSD11a1, Prol, RATPRLSD1, RNPROL, Prl "	mRNA	Rattus norvegicus	7843989	Endoplasmic reticulum	Pituitary cell	In situ hybridization	"Preembedding electron microscopic ISH localized rat growth hormone and prolactin mRNAs on the polysomes of the rough endoplasmic reticulum (RER). Rat growth hormone mRNA was distributed diffusely on the RER, whereas rat prolactin mRNA was scattered and distributed focally. Thus there might be a specific translational site for prolactin mRNA on the RER. Rat growth hormone mRNA signals were also recognized on the polysomes of the RER, using the postembedding method with streptavidin gold conjugate. "
RLID00007905	24683	Prl	http://www.ncbi.nlm.nih.gov/gene/?term=24683	"Gha1, PRLB, PRLSD11a1, Prol, RATPRLSD1, RNPROL, Prl "	mRNA	Rattus norvegicus	9361267	Endoplasmic reticulum	Pituitary glands	In situ hybridization	"With ISH, the expression and distribution of PRL messenger ribonucleic acid (mRNA) was observed in a fashion suggesting polysome-like structures on RER. These observations were confirmed by immunoelectron microscopy and electron microscopic ISH. "
RLID00007906	24683	Prl	http://www.ncbi.nlm.nih.gov/gene/?term=24683	"Gha1, PRLB, PRLSD11a1, Prol, RATPRLSD1, RNPROL, Prl "	mRNA	Rattus norvegicus	2703695	Endoplasmic reticulum	Pituitary	In situ hybridization	Figure 5. Ultra-thin section which was immunolabeled for PAL localization before the autoradiographic procedure. The small secretory granules are decorated with gold particles (arrows) and silver grains are seen over the rough endoplasmic reticulum (AER). An adjacent GH cell is unlabeled. Exposure time 14 days.
RLID00007907	24684	Prlr	http://www.ncbi.nlm.nih.gov/gene/?term=24684	RATPRLR	mRNA	Rattus norvegicus	7606212	Endoplasmic reticulum	Hepatocyte	In situ hybridization	"The expression of both the long and short forms of PRL-receptor mRNA was readily identified in the cytoplasmic matrix, and in association with the endoplasmic reticulum, but a low expression of these forms was detected in the nucleus of hepatocyte. "
RLID00007908	24684	Prlr	http://www.ncbi.nlm.nih.gov/gene/?term=24684	RATPRLR	mRNA	Rattus norvegicus	7606212	Nucleus	Hepatocyte	In situ hybridization	"The expression of both the long and short forms of PRL-receptor mRNA was readily identified in the cytoplasmic matrix, and in association with the endoplasmic reticulum, but a low expression of these forms was detected in the nucleus of hepatocyte. "
RLID00007909	24684	Prlr	http://www.ncbi.nlm.nih.gov/gene/?term=24684	RATPRLR	mRNA	Rattus norvegicus	7606212	Cytoplasm	Hepatocyte	In situ hybridization	"The expression of both the long and short forms of PRL-receptor mRNA was readily identified in the cytoplasmic matrix, and in association with the endoplasmic reticulum, but a low expression of these forms was detected in the nucleus of hepatocyte. "
RLID00007910	24685	Prm1	http://www.ncbi.nlm.nih.gov/gene/?term=24685		mRNA	Rattus norvegicus	1795020	Nucleus	Spermatids	In situ hybridization	During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm. During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm.
RLID00007911	24685	Prm1	http://www.ncbi.nlm.nih.gov/gene/?term=24685		mRNA	Rattus norvegicus	1795020	Cytoplasm	Spermatids	In situ hybridization	During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm. During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm.
RLID00007912	24688	Prph	http://www.ncbi.nlm.nih.gov/gene/?term=24688	"Perf1, Prph "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00007913	24688	Prph	http://www.ncbi.nlm.nih.gov/gene/?term=24688	"Perf1, Prph "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007914	246	ALOX15	http://www.ncbi.nlm.nih.gov/gene/?term=246	"12-LOX, 15-LOX-1, 15LOX-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007915	246	ALOX15	http://www.ncbi.nlm.nih.gov/gene/?term=246	"12-LOX, 15-LOX-1, 15LOX-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007916	24720	Rn5s	http://www.ncbi.nlm.nih.gov/gene/?term=24720	Rn5s2	rRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"These axons also contain 5S rRNA, phosphorylated S6 ribosomal protein, eIF2α translation factor, and 4EBP1 translation factor inhibitory protein. "
RLID00007917	2475	MTOR	http://www.ncbi.nlm.nih.gov/gene/?term=2475	"FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007918	24773	Sftpa1	http://www.ncbi.nlm.nih.gov/gene/?term=24773	"PSAP, PSP-A, SP-A, Sftp1, Sftpa, Sftpl "	mRNA	Rattus norvegicus	1540394	Endoplasmic reticulum	Lung cell	In situ hybridization|Northern blot	"The present study demonstrates an overexpression of SP-A mRNA despite the ultrastructural changes in the endoplasmic reticulum of alveolar type II cells in the diabetic lungs, which will provide new information on the regulatory mechanism of SP-A gene expression. "
RLID00007919	24786	Sod1	http://www.ncbi.nlm.nih.gov/gene/?term=24786	CuZnSOD	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00007920	24786	Sod1	http://www.ncbi.nlm.nih.gov/gene/?term=24786	CuZnSOD	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007921	24837	Tnnt2	http://www.ncbi.nlm.nih.gov/gene/?term=24837	"CTTG, Ctt, RATCTTG, Tnnt3 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007922	24839	Tnp1	http://www.ncbi.nlm.nih.gov/gene/?term=24839		mRNA	Rattus norvegicus	1795020	Nucleus	Spermatids	In situ hybridization	During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm. During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm.
RLID00007923	24839	Tnp1	http://www.ncbi.nlm.nih.gov/gene/?term=24839		mRNA	Rattus norvegicus	1795020	Cytoplasm	Spermatids	In situ hybridization	During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm. During early spermiogenesis (before step 7) nuclear transcripts of both TP 1 and Prm 1 were seen. After step 7 the TP 1 and Prm 1 mRNAs were only detected in the cytoplasm.
RLID00007924	2483	FRG1	http://www.ncbi.nlm.nih.gov/gene/?term=2483	"FRG1A, FSG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007925	24851	Tpm1	http://www.ncbi.nlm.nih.gov/gene/?term=24851	"Alpha-tm, Tma2, Tmsa "	mRNA	Rattus norvegicus	8581312	Cell body	Embryoneuron	In situ hybridization	TmBr-2 mRNA was distributed throughout the cell body (Figure 1C).
RLID00007926	248	ALPI	http://www.ncbi.nlm.nih.gov/gene/?term=248	IAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007927	24917	Kpnb1	http://www.ncbi.nlm.nih.gov/gene/?term=24917	Impnb	mRNA	Rattus norvegicus	14687545	Axon	Sciatic nerve	In situ hybridization|RT-PCR	We then conducted RT-PCR for importin β in the axons and observed a clear signal indicating the presence of importin β transcripts in the axonal mRNA (Figure 2E).
RLID00007928	2491	CENPI	http://www.ncbi.nlm.nih.gov/gene/?term=2491	"CENP-I, FSHPRH1, LRPR1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007929	2491	CENPI	http://www.ncbi.nlm.nih.gov/gene/?term=2491	"CENP-I, FSHPRH1, LRPR1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007930	2495	FTH1	http://www.ncbi.nlm.nih.gov/gene/?term=2495	"FHC, FTH, FTHL6, HFE5, PIG15, PLIF "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007931	2495	FTH1	http://www.ncbi.nlm.nih.gov/gene/?term=2495	"FHC, FTH, FTHL6, HFE5, PIG15, PLIF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007932	2495	FTH1	http://www.ncbi.nlm.nih.gov/gene/?term=2495	"FHC, FTH, FTHL6, HFE5, PIG15, PLIF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007933	249	ALPL	http://www.ncbi.nlm.nih.gov/gene/?term=249	"AP-TNAP, APTNAP, HOPS, TNAP, TNSALP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007934	24	ABCA4	http://www.ncbi.nlm.nih.gov/gene/?term=24	"ABC10, ABCR, ARMD2, CORD3, FFM, RMP, RP19, STGD, STGD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007935	25054	Ntrk2	http://www.ncbi.nlm.nih.gov/gene/?term=25054	"RATTRKB1, TRKB1, Tkrb, trk-B, trkB "	mRNA	Rattus norvegicus	11043561	Dendrite	ForeBrain	In situ hybridization	"In striking contrast with TrkA, the TrkB mRNA showed a clear somatodendritic localization in the majority of the labelled neurons. "
RLID00007936	25054	Ntrk2	http://www.ncbi.nlm.nih.gov/gene/?term=25054	"RATTRKB1, TRKB1, Tkrb, trk-B, trkB "	mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Nonstimulated rats: BDNF, TrkB, and CaMKII-β mRNAs localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of dentate gyrus (DG) granule cells; CaMKII-α mRNA localized throughout the dendritic length in neurons of all hippocampal subfields.  In contrast, CaMKII-? (Figs. 1C and 2D), BDNF (Figs. 1E and 2G), and TrkB mRNAs (Figs.1G and 2J) were localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of DG granule cells. "
RLID00007937	25054	Ntrk2	http://www.ncbi.nlm.nih.gov/gene/?term=25054	"RATTRKB1, TRKB1, Tkrb, trk-B, trkB "	mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Pilocarpine seizures: increased staining levels of CaMKII-β mRNA throughout the whole dendritic length in all hippocampal subfields; induction of CaMKII-α, BDNF, and TrkB mRNAs dendritic targeting in CA1, CA3, and DG neurons.  Data provide evidence that BDNF, TrkB, and CaMKII-α and -β mRNAs are accumulated in the dendrites of specific hippocampal neurons during pilocarpine seizures and kindling development. "
RLID00007938	25054	Ntrk2	http://www.ncbi.nlm.nih.gov/gene/?term=25054	"RATTRKB1, TRKB1, Tkrb, trk-B, trkB "	mRNA	Rattus norvegicus	18497100	Dendrite	Hippocampus	In situ hybridization	"The first clear evidence that BDNF and TrkB mRNAs are located in dendrites was found in primary cultures of rat hippocampal neurons where, under basal conditions, these two mRNAs are localized in the initial dendritic compartment (an average of 31.5m from the cell soma considering all types of dendrites and within a range of 30-100m from the cell soma, when considering apical dendrites only).  "
RLID00007939	25085	Th	http://www.ncbi.nlm.nih.gov/gene/?term=25085	The	mRNA	Rattus norvegicus	9691425	Cytoplasm	Brain	In situ hybridization	"Using exon-specific probes and electron microscopic in situ hybridization in reserpine-treated animals, we have demonstrated that the TH mRNA is localized both in the perikaryal cytoplasm (in association with domains of the endoplasmic reticulum) and in the nucleus (in large and smaller aggregates). "
RLID00007940	25085	Th	http://www.ncbi.nlm.nih.gov/gene/?term=25085	The	mRNA	Rattus norvegicus	9691425	Nucleus	Brain	In situ hybridization	"Using exon-specific probes and electron microscopic in situ hybridization in reserpine-treated animals, we have demonstrated that the TH mRNA is localized both in the perikaryal cytoplasm (in association with domains of the endoplasmic reticulum) and in the nucleus (in large and smaller aggregates). "
RLID00007941	250	ALPP	http://www.ncbi.nlm.nih.gov/gene/?term=250	"ALP, PALP, PLAP, PLAP-1 "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00007942	250	ALPP	http://www.ncbi.nlm.nih.gov/gene/?term=250	"ALP, PALP, PLAP, PLAP-1 "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00007943	250	ALPP	http://www.ncbi.nlm.nih.gov/gene/?term=250	"ALP, PALP, PLAP, PLAP-1 "	mRNA	Homo sapiens	26272916	Endoplasmic reticulum	U2OS cell	Fluorescence in situ hybridization	"As mentioned above, we have previously demonstrated that >50% of ALPP mRNA is associated with the ER in a translation-dependent manner and that the remaining fraction is largely dependent on p180 (Cui et al., 2012). "
RLID00007944	250	ALPP	http://www.ncbi.nlm.nih.gov/gene/?term=250	"ALP, PALP, PLAP, PLAP-1 "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00007945	250	ALPP	http://www.ncbi.nlm.nih.gov/gene/?term=250	"ALP, PALP, PLAP, PLAP-1 "	mRNA	Homo sapiens	22679391	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00007946	25113	Ddn	http://www.ncbi.nlm.nih.gov/gene/?term=25113	Den	mRNA	Rattus norvegicus	9073398	Dendrite	Hippocamus	In situ hybridization	"In the hippocamus, DEN mRNA is highly expressed in the cell laminae and dendritic layers of the dentate gyrus and CA1 field, but expression is markedly reduced in the CA3 and CA4 areas.  The most compelling observation regarding DEN mRNA localization in the adult rat brain is the clear dendritic distribution of the transcripts in the hippocampus (Figs. 1A and 1C). "
RLID00007947	25116	Hsd11b1	http://www.ncbi.nlm.nih.gov/gene/?term=25116	LRRGT00065	mRNA	Oryctolagus cuniculus	9699885	Endoplasmic reticulum	Kidney	RT-PCR|Northern analysis	"Co-staining with markers for ER proteins, the Golgi membrane, mitochondria and nucleus confirmed that 11beta-HSD2 is localized exclusively to the ER. "
RLID00007948	2512	FTL	http://www.ncbi.nlm.nih.gov/gene/?term=2512	"LFTD, NBIA3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007949	2512	FTL	http://www.ncbi.nlm.nih.gov/gene/?term=2512	"LFTD, NBIA3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007950	2512	FTL	http://www.ncbi.nlm.nih.gov/gene/?term=2512	"LFTD, NBIA3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007951	2512	FTL	http://www.ncbi.nlm.nih.gov/gene/?term=2512	"LFTD, NBIA3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007952	251414	zpg	http://www.ncbi.nlm.nih.gov/gene/?term=251414	"Dmel_CG10125, CG10125, Dm-inx4, Dmel\CG10125, FBpp0076692, Inx4, Zpg, inx-4, inx4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00007953	251645	CG32276	http://www.ncbi.nlm.nih.gov/gene/?term=251645	"Dmel_ BcDNA:RE27904, Dmel\CG32276 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00007954	2516	NR5A1	http://www.ncbi.nlm.nih.gov/gene/?term=2516	"AD4BP, ELP, FTZ1, FTZF1, POF7, SF-1, SF1, SPGF8, SRXY3 "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmids containing either ALPP, t-ftz, or the AF1, AF2 fusion constructs and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (Ctrl), puromycin (Puro), or HHT for 30 min and then extracted with either digitonin alone, or for puromycin-treated cells, with 20 mM EDTA. The cells were then fixed, stained for mRNA using specific FISH probes (ALPP probe for AF1, ftz probe for AF2), and imaged. FIGURE 2B: quantification of the fluorescence intensities of mRNA in the ER and nucleus.  Data are collected from Figure 2. "
RLID00007955	2516	NR5A1	http://www.ncbi.nlm.nih.gov/gene/?term=2516	"AD4BP, ELP, FTZ1, FTZF1, POF7, SF-1, SF1, SPGF8, SRXY3 "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmids containing either ALPP, t-ftz, or the AF1, AF2 fusion constructs and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (Ctrl), puromycin (Puro), or HHT for 30 min and then extracted with either digitonin alone, or for puromycin-treated cells, with 20 mM EDTA. The cells were then fixed, stained for mRNA using specific FISH probes (ALPP probe for AF1, ftz probe for AF2), and imaged. FIGURE 2B: quantification of the fluorescence intensities of mRNA in the ER and nucleus.  Data are collected from Figure 2. "
RLID00007956	2516	NR5A1	http://www.ncbi.nlm.nih.gov/gene/?term=2516	"AD4BP, ELP, FTZ1, FTZF1, POF7, SF-1, SF1, SPGF8, SRXY3 "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"In order to ensure that this technique effectively separates these two classes of mRNA while simultaneously preserving the ultrastructure of the ER, the distribution of various versions of the fushi tarazu (ftz) mRNA fragment were examined in COS-7 cells by fluorescent in situ hybridization (FISH). First we monitored t-ftz mRNA, which encodes a secreted version of the ftz protein [30]. This mRNA, which localizes to the ER ([30] and Figure S1A), remained associated with the cells after digitonin extraction (Figure S1B-C). "
RLID00007957	2516	NR5A1	http://www.ncbi.nlm.nih.gov/gene/?term=2516	"AD4BP, ELP, FTZ1, FTZF1, POF7, SF-1, SF1, SPGF8, SRXY3 "	mRNA	Homo sapiens	22679391	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00007958	2517	FUCA1	http://www.ncbi.nlm.nih.gov/gene/?term=2517	FUCA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007959	2517	FUCA1	http://www.ncbi.nlm.nih.gov/gene/?term=2517	FUCA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007960	2517	FUCA1	http://www.ncbi.nlm.nih.gov/gene/?term=2517	FUCA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007961	2519	FUCA2	http://www.ncbi.nlm.nih.gov/gene/?term=2519	dJ20N2.5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007962	2519	FUCA2	http://www.ncbi.nlm.nih.gov/gene/?term=2519	dJ20N2.5	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00007963	25203	Ccnb1	http://www.ncbi.nlm.nih.gov/gene/?term=25203		mRNA	Rattus norvegicus	8809408	Ribosome	Liver	RNase protection analysis	"In addition, cytoplasmic protein levels of cyclin B1 exhibited a constant distribution in subfractions of microsome- and polysome-associated and free proteins. Cyclin B1 RNA also localized to these three cytoplasmic subfractions. "
RLID00007964	2521	FUS	http://www.ncbi.nlm.nih.gov/gene/?term=2521	"ALS6, ETM4, FUS1, HNRNPP2, POMP75, TLS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007965	2521	FUS	http://www.ncbi.nlm.nih.gov/gene/?term=2521	"ALS6, ETM41, HNRNPP2, POMP75, TLS, FUS "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007966	2521	FUS	http://www.ncbi.nlm.nih.gov/gene/?term=2521	"ALS6, ETM41, HNRNPP2, POMP75, TLS, FUS "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00007967	2523	FUT1	http://www.ncbi.nlm.nih.gov/gene/?term=2523	"H, HH, HSC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007968	2523	FUT1	http://www.ncbi.nlm.nih.gov/gene/?term=2523	"H, HH, HSC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007969	2524	FUT2	http://www.ncbi.nlm.nih.gov/gene/?term=2524	"B12QTL1, SE, SEC2, Se2, sej "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007970	2524	FUT2	http://www.ncbi.nlm.nih.gov/gene/?term=2524	"B12QTL1, SE, SEC2, Se2, sej "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007971	2525	FUT3	http://www.ncbi.nlm.nih.gov/gene/?term=2525	"CD174, FT3B, FucT-III, LE, Les "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007972	25262	Itpr1	http://www.ncbi.nlm.nih.gov/gene/?term=25262	"I145TR, IP3R1, InsP3R, InsP3R1, P400 "	mRNA	Mus musculus	8081710	Dendrite	Purkinje cell	In situ hybridization	"In the most abundantly expressing Purkinje cells, InsP3R1 mRNA appeared to be translocated to the distal dendrites, since a strong hybridization density was observed in the molecular layer of the cerebellum. "
RLID00007973	25267	Pdgfra	http://www.ncbi.nlm.nih.gov/gene/?term=25267	"APDGFR, PDGFACE "	mRNA	Rattus norvegicus	9073394	Cell body	Medullary velum 	In situ hybridization	"The high level of expression of PDGF-alphaR mRNA in the AMV of juvenile rats, localized to cell bodies within the myelinated axon tracts, strongly suggesting that oligodendrocyte precursors persisted in the mature velum "
RLID00007974	2526	FUT4	http://www.ncbi.nlm.nih.gov/gene/?term=2526	"CD15, ELFT, FCT3A, FUC-TIV, FUTIV, LeX, SSEA-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007975	252829	Obox5	http://www.ncbi.nlm.nih.gov/gene/?term=252829	C87544	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007976	252839	TMEM9	http://www.ncbi.nlm.nih.gov/gene/?term=252839	TMEM9A	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007977	252839	TMEM9	http://www.ncbi.nlm.nih.gov/gene/?term=252839	"DERM4A, TMEM9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007978	252866	Adam34	http://www.ncbi.nlm.nih.gov/gene/?term=252866		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00007979	252870	Usp7	http://www.ncbi.nlm.nih.gov/gene/?term=252870	"2210010O09Rik, AA409944, AA617399, AU019296, AW548146, C80752, Hausp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007980	252875	Mios	http://www.ncbi.nlm.nih.gov/gene/?term=252875	C81488	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007981	2528	FUT6	http://www.ncbi.nlm.nih.gov/gene/?term=2528	"FCT3A, FT1A, Fuc-TVI, FucT-VI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007982	252948	TTTY16	http://www.ncbi.nlm.nih.gov/gene/?term=252948	NCRNA00139	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00007983	252952	TTTY19	http://www.ncbi.nlm.nih.gov/gene/?term=252952	NCRNA00144	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00007984	252969	NEIL2	http://www.ncbi.nlm.nih.gov/gene/?term=252969	"NEH2, NEI2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007985	252969	NEIL2	http://www.ncbi.nlm.nih.gov/gene/?term=252969	"NEH2, NEI2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007986	252969	NEIL2	http://www.ncbi.nlm.nih.gov/gene/?term=252969	"NEH2, NEI2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00007987	252974	Tspear	http://www.ncbi.nlm.nih.gov/gene/?term=252974	"C330046G03Rik, ORF65, TSP-EAR, Tnep1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00007988	252995	FNDC5	http://www.ncbi.nlm.nih.gov/gene/?term=252995	"FRCP2, irisin "	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00007989	253012	HEPACAM2	http://www.ncbi.nlm.nih.gov/gene/?term=253012	MIKI	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007990	25307	Cst3	http://www.ncbi.nlm.nih.gov/gene/?term=25307	CYSC	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007991	2530	FUT8	http://www.ncbi.nlm.nih.gov/gene/?term=2530		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007992	253143	PRR14L	http://www.ncbi.nlm.nih.gov/gene/?term=253143	C22orf30	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007993	253143	PRR14L	http://www.ncbi.nlm.nih.gov/gene/?term=253143	C22orf30	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00007994	2531	KDSR	http://www.ncbi.nlm.nih.gov/gene/?term=2531	"DHSR, FVT1, SDR35C1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007995	25320	Gast	http://www.ncbi.nlm.nih.gov/gene/25320	"Gas, PPG34 "	mRNA	Rattus norvegicus	8812056	Endoplasmic reticulum	Hypothalamus	In situ hybridization	"Altogether, these ultrastructural studies strongly suggested that the Gas and AVP mRNAs might be associated with distinct domains of the RER. "
RLID00007996	25327	Kcnc1	http://www.ncbi.nlm.nih.gov/gene/?term=25327	"KShIIIB, Kv3.1, Kv4, NGK2-KV4 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00007997	2532	ACKR1	http://www.ncbi.nlm.nih.gov/gene/?term=2532	"CCBP1, CD234, DARC, Dfy, FY, GPD, GpFy, WBCQ1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007998	2533	FYB	http://www.ncbi.nlm.nih.gov/gene/?term=2533	"ADAP, PRO0823, SLAP-130, SLAP130 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00007999	253430	IPMK	http://www.ncbi.nlm.nih.gov/gene/?term=253430		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008000	2534	FYN	http://www.ncbi.nlm.nih.gov/gene/?term=2534	"SLK, SYN, p59-FYN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008001	253558	LCLAT1	http://www.ncbi.nlm.nih.gov/gene/?term=253558	"1AGPAT8, AGPAT8, ALCAT1, HSRG1849, LYCAT, UNQ1849 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008002	253558	LCLAT1	http://www.ncbi.nlm.nih.gov/gene/?term=253558	"1AGPAT8, AGPAT8, ALCAT1, HSRG1849, LYCAT, UNQ1849 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008003	253650	ANKRD18A	http://www.ncbi.nlm.nih.gov/gene/?term=253650		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008004	253714	MMS22L	http://www.ncbi.nlm.nih.gov/gene/?term=253714	"C6orf167, dJ39B17.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008005	253714	MMS22L	http://www.ncbi.nlm.nih.gov/gene/?term=253714	"C6orf167, dJ39B17.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008006	253714	MMS22L	http://www.ncbi.nlm.nih.gov/gene/?term=253714	"C6orf167, dJ39B17.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008007	253738	EBF3	http://www.ncbi.nlm.nih.gov/gene/?term=253738	"COE3, EBF-3, O/E-2, OE-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008008	253769	WDR27	http://www.ncbi.nlm.nih.gov/gene/?term=253769		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008009	253769	WDR27	http://www.ncbi.nlm.nih.gov/gene/?term=253769		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008010	253782	CERS6	http://www.ncbi.nlm.nih.gov/gene/?term=253782	"CERS5, LASS6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008011	253782	CERS6	http://www.ncbi.nlm.nih.gov/gene/?term=253782	"CERS5, LASS6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008012	253782	CERS6	http://www.ncbi.nlm.nih.gov/gene/?term=253782	"CERS5, LASS6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008013	2537	IFI6	http://www.ncbi.nlm.nih.gov/gene/?term=2537	"6-16, FAM14C, G1P3, IFI-6-16, IFI616 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008014	2537	IFI6	http://www.ncbi.nlm.nih.gov/gene/?term=2537	"6-16, FAM14C, G1P3, IFI-6-1616, IFI6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008015	253832	ZDHHC20	http://www.ncbi.nlm.nih.gov/gene/?term=253832	"4933421L13Rik, DHHC-20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008016	2538	G6PC	http://www.ncbi.nlm.nih.gov/gene/?term=2538	"G6PC1, G6PT, GSD1, GSD1a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008017	2538	G6PC	http://www.ncbi.nlm.nih.gov/gene/?term=2538	"G6PC1, G6PT, GSD1, GSD1a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008018	2539667	ash2	http://www.ncbi.nlm.nih.gov/gene/?term=2539667	SPBC13G1.08c	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00008019	253980	KCTD13	http://www.ncbi.nlm.nih.gov/gene/?term=253980	"BACURD1, FKSG86, PDIP1, POLDIP1, hBACURD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008020	25398	Cacna1a	http://www.ncbi.nlm.nih.gov/gene/?term=25398	"BccA1, Cav2.1, rbA-1 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00008021	2539	G6PD	http://www.ncbi.nlm.nih.gov/gene/?term=2539	G6PD1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008022	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	1311815	Dendrite	Hippocampus	In situ hybridization	"These data suggest that CaM II kinase a mRNA is expressed in the dendrites of hippocampal pyramidal cells and, therefore, is likely to be expressed in dendrites in other regions of the central nervous system exhibiting CaM II kinase a: cRNA labeling in the neuropil. "
RLID00008023	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	7500833	Dendrite	Neuron	In situ hybridization	In each of these region hybridization was decreased in the molecular layers which is consistent with the reported dendritic localization of alpha CamKII mRNA.
RLID00008024	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	7773006	Dendrite	Neuron	In situ hybridization	"Table 1. As of 1994, mRNAs that have been localized within dendrites by in situ hybridization.  Data are collected from Table 1. "
RLID00008025	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	9322162	Cell body	Hippocampus	In situ hybridization	"In most neurons that express a CaMII kinase, the highest levels of the mRNA were in the cell body, but labeling was also present throughout dendrites. "
RLID00008026	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Nonstimulated rats: BDNF, TrkB, and CaMKII-β mRNAs localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of dentate gyrus (DG) granule cells; CaMKII-α mRNA localized throughout the dendritic length in neurons of all hippocampal subfields.  In contrast, CaMKII-? (Figs. 1C and 2D), BDNF (Figs. 1E and 2G), and TrkB mRNAs (Figs.1G and 2J) were localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of DG granule cells. "
RLID00008027	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Pilocarpine seizures: increased staining levels of CaMKII-β mRNA throughout the whole dendritic length in all hippocampal subfields; induction of CaMKII-α, BDNF, and TrkB mRNAs dendritic targeting in CA1, CA3, and DG neurons.  Data provide evidence that BDNF, TrkB, and CaMKII-α and -β mRNAs are accumulated in the dendrites of specific hippocampal neurons during pilocarpine seizures and kindling development. "
RLID00008028	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	20237286	Dendrite	Hippocampus	Fluorescence in situ hybridization	"When MAP2 3'-UTR/GAPDH and CaMKIIa 3'-UTR/GAPDH pairs (Fig. 2A,B) were coinjected in mature neurons, MAP2 and CaMKIIa 3'-UTRs were transported as particles into dendrites, whereas GAPDH was retained in the soma.  "
RLID00008029	25400	Camk2a	http://www.ncbi.nlm.nih.gov/gene/?term=25400	"PK2CDD, PKCCD "	mRNA	Rattus norvegicus	2162385	Dendrite	Brain	In situ hybridization	Our results indicate that CaM-KII alpha- but not beta-subunit mRNA is transported into dendrites.
RLID00008030	254048	UBN2	http://www.ncbi.nlm.nih.gov/gene/?term=254048		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008031	254048	UBN2	http://www.ncbi.nlm.nih.gov/gene/?term=254048		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008032	254048	UBN2	http://www.ncbi.nlm.nih.gov/gene/?term=254048		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008033	254065	BRWD3	http://www.ncbi.nlm.nih.gov/gene/?term=254065	"BRODL, MRX93 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00008034	254170	FBXO33	http://www.ncbi.nlm.nih.gov/gene/?term=254170	"BMND12, Fbx33, c14_5247 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008035	2541815	bip1	http://www.ncbi.nlm.nih.gov/gene/?term=2541815	"SPAC22A12.15c, bip "	mRNA	Saccharomyces cerevisiae	23066505	Ribosome	Yeast	Northern blot	"Northern blot analysis of the distribution of total or tBip1 mRNA in polyribosomes from extracts of unstressed or ER-stressed (2 mM DTT, 1 hr) cells. "
RLID00008036	25420	Cryab	http://www.ncbi.nlm.nih.gov/gene/?term=25420	AACRYA	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00008037	25420	Cryab	http://www.ncbi.nlm.nih.gov/gene/?term=25420	AACRYA	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. Data collected from Table 1.
RLID00008038	254225	RNF169	http://www.ncbi.nlm.nih.gov/gene/?term=254225		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008039	254295	PHYHD1	http://www.ncbi.nlm.nih.gov/gene/?term=254295		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008040	254295	PHYHD1	http://www.ncbi.nlm.nih.gov/gene/?term=254295		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008041	2542	SLC37A4	http://www.ncbi.nlm.nih.gov/gene/?term=2542	"G6PT1, G6PT2, G6PT3, GSD1b, GSD1c, GSD1d, PRO0685, TRG-19, TRG19 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008042	254359	ZDHHC24	http://www.ncbi.nlm.nih.gov/gene/?term=254359		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008043	25438	Eno3	http://www.ncbi.nlm.nih.gov/gene/?term=25438	"BBE, MSE "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00008044	254394	MCM9	http://www.ncbi.nlm.nih.gov/gene/?term=254394	"C6orf61, MCMDC1, ODG4, dJ329L24.1, dJ329L24.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008045	2543	GAGE1	http://www.ncbi.nlm.nih.gov/gene/?term=2543	"CT4.1, GAGE-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008046	254531	LPCAT4	http://www.ncbi.nlm.nih.gov/gene/?term=254531	"AGPAT7, AYTL3, LPAAT-eta, LPEAT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008047	254552	NUDT8	http://www.ncbi.nlm.nih.gov/gene/?term=254552		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008048	25459	Hmgb1	http://www.ncbi.nlm.nih.gov/gene/?term=25459	"Ac2-008, Hmg1 "	mRNA	Rattus norvegicus	25855182	Axon	Neuron 	Fluorescence in situ hybridization|qRT-PCR	"Here, we show that amphoterin mRNA localizes into axons via its proximal 3�UTR. "
RLID00008049	25459	Hmgb1	http://www.ncbi.nlm.nih.gov/gene/?term=25459	"Ac2-008, Hmg1 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00008050	25473	Lamb2	http://www.ncbi.nlm.nih.gov/gene/?term=25473	SLAM	mRNA	Rattus norvegicus	7599960	Synapse	Muscle fibers	In situ hybridization	"N-CAM, 45K-rapsyn, and S-laminin mRNAs are concentrated at synaptic sites in muscle fibers "
RLID00008051	2547	XRCC6	http://www.ncbi.nlm.nih.gov/gene/?term=2547	"CTC75, CTCBF, G22P1, KU70, ML8, TLAA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008052	2547	XRCC6	http://www.ncbi.nlm.nih.gov/gene/?term=2547	"CTC75, CTCBF, G22P1, KU70, ML8, TLAA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008053	2547	XRCC6	http://www.ncbi.nlm.nih.gov/gene/?term=2547	"CTC75, CTCBF, G22P1, KU70, ML8, TLAA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008054	254863	TMEM256	http://www.ncbi.nlm.nih.gov/gene/?term=254863	C17orf61	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008055	254887	ZDHHC23	http://www.ncbi.nlm.nih.gov/gene/?term=254887	"DHHC-23, NIDD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008056	2548	GAA	http://www.ncbi.nlm.nih.gov/gene/?term=2548	LYAG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008057	255027	MPV17L	http://www.ncbi.nlm.nih.gov/gene/?term=255027	"M-LPH, MLPH1, MLPH21, MPV17L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008058	255027	MPV17L	http://www.ncbi.nlm.nih.gov/gene/?term=255027	"M-LPH, MLPH1, MLPH21, MPV17L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008059	2550	GABBR1	http://www.ncbi.nlm.nih.gov/gene/?term=2550	"GABABR1, GABBR1-3, GB1, GPRC3A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008060	25518	Ppia	http://www.ncbi.nlm.nih.gov/gene/?term=25518	"CYCA, CyP-A "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00008061	2551	GABPA	http://www.ncbi.nlm.nih.gov/gene/?term=2551	"E4TF1-60, E4TF1A, NFT2, NRF2, NRF2A, RCH04A07 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008062	25522	Prkcz	http://www.ncbi.nlm.nih.gov/gene/?term=25522	"14-3-3-zetaisoform, Pkcz, r14-3-3 "	mRNA	Rattus norvegicus	15371429	Dendrite	Hippocampus	In situ hybridization	"Fig. 1 shows that substantial signal intensities, indicating the presence of PKM-Zeta mRNA, were observed in both somata and dendrites of hippocampal neurons. Again, the labeling signal for PKM-Zeta mRNA was discontinuously distributed along dendritic arborizations.  "
RLID00008063	255252	LRRC57	http://www.ncbi.nlm.nih.gov/gene/?term=255252		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008064	255252	LRRC57	http://www.ncbi.nlm.nih.gov/gene/?term=255252		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008065	2553	GABPB1	http://www.ncbi.nlm.nih.gov/gene/?term=2553	"BABPB2, E4TF1, E4TF1-47, E4TF1-53, E4TF1B, GABPB, GABPB2, NRF2B1, NRF2B2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008066	2553	GABPB1	http://www.ncbi.nlm.nih.gov/gene/?term=2553	"BABPB2, E4TF1, E4TF1-47, E4TF1-53, E4TF1B, GABPB, GABPB-1, GABPB2, NRF2B1, NRF2B2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008067	255403	ZNF718	http://www.ncbi.nlm.nih.gov/gene/?term=255403		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008068	255488	RNF144B	http://www.ncbi.nlm.nih.gov/gene/?term=255488	"IBRDC2, PIR2, bA528A10.3, p53RFP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008069	255488	RNF144B	http://www.ncbi.nlm.nih.gov/gene/?term=255488	"IBRDC2, PIR2, bA528A10.3, p53RFP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008070	25550	Slc1a1	http://www.ncbi.nlm.nih.gov/gene/?term=25550	"Eaac1, Eaat3, REAAC1 "	mRNA	Rattus norvegicus	21185901	Dendrite	Hippocampus	In situ hybridization	"These studies provide the first evidence that EAAC1 mRNA localizes to dendrites and suggest that dendritic targeting of EAAC1 mRNA is increased by seizure activity and may be regulated by neuronal activity/depolarization.restricted to the cell body and proximal dendrites of hippocampal pyramidal neurons in vivo under control conditions.  Together, these data provide strong evidence that EAAC1 mRNA is localized in dendrites in vitro. "
RLID00008071	255626	HIST1H2BA	http://www.ncbi.nlm.nih.gov/gene/?term=255626	"H2BFU, STBP, TH2B, TSH2B, TSH2B.1, bA317E16.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008072	255738	PCSK9	http://www.ncbi.nlm.nih.gov/gene/?term=255738	"FH3, HCHOLA3, LDLCQ1, NARC-1, NARC1, PC9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008073	255812	SDHAP1	http://www.ncbi.nlm.nih.gov/gene/?term=255812	"SDHAL1, SDHALP1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008074	255877	BCL6B	http://www.ncbi.nlm.nih.gov/gene/?term=255877	"BAZF, ZBTB28, ZNF62 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008075	255919	CNEP1R1	http://www.ncbi.nlm.nih.gov/gene/?term=255919	"C16orf69, NEP1-R1, TMEM188, TMP125 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008076	255919	CNEP1R1	http://www.ncbi.nlm.nih.gov/gene/?term=255919	"C16orf69, NEP1-R1, NEP1R1, TMEM188, TMP125 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008077	255919	CNEP1R1	http://www.ncbi.nlm.nih.gov/gene/?term=255919	"C16orf69, NEP1-R1, NEP1R1, TMEM188, TMP125 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008078	255919	CNEP1R1	http://www.ncbi.nlm.nih.gov/gene/?term=255919	"C16orf69, NEP1-R1, NEP1R1, TMEM188, TMP125 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008079	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	2148487	Cell body	Neuron	In situ hybridization	"In situ hybridization revealed a differential localization of mRNA within dendrites. mRNA encoding MAP2 was abundant in cell bodies and distributed nonhomogeneously throughout the dendritic compartment, but was not detected in axons. "
RLID00008080	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	3200318	Dendrite	Neuron	In situ hybridization	"Here, we use in situ hybridization with specific complementary DNA probes to show that messenger RNA for the dendritic-spcific microtubule associated protein MAP2 is presented in dendrites in developing brain. "
RLID00008081	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	7773006	Dendrite	Neuron	In situ hybridization	"Table 1. As of 1994, mRNAs that have been localized within dendrites by in situ hybridization.  Data are collected from Table 1. "
RLID00008082	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	7877439	Dendrite	Neuron	In situ hybridization	"These included MAP2 mRNA, which was identified by deep staining within dendritic fields but by only light staining within neuronal cell bodies.  The dendrite-rich molecular layers, in contrast, were deeply and diffusely stained suggesting that most MAP2 mRNA was translocated into the dendrites of hippocampal neurons (Fig. 1B). "
RLID00008083	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	7877439	Cytoplasm	Neuron	In situ hybridization	"Within specific brainstem nuclei, such as the trapezoid nucleus, stain corresponding to MAP2 mRNA was confined to the perinuclear cytoplasm of neurons (Fig. 3A). "
RLID00008084	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	9322162	Dendrite	Hippocampus	In situ hybridization	"In some neurons that express MAP2, the mRNA was present at the highest levels in the proximal third to half of the dendritic arbor, whereas in other neurons the highest levels of labeling were in the cell body.  This labeling presumably reflects the presence of MAP2 mRNA in the dendrites of most of the neurons that inhabit the cortex. "
RLID00008085	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	20237286	Dendrite	Hippocampus	Fluorescence in situ hybridization	"When MAP2 3'-UTR/GAPDH and CaMKIIa 3'-UTR/GAPDH pairs (Fig. 2A,B) were coinjected in mature neurons, MAP2 and CaMKIIa 3'-UTRs were transported as particles into dendrites, whereas GAPDH was retained in the soma.  "
RLID00008086	25595	Map2	http://www.ncbi.nlm.nih.gov/gene/?term=25595	"MAP2R, Mtap2 "	mRNA	Rattus norvegicus	26512708	Dendrite	ForeBrain	Immunoprecipitation|RIP-Chip	"Rat MARTA-1, a protein that transports MAP-2 mRNA to dendrites  "
RLID00008087	255967	PAN3	http://www.ncbi.nlm.nih.gov/gene/?term=255967		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008088	2560	GABRB1	http://www.ncbi.nlm.nih.gov/gene/?term=2560		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008089	25617	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=25617	"BIP, GRP78 "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00008090	25617	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=25617	"BIP, GRP78 "	mRNA	Rattus norvegicus	20308067	Axon	Neuron	Fluorescence in situ hybridization	"MRNAs encoding the endoplasmic reticulum chaperone proteins calreticulin and Grp78/BiP were previously detected in sensory axons by RT-PCR and array hybridization (7, 30). Because these analyses used lysed axons that could contain proximal axonal segments, we used FISH to directly visualize the mRNAs in dissociated cultures of DRG neurons. DRG neurons showed punctate FISH signals for beta-actin, calreticulin, and Grp78/BiP mRNAs that extended into growth cones (Fig. 1A). This granular distribution is similar to other mRNAs localizing to dendrites and axons (21).mRNAs encoding the endoplasmic reticulum chaperone proteins calreticulin and Grp78/BiP were previously detected in sensory axons by RT-PCR and array hybridization (7, 30). Because these analyses used lysed axons that could contain proximal axonal segments, we used FISH to directly visualize the mRNAs in dissociated cultures of DRG neurons. DRG neurons showed punctate FISH signals for beta-actin, calreticulin, and Grp78/BiP mRNAs that extended into growth cones (Fig. 1A). This granular distribution is similar to other mRNAs localizing to dendrites and axons (21). "
RLID00008091	25617	Hspa5	http://www.ncbi.nlm.nih.gov/gene/?term=25617	"BIP, GRP78 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00008092	256281	NUDT14	http://www.ncbi.nlm.nih.gov/gene/?term=256281	"UGPP, UGPPase "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008093	256281	NUDT14	http://www.ncbi.nlm.nih.gov/gene/?term=256281	"UGPP, UGPPase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008094	2562	GABRB3	http://www.ncbi.nlm.nih.gov/gene/?term=2562	ECA5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008095	2562	GABRB3	http://www.ncbi.nlm.nih.gov/gene/?term=2562	ECA5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008096	256302	NATD1	http://www.ncbi.nlm.nih.gov/gene/?term=256302	"C17orf103, Gtlf3b "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008097	256302	NATD1	http://www.ncbi.nlm.nih.gov/gene/?term=256302	"C17orf103, Gtlf3b "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008098	256302	NATD1	http://www.ncbi.nlm.nih.gov/gene/?term=256302	"C17orf103, Gtlf3b "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008099	256356	GK5	http://www.ncbi.nlm.nih.gov/gene/?term=256356		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008100	256356	GK5	http://www.ncbi.nlm.nih.gov/gene/?term=256356		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008101	256356	GK5	http://www.ncbi.nlm.nih.gov/gene/?term=256356		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008102	256364	EML3	http://www.ncbi.nlm.nih.gov/gene/?term=256364	ELP95	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008103	256364	EML3	http://www.ncbi.nlm.nih.gov/gene/?term=256364	ELP95	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008104	256380	SCML4	http://www.ncbi.nlm.nih.gov/gene/?term=256380	dJ47M23.1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008105	256380	SCML4	http://www.ncbi.nlm.nih.gov/gene/?term=256380	dJ47M23.1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008106	2563	GABRD	http://www.ncbi.nlm.nih.gov/gene/?term=2563	"EIG10, EJM7, GEFSP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008107	256471	MFSD8	http://www.ncbi.nlm.nih.gov/gene/?term=256471	"CCMD, CLN7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008108	2564	GABRE	http://www.ncbi.nlm.nih.gov/gene/?term=2564		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008109	256586	LYSMD2	http://www.ncbi.nlm.nih.gov/gene/?term=256586		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008110	256815	C10orf67	http://www.ncbi.nlm.nih.gov/gene/?term=256815	"C10orf115, LINC01552, bA215C7.4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008111	256815	C10orf67	http://www.ncbi.nlm.nih.gov/gene/?term=256815	"C10orf115, LINC01552, bA215C7.4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008112	2568	GABRP	http://www.ncbi.nlm.nih.gov/gene/?term=2568		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008113	25695	Cebpd	http://www.ncbi.nlm.nih.gov/gene/?term=25695	"C/EBPd, CELF "	mRNA	Rattus norvegicus	23426691	Dendrite	Hippocampus	Fluorescence in situ hybridization	"C/EBPδ is found in nuclear, somatic, and dendritic compartments, and a dendritic localization of C/EBPδ mRNA in hippocampal neuronal cultures suggests that this transcription factor may be translated at synapses. "
RLID00008114	256987	SERINC5	http://www.ncbi.nlm.nih.gov/gene/?term=256987	"C5orf12, TPO1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008115	256987	SERINC5	http://www.ncbi.nlm.nih.gov/gene/?term=256987	"C5orf12, TPO1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008116	25698	Ass1	http://www.ncbi.nlm.nih.gov/gene/?term=25698	"ASSA, Ass "	mRNA	Rattus norvegicus	8726358	Endoplasmic reticulum	Liver	In situ hybridization	"These ratios showed that the mRNAs for argininosuccinate synthetase and argininosuccinate lyase were located next to the cytoplasmic side of the mitochondrial membrane and in the nearby endoplasmic reticulum. These data show that ASL mRNA is preferentially located at the mitochondrial outer membrane and in the ER. Thus,ASS mRNA, likeASL mRNA, is preferentially located at the mitochondrial outer membrane and in the ER. This suggests that COIII mRNA is actually predominantly associated with those portions of the inner membrane which lie at the mitochondrial perimeter rather than along the cristae. "
RLID00008117	25698	Ass1	http://www.ncbi.nlm.nih.gov/gene/?term=25698	"ASSA, Ass "	mRNA	Rattus norvegicus	8726358	Mitochondrion	Liver	In situ hybridization	"A method was developed to study the intracellular distribution of ASS and ASL mRNAs in rat liver at the ultrastructural level, using in situ RT-PCR (reverse transcription and the polymerase chain reaction). The results indicate that these mRNAs are localized to areas of the cytoplasm adjacent to, or in the immediate vicinity of, the mitochondria.For experiments using the ASS primers, ratios similar to those for ASL were obtained, again regardless of the specific experimental procedures followed. For all silver grains, the ratios for mitochondrial outer membrane were 2.36 & 0.40 and 2.18 -+ 0.33, and those for ER were 1.36 * 0.20 and 1.19 2 0.18 after in situ RT-PCR or in situ RT, respectively, while the ratios for mitochondrial matrix and other structures were < 1.0 (Table I, ASS data). Consideration of only medium/large grains gave similar ratios (not shown). Thus, ASS mRNA, like ASL mRNA, is preferentially located at the mitochondrial outer membrane and in the ER. "
RLID00008118	257000	TINCR	http://www.ncbi.nlm.nih.gov/gene/?term=257000	"LINC00036, NCRNA00036, PLAC2, onco-lncRNA-16 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008119	257000	TINCR	http://www.ncbi.nlm.nih.gov/gene/?term=257000	"LINC00036, NCRNA00036, PLAC2, onco-lncRNA-16 "	lncRNA	Homo sapiens	23201690	Cytoplasm	Keratinocytes	In situ hybridization	"Single-molecule RNA fluorescence in situ hybridization (FISH) identified 80.6% of TINCR molecules newly acquired during differentiation within the cytoplasm (Supplementary Fig. 1e, f). "
RLID00008120	257106	ARHGAP30	http://www.ncbi.nlm.nih.gov/gene/?term=257106		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008121	25718	Igf1r	http://www.ncbi.nlm.nih.gov/gene/?term=25718	"IGF-1 receptor, IGFIRC, Igfr1, JTK13 "	mRNA	Rattus norvegicus	1658638	Cell body	Brain	In situ hybridization	"IGF-I-R mRNA is synthesized in neuronal cell bodies, and the receptors are transported to axons and dendrites in adjacent synapse-rich layers. "
RLID00008122	2571	GAD1	http://www.ncbi.nlm.nih.gov/gene/?term=2571	"CPSQ1, GAD, SCP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008123	25728	Apoe	http://www.ncbi.nlm.nih.gov/gene/?term=25728	APOEA	mRNA	Rattus norvegicus	20456011	Cell body	Hippocampus	In situ hybridization	The in situ signals of APOE mRNA (Fig. 1a and b) and other candidates (see Figure S2) were detected in both the cell bodies and dendrites of the cultured hippocampal neurons.
RLID00008124	25728	Apoe	http://www.ncbi.nlm.nih.gov/gene/?term=25728	APOEA	mRNA	Rattus norvegicus	20456011	Dendrite	Hippocampus	In situ hybridization	The in situ signals of APOE mRNA (Fig. 1a and b) and other candidates (see Figure S2) were detected in both the cell bodies and dendrites of the cultured hippocampal neurons.
RLID00008125	257397	TAB3	http://www.ncbi.nlm.nih.gov/gene/?term=257397	"MAP3K7IP3, NAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008126	25739	Pygb	http://www.ncbi.nlm.nih.gov/gene/?term=25739	GLYPHOA	mRNA	Rattus norvegicus	24898526	Axon	Spinal motoneuron 	In situ hybridization|qRT-PCR	"To study the mRNA expression of GP and GS, the key enzymes of glycogen metabolism, we applied FISH on cultured spinal motoneurons. This also allowed us to investigate the distribution of these mRNAs in soma, dendrites and axons. GP mRNA was present in the cell soma as well as in processes (Figure 1a, d, arrows). The signal overlapped with the signal for MAP2 (Figure 1b,c) as well as that for tau (Figure 1e, f) indicating the presence of the mRNA in dendrites as well as in axons. "
RLID00008127	25739	Pygb	http://www.ncbi.nlm.nih.gov/gene/?term=25739	GLYPHOA	mRNA	Rattus norvegicus	24898526	Dendrite	Spinal motoneuron 	In situ hybridization|qRT-PCR	"To study the mRNA expression of GP and GS, the key enzymes of glycogen metabolism, we applied FISH on cultured spinal motoneurons. This also allowed us to investigate the distribution of these mRNAs in soma, dendrites and axons. GP mRNA was present in the cell soma as well as in processes (Figure? 1a, d, arrows). The signal overlapped with the signal for MAP2 (Figure? 1b,c) as well as that for tau (Figure? 1e, f) indicating the presence of the mRNA in dendrites as well as in axons. "
RLID00008128	257407	C2orf72	http://www.ncbi.nlm.nih.gov/gene/?term=257407		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008129	257415	FAM133B	http://www.ncbi.nlm.nih.gov/gene/?term=257415		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008130	25764	HYPK	http://www.ncbi.nlm.nih.gov/gene/?term=25764	"C15orf63, HSPC136 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008131	25766	PRPF40B	http://www.ncbi.nlm.nih.gov/gene/?term=25766	HYPC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008132	25771	TBC1D22A	http://www.ncbi.nlm.nih.gov/gene/?term=25771	"C22orf4, HSC79E021 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008133	25771	TBC1D22A	http://www.ncbi.nlm.nih.gov/gene/?term=25771	"C22orf4, HSC79E021 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008134	25776	CBY1	http://www.ncbi.nlm.nih.gov/gene/?term=25776	"C22orf2, CBY, HS508I15A, PGEA1, PIGEA-14, PIGEA14, arb1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008135	25777	SUN2	http://www.ncbi.nlm.nih.gov/gene/?term=25777	UNC84B	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008136	25778	DSTYK	http://www.ncbi.nlm.nih.gov/gene/?term=25778	"CAKUT1, DustyPK, HDCMD38P, RIP5, RIPK5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008137	25782	RAB3GAP2	http://www.ncbi.nlm.nih.gov/gene/?term=25782	"RAB3-GAP150, RAB3GAP150, SPG69, WARBM2, p150 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008138	25782	RAB3GAP2	http://www.ncbi.nlm.nih.gov/gene/?term=25782	"RAB3-GAP150, RAB3GAP150, SPG69, WARBM2, p150 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008139	25782	RAB3GAP2	http://www.ncbi.nlm.nih.gov/gene/?term=25782	"RAB3-GAP150, RAB3GAP150, SPG69, WARBM2, p150 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008140	257872	Olfr835	http://www.ncbi.nlm.nih.gov/gene/?term=257872	MOR150-3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008141	257885	Olfr885	http://www.ncbi.nlm.nih.gov/gene/?term=257885	MOR162-12	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008142	25789	TMEM59L	http://www.ncbi.nlm.nih.gov/gene/?term=25789	"BSMAP, C19orf4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008143	257906	Olfr293	http://www.ncbi.nlm.nih.gov/gene/?term=257906	MOR221-3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008144	257914	Olfr663	http://www.ncbi.nlm.nih.gov/gene/?term=257914	MOR40-12	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008145	257919	Olfr467	http://www.ncbi.nlm.nih.gov/gene/?term=257919	"GA_x5J8B7W6B6J-2556603-2556836, MOR204-33P "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008146	257921	Olfr1229	http://www.ncbi.nlm.nih.gov/gene/?term=257921	"MOR233-19, MOR233-22 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008147	257929	Olfr299	http://www.ncbi.nlm.nih.gov/gene/?term=257929	MOR221-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008148	25792	CIZ1	http://www.ncbi.nlm.nih.gov/gene/?term=25792	"LSFR1, NP94, ZNF356 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008149	25796	PGLS	http://www.ncbi.nlm.nih.gov/gene/?term=25796	"6PGL, HEL-S-304 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008150	25796	PGLS	http://www.ncbi.nlm.nih.gov/gene/?term=25796	"6PGL, HEL-S-304 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008151	257979	Olfr1281	http://www.ncbi.nlm.nih.gov/gene/?term=257979	"MOR248-14P, MOR248-18 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008152	25798	BRI3	http://www.ncbi.nlm.nih.gov/gene/?term=25798	I3	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008153	25799	ZNF324	http://www.ncbi.nlm.nih.gov/gene/?term=25799	"ZF5128, ZNF324A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008154	25799	ZNF324	http://www.ncbi.nlm.nih.gov/gene/?term=25799	"ZF5128A, ZNF324 "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00008155	25800	SLC39A6	http://www.ncbi.nlm.nih.gov/gene/?term=25800	"LIV-1, ZIP6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008156	25800	SLC39A6	http://www.ncbi.nlm.nih.gov/gene/?term=25800	"LIV-1, ZIP6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008157	258010	SVIP	http://www.ncbi.nlm.nih.gov/gene/?term=258010		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008158	258010	SVIP	http://www.ncbi.nlm.nih.gov/gene/?term=258010		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008159	25801	GCA	http://www.ncbi.nlm.nih.gov/gene/?term=25801	GCL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008160	25804	LSM4	http://www.ncbi.nlm.nih.gov/gene/?term=25804	"GRP, YER112W "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008161	25804	LSM4	http://www.ncbi.nlm.nih.gov/gene/?term=25804	"GRP, YER112W "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008162	25805	BAMBI	http://www.ncbi.nlm.nih.gov/gene/?term=25805	NMA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008163	25807	RHBDD3	http://www.ncbi.nlm.nih.gov/gene/?term=25807	"C22orf3, HS984G1A, PTAG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008164	2580	GAK	http://www.ncbi.nlm.nih.gov/gene/?term=2580	"DNAJ26, DNAJC26 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008165	2580	GAK	http://www.ncbi.nlm.nih.gov/gene/?term=2580	"DNAJ26, DNAJC26 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008166	25813	SAMM50	http://www.ncbi.nlm.nih.gov/gene/?term=25813	"CGI-51, OMP85, SAM50, TOB55, TRG-3, YNL026W "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008167	25813	SAMM50	http://www.ncbi.nlm.nih.gov/gene/?term=25813	"CGI-51, OMP85, SAM50, TOB55, TRG-3, YNL026W "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008168	25814	ATXN10	http://www.ncbi.nlm.nih.gov/gene/?term=25814	"E46L, HUMEEP, SCA10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008169	25814	ATXN10	http://www.ncbi.nlm.nih.gov/gene/?term=25814	"E46L, HUMEEP, SCA10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008170	25814	ATXN10	http://www.ncbi.nlm.nih.gov/gene/?term=25814	"E46L, HUMEEP, SCA10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008171	258163	Olfr504	http://www.ncbi.nlm.nih.gov/gene/?term=258163	"MOR40-15, MOR40-7P "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008172	25816	TNFAIP8	http://www.ncbi.nlm.nih.gov/gene/?term=25816	"GG2-1, MDC-3.13, NDED, SCC-S2, SCCS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008173	25816	TNFAIP8	http://www.ncbi.nlm.nih.gov/gene/?term=25816	"GG2-1, MDC-3.13, NDED, SCC-S2, SCCS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008174	25816	TNFAIP8	http://www.ncbi.nlm.nih.gov/gene/?term=25816	"GG2-1, MDC-3.13, NDED, SCC-S2, SCCS2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008175	2581	GALC	http://www.ncbi.nlm.nih.gov/gene/?term=2581		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008176	25820	ARIH1	http://www.ncbi.nlm.nih.gov/gene/?term=25820	"ARI, HARI, HHARI, UBCH7BP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008177	25820	ARIH1	http://www.ncbi.nlm.nih.gov/gene/?term=25820	"ARI, HARI, HHARI, UBCH7BP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008178	25820	ARIH1	http://www.ncbi.nlm.nih.gov/gene/?term=25820	"ARI, HARI, HHARI, UBCH7BP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008179	25821	MTO1	http://www.ncbi.nlm.nih.gov/gene/?term=25821	"CGI-02, COXPD10 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008180	258238	Olfr417	http://www.ncbi.nlm.nih.gov/gene/?term=258238	"GA_x5J8B7W3B3M-312879-313274, GA_x6K02T2P20D-20787051-20786119, MOR267-11 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008181	25824	PRDX5	http://www.ncbi.nlm.nih.gov/gene/?term=25824	"ACR1, AOEB166, B166, HEL-S-55, PLP, PMP20, PRDX6, PRXV, SBBI10, prx-V "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008182	25824	PRDX5	http://www.ncbi.nlm.nih.gov/gene/?term=25824	"ACR1, AOEB166, B166, HEL-S-55, PLP, PMP20, PRDX6, PRXV, SBBI10, prx-V "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008183	25824	PRDX5	http://www.ncbi.nlm.nih.gov/gene/?term=25824	"ACR1, AOEB166, B166, HEL-S-55, PLP, PMP20, PRDX6, PRXV, SBBI10, prx-V "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008184	25825	BACE2	http://www.ncbi.nlm.nih.gov/gene/?term=25825	"AEPLC, ALP56, ASP1, ASP21, BAE2, CDA13, CEAP1, DRAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008185	25826	SNORD82	http://www.ncbi.nlm.nih.gov/gene/?term=25826	"RNU82, U82, Z25 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008186	25826	SNORD82	http://www.ncbi.nlm.nih.gov/gene/?term=25826	"RNU82, U82, Z25 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008187	25828	TXN2	http://www.ncbi.nlm.nih.gov/gene/?term=25828	"COXPD29, MT-TRX, MTRX, TRX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008188	2582	GALE	http://www.ncbi.nlm.nih.gov/gene/?term=2582	SDR1E1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008189	2582	GALE	http://www.ncbi.nlm.nih.gov/gene/?term=2582	SDR1E1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008190	25830	SULT4A1	http://www.ncbi.nlm.nih.gov/gene/?term=25830	"BR-STL-1, BRSTL1, DJ388M5.3, NST, SULTX3, hBR-STL-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008191	25831	HECTD1	http://www.ncbi.nlm.nih.gov/gene/?term=25831	EULIR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008192	25831	HECTD1	http://www.ncbi.nlm.nih.gov/gene/?term=25831	EULIR	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008193	258320	Olfr1232	http://www.ncbi.nlm.nih.gov/gene/?term=258320	MOR233-18	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008194	258329	Olfr135	http://www.ncbi.nlm.nih.gov/gene/?term=258329	MOR256-48	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008195	258336	Olfr77	http://www.ncbi.nlm.nih.gov/gene/?term=258336	"18A, MOR143-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008196	25833	POU2F3	http://www.ncbi.nlm.nih.gov/gene/?term=25833	"Epoc-1, OCT-11, OCT11, OTF-11, PLA-1, PLA1, Skn-1a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008197	25833	POU2F3	http://www.ncbi.nlm.nih.gov/gene/?term=25833	"Epoc-1, OCT-11, OCT11, OTF-11, PLA-1, PLA1, Skn-1a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008198	258378	Olfr593	http://www.ncbi.nlm.nih.gov/gene/?term=258378	MOR24-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008199	258388	Olfr1279	http://www.ncbi.nlm.nih.gov/gene/?term=258388	MOR245-12	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008200	258398	Olfr1295	http://www.ncbi.nlm.nih.gov/gene/?term=258398	MOR248-10	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008201	25839	COG4	http://www.ncbi.nlm.nih.gov/gene/?term=25839	"CDG2J, COD1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008202	2583	B4GALNT1	http://www.ncbi.nlm.nih.gov/gene/?term=2583	"GALGT, GALNACT, GalNAc-T, SPG26 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008203	258402	Olfr1079	http://www.ncbi.nlm.nih.gov/gene/?term=258402	MOR189-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008204	25840	METTL7A	http://www.ncbi.nlm.nih.gov/gene/?term=25840	AAM-B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008205	25842	ASF1A	http://www.ncbi.nlm.nih.gov/gene/?term=25842	"CGI-98, CIA, HSPC146 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008206	25842	ASF1A	http://www.ncbi.nlm.nih.gov/gene/?term=25842	"CGI-98, CIA, HSPC146 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008207	258430	Olfr938	http://www.ncbi.nlm.nih.gov/gene/?term=258430	MOR171-25	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008208	25843	MOB4	http://www.ncbi.nlm.nih.gov/gene/?term=25843	"2C4D, CGI-95, MOB1, MOB3, MOBKL3, PHOCN, PREI3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008209	25843	MOB4	http://www.ncbi.nlm.nih.gov/gene/?term=25843	"2C4D, CGI-95, MOB1, MOB3, MOBKL3, PHOCN, PREI3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008210	25843	MOB4	http://www.ncbi.nlm.nih.gov/gene/?term=25843	"2C4D, CGI-95, MOB1, MOB3, MOBKL3, PHOCN, PREI3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008211	25844	YIPF3	http://www.ncbi.nlm.nih.gov/gene/?term=25844	"C6orf109, FinGER3, KLIP1, dJ337H4.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008212	25847	ANAPC13	http://www.ncbi.nlm.nih.gov/gene/?term=25847	"APC13, SWM1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008213	25847	ANAPC13	http://www.ncbi.nlm.nih.gov/gene/?term=25847	"APC13, SWM1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008214	258487	Olfr722	http://www.ncbi.nlm.nih.gov/gene/?term=258487	MOR241-3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008215	2584	GALK1	http://www.ncbi.nlm.nih.gov/gene/?term=2584	"GALK, GK1, HEL-S-19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008216	25850	ZNF345	http://www.ncbi.nlm.nih.gov/gene/?term=25850	HZF10	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008217	25850	ZNF345	http://www.ncbi.nlm.nih.gov/gene/?term=25850	HZF10	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008218	25852	ARMC8	http://www.ncbi.nlm.nih.gov/gene/?term=25852	"GID5, HSPC056, S863-2, VID28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008219	258534	Olfr1361	http://www.ncbi.nlm.nih.gov/gene/?term=258534	MOR256-12	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008220	25853	DCAF12	http://www.ncbi.nlm.nih.gov/gene/?term=25853	"CT102, KIAA1892, TCC52, WDR40A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008221	25853	DCAF12	http://www.ncbi.nlm.nih.gov/gene/?term=25853	"CT102, KIAA1892, TCC52, WDR40A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008222	258549	Olfr798	http://www.ncbi.nlm.nih.gov/gene/?term=258549	MOR108-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008223	25854	FAM149A	http://www.ncbi.nlm.nih.gov/gene/?term=25854	"MST119, MSTP119 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008224	25855	BRMS1	http://www.ncbi.nlm.nih.gov/gene/?term=25855		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008225	25855	BRMS1	http://www.ncbi.nlm.nih.gov/gene/?term=25855		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008226	258561	Olfr1012	http://www.ncbi.nlm.nih.gov/gene/?term=258561	MOR213-6	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008227	25858	TEX40	http://www.ncbi.nlm.nih.gov/gene/?term=25858	C11orf20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008228	258597	Olfr716	http://www.ncbi.nlm.nih.gov/gene/?term=258597	MOR260-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008229	2585	GALK2	http://www.ncbi.nlm.nih.gov/gene/?term=2585	GK2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008230	25861	DFNB31	http://www.ncbi.nlm.nih.gov/gene/?term=25861	"CIP98, PDZD7B, USH2D, WHRN, WI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008231	258632	Olfr1138	http://www.ncbi.nlm.nih.gov/gene/?term=258632	MOR177-8	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008232	258644	Olfr1166	http://www.ncbi.nlm.nih.gov/gene/?term=258644	MOR174-6	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008233	25864	ABHD14A	http://www.ncbi.nlm.nih.gov/gene/?term=25864	DORZ1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008234	25865	PRKD2	http://www.ncbi.nlm.nih.gov/gene/?term=25865	"HSPC187, PKD2, nPKC-D2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008235	258675	Olfr1423	http://www.ncbi.nlm.nih.gov/gene/?term=258675	MOR239-3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008236	258677	Olfr76	http://www.ncbi.nlm.nih.gov/gene/?term=258677	"MOR215-3, V5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008237	258679	Olfr1440	http://www.ncbi.nlm.nih.gov/gene/?term=258679	MOR215-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008238	258690	Olfr1469	http://www.ncbi.nlm.nih.gov/gene/?term=258690	MOR202-11	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008239	25870	SUMF2	http://www.ncbi.nlm.nih.gov/gene/?term=25870	pFGE	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008240	25870	SUMF2	http://www.ncbi.nlm.nih.gov/gene/?term=25870	pFGE	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008241	25870	SUMF2	http://www.ncbi.nlm.nih.gov/gene/?term=25870	pFGE	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008242	25871	C3orf17	http://www.ncbi.nlm.nih.gov/gene/?term=25871	"NEPRO, NET17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008243	258720	Olfr516	http://www.ncbi.nlm.nih.gov/gene/?term=258720	MOR268-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008244	258736	Olfr1497	http://www.ncbi.nlm.nih.gov/gene/?term=258736	MOR212-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008245	25873	RPL36	http://www.ncbi.nlm.nih.gov/gene/?term=25873	L36	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008246	25874	MPC2	http://www.ncbi.nlm.nih.gov/gene/?term=25874	BRP44	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008247	25874	MPC2	http://www.ncbi.nlm.nih.gov/gene/?term=25874	BRP44	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008248	258768	Olfr1189	http://www.ncbi.nlm.nih.gov/gene/?term=258768	MOR237-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008249	25878	MXRA5	http://www.ncbi.nlm.nih.gov/gene/?term=25878		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008250	25879	DCAF13	http://www.ncbi.nlm.nih.gov/gene/?term=25879	"GM83, HSPC064, WDSOF1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008251	25880	TMEM186	http://www.ncbi.nlm.nih.gov/gene/?term=25880	C16orf51	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008252	25885	POLR1A	http://www.ncbi.nlm.nih.gov/gene/?term=25885	"A190, AFDCIN, RPA1, RPA194, RPO1-4, RPO14 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008253	25886	POC1A	http://www.ncbi.nlm.nih.gov/gene/?term=25886	"PIX2, SOFT, WDR51A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008254	258886	Olfr1299	http://www.ncbi.nlm.nih.gov/gene/?term=258886	MOR248-8	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008255	258887	Olfr1294	http://www.ncbi.nlm.nih.gov/gene/?term=258887	MOR248-7	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008256	25888	ZNF473	http://www.ncbi.nlm.nih.gov/gene/?term=25888	"HZFP100, ZN473 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008257	258890	Olfr1297	http://www.ncbi.nlm.nih.gov/gene/?term=258890	MOR248-4	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008258	258895	Olfr1216	http://www.ncbi.nlm.nih.gov/gene/?term=258895	MOR233-9	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008259	25893	TRIM58	http://www.ncbi.nlm.nih.gov/gene/?term=25893	BIA2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008260	25894	PLEKHG4	http://www.ncbi.nlm.nih.gov/gene/?term=25894	"ARHGEF44, PRTPHN1, SCA4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008261	258951	Olfr339	http://www.ncbi.nlm.nih.gov/gene/?term=258951	MOR136-3	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008262	258959	Olfr170	http://www.ncbi.nlm.nih.gov/gene/?term=258959	MOR273-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008263	25895	METTL21B	http://www.ncbi.nlm.nih.gov/gene/?term=25895	FAM119B	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008264	25895	METTL21B	http://www.ncbi.nlm.nih.gov/gene/?term=25895	FAM119B	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008265	25896	INTS7	http://www.ncbi.nlm.nih.gov/gene/?term=25896	"C1orf73, INT7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008266	25896	INTS7	http://www.ncbi.nlm.nih.gov/gene/?term=25896	"C1orf73, INT7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008267	258971	Olfr1243	http://www.ncbi.nlm.nih.gov/gene/?term=258971	MOR231-4	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008268	25897	RNF19A	http://www.ncbi.nlm.nih.gov/gene/?term=25897	RNF19	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008269	25898	RCHY1	http://www.ncbi.nlm.nih.gov/gene/?term=25898	"ARNIP, CHIMP, PIRH2, PRO1996, RNF199, ZCHY, ZNF363 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008270	25898	RCHY1	http://www.ncbi.nlm.nih.gov/gene/?term=25898	"ARNIP, CHIMP, PIRH2, PRO1996, RNF199, ZCHY, ZNF363 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008271	2589	GALNT1	http://www.ncbi.nlm.nih.gov/gene/?term=2589	GALNAC-T1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008272	2589	GALNT1	http://www.ncbi.nlm.nih.gov/gene/?term=2589	GALNAC-T1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008273	2589	GALNT1	http://www.ncbi.nlm.nih.gov/gene/?term=2589	GALNAC-T1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008274	25901	CCDC28A	http://www.ncbi.nlm.nih.gov/gene/?term=25901	"C6orf80, CCRL1AP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008275	259026	Olfr378	http://www.ncbi.nlm.nih.gov/gene/?term=259026	MOR135-2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008276	25902	MTHFD1L	http://www.ncbi.nlm.nih.gov/gene/?term=25902	"FTHFSDC1, MTC1THFS, dJ292B18.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008277	25902	MTHFD1L	http://www.ncbi.nlm.nih.gov/gene/?term=25902	"FTHFSDC1, MTC1THFS, dJ292B18.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008278	25904	CNOT10	http://www.ncbi.nlm.nih.gov/gene/?term=25904		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008279	25904	CNOT10	http://www.ncbi.nlm.nih.gov/gene/?term=25904		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008280	25906	ANAPC15	http://www.ncbi.nlm.nih.gov/gene/?term=25906	"APC15, C11orf51, HSPC020 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008281	25906	ANAPC15	http://www.ncbi.nlm.nih.gov/gene/?term=25906	"APC15, C11orf51, HSPC020 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008282	259074	Olfr1352	http://www.ncbi.nlm.nih.gov/gene/?term=259074	MOR139-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008283	25907	TMEM158	http://www.ncbi.nlm.nih.gov/gene/?term=25907	"BBP, RIS1, p40BBP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008284	2590	GALNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2590	GalNAc-T2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008285	2590	GALNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2590	GalNAc-T2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008286	2590	GALNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2590	GalNAc-T2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008287	259111	Olfr974	http://www.ncbi.nlm.nih.gov/gene/?term=259111	MOR171-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008288	259112	Olfr979	http://www.ncbi.nlm.nih.gov/gene/?term=259112	MOR223-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008289	25911	DPCD	http://www.ncbi.nlm.nih.gov/gene/?term=25911		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008290	25912	C1orf43	http://www.ncbi.nlm.nih.gov/gene/?term=25912	"HSPC012, NICE-3, NS5ATP4, S863-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008291	25913	POT1	http://www.ncbi.nlm.nih.gov/gene/?term=25913	"CMM10, GLM9, HPOT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008292	25914	RTTN	http://www.ncbi.nlm.nih.gov/gene/?term=25914		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008293	25915	NDUFAF3	http://www.ncbi.nlm.nih.gov/gene/?term=25915	"2P1, C3orf60, E3-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008294	259173	ALS2CL	http://www.ncbi.nlm.nih.gov/gene/?term=259173	RN49018	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008295	25917	THUMPD3	http://www.ncbi.nlm.nih.gov/gene/?term=25917		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008296	25917	THUMPD3	http://www.ncbi.nlm.nih.gov/gene/?term=25917		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008297	259197	NCR3	http://www.ncbi.nlm.nih.gov/gene/?term=259197	"1C7, CD337, LY117, MALS, NKp30 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008298	25920	NELFB	http://www.ncbi.nlm.nih.gov/gene/?term=25920	"COBRA1, NELF-B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008299	259215	LY6G6F	http://www.ncbi.nlm.nih.gov/gene/?term=259215	"C6orf21, G6f, LY6G6D, NG32 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008300	25921	ZDHHC5	http://www.ncbi.nlm.nih.gov/gene/?term=25921	"DHHC5, ZNF375 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008301	25921	ZDHHC5	http://www.ncbi.nlm.nih.gov/gene/?term=25921	"DHHC5, ZNF375 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008302	259230	SGMS1	http://www.ncbi.nlm.nih.gov/gene/?term=259230	"MOB, MOB1, SMS1, TMEM23, hmob33 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008303	259230	SGMS1	http://www.ncbi.nlm.nih.gov/gene/?term=259230	"MOB, MOB1, SMS1, TMEM23, hmob33 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008304	259230	SGMS1	http://www.ncbi.nlm.nih.gov/gene/?term=259230	"MOB, MOB1, SMS1, TMEM23, hmob33 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008305	25923	ATL3	http://www.ncbi.nlm.nih.gov/gene/?term=25923	HSN1F	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008306	25923	ATL3	http://www.ncbi.nlm.nih.gov/gene/?term=25923	HSN1F	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008307	25925	ZNF521	http://www.ncbi.nlm.nih.gov/gene/?term=25925	"EHZF, Evi3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008308	259266	ASPM	http://www.ncbi.nlm.nih.gov/gene/?term=259266	"ASP, Calmbp1, MCPH5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008309	25926	NOL11	http://www.ncbi.nlm.nih.gov/gene/?term=25926		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008310	259279	Tubgcp3	http://www.ncbi.nlm.nih.gov/gene/?term=259279	"GCP3, Spc98p "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008311	259282	BOD1L1	http://www.ncbi.nlm.nih.gov/gene/?term=259282	"BOD1L, FAM44A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008312	259282	BOD1L1	http://www.ncbi.nlm.nih.gov/gene/?term=259282	"BOD1L, FAM44A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008313	2592	GALT	http://www.ncbi.nlm.nih.gov/gene/?term=2592		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008314	2592	GALT	http://www.ncbi.nlm.nih.gov/gene/?term=2592		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008315	259300	Ehd2	http://www.ncbi.nlm.nih.gov/gene/?term=259300	"BC027084, C130052H20Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008316	259302	Srgap3	http://www.ncbi.nlm.nih.gov/gene/?term=259302	"AI452337, Arhgap14, D130026O08Rik, Gbi, MEGAP, WRP, mKIAA0411 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008317	25932	CLIC4	http://www.ncbi.nlm.nih.gov/gene/?term=25932	"CLIC4L, H1, MTCLIC, huH1, p64H1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008318	25934	NIPSNAP3A	http://www.ncbi.nlm.nih.gov/gene/?term=25934	"HSPC299, NIPSNAP4, TASSC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008319	25936	NSL1	http://www.ncbi.nlm.nih.gov/gene/?term=25936	"C1orf48, DC8, MIS14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008320	25936	NSL1	http://www.ncbi.nlm.nih.gov/gene/?term=25936	"C1orf48, DC8, MIS14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008321	25937	WWTR1	http://www.ncbi.nlm.nih.gov/gene/?term=25937	TAZ	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008322	25937	WWTR1	http://www.ncbi.nlm.nih.gov/gene/?term=25937	TAZ	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008323	2593	GAMT	http://www.ncbi.nlm.nih.gov/gene/?term=2593	"CCDS2, HEL-S-20, PIG2, TP53I2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008324	2593	GAMT	http://www.ncbi.nlm.nih.gov/gene/?term=2593	"CCDS2, HEL-S-20, PIG2, TP53I2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008325	25940	FAM98A	http://www.ncbi.nlm.nih.gov/gene/?term=25940		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008326	25941	TPGS2	http://www.ncbi.nlm.nih.gov/gene/?term=25941	"C18orf10, HMFN0601, L17, PGs2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008327	25942	SIN3A	http://www.ncbi.nlm.nih.gov/gene/?term=25942		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008328	25942	SIN3A	http://www.ncbi.nlm.nih.gov/gene/?term=25942		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008329	25943	C20orf194	http://www.ncbi.nlm.nih.gov/gene/?term=25943		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008330	25945	NECTIN3	http://www.ncbi.nlm.nih.gov/gene/?term=25945	"CD113, CDW113, NECTIN-3, PPR3, PRR3, PVRL3, PVRR3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008331	25946	ZNF385A	http://www.ncbi.nlm.nih.gov/gene/?term=25946	"HZF, RZF, ZFP385, ZNF385 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008332	25948	KBTBD2	http://www.ncbi.nlm.nih.gov/gene/?term=25948	BKLHD1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008333	25948	KBTBD2	http://www.ncbi.nlm.nih.gov/gene/?term=25948	BKLHD1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008334	25949	SYF2	http://www.ncbi.nlm.nih.gov/gene/?term=25949	"CBPIN, NTC31, P29, fSAP29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008335	25949	SYF2	http://www.ncbi.nlm.nih.gov/gene/?term=25949	"CBPIN, NTC31, P29, fSAP29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008336	25950	RWDD3	http://www.ncbi.nlm.nih.gov/gene/?term=25950	RSUME	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008337	25950	RWDD3	http://www.ncbi.nlm.nih.gov/gene/?term=25950	RSUME	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008338	25953	PNKD	http://www.ncbi.nlm.nih.gov/gene/?term=25953	"BRP17, DYT8, FKSG19, FPD1, KIPP1184, MR-1, MR1, PDC, PKND1, TAHCCP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008339	25953	PNKD	http://www.ncbi.nlm.nih.gov/gene/?term=25953	"BRP17, DYT8, FKSG19, FPD1, KIPP1184, MR-1, MR1, PDC, PKND1, TAHCCP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008340	25957	PNISR	http://www.ncbi.nlm.nih.gov/gene/?term=25957	"C6orf111, HSPC306, SFRS18, SRrp130, bA98I9.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008341	25957	PNISR	http://www.ncbi.nlm.nih.gov/gene/?term=25957	"C6orf111, HSPC306, SFRS18, SRrp130, bA98I9.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008342	25959	KANK2	http://www.ncbi.nlm.nih.gov/gene/?term=25959	"ANKRD25, MXRA3, PPKWH, SIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008343	25959	KANK2	http://www.ncbi.nlm.nih.gov/gene/?term=25959	"ANKRD25, MXRA3, PPKWH, SIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008344	25961	NUDT13	http://www.ncbi.nlm.nih.gov/gene/?term=25961		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008345	25963	TMEM87A	http://www.ncbi.nlm.nih.gov/gene/?term=25963		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008346	25963	TMEM87A	http://www.ncbi.nlm.nih.gov/gene/?term=25963		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008347	25966	C2CD2	http://www.ncbi.nlm.nih.gov/gene/?term=25966	"C21orf25, C21orf258, TMEM24L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008348	25970	SH2B1	http://www.ncbi.nlm.nih.gov/gene/?term=25970	"PSM, SH2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008349	25972	UNC50	http://www.ncbi.nlm.nih.gov/gene/?term=25972	"GMH1, HSD23, UNCL, URP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008350	25972	UNC50	http://www.ncbi.nlm.nih.gov/gene/?term=25972	"GMH1, HSD23, UNCL, URP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008351	25972	UNC50	http://www.ncbi.nlm.nih.gov/gene/?term=25972	"GMH1, HSD23, UNCL, URP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008352	25973	PARS2	http://www.ncbi.nlm.nih.gov/gene/?term=25973	"MT-PRORS, proRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008353	25974	MMACHC	http://www.ncbi.nlm.nih.gov/gene/?term=25974	cblC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008354	25974	MMACHC	http://www.ncbi.nlm.nih.gov/gene/?term=25974	cblC	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008355	25974	MMACHC	http://www.ncbi.nlm.nih.gov/gene/?term=25974	cblC	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008356	25976	TIPARP	http://www.ncbi.nlm.nih.gov/gene/?term=25976	"ARTD14, PARP7, pART14 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008357	25977	NECAP1	http://www.ncbi.nlm.nih.gov/gene/?term=25977	EIEE21	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008358	25978	CHMP2B	http://www.ncbi.nlm.nih.gov/gene/?term=25978	"ALS17, CHMP2.5, DMT1, VPS2-2, VPS2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008359	25978	CHMP2B	http://www.ncbi.nlm.nih.gov/gene/?term=25978	"ALS17, CHMP2.5, DMT1, VPS2-2, VPS2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008360	25978	CHMP2B	http://www.ncbi.nlm.nih.gov/gene/?term=25978	"ALS17, CHMP2.5, DMT1, VPS2-2, VPS2B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008361	25979	DHRS7B	http://www.ncbi.nlm.nih.gov/gene/?term=25979	"CGI-93, SDR32C1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008362	25979	DHRS7B	http://www.ncbi.nlm.nih.gov/gene/?term=25979	"CGI-93, SDR32C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008363	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00008364	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	19175411	Ribosome	T-cell|SeAx	qRT-PCR	"Using quantitative real-time RT-PCR we evaluated, whether mRNAs coding for differently located proteins are selectively enriched in one of the two analysed compartments, namely free versus membrane-associated polysomes. We selected genes coding for proteins located in the plasma membrane (GPR137B), secreted proteins (TIC2, IBP2, PAI) and cytosolic proteins (the house keeping genes GAPDH and HMBS). In fact, the distribution of the specific mRNA was as predicted ( Fig. 1): The average ratio of specific mRNA at bound ribosomes versus free ribosomes was 1 ? 4.4 for the housekeeping genes (GAPDH and HMBS) and 13.3 ? 1 for genes coding for membrane-bound or secreted proteins. Ratios for genes coding for cytosolic proteins were always below 0.6 and those for membrane or secreted genes were always above 1. The highest values were observed for PAI in MyLa (57 ? 1) and GPR137B in SeAx (34 ? 1), while the lowest ratios were detected for HMBS (1 ? 55) and GAPDH (1 ? 12) in HuT78. "
RLID00008365	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008366	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	22895844	Exosome	Colon|Liver|Lung	qRT-PCR	"When the RNA species within exosomes derived from the three CRC cell lines were examined, the mRNAs of housekeeping genes such as ACTB and GAPDH, the microRNAs such as miR-21, miR-192 and miR-221, and the natural antisense RNAs of LRRC24, MDM2 and CDKN1A genes, were detected. "
RLID00008367	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	Northern blot	"In this report, we use multiple cell fractionation protocols, in combination with cDNA microarray, nuclease protection, and Northern blot analyses, to assess the distribution of mRNAs between free and ER-bound ribosomes. We find a broad representation of mRNAs encoding soluble proteins in the ER fraction, with a subset of such mRNAs displaying substantial ER partitioning. In addition, we present evidence that membrane-bound ribosomes engage in the translation of mRNAs encoding soluble proteins. Single-cell in situ hybridization analysis of the subcellular distribution of mRNAs encoding ER-localized and soluble proteins identify two overall patterns of mRNA distribution in the cell-endoplasmic reticular and cytosolic. FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells.  "
RLID00008368	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00008369	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	16178658	Mitochondrion	HDF cell	Fluorescence in situ hybridization	"Unexpectedly, we found that both K-ras and GAPDH mRNAs colocalize with mitochondria. Extensive control studies are performed, including the use of fluorescence in-situ hybridization (FISH), negative-control beacons, and the detection of colocalization of 28S ribosomal RNA with the rough endoplasmic reticulum (ER), suggesting that the mRNA localization and colocalization patterns observed in our study are true and specific.  "
RLID00008370	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	21431749	Cytosol	HEK293 cell	Northern blot	"Similarly, Northern blot analysis of the mRNA composition of the cytosol and membrane fractions show that the cytosol fraction is enriched for mRNAs encoding histone (H3F3A) and GAPDH, whereas the membrane fraction is enriched in mRNAs encoding ER resident proteins, such as GRP94 and calreticulin (Fig. 2 B). "
RLID00008371	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	25142066	Endoplasmic reticulum	HEK293|HeLa|HDF|J558 cell	qRT-PCR	"Figure 3: Correlation between paired measurements of the fraction of 18S rRNA and GAPDH mRNA on the ER membrane.  Correlation between paired measurements of the fraction of 18S rRNA and GAPDH mRNA on the ER membrane. (A) Ribosome and GAPDH mRNA distributions were determined in the indicated cell lines and in 16 independent experiments conducted with HEK293 cells (B). qPCR array data comparing RNA distribution in cytosol and membrane fractions of HEK293 (C) and J558 (D) cells. Data are represented as a histogram of the fractional value of RNA in the membrane fraction for various cohorts of RNAs. mRNAcyt represent RNAs that encode cytosolic and nucleoplasmic proteins; mRNAsec include RNAs encoding secretory and membrane proteins as well as resident proteins of endomembrane organelles. (?) Mean, (σ) deviation. Data are collected from Figure 3. "
RLID00008372	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	25142066	Cytosol	HeLa cell|HEK293 cell	In situ hybridization	"Here, using single molecule RNA fluorescence in situ hybridization and cell fractionation, we have demonstrated that a candidate RNA with an expected cytosolic distribution, GAPDH, does, indeed, reside in close proximity to the ER membrane and, by virtue of its extractability in detergent, can be translated on ER-bound ribosomes. "
RLID00008373	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	25142066	Ribosome	HEK293|HeLa|HDF|J558 cell	qRT-PCR	"Figure 3: Correlation between paired measurements of the fraction of 18S rRNA and GAPDH mRNA on the ER membrane.  Correlation between paired measurements of the fraction of 18S rRNA and GAPDH mRNA on the ER membrane. (A) Ribosome and GAPDH mRNA distributions were determined in the indicated cell lines and in 16 independent experiments conducted with HEK293 cells (B). qPCR array data comparing RNA distribution in cytosol and membrane fractions of HEK293 (C) and J558 (D) cells. Data are represented as a histogram of the fractional value of RNA in the membrane fraction for various cohorts of RNAs. mRNAcyt represent RNAs that encode cytosolic and nucleoplasmic proteins; mRNAsec include RNAs encoding secretory and membrane proteins as well as resident proteins of endomembrane organelles. (?) Mean, (σ) deviation. Data are collected from Figure 3. "
RLID00008374	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	26272916	Endoplasmic reticulum	U2OS cell	Fluorescence in situ hybridization	"To determine whether partial ER association was a general phenomenon for all mRNAs, we next investigated the localization of an mRNA encoding a cytosolic protein, glyceraldehyde 3-phosphate dehydrogenase (GAPDH). We could reproducibly find 15% of the GAPDH puncta in digitonin-extracted cells (Fig. 1A,B). However, in contrast to what we had seen for Sec61b and nesprin-2, most of the GAPDH mRNAs were extracted in cells treated with either HHT, or puromycin+EDTA (Fig. 1), suggesting that the small amount of ER association was mediated by translating ribosomes. Data are collected from Figure 1. "
RLID00008375	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008376	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008377	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008378	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	22193719	Cytoplasm	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00008379	2597	GAPDH	http://www.ncbi.nlm.nih.gov/gene/?term=2597	"G3PD, GAPD, HEL-S-162eP "	mRNA	Homo sapiens	25753659	Cytosol	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00008380	25980	AAR2	http://www.ncbi.nlm.nih.gov/gene/?term=25980	"C20orf4, CGI-23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008381	25983	NGDN	http://www.ncbi.nlm.nih.gov/gene/?term=25983	"C14orf120, CANu1, LCP5, NGD, lpd-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008382	25983	NGDN	http://www.ncbi.nlm.nih.gov/gene/?term=25983	"C14orf120, CANu1, LCP5, NGD, lpd-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008383	25983	NGDN	http://www.ncbi.nlm.nih.gov/gene/?term=25983	"C14orf120, CANu1, LCP5, NGD, lpd-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008384	25987	TSKU	http://www.ncbi.nlm.nih.gov/gene/?term=25987	"E2IG4, LRRC54, TSK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008385	25988	HINFP	http://www.ncbi.nlm.nih.gov/gene/?term=25988	"HiNF-P, MIZF, ZNF743 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008386	25994	HIGD1A	http://www.ncbi.nlm.nih.gov/gene/?term=25994	"HIG1, RCF1a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008387	25994	HIGD1A	http://www.ncbi.nlm.nih.gov/gene/?term=25994	"HIG1, RCF1a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008388	25994	HIGD1A	http://www.ncbi.nlm.nih.gov/gene/?term=25994	"HIG1, RCF1a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008389	25996	REXO2	http://www.ncbi.nlm.nih.gov/gene/?term=25996	"CGI-114, REX2, RFN, SFN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008390	25998	IBTK	http://www.ncbi.nlm.nih.gov/gene/?term=25998	"BTBD26, BTKI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008391	25	ABL1	http://www.ncbi.nlm.nih.gov/gene/?term=25	"ABL, JTK7, bcr/abl, c-ABL, c-ABL1, p150, v-abl "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008392	25	ABL1	http://www.ncbi.nlm.nih.gov/gene/?term=25	"ABL, JTK7, bcr/abl, c-ABL, c-ABL1, p150, v-abl "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008393	25	ABL1	http://www.ncbi.nlm.nih.gov/gene/?term=25	"ABL, JTK7, bcr/abl, c-ABL, c-ABL1, p150, v-abl "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008394	26000	TBC1D10B	http://www.ncbi.nlm.nih.gov/gene/?term=26000	"EPI64B, FP2461 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008395	26001	RNF167	http://www.ncbi.nlm.nih.gov/gene/?term=26001	"5730408C10Rik, LP2254, RING105 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008396	26003	GORASP2	http://www.ncbi.nlm.nih.gov/gene/?term=26003	"GOLPH6, GRASP55, GRS2, p59 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008397	26005	C2CD3	http://www.ncbi.nlm.nih.gov/gene/?term=26005	OFD14	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008398	26007	TKFC	http://www.ncbi.nlm.nih.gov/gene/?term=26007	"DAK, NET45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008399	26007	TKFC	http://www.ncbi.nlm.nih.gov/gene/?term=26007	"DAK, NET45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008400	26009	ZZZ3	http://www.ncbi.nlm.nih.gov/gene/?term=26009	ATAC1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008401	26010	SPATS2L	http://www.ncbi.nlm.nih.gov/gene/?term=26010	"DNAPTP6, SGNP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008402	26010	SPATS2L	http://www.ncbi.nlm.nih.gov/gene/?term=26010	"DNAPTP6, SGNP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008403	26011	TENM4	http://www.ncbi.nlm.nih.gov/gene/?term=26011	"Doc4, ETM5, ODZ4, TNM4, Ten-M4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008404	26012	NSMF	http://www.ncbi.nlm.nih.gov/gene/?term=26012	"HH9, NELF "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008405	26017	FAM32A	http://www.ncbi.nlm.nih.gov/gene/?term=26017	"OTAG-12, OTAG12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008406	26018	LRIG1	http://www.ncbi.nlm.nih.gov/gene/?term=26018	"LIG-1, LIG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008407	26019	UPF2	http://www.ncbi.nlm.nih.gov/gene/?term=26019	"HUPF2, RENT2, smg-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008408	26019	UPF2	http://www.ncbi.nlm.nih.gov/gene/?term=26019	"HUPF2, RENT2, smg-3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008409	26020	LRP10	http://www.ncbi.nlm.nih.gov/gene/?term=26020	"LRP9, MST087, MSTP087 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008410	260293	CYP4X1	http://www.ncbi.nlm.nih.gov/gene/?term=260293	CYPIVX1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008411	260294	NSUN5P2	http://www.ncbi.nlm.nih.gov/gene/?term=260294	"NOL1R2, NSUN5C, WBSCR20B, WBSCR20C "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008412	26030	PLEKHG3	http://www.ncbi.nlm.nih.gov/gene/?term=26030	"ARHGEF43, KIAA0599 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008413	26031	OSBPL3	http://www.ncbi.nlm.nih.gov/gene/?term=26031	"ORP-3, ORP3, OSBP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008414	26032	SUSD5	http://www.ncbi.nlm.nih.gov/gene/?term=26032		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008415	26034	IPCEF1	http://www.ncbi.nlm.nih.gov/gene/?term=26034	PIP3-E	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008416	26034	IPCEF1	http://www.ncbi.nlm.nih.gov/gene/?term=26034	PIP3-E	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008417	26035	GLCE	http://www.ncbi.nlm.nih.gov/gene/?term=26035	HSEPI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008418	26037	SIPA1L1	http://www.ncbi.nlm.nih.gov/gene/?term=26037	E6TP1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008419	260425	MAGI3	http://www.ncbi.nlm.nih.gov/gene/?term=260425	"MAGI-3, dJ730K3.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008420	26046	LTN1	http://www.ncbi.nlm.nih.gov/gene/?term=26046	"C21orf10, C21orf98, RNF160, ZNF294 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008421	26047	CNTNAP2	http://www.ncbi.nlm.nih.gov/gene/?term=26047	"AUTS15, CASPR2, CDFE, NRXN4, PTHSL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008422	26048	ZNF500	http://www.ncbi.nlm.nih.gov/gene/?term=26048	"ZKSCAN18, ZSCAN50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008423	26049	FAM169A	http://www.ncbi.nlm.nih.gov/gene/?term=26049	SLAP75	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008424	26051	PPP1R16B	http://www.ncbi.nlm.nih.gov/gene/?term=26051	"ANKRD4, TIMAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008425	26054	SENP6	http://www.ncbi.nlm.nih.gov/gene/?term=26054	"SSP1, SUSP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008426	26054	SENP6	http://www.ncbi.nlm.nih.gov/gene/?term=26054	"SSP1, SUSP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008427	26054	SENP6	http://www.ncbi.nlm.nih.gov/gene/?term=26054	"SSP1, SUSP1 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00008428	26056	RAB11FIP5	http://www.ncbi.nlm.nih.gov/gene/?term=26056	"GAF1, RIP11, pp75 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008429	26056	RAB11FIP5	http://www.ncbi.nlm.nih.gov/gene/?term=26056	"GAF1, RIP11, pp75 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008430	26057	ANKRD17	http://www.ncbi.nlm.nih.gov/gene/?term=26057	"GTAR, MASK2, NY-BR-16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008431	26057	ANKRD17	http://www.ncbi.nlm.nih.gov/gene/?term=26057	"GTAR, MASK2, NY-BR-16 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008432	26057	ANKRD17	http://www.ncbi.nlm.nih.gov/gene/?term=26057	"GTAR, MASK2, NY-BR-16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008433	26058	GIGYF2	http://www.ncbi.nlm.nih.gov/gene/?term=26058	"GYF2, PARK11, PERQ2, PERQ3, TNRC15 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008434	26060	APPL1	http://www.ncbi.nlm.nih.gov/gene/?term=26060	"APPL, DIP13alpha, MODY14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008435	26060	APPL1	http://www.ncbi.nlm.nih.gov/gene/?term=26060	"APPL, DIP13alpha, MODY14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008436	26060	APPL1	http://www.ncbi.nlm.nih.gov/gene/?term=26060	"APPL, DIP13alpha, MODY14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008437	26060	APPL1	http://www.ncbi.nlm.nih.gov/gene/?term=26060	"APPL, DIP13alpha, MODY14 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008438	26060	APPL1	http://www.ncbi.nlm.nih.gov/gene/?term=26060	"APPL, DIP13alpha, MODY14 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008439	26061	HACL1	http://www.ncbi.nlm.nih.gov/gene/?term=26061	"2-HPCL, HPCL, HPCL2, PHYH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008440	26063	DECR2	http://www.ncbi.nlm.nih.gov/gene/?term=26063	"PDCR, SDR17C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008441	26063	DECR2	http://www.ncbi.nlm.nih.gov/gene/?term=26063	"PDCR, SDR17C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008442	26064	RAI14	http://www.ncbi.nlm.nih.gov/gene/?term=26064	"NORPEG, RAI13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008443	26064	RAI14	http://www.ncbi.nlm.nih.gov/gene/?term=26064	"NORPEG, RAI13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008444	26065	LSM14A	http://www.ncbi.nlm.nih.gov/gene/?term=26065	"C19orf13, FAM61A, RAP55, RAP55A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008445	26067080	vas	http://www.ncbi.nlm.nih.gov/gene/?term=26067080	"Dmel_CG46283, BG:DS00929.14, CG3506, CG43081, CG46283, DmRH25, Dmel\CG46283, Dmel_CG33678, Dmel_CG3506, Dmel_CG43081, EP(2)0812, VAS, VASA, Vas, Vasa, cgt, fs(2)ltoRJ36 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00008446	26073	POLDIP2	http://www.ncbi.nlm.nih.gov/gene/?term=26073	"PDIP38, POLD4, p38 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008447	26073	POLDIP2	http://www.ncbi.nlm.nih.gov/gene/?term=26073	"PDIP38, POLD4, p38 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008448	26085	KLK13	http://www.ncbi.nlm.nih.gov/gene/?term=26085	"KLK-L4, KLKL4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008449	26086	GPSM1	http://www.ncbi.nlm.nih.gov/gene/?term=26086	AGS3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008450	26090	ABHD12	http://www.ncbi.nlm.nih.gov/gene/?term=26090	"ABHD12A, BEM46L2, C20orf22, PHARC, dJ965G21.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008451	26091	HERC4	http://www.ncbi.nlm.nih.gov/gene/?term=26091		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008452	26091	HERC4	http://www.ncbi.nlm.nih.gov/gene/?term=26091		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008453	26092	TOR1AIP1	http://www.ncbi.nlm.nih.gov/gene/?term=26092	"LAP1, LAP1B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008454	26097	CHTOP	http://www.ncbi.nlm.nih.gov/gene/?term=26097	"C1orf77, FL-SRAG, FOP, SRAG, SRAG-3, SRAG-5, pp7704 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008455	26097	CHTOP	http://www.ncbi.nlm.nih.gov/gene/?term=26097	"C1orf77, FL-SRAG, FOP, SRAG, SRAG-3, SRAG-5, pp7704 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008456	26098	EDRF1	http://www.ncbi.nlm.nih.gov/gene/?term=26098	C10orf137	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008457	26099	SZRD1	http://www.ncbi.nlm.nih.gov/gene/?term=26099	C1orf144	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008458	26099	SZRD1	http://www.ncbi.nlm.nih.gov/gene/?term=26099	C1orf144	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008459	26100	WIPI2	http://www.ncbi.nlm.nih.gov/gene/?term=26100	"ATG18B, Atg21, CGI-50, WIPI-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008460	26112	CCDC69	http://www.ncbi.nlm.nih.gov/gene/?term=26112		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008461	26112	CCDC69	http://www.ncbi.nlm.nih.gov/gene/?term=26112		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008462	26115	TANC2	http://www.ncbi.nlm.nih.gov/gene/?term=26115	"ROLSA, rols "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008463	26118	WSB1	http://www.ncbi.nlm.nih.gov/gene/?term=26118	"SWIP1, WSB-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008464	26118	WSB1	http://www.ncbi.nlm.nih.gov/gene/?term=26118	"SWIP1, WSB-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008465	26119	LDLRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=26119	"ARH, ARH1, ARH2, FHCB1, FHCB2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008466	26121	PRPF31	http://www.ncbi.nlm.nih.gov/gene/?term=26121	"NY-BR-99, PRP31, RP11, SNRNP61 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008467	26121	PRPF31	http://www.ncbi.nlm.nih.gov/gene/?term=26121	"NY-BR-99, PRP31, RP11, SNRNP61 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008468	26122	EPC2	http://www.ncbi.nlm.nih.gov/gene/?term=26122	EPC-LIKE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008469	26123	TCTN3	http://www.ncbi.nlm.nih.gov/gene/?term=26123	"C10orf61, JBTS18, OFD4, TECT3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008470	26123	TCTN3	http://www.ncbi.nlm.nih.gov/gene/?term=26123	"C10orf61, JBTS18, OFD4, TECT3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008471	26127	FGFR1OP2	http://www.ncbi.nlm.nih.gov/gene/?term=26127	"HSPC123-like, WIT3.0 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008472	26127	FGFR1OP2	http://www.ncbi.nlm.nih.gov/gene/?term=26127	"HSPC123-like, WIT3.0 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008473	26127	FGFR1OP2	http://www.ncbi.nlm.nih.gov/gene/?term=26127	"HSPC123-like, WIT3.0 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008474	26130	GAPVD1	http://www.ncbi.nlm.nih.gov/gene/?term=26130	"GAPEX5, GAPex-5, RAP6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008475	26133	TRPC4AP	http://www.ncbi.nlm.nih.gov/gene/?term=26133	"C20orf188, PPP1R158, TRRP4AP, TRUSS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008476	26135	SERBP1	http://www.ncbi.nlm.nih.gov/gene/?term=26135	"CGI-55, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008477	26135	SERBP1	http://www.ncbi.nlm.nih.gov/gene/?term=26135	"CGI-55, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008478	26135	SERBP1	http://www.ncbi.nlm.nih.gov/gene/?term=26135	"CGI-55, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008479	26135	SERBP1	http://www.ncbi.nlm.nih.gov/gene/?term=26135	"CGI-55, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008480	26135	SERBP1	http://www.ncbi.nlm.nih.gov/gene/?term=26135	"CGI-55, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008481	26136	TES	http://www.ncbi.nlm.nih.gov/gene/?term=26136	"TESS, TESS-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008482	26136	TES	http://www.ncbi.nlm.nih.gov/gene/?term=26136	"TESSS-2, TES "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008483	26136	TES	http://www.ncbi.nlm.nih.gov/gene/?term=26136	"TESSS-2, TES "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008484	26136	TES	http://www.ncbi.nlm.nih.gov/gene/?term=26136	"TESSS-2, TES "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008485	26145	IRF2BP1	http://www.ncbi.nlm.nih.gov/gene/?term=26145		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008486	26146	TRAF3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=26146	"IFT54, MIP-T3, MIPT3, SLSN9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008487	26147	PHF19	http://www.ncbi.nlm.nih.gov/gene/?term=26147	"MTF2L1, PCL3, TDRD19B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008488	26152	ZNF337	http://www.ncbi.nlm.nih.gov/gene/?term=26152		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008489	26153	KIF26A	http://www.ncbi.nlm.nih.gov/gene/?term=26153		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008490	26155	NOC2L	http://www.ncbi.nlm.nih.gov/gene/?term=26155	"NET15, NET7, NIR, PPP1R112 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008491	26155	NOC2L	http://www.ncbi.nlm.nih.gov/gene/?term=26155	"NET15, NET7, NIR, PPP1R112 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008492	26156	RSL1D1	http://www.ncbi.nlm.nih.gov/gene/?term=26156	"CSIG, L12, PBK1, UTP30 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008493	26164	MTG2	http://www.ncbi.nlm.nih.gov/gene/?term=26164	"GTPBP5, ObgH1, dJ1005F21.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008494	26166	RGS22	http://www.ncbi.nlm.nih.gov/gene/?term=26166	"CT145, PRTD-NY2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008495	26166	RGS22	http://www.ncbi.nlm.nih.gov/gene/?term=26166	"CT145, PRTD-NY2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008496	26167	PCDHB5	http://www.ncbi.nlm.nih.gov/gene/?term=26167	PCDH-BETA5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008497	26168	SENP3	http://www.ncbi.nlm.nih.gov/gene/?term=26168	"SMT3IP1, SSP3, Ulp1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008498	26168	SENP3	http://www.ncbi.nlm.nih.gov/gene/?term=26168	"SMT3IP1, SSP3, Ulp1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008499	261726	TIPRL	http://www.ncbi.nlm.nih.gov/gene/?term=261726	"TIP, TIP41 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008500	261729	STEAP2	http://www.ncbi.nlm.nih.gov/gene/?term=261729	"IPCA1, PCANAP1, PUMPCn, STAMP1, STMP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008501	261729	STEAP2	http://www.ncbi.nlm.nih.gov/gene/?term=261729	"IPCA1, PCANAP1, PUMPCn, STAMP1, STMP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008502	261734	NPHP4	http://www.ncbi.nlm.nih.gov/gene/?term=261734	"POC10, SLSN4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008503	26173	INTS1	http://www.ncbi.nlm.nih.gov/gene/?term=26173	"INT1, NET28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008504	26173	INTS1	http://www.ncbi.nlm.nih.gov/gene/?term=26173	"INT1, NET28 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008505	26175	TMEM251	http://www.ncbi.nlm.nih.gov/gene/?term=26175	C14orf109	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008506	2617	GARS	http://www.ncbi.nlm.nih.gov/gene/?term=2617	"CMT2D, DSMAV, GlyRS, HMN5, SMAD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008507	2617	GARS	http://www.ncbi.nlm.nih.gov/gene/?term=2617	"CMT2D, DSMAV, GlyRS, HMN5, SMAD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008508	2617	GARS	http://www.ncbi.nlm.nih.gov/gene/?term=2617	"CMT2D, DSMAV, GlyRS, HMN5, SMAD1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008509	2618	GART	http://www.ncbi.nlm.nih.gov/gene/?term=2618	"AIRS, GARS, GARTF, PAIS, PGFT, PRGS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008510	2618	GART	http://www.ncbi.nlm.nih.gov/gene/?term=2618	"AIRS, GARSF, PAIS, PGFT, PRGS, GART "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008511	2618	GART	http://www.ncbi.nlm.nih.gov/gene/?term=2618	"AIRS, GARSF, PAIS, PGFT, PRGS, GART "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008512	2618	GART	http://www.ncbi.nlm.nih.gov/gene/?term=2618	"AIRS, GARSF, PAIS, PGFT, PRGS, GART "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008513	2618	GART	http://www.ncbi.nlm.nih.gov/gene/?term=2618	"AIRS, GARSF, PAIS, PGFT, PRGS, GART "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008514	26190	FBXW2	http://www.ncbi.nlm.nih.gov/gene/?term=26190	"FBW2, Fwd2, Md6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008515	26190	FBXW2	http://www.ncbi.nlm.nih.gov/gene/?term=26190	"FBW2, Fwd2, Md6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008516	26190	FBXW2	http://www.ncbi.nlm.nih.gov/gene/?term=26190	"FBW2, Fwd2, Md6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008517	26190	FBXW2	http://www.ncbi.nlm.nih.gov/gene/?term=26190	"FBW2, Fwd2, Md6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008518	26193	mt-Nd1	http://www.ncbi.nlm.nih.gov/gene/?term=26193	ND1	mRNA	Rattus norvegicus	23487039	Cell body	Hippocampus	In situ hybridization	"As expected, in situ signals of Nd1 mRNA showed a particular pattern and Nd1 mRNAs were strongly colocalized with Dcp1a-bodies in both the cell bodies and the dendrites (supplementary material Fig. S6C).  Intriguingly, the neuronal activity released P-body-bound Nd1 and Arp2 mRNAs, and consequently reversed the decrease of F-actin, which are induced by expression of Dcp1a, in the dendrites. "
RLID00008519	26193	mt-Nd1	http://www.ncbi.nlm.nih.gov/gene/?term=26193	ND1	mRNA	Rattus norvegicus	23487039	Dendrite	Hippocampus	In situ hybridization	"As expected, in situ signals of Nd1 mRNA showed a particular pattern and Nd1 mRNAs were strongly colocalized with Dcp1a-bodies in both the cell bodies and the dendrites (supplementary material Fig. S6C).  Intriguingly, the neuronal activity released P-body-bound Nd1 and Arp2 mRNAs, and consequently reversed the decrease of F-actin, which are induced by expression of Dcp1a, in the dendrites. "
RLID00008520	26204	mt-Co3	http://www.ncbi.nlm.nih.gov/gene/?term=26204	COX3	mRNA	Rattus norvegicus	8726358	Mitochondrion	Liver	In situ hybridization	"These ratios showed that the mRNAs for argininosuccinate synthetase and argininosuccinate lyase were located next to the cytoplasmic side of the mitochondrial membrane and in the nearby endoplasmic reticulum. These data show that ASL mRNA is preferentially located at the mitochondrial outer membrane and in the ER. Thus,ASS mRNA, likeASL mRNA, is preferentially located at the mitochondrial outer membrane and in the ER. This suggests that COIII mRNA is actually predominantly associated with those portions of the inner membrane which lie at the mitochondrial perimeter rather than along the cristae. "
RLID00008521	26205	GMEB2	http://www.ncbi.nlm.nih.gov/gene/?term=26205	"GMEB-2, P79PIF, PIF79 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008522	26207	PITPNC1	http://www.ncbi.nlm.nih.gov/gene/?term=26207	"M-RDGB-beta, MRDGBbeta, RDGB-BETA, RDGBB, RDGBB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008523	26207	PITPNC1	http://www.ncbi.nlm.nih.gov/gene/?term=26207	"M-RDGB-beta, MRDGBbeta, RDGB-BETA, RDGBB, RDGBB1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008524	2620	GAS2	http://www.ncbi.nlm.nih.gov/gene/?term=2620		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008525	2621	GAS6	http://www.ncbi.nlm.nih.gov/gene/?term=2621	"AXLLG, AXSF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008526	2621	GAS6	http://www.ncbi.nlm.nih.gov/gene/?term=2621	"AXLLG, AXSF "	mRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00008527	2621	GAS6	http://www.ncbi.nlm.nih.gov/gene/?term=2621	"AXLLG, AXSF "	mRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00008528	26224	FBXL3	http://www.ncbi.nlm.nih.gov/gene/?term=26224	"FBL3, FBL3AA, FBXL3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008529	26225	ARL5A	http://www.ncbi.nlm.nih.gov/gene/?term=26225	"ARFLP5, ARL5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008530	26227	PHGDH	http://www.ncbi.nlm.nih.gov/gene/?term=26227	"3-PGDH, 3PGDH, HEL-S-113, NLS, NLS1, PDG, PGAD, PGD, PGDHD, SERA, PHGDH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008531	26229	B3GAT3	http://www.ncbi.nlm.nih.gov/gene/?term=26229	"GLCATI, glcUAT-I "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008532	26229	B3GAT3	http://www.ncbi.nlm.nih.gov/gene/?term=26229	"GLCATI, glcUAT-I "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008533	2622	GAS8	http://www.ncbi.nlm.nih.gov/gene/?term=2622	"CILD33, DRC4, GAS11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008534	26230	TIAM2	http://www.ncbi.nlm.nih.gov/gene/?term=26230	"STEF, TIAM-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008535	26233	FBXL6	http://www.ncbi.nlm.nih.gov/gene/?term=26233	"FBL6, FBL6A, PP14630 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008536	26235	FBXL4	http://www.ncbi.nlm.nih.gov/gene/?term=26235	"FBL4, FBL5, MTDPS13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008537	2623	GATA1	http://www.ncbi.nlm.nih.gov/gene/?term=2623	"ERYF1, GATA-1, GF-1, GF1, NF-E1, NFE1, XLANP, XLTDA, XLTT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008538	26249	KLHL3	http://www.ncbi.nlm.nih.gov/gene/?term=26249	PHA2D	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008539	2624	GATA2	http://www.ncbi.nlm.nih.gov/gene/?term=2624	"DCML, IMD21, MONOMAC, NFE1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008540	26258	BLOC1S6	http://www.ncbi.nlm.nih.gov/gene/?term=26258	"BLOS6, HPS9, PA, PALLID, PLDN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008541	26258	BLOC1S6	http://www.ncbi.nlm.nih.gov/gene/?term=26258	"BLOS6, HPS9, PA, PALLID, PLDN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008542	26258	BLOC1S6	http://www.ncbi.nlm.nih.gov/gene/?term=26258	"BLOS6, HPS9, PA, PALLID, PLDN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008543	26259	FBXW8	http://www.ncbi.nlm.nih.gov/gene/?term=26259	"FBW6, FBW8, FBX29, FBXO29, FBXW6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008544	26259	FBXW8	http://www.ncbi.nlm.nih.gov/gene/?term=26259	"FBW6, FBW8, FBX29, FBXO29, FBXW6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008545	26259	FBXW8	http://www.ncbi.nlm.nih.gov/gene/?term=26259	"FBW6, FBW8, FBX29, FBXO29, FBXW6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008546	2625	GATA3	http://www.ncbi.nlm.nih.gov/gene/?term=2625	"HDR, HDRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008547	26260	FBXO25	http://www.ncbi.nlm.nih.gov/gene/?term=26260	FBX25	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008548	26262	TSPAN17	http://www.ncbi.nlm.nih.gov/gene/?term=26262	"FBX23, FBXO23, TM4SF17 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008549	26262	TSPAN17	http://www.ncbi.nlm.nih.gov/gene/?term=26262	"FBX23, FBXO23, TM4SF17 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008550	26263	FBXO22	http://www.ncbi.nlm.nih.gov/gene/?term=26263	"FBX22, FISTC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008551	26263	FBXO22	http://www.ncbi.nlm.nih.gov/gene/?term=26263	"FBX22, FISTC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008552	26267	FBXO10	http://www.ncbi.nlm.nih.gov/gene/?term=26267	"FBX10, PRMT11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008553	26268	FBXO9	http://www.ncbi.nlm.nih.gov/gene/?term=26268	"FBX9, NY-REN-57, VCIA1, dJ341E18.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008554	26268	FBXO9	http://www.ncbi.nlm.nih.gov/gene/?term=26268	"FBX9, NY-REN-57, VCIA1, dJ341E18.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008555	26269	FBXO8	http://www.ncbi.nlm.nih.gov/gene/?term=26269	"DC10, FBS, FBX8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008556	26269	FBXO8	http://www.ncbi.nlm.nih.gov/gene/?term=26269	"DC10, FBS, FBX8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008557	26270	FBXO6	http://www.ncbi.nlm.nih.gov/gene/?term=26270	"FBG2, FBS2, FBX6, Fbx6b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008558	26271	FBXO5	http://www.ncbi.nlm.nih.gov/gene/?term=26271	"EMI1, FBX5, Fbxo31 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008559	26272	FBXO4	http://www.ncbi.nlm.nih.gov/gene/?term=26272	FBX4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008560	26272	FBXO4	http://www.ncbi.nlm.nih.gov/gene/?term=26272	FBX4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008561	26273	FBXO3	http://www.ncbi.nlm.nih.gov/gene/?term=26273	"FBA, FBX3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008562	26275	HIBCH	http://www.ncbi.nlm.nih.gov/gene/?term=26275	HIBYLCOAH	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008563	26277	TINF2	http://www.ncbi.nlm.nih.gov/gene/?term=26277	"DKCA3, TIN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008564	26277	TINF2	http://www.ncbi.nlm.nih.gov/gene/?term=26277	"DKCA3, TIN2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008565	26278	SACS	http://www.ncbi.nlm.nih.gov/gene/?term=26278	"ARSACS, DNAJC29, PPP1R138, SPAX6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008566	26278	SACS	http://www.ncbi.nlm.nih.gov/gene/?term=26278	"ARSACS, DNAJC29, PPP1R138, SPAX6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008567	2627	GATA6	http://www.ncbi.nlm.nih.gov/gene/?term=2627		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008568	2627	GATA6	http://www.ncbi.nlm.nih.gov/gene/?term=2627		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008569	26284	ERAL1	http://www.ncbi.nlm.nih.gov/gene/?term=26284	"CEGA, ERA, ERA-WA, H-ERA, HERA-A, HERA-B, ERAL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008570	2628	GATM	http://www.ncbi.nlm.nih.gov/gene/?term=2628	"AGAT, AT, CCDS3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008571	26292	MYCBP	http://www.ncbi.nlm.nih.gov/gene/?term=26292	AMY-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008572	26292	MYCBP	http://www.ncbi.nlm.nih.gov/gene/?term=26292	AMY-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008573	26292	MYCBP	http://www.ncbi.nlm.nih.gov/gene/?term=26292	AMY-1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008574	26298	EHF	http://www.ncbi.nlm.nih.gov/gene/?term=26298	"ESE3, ESE3B, ESEJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008575	2629	GBA	http://www.ncbi.nlm.nih.gov/gene/?term=2629	"GBA1, GCB, GLUC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008576	2629	GBA	http://www.ncbi.nlm.nih.gov/gene/?term=2629	"GBA1, GCB, GLUC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008577	262	AMD1	http://www.ncbi.nlm.nih.gov/gene/?term=262	"ADOMETDC, AMD, SAMDC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008578	262	AMD1	http://www.ncbi.nlm.nih.gov/gene/?term=262	"ADOMETDC, AMD, SAMDC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008579	26301	GBGT1	http://www.ncbi.nlm.nih.gov/gene/?term=26301	"A3GALNT, FS, UNQ2513 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008580	2631	GBAS	http://www.ncbi.nlm.nih.gov/gene/?term=2631	NIPSNAP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008581	2632	GBE1	http://www.ncbi.nlm.nih.gov/gene/?term=2632	"APBD, GBE, GSD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008582	263406	Plekhg3	http://www.ncbi.nlm.nih.gov/gene/?term=263406	BC030417	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008583	26354	GNL3	http://www.ncbi.nlm.nih.gov/gene/?term=26354	"C77032, E2IG3, NNP47, NS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008584	26354	GNL3	http://www.ncbi.nlm.nih.gov/gene/?term=26354	"C77032, E2IG3, NNP47, NS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008585	26355	FAM162A	http://www.ncbi.nlm.nih.gov/gene/?term=26355	"C3orf28, E2IG5, HGTD-P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008586	26356	Ing1	http://www.ncbi.nlm.nih.gov/gene/?term=26356	"2610028J21Rik, AA407184, AI875420, mING1h, p33Ing1, p37Ing1b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008587	2635	GBP3	http://www.ncbi.nlm.nih.gov/gene/?term=2635		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008588	26374	Rfwd2	http://www.ncbi.nlm.nih.gov/gene/?term=26374	"AI316802, C80879, Cop1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008589	26374	Rfwd2	http://www.ncbi.nlm.nih.gov/gene/?term=26374	"AI316802, C80879, Cop1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008590	26385	Grk6	http://www.ncbi.nlm.nih.gov/gene/?term=26385	Gprk6	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008591	26388	Ifi202b	http://www.ncbi.nlm.nih.gov/gene/?term=26388	"Ifbip-1, Ifi202, Ifi202a, p202 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008592	2639	GCDH	http://www.ncbi.nlm.nih.gov/gene/?term=2639	"ACAD5, GCD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008593	26400	Map2k7	http://www.ncbi.nlm.nih.gov/gene/?term=26400	"5930412N11Rik, JNKK 2, Jnkk2, MAPKK 7, MEK 7, Mapkk7, Mek7, Mkk7, Prkmk7, sek2 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00008594	264064	Cdk8	http://www.ncbi.nlm.nih.gov/gene/?term=264064		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008595	26407	Map3k4	http://www.ncbi.nlm.nih.gov/gene/?term=26407	"D17Rp17, D17Rp17e, MAPKKK4, MEKK 4, MTK1, Mek4b, Mekk4, RP17, Rp17a, Tas, mKIAA0213 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008596	26409	Map3k7	http://www.ncbi.nlm.nih.gov/gene/?term=26409	"B430101B05, C87327, Tak1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008597	26412	Map4k2	http://www.ncbi.nlm.nih.gov/gene/?term=26412	"AI385662, BL44, GCK, Rab8ip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008598	26419	Mapk8	http://www.ncbi.nlm.nih.gov/gene/?term=26419	"AI849689, JNK, JNK1, Prkm8, SAPK1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008599	26420	Mapk9	http://www.ncbi.nlm.nih.gov/gene/?term=26420	"AI851083, JNK2, Prkm9, p54aSAPK "	mRNA	Mus musculus	21281539	Mitotic spindle	Oocyte	Beckman DU 530 Analyzer	"The association of JNK2 with spindle poles was further confirmed by colocalization with the centrosomal proteins, r-tubulin and Plk1. "
RLID00008600	26422	Nbea	http://www.ncbi.nlm.nih.gov/gene/?term=26422	"Lyst2, mKIAA1544 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008601	26424	Nr5a2	http://www.ncbi.nlm.nih.gov/gene/?term=26424	"AU020803, D1Ertd308e, Ftf, LRH-1, UF2-H3B "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008602	26424	Nr5a2	http://www.ncbi.nlm.nih.gov/gene/?term=26424	"AU020803, D1Ertd308e, Ftf, LRH-1, UF2-H3B "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008603	26427	Creb3l1	http://www.ncbi.nlm.nih.gov/gene/?term=26427	Oasis	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008604	26428	Orc4	http://www.ncbi.nlm.nih.gov/gene/?term=26428	"Orc4Pl, mMmORC4, Orc4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008605	26429	Orc5	http://www.ncbi.nlm.nih.gov/gene/?term=26429	"AL033327, MmORC5l, Orc5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008606	2643	GCH1	http://www.ncbi.nlm.nih.gov/gene/?term=2643	"DYT14, DYT5, DYT5a, GCH, GTP-CH-1, GTPCH1, HPABH4B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008607	26442	Psma5	http://www.ncbi.nlm.nih.gov/gene/?term=26442	ZETA	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008608	26446	Psmb3	http://www.ncbi.nlm.nih.gov/gene/?term=26446	"AL033320, C10-II "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008609	2644	GCHFR	http://www.ncbi.nlm.nih.gov/gene/?term=2644	"GFRP, HsT16933, P35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008610	2644	GCHFR	http://www.ncbi.nlm.nih.gov/gene/?term=2644	"GFRP, HsT16933, P35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008611	26451	Rpl27a	http://www.ncbi.nlm.nih.gov/gene/?term=26451	"L27', L27A, L29 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008612	26466	Zfp260	http://www.ncbi.nlm.nih.gov/gene/?term=26466	"AI480997, Ozrf1, PEX1, Zfp63, Znf260 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008613	26469	PTPN18	http://www.ncbi.nlm.nih.gov/gene/?term=26469	"BDP1, PTP-HSCF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008614	26470	SEZ6L2	http://www.ncbi.nlm.nih.gov/gene/?term=26470	"BSRPA, PSK-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008615	26471	NUPR1	http://www.ncbi.nlm.nih.gov/gene/?term=26471	"COM1, P8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008616	26471	NUPR1	http://www.ncbi.nlm.nih.gov/gene/?term=26471	"COM1, P8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008617	26472	PPP1R14B	http://www.ncbi.nlm.nih.gov/gene/?term=26472	"PHI-1, PLCB3N, PNG, SOM172 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008618	2647	BLOC1S1	http://www.ncbi.nlm.nih.gov/gene/?term=2647	"BLOS1, BORCS1, GCN5L1, MICoA, RT14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008619	2648	KAT2A	http://www.ncbi.nlm.nih.gov/gene/?term=2648	"GCN5, GCN5L2, PCAF-b, hGCN5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008620	26499	PLEK2	http://www.ncbi.nlm.nih.gov/gene/?term=26499		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008621	2649	NR6A1	http://www.ncbi.nlm.nih.gov/gene/?term=2649	"CT150, GCNF, GCNF1, NR61, RTR, hGCNF, hRTR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008622	26502	NARF	http://www.ncbi.nlm.nih.gov/gene/?term=26502	IOP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008623	26502	NARF	http://www.ncbi.nlm.nih.gov/gene/?term=26502	IOP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008624	26503	SLC17A5	http://www.ncbi.nlm.nih.gov/gene/?term=26503	"AST, ISSD, NSD, SD, SIALIN, SIASD, SLD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008625	26505	CNNM3	http://www.ncbi.nlm.nih.gov/gene/?term=26505	ACDP3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008626	26505	CNNM3	http://www.ncbi.nlm.nih.gov/gene/?term=26505	ACDP3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008627	26505	CNNM3	http://www.ncbi.nlm.nih.gov/gene/?term=26505	ACDP3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008628	26509	MYOF	http://www.ncbi.nlm.nih.gov/gene/?term=26509	FER1L3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008629	26511	CHIC2	http://www.ncbi.nlm.nih.gov/gene/?term=26511	BTL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008630	26512	INTS6	http://www.ncbi.nlm.nih.gov/gene/?term=26512	"DBI-1, DDX26, DDX26A, DICE1, HDB, INT6, Notchl2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008631	26515	TIMM10B	http://www.ncbi.nlm.nih.gov/gene/?term=26515	"FXC1, TIM10B, Tim9b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008632	26515	TIMM10B	http://www.ncbi.nlm.nih.gov/gene/?term=26515	"FXC1, TIM10B, Tim9b "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008633	26515	TIMM10B	http://www.ncbi.nlm.nih.gov/gene/?term=26515	"FXC1, TIM10B, Tim9b "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008634	26517	TIMM13	http://www.ncbi.nlm.nih.gov/gene/?term=26517	"TIM13, TIM13B, TIMM13A, TIMM13B, ppv1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008635	26517	TIMM13	http://www.ncbi.nlm.nih.gov/gene/?term=26517	"TIM13, TIM13BA, TIMM13B, ppv1, TIMM13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008636	26519	TIMM10	http://www.ncbi.nlm.nih.gov/gene/?term=26519	"TIM10, TIM10A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008637	26520	TIMM9	http://www.ncbi.nlm.nih.gov/gene/?term=26520	"TIM9, TIM9A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008638	26521	TIMM8B	http://www.ncbi.nlm.nih.gov/gene/?term=26521	"DDP2, TIM8B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008639	26523	AGO1	http://www.ncbi.nlm.nih.gov/gene/?term=26523	"EIF2C, EIF2C1, GERP95, Q99, hAgo1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008640	26523	AGO1	http://www.ncbi.nlm.nih.gov/gene/?term=26523	"EIF2C, EIF2C1, GERP95, Q99, hAgo1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008641	26523	AGO1	http://www.ncbi.nlm.nih.gov/gene/?term=26523	"EIF2C, EIF2C1, GERP95, Q99, hAgo1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008642	2653	GCSH	http://www.ncbi.nlm.nih.gov/gene/?term=2653	"GCE, NKH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008643	2653	GCSH	http://www.ncbi.nlm.nih.gov/gene/?term=2653	"GCE, NKH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008644	26562	Ncdn	http://www.ncbi.nlm.nih.gov/gene/?term=26562	"AU042419, MMS10-AE, Ms10ae, mKIAA0607, norbin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008645	26572	Cops3	http://www.ncbi.nlm.nih.gov/gene/?term=26572	"Csn3, Sgn3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008646	26577	PCOLCE2	http://www.ncbi.nlm.nih.gov/gene/?term=26577	PCPE2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008647	26578	OSTF1	http://www.ncbi.nlm.nih.gov/gene/?term=26578	"OSF, SH3P2, bA235O14.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008648	26578	OSTF1	http://www.ncbi.nlm.nih.gov/gene/?term=26578	"OSF, SH3P2, bA235O14.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008649	26578	OSTF1	http://www.ncbi.nlm.nih.gov/gene/?term=26578	"OSF, SH3P2, bA235O14.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008650	26579	MYEOV	http://www.ncbi.nlm.nih.gov/gene/?term=26579	OCIM	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008651	26580	BSCL2	http://www.ncbi.nlm.nih.gov/gene/?term=26580	"GNG3LG, HMN5, PELD, SPG17 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008652	26586	CKAP2	http://www.ncbi.nlm.nih.gov/gene/?term=26586	"LB1, TMAP, se20-10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008653	26586	CKAP2	http://www.ncbi.nlm.nih.gov/gene/?term=26586	"LB1, TMAP, se20-10 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008654	26586	CKAP2	http://www.ncbi.nlm.nih.gov/gene/?term=26586	"LB1, TMAP, se20-10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008655	26589	MRPL46	http://www.ncbi.nlm.nih.gov/gene/?term=26589	"C15orf4, LIECG2, P2ECSL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008656	26608	TBL2	http://www.ncbi.nlm.nih.gov/gene/?term=26608	"WBSCR13, WS-betaTRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008657	26608	TBL2	http://www.ncbi.nlm.nih.gov/gene/?term=26608	"WBSCR13, WS-betaTRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008658	26611	Rcn2	http://www.ncbi.nlm.nih.gov/gene/?term=26611	"AA408742, Tcbp49 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008659	26628	OR7E47P	http://www.ncbi.nlm.nih.gov/gene/?term=26628	OR7E141	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008660	2662	GDF10	http://www.ncbi.nlm.nih.gov/gene/?term=2662	"BMP-3b, BMP3B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008661	2664	GDI1	http://www.ncbi.nlm.nih.gov/gene/?term=2664	"1A, GDIL, MRX41, MRX48, OPHN2, RABGD1A, RABGDIA, XAP-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008662	2664	GDI1	http://www.ncbi.nlm.nih.gov/gene/?term=2664	"1A, GDIL, MRX41, MRX48, OPHN2, RABGD1A, RABGDIA, XAP-4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008663	2664	GDI1	http://www.ncbi.nlm.nih.gov/gene/?term=2664	"1A, GDIL, MRX41, MRX48, OPHN2, RABGD1A, RABGDIA, XAP-4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008664	2665	GDI2	http://www.ncbi.nlm.nih.gov/gene/?term=2665	"HEL-S-46e, RABGDIB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008665	2665	GDI2	http://www.ncbi.nlm.nih.gov/gene/?term=2665	"HEL-S-46e, RABGDIB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008666	2665	GDI2	http://www.ncbi.nlm.nih.gov/gene/?term=2665	"HEL-S-46e, RABGDIB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008667	266629	SEC14L3	http://www.ncbi.nlm.nih.gov/gene/?term=266629	TAP2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008668	266655	LINC00094	http://www.ncbi.nlm.nih.gov/gene/?term=266655	"LP2477, NCRNA00094, bA374P20.3 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008669	266740	MAGEA2B	http://www.ncbi.nlm.nih.gov/gene/?term=266740	"CT1.2, MAGE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008670	266759	Hspa4	http://www.ncbi.nlm.nih.gov/gene/?term=266759	"Hsp110, Hsp70, irp94 "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00008671	266759	Hspa4	http://www.ncbi.nlm.nih.gov/gene/?term=266759	"Hsp110, Hsp70, irp94 "	mRNA	Rattus norvegicus	17439344	Cytoplasm	Brain	In situ hybridization	"In contrast, mRNA of the cytoplasmic hsp70 was strongly induced at 4 h after brain injury in multiple brain regions within the injured hemisphere, and this expression was greatly en- hanced by secondary hypoxia.  "
RLID00008672	266759	Hspa4	http://www.ncbi.nlm.nih.gov/gene/?term=266759	"Hsp110, Hsp70, irp94 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00008673	266781	Snx17	http://www.ncbi.nlm.nih.gov/gene/?term=266781	"5830447M19Rik, AI790646, D5Ertd260e, b2b1625.1Clo, mKIAA0064 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008674	266977	ADGRF1	http://www.ncbi.nlm.nih.gov/gene/?term=266977	"GPR110, KPG_012, PGR19, hGPCR36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008675	267002	PGBD2	http://www.ncbi.nlm.nih.gov/gene/?term=267002		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008676	267010	RNU12	http://www.ncbi.nlm.nih.gov/gene/?term=267010	"RNU12-1L, RNU12P, dJ222E13.7, RNU12 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008677	267010	RNU12	http://www.ncbi.nlm.nih.gov/gene/?term=267010	"RNU12-1L, RNU12P, dJ222E13.7, RNU12 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008678	267019	Rps15a	http://www.ncbi.nlm.nih.gov/gene/?term=267019	A630031B11Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008679	267020	ATP5L2	http://www.ncbi.nlm.nih.gov/gene/?term=267020	ATP5K2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008680	2670	GFAP	http://www.ncbi.nlm.nih.gov/gene/?term=2670	ALXDRD	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008681	2671	GFER	http://www.ncbi.nlm.nih.gov/gene/?term=2671	"ALR, ERV1, HERV1, HPO, HPO1, HPO2, HSS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008682	2671	GFER	http://www.ncbi.nlm.nih.gov/gene/?term=2671	"ALR, ERV1, HERV1, HPO, HPO1, HPO2, HSS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008683	2673	GFPT1	http://www.ncbi.nlm.nih.gov/gene/?term=2673	"CMS12, CMSTA1, GFA, GFAT, GFAT 1, GFAT1, GFAT1m, GFPTL, MSLG, GFPT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008684	26762	HAVCR1	http://www.ncbi.nlm.nih.gov/gene/?term=26762	"CD365, HAVCR, HAVCR-1, KIM-1, KIM1, TIM, TIM-1, TIM1, TIMD-1, TIMD1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008685	26762	HAVCR1	http://www.ncbi.nlm.nih.gov/gene/?term=26762	"CD365, HAVCR, HAVCR-1, KIM-1, KIM1, TIM, TIM-1, TIM1, TIMD-1, TIMD1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008686	26765	SNORD12C	http://www.ncbi.nlm.nih.gov/gene/?term=26765	"E2, E2-1, E3, RNU106, SNORD106, U106 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008687	26767	RNU105B	http://www.ncbi.nlm.nih.gov/gene/?term=26767	"105B, E1-2 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008688	26767	RNU105B	http://www.ncbi.nlm.nih.gov/gene/?term=26767	"105B, E1-2 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008689	26768	SNORA73B	http://www.ncbi.nlm.nih.gov/gene/?term=26768	"105A, E1c, RNU105A, RNU17B, U17B "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008690	26768	SNORA73B	http://www.ncbi.nlm.nih.gov/gene/?term=26768	"105A, E1c, RNU105A, RNU17B, U17B "	snoRNA	Homo sapiens	9671460	Nucleus	HeLa cell	Northern blot	"We investigated the cellular localization of the U17HG RNA. Cell fractionation experiments indicated that U17HG RNA is enriched in the cytoplasm (Fig.5A), similar to UHG RNA, another noncoding snoRNA host having no protein-coding potential (Fig.5B). As expected, U17 snoRNA, used as a control, was found mainly in the nuclear fraction (Fig.5C). "
RLID00008691	26768	SNORA73B	http://www.ncbi.nlm.nih.gov/gene/?term=26768	"105A, E1c, RNU105A, RNU17B, U17B "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008692	26768	SNORA73B	http://www.ncbi.nlm.nih.gov/gene/?term=26768	"105A, E1c, RNU105A, RNU17B, U17B "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008693	26768	SNORA73B	http://www.ncbi.nlm.nih.gov/gene/?term=26768	"105A, E1c, RNU105A, RNU17B, U17B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008694	26768	SNORA73B	http://www.ncbi.nlm.nih.gov/gene/?term=26768	"105A, E1c, RNU105A, RNU17B, U17B "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008695	26769	SNORD81	http://www.ncbi.nlm.nih.gov/gene/?term=26769	"RNU104, U81, Z23 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008696	26769	SNORD81	http://www.ncbi.nlm.nih.gov/gene/?term=26769	"RNU104, U81, Z23 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008697	26769	SNORD81	http://www.ncbi.nlm.nih.gov/gene/?term=26769	"RNU104, U81, Z23 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008698	26769	SNORD81	http://www.ncbi.nlm.nih.gov/gene/?term=26769	"RNU104, U81, Z23 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008699	2676	GFRA3	http://www.ncbi.nlm.nih.gov/gene/?term=2676	GDNFR3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008700	26770	SNORD79	http://www.ncbi.nlm.nih.gov/gene/?term=26770	"RNU103, U79, Z22 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008701	26771	SNORD102	http://www.ncbi.nlm.nih.gov/gene/?term=26771	"RNU102, Z18 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008702	26771	SNORD102	http://www.ncbi.nlm.nih.gov/gene/?term=26771	"RNU102, Z18 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008703	26773	SNORD4A	http://www.ncbi.nlm.nih.gov/gene/?term=26773	"RNU101A, Z17A, mgh18S-121 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008704	26773	SNORD4A	http://www.ncbi.nlm.nih.gov/gene/?term=26773	"RNU101A, Z17A, mgh18S-121 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008705	26773	SNORD4A	http://www.ncbi.nlm.nih.gov/gene/?term=26773	"RNU101A, Z17A, mgh18S-121 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008706	26773	SNORD4A	http://www.ncbi.nlm.nih.gov/gene/?term=26773	"RNU101A, Z17A, mgh18S-121 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008707	26774	SNORD80	http://www.ncbi.nlm.nih.gov/gene/?term=26774	"RNU100, U80, Z15 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008708	26774	SNORD80	http://www.ncbi.nlm.nih.gov/gene/?term=26774	"RNU100, U80, Z15 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008709	26775	SNORA72	http://www.ncbi.nlm.nih.gov/gene/?term=26775	"RNU72, U72 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008710	26775	SNORA72	http://www.ncbi.nlm.nih.gov/gene/?term=26775	"RNU72, U72 "	snoRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00008711	26776	SNORA71B	http://www.ncbi.nlm.nih.gov/gene/?term=26776	"RNU71B, U71b "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008712	26776	SNORA71B	http://www.ncbi.nlm.nih.gov/gene/?term=26776	"RNU71B, U71b "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008713	26776	SNORA71B	http://www.ncbi.nlm.nih.gov/gene/?term=26776	"RNU71B, U71b "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008714	26777	SNORA71A	http://www.ncbi.nlm.nih.gov/gene/?term=26777	"RNU71A, U71a "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008715	26778	SNORA70	http://www.ncbi.nlm.nih.gov/gene/?term=26778	"DXS648E, RNU70, U70 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008716	26779	SNORA69	http://www.ncbi.nlm.nih.gov/gene/?term=26779	"RNU69, U69, U69A "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008717	26779	SNORA69	http://www.ncbi.nlm.nih.gov/gene/?term=26779	"RNU69, U69, U69A "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008718	2677	GGCX	http://www.ncbi.nlm.nih.gov/gene/?term=2677	VKCFD1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008719	2677	GGCX	http://www.ncbi.nlm.nih.gov/gene/?term=2677	VKCFD1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008720	26782	SNORA66	http://www.ncbi.nlm.nih.gov/gene/?term=26782	"RNU66, U66 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008721	26783	SNORA65	http://www.ncbi.nlm.nih.gov/gene/?term=26783	"RNU65, U65 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008722	26784	SNORA64	http://www.ncbi.nlm.nih.gov/gene/?term=26784	"RNU64, U64 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008723	26784	SNORA64	http://www.ncbi.nlm.nih.gov/gene/?term=26784	"RNU64, U64 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008724	26784	SNORA64	http://www.ncbi.nlm.nih.gov/gene/?term=26784	"RNU64, U64 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008725	26785	SNORD63	http://www.ncbi.nlm.nih.gov/gene/?term=26785	"RNU63A, U63, SNORD63 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008726	26785	SNORD63	http://www.ncbi.nlm.nih.gov/gene/?term=26785	"RNU63A, U63, SNORD63 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008727	26785	SNORD63	http://www.ncbi.nlm.nih.gov/gene/?term=26785	"RNU63A, U63, SNORD63 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008728	26786	SNORD62A	http://www.ncbi.nlm.nih.gov/gene/?term=26786	"RNU62, U62, U62A "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008729	26786	SNORD62A	http://www.ncbi.nlm.nih.gov/gene/?term=26786	"RNU62, U62, U62A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008730	26786	SNORD62A	http://www.ncbi.nlm.nih.gov/gene/?term=26786	"RNU62, U62, U62A "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008731	26786	SNORD62A	http://www.ncbi.nlm.nih.gov/gene/?term=26786	"RNU62, U62, U62A "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008732	26788	SNORD60	http://www.ncbi.nlm.nih.gov/gene/?term=26788	"RNU60, U60 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008733	26788	SNORD60	http://www.ncbi.nlm.nih.gov/gene/?term=26788	"RNU60, U60 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008734	26788	SNORD60	http://www.ncbi.nlm.nih.gov/gene/?term=26788	"RNU60, U60 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00008735	26788	SNORD60	http://www.ncbi.nlm.nih.gov/gene/?term=26788	"RNU60, U60 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008736	26788	SNORD60	http://www.ncbi.nlm.nih.gov/gene/?term=26788	"RNU60, U60 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008737	26789	SNORD59A	http://www.ncbi.nlm.nih.gov/gene/?term=26789	"RNU59, U59 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008738	26791	SNORD58A	http://www.ncbi.nlm.nih.gov/gene/?term=26791	"RNU58A, U58a "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008739	26791	SNORD58A	http://www.ncbi.nlm.nih.gov/gene/?term=26791	"RNU58A, U58a "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008740	26792	SNORD57	http://www.ncbi.nlm.nih.gov/gene/?term=26792	"RNU57, U57 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008741	26792	SNORD57	http://www.ncbi.nlm.nih.gov/gene/?term=26792	"RNU57, U57 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008742	26792	SNORD57	http://www.ncbi.nlm.nih.gov/gene/?term=26792	"RNU57, U57 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008743	26792	SNORD57	http://www.ncbi.nlm.nih.gov/gene/?term=26792	"RNU57, U57 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008744	26796	SNORD53	http://www.ncbi.nlm.nih.gov/gene/?term=26796	"RNU53A, U53, SNORD53 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008745	26798	SNORD51	http://www.ncbi.nlm.nih.gov/gene/?term=26798	"RNU51, U51 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008746	26799	SNORD50A	http://www.ncbi.nlm.nih.gov/gene/?term=26799	"RNU50, U50 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008747	26799	SNORD50A	http://www.ncbi.nlm.nih.gov/gene/?term=26799	"RNU50, U50 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008748	267	AMFR	http://www.ncbi.nlm.nih.gov/gene/?term=267	"GP78, RNF45 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008749	267	AMFR	http://www.ncbi.nlm.nih.gov/gene/?term=267	"GP78, RNF45 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008750	26800	SNORD49A	http://www.ncbi.nlm.nih.gov/gene/?term=26800	"RNU49, U49, U49A "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008751	26800	SNORD49A	http://www.ncbi.nlm.nih.gov/gene/?term=26800	"RNU49, U49, U49A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008752	26800	SNORD49A	http://www.ncbi.nlm.nih.gov/gene/?term=26800	"RNU49, U49, U49A "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008753	26801	SNORD48	http://www.ncbi.nlm.nih.gov/gene/?term=26801	"RNU48, U48 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008754	26801	SNORD48	http://www.ncbi.nlm.nih.gov/gene/?term=26801	"RNU48, U48 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008755	26802	SNORD47	http://www.ncbi.nlm.nih.gov/gene/?term=26802	"RNU47, U47 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008756	26802	SNORD47	http://www.ncbi.nlm.nih.gov/gene/?term=26802	"RNU47, U47 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008757	26805	SNORD45A	http://www.ncbi.nlm.nih.gov/gene/?term=26805	"RNU45A, U45a "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008758	26805	SNORD45A	http://www.ncbi.nlm.nih.gov/gene/?term=26805	"RNU45A, U45a "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008759	26805	SNORD45A	http://www.ncbi.nlm.nih.gov/gene/?term=26805	"RNU45A, U45a "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008760	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008761	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008762	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008763	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	25203660	Cytoplasm	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008764	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00008765	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008766	26806	SNORD44	http://www.ncbi.nlm.nih.gov/gene/?term=26806	"RNU44, U44 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008767	26807	SNORD43	http://www.ncbi.nlm.nih.gov/gene/?term=26807	"RNU43, U43 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008768	26807	SNORD43	http://www.ncbi.nlm.nih.gov/gene/?term=26807	"RNU43, U43 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008769	26808	SNORD42B	http://www.ncbi.nlm.nih.gov/gene/?term=26808	"RNU42B, U42B "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008770	26809	SNORD42A	http://www.ncbi.nlm.nih.gov/gene/?term=26809	"RNU42A, U42, U42A "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008771	26810	SNORD41	http://www.ncbi.nlm.nih.gov/gene/?term=26810	"RNU41, U41 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008772	26811	SNORD55	http://www.ncbi.nlm.nih.gov/gene/?term=26811	"RNU39, RNU55, SNORD39, U39, U55 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008773	26811	SNORD55	http://www.ncbi.nlm.nih.gov/gene/?term=26811	"RNU39, RNU55, SNORD39, U39, U55 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008774	26811	SNORD55	http://www.ncbi.nlm.nih.gov/gene/?term=26811	"RNU39, RNU55, SNORD39, U39, U55 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008775	26812	SNORD37	http://www.ncbi.nlm.nih.gov/gene/?term=26812	"RNU37, U37 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008776	26812	SNORD37	http://www.ncbi.nlm.nih.gov/gene/?term=26812	"RNU37, U37 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008777	26813	SNORD36C	http://www.ncbi.nlm.nih.gov/gene/?term=26813	"RNU36C, U36c "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008778	26814	SNORD36B	http://www.ncbi.nlm.nih.gov/gene/?term=26814	"RNU36B, U36b "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008779	26817	SNORD34	http://www.ncbi.nlm.nih.gov/gene/?term=26817	"RNU34, U34 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008780	26817	SNORD34	http://www.ncbi.nlm.nih.gov/gene/?term=26817	"RNU34, U34 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008781	26818	SNORD33	http://www.ncbi.nlm.nih.gov/gene/?term=26818	"RNU33, U33 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008782	26818	SNORD33	http://www.ncbi.nlm.nih.gov/gene/?term=26818	"RNU33, U33 "	snoRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008783	26820	SNORD24	http://www.ncbi.nlm.nih.gov/gene/?term=26820	"RNU24, U24 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008784	26820	SNORD24	http://www.ncbi.nlm.nih.gov/gene/?term=26820	"RNU24, U24 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00008785	26820	SNORD24	http://www.ncbi.nlm.nih.gov/gene/?term=26820	"RNU24, U24 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00008786	26820	SNORD24	http://www.ncbi.nlm.nih.gov/gene/?term=26820	"RNU24, U24 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008787	26820	SNORD24	http://www.ncbi.nlm.nih.gov/gene/?term=26820	"RNU24, U24 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008788	26821	SNORA74A	http://www.ncbi.nlm.nih.gov/gene/?term=26821	"RNU19, U19 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008789	26821	SNORA74A	http://www.ncbi.nlm.nih.gov/gene/?term=26821	"RNU19, U19 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008790	26821	SNORA74A	http://www.ncbi.nlm.nih.gov/gene/?term=26821	"RNU19, U19 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008791	26822	SNORD14A	http://www.ncbi.nlm.nih.gov/gene/?term=26822	"RNU14, RNU14A, U14, U14-S13-5 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008792	26822	SNORD14A	http://www.ncbi.nlm.nih.gov/gene/?term=26822	"RNU14, RNU14A, U14, U14-S13-5 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008793	26822	SNORD14A	http://www.ncbi.nlm.nih.gov/gene/?term=26822	"RNU14, RNU14A, U14, U14-S13-5 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008794	26823	RNU12-2P	http://www.ncbi.nlm.nih.gov/gene/?term=26823	"RNU12, RNU12P, U12 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008795	26824	RNU11	http://www.ncbi.nlm.nih.gov/gene/?term=26824	"RNU11-1, U11 "	snRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00008796	26824	RNU11	http://www.ncbi.nlm.nih.gov/gene/?term=26824	"RNU11-1, U11 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008797	26824	RNU11	http://www.ncbi.nlm.nih.gov/gene/?term=26824	"RNU11-1, U11 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008798	26824	RNU11	http://www.ncbi.nlm.nih.gov/gene/?term=26824	"RNU11-1, U11 "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008799	26826	RNU6-6P	http://www.ncbi.nlm.nih.gov/gene/?term=26826	"RNU6-6, RNU6B, U6-6 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008800	26826	RNU6-6P	http://www.ncbi.nlm.nih.gov/gene/?term=26826	"RNU6-6, RNU6B, U6-6 "	snoRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00008801	26826	RNU6-6P	http://www.ncbi.nlm.nih.gov/gene/?term=26826	"RNU6-6, RNU6B, U6-6 "	snoRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00008802	26827	RNU6-1	http://www.ncbi.nlm.nih.gov/gene/?term=26827	"RNU6, RNU6A, U6, U6-1 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008803	26827	RNU6-1	http://www.ncbi.nlm.nih.gov/gene/?term=26827	"RNU6, RNU6A, U6, U6-1 "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008804	26827	RNU6-1	http://www.ncbi.nlm.nih.gov/gene/?term=26827	"RNU6, RNU6A, U6, U6-1 "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008805	268288	Samd3	http://www.ncbi.nlm.nih.gov/gene/?term=268288	Gm623	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008806	26828	RNU5F-1	http://www.ncbi.nlm.nih.gov/gene/?term=26828	"RNU5F, U5F "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008807	26829	RNU5E-1	http://www.ncbi.nlm.nih.gov/gene/?term=26829	"RNU5E, U5E "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008808	26829	RNU5E-1	http://www.ncbi.nlm.nih.gov/gene/?term=26829	"RNU5E, U5E "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008809	26829	RNU5E-1	http://www.ncbi.nlm.nih.gov/gene/?term=26829	"RNU5E, U5E "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008810	26829	RNU5E-1	http://www.ncbi.nlm.nih.gov/gene/?term=26829	"RNU5E, U5E "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008811	268307	4833431D13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=268307		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008812	26830	RNU5D-1	http://www.ncbi.nlm.nih.gov/gene/?term=26830	"RNU5D, U5DL, U5DS "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008813	26831	RNU5A-1	http://www.ncbi.nlm.nih.gov/gene/?term=26831	"RNU5, RNU5A, RNU5C, U5A, U5B1 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008814	26831	RNU5A-1	http://www.ncbi.nlm.nih.gov/gene/?term=26831	"RNU5, RNU5A, RNU5C, U5A, U5B1 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008815	26831	RNU5A-1	http://www.ncbi.nlm.nih.gov/gene/?term=26831	"RNU5, RNU5A, RNU5C, U5A, U5B1 "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008816	26831	RNU5A-1	http://www.ncbi.nlm.nih.gov/gene/?term=26831	"RNU5, RNU5A, RNU5C, U5A, U5B1 "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008817	26832	RNU5B-1	http://www.ncbi.nlm.nih.gov/gene/?term=26832	"RNU5BP, U5B1, RNU5B-1 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008818	26832	RNU5B-1	http://www.ncbi.nlm.nih.gov/gene/?term=26832	"RNU5BP, U5B1, RNU5B-1 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008819	26832	RNU5B-1	http://www.ncbi.nlm.nih.gov/gene/?term=26832	"RNU5BP, U5B1, RNU5B-1 "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008820	26832	RNU5B-1	http://www.ncbi.nlm.nih.gov/gene/?term=26832	"RNU5BP, U5B1, RNU5B-1 "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008821	26834	RNU4-2	http://www.ncbi.nlm.nih.gov/gene/?term=26834	"RNU4-1B, RNU4B1, RNU4C, U4A, U4b, U4c "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008822	26834	RNU4-2	http://www.ncbi.nlm.nih.gov/gene/?term=26834	"RNU4-1B, RNU4B1, RNU4C, U4A, U4b, U4c "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008823	26835	RNU4-1	http://www.ncbi.nlm.nih.gov/gene/?term=26835	"RNU4A, RNU4B2, U4, U4BL "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008824	26835	RNU4-1	http://www.ncbi.nlm.nih.gov/gene/?term=26835	"RNU4A, RNU4B2, U4, U4BL "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008825	26835	RNU4-1	http://www.ncbi.nlm.nih.gov/gene/?term=26835	"RNU4A, RNU4B2, U4, U4BL "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008826	26835	RNU4-1	http://www.ncbi.nlm.nih.gov/gene/?term=26835	"RNU4A, RNU4B2, U4, U4BL "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008827	268373	Ppia	http://www.ncbi.nlm.nih.gov/gene/?term=268373	"2700098C05, Cphn, CyP-18, CypA "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008828	26838	RNU4-6P	http://www.ncbi.nlm.nih.gov/gene/?term=26838	"RNU4P6, U4, U4/8 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008829	268390	Ahsa2	http://www.ncbi.nlm.nih.gov/gene/?term=268390		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008830	268395	Mpg	http://www.ncbi.nlm.nih.gov/gene/?term=268395	"9830006D05, AI326268, APNG, Aag, Mid1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008831	2683	B4GALT1	http://www.ncbi.nlm.nih.gov/gene/?term=2683	"B4GAL-T1, CDG2D, GGTB2, GT1, GTB, beta4Gal-T1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008832	2683	B4GALT1	http://www.ncbi.nlm.nih.gov/gene/?term=2683	"B4GAL-T1, CDG2D, GGTB2, GT1, GTB, beta4Gal-T1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008833	268417	Zkscan17	http://www.ncbi.nlm.nih.gov/gene/?term=268417	"Nizp1, Zfp496, Znf496 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008834	268449	Rpl23a	http://www.ncbi.nlm.nih.gov/gene/?term=268449	"BC029892, MDA20 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008835	268449	Rpl23a	http://www.ncbi.nlm.nih.gov/gene/?term=268449	"BC029892, MDA20 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00008836	26844	RNU3P2	http://www.ncbi.nlm.nih.gov/gene/?term=26844	"U3, U3.2 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008837	26844	RNU3P2	http://www.ncbi.nlm.nih.gov/gene/?term=26844	"U3, U3.2 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008838	268482	Krt12	http://www.ncbi.nlm.nih.gov/gene/?term=268482	"AI835216, K12, Krt-12, Krt1-12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008839	268512	Slc26a11	http://www.ncbi.nlm.nih.gov/gene/?term=268512	F630021I08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008840	26851	SNORD3B-1	http://www.ncbi.nlm.nih.gov/gene/?term=26851	"RNU3A1, U3a, U3b1, U3b2 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008841	268527	Greb1	http://www.ncbi.nlm.nih.gov/gene/?term=268527	"5730583K22Rik, 9130004E13, AF180470, AU023194, mKIAA0575 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008842	26852	RNU2-5P	http://www.ncbi.nlm.nih.gov/gene/?term=26852	RNU2P3	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008843	268534	Sntg2	http://www.ncbi.nlm.nih.gov/gene/?term=268534	"2210008K22Rik, 9530013L23, BB121248 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008844	26854	RNU2-3P	http://www.ncbi.nlm.nih.gov/gene/?term=26854	"RNU2P1, U2 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008845	268566	Gphn	http://www.ncbi.nlm.nih.gov/gene/?term=268566	"5730552E08Rik, AI662856, BC027112, C230040D23, GPH, GPHRYN, geph "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008846	26859	RNU1-14P	http://www.ncbi.nlm.nih.gov/gene/?term=26859	"RNU1P7, U1P17 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008847	26860	RNU1-13P	http://www.ncbi.nlm.nih.gov/gene/?term=26860	"RNU1-71, RNU1P6, RNVU1-2, U1.1, U1P1, vU1.2 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008848	26861	RNU1-11P	http://www.ncbi.nlm.nih.gov/gene/?term=26861	"RNU1P1, RNU1P5, U1P1A "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008849	26863	RNVU1-18	http://www.ncbi.nlm.nih.gov/gene/?term=26863	"RNU1-25, RNU1-25P, RNU1-5, RNU1P1, RNU1P9, U1.15, U1P101, U1P15, vU1.18 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008850	26863	RNVU1-18	http://www.ncbi.nlm.nih.gov/gene/?term=26863	"RNU1-25, RNU1-25P, RNU1-5, RNU1P1, RNU1P9, U1.15, U1P101, U1P15, vU1.18 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008851	26864	RNVU1-7	http://www.ncbi.nlm.nih.gov/gene/?term=26864	"RNU1-26P, RNU1-6, RNU1-6P, RNU1-9, RNU1-9P, RNVU1-9, vU1.7, vU1.9 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008852	26864	RNVU1-7	http://www.ncbi.nlm.nih.gov/gene/?term=26864	"RNU1-26P, RNU1-6, RNU1-6P, RNU1-9, RNU1-9P, RNVU1-9, vU1.7, vU1.9 "	snRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00008853	268656	Sptlc1	http://www.ncbi.nlm.nih.gov/gene/?term=268656	"AW552086, C77762, E030036H05, Lcb1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008854	26865	RNU1-27P	http://www.ncbi.nlm.nih.gov/gene/?term=26865	"RNU1-7, RNU1-7P "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008855	26865	RNU1-27P	http://www.ncbi.nlm.nih.gov/gene/?term=26865	"RNU1-7, RNU1-7P "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008856	26866	RNU1-28P	http://www.ncbi.nlm.nih.gov/gene/?term=26866	"RNU1-8, RNU1-8P "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008857	26866	RNU1-28P	http://www.ncbi.nlm.nih.gov/gene/?term=26866	"RNU1-8, RNU1-8P "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008858	268697	Ccnb1	http://www.ncbi.nlm.nih.gov/gene/?term=268697	"Ccnb1-rs1-rs13, CycB1, Cycb-4, Cycb-5, Cycb1-rs1, Ccnb1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008859	268697	Ccnb1	http://www.ncbi.nlm.nih.gov/gene/?term=268697	"Ccnb1-rs1-rs13, CycB1, Cycb-4, Cycb-5, Cycb1-rs1, Ccnb1 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00008860	26869	RNU1-3	http://www.ncbi.nlm.nih.gov/gene/?term=26869	"HSD4, RNU1G3 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008861	26869	RNU1-3	http://www.ncbi.nlm.nih.gov/gene/?term=26869	"HSD4, RNU1G3 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008862	2686	GGT7	http://www.ncbi.nlm.nih.gov/gene/?term=2686	"D20S101, GGT4, GGTL3, GGTL5, dJ18C9.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008863	26870	RNU1-2	http://www.ncbi.nlm.nih.gov/gene/?term=26870	"RNU1C1, RNU1C2, U1C1, U1C21 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008864	26870	RNU1-2	http://www.ncbi.nlm.nih.gov/gene/?term=26870	"RNU1C1, RNU1C2, U1C1, U1C21 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008865	26871	RNU1-1	http://www.ncbi.nlm.nih.gov/gene/?term=26871	"HSD1, HU1-1, RNU1, RNU1A, RNU1A3, RNU1G4, Rnu1a1, U1, U1A1 "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00008866	26871	RNU1-1	http://www.ncbi.nlm.nih.gov/gene/?term=26871	"HSD1, HU1-1, RNU1, RNU1A, RNU1A3, RNU1G4, Rnu1a1, U1, U1A1 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008867	26871	RNU1-1	http://www.ncbi.nlm.nih.gov/gene/?term=26871	"HSD1, HU1-1, RNU1, RNU1A, RNU1A3, RNU1G4, Rnu1a1, U1, U1A1 "	snRNA	Homo sapiens	1530887	Nucleus	HeLa cell	In situ hybridization	"The localization of U1 and U2 small nuclear RNAs (snRNAs) has been examined by in situ hybridization using 2'-O-alkyl oligonucleotide probes. We have found that these snRNAs, which are essential for pre-mRNA splicing, localize in a speckled distribution, in addition to being present in three of four foci, in HeLa cell nuclei. However, in cells of defined passage, such as Detroit 551 and WI-38 fibroblasts, these snRNAs are concentrated in nuclear speckles, and foci are not observed. "
RLID00008868	26871	RNU1-1	http://www.ncbi.nlm.nih.gov/gene/?term=26871	"HSD1, HU1-1, RNU1, RNU1A, RNU1A3, RNU1G4, Rnu1a1, U1, U1A1 "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008869	26871	RNU1-1	http://www.ncbi.nlm.nih.gov/gene/?term=26871	"HSD1, HU1-1, RNU1, RNU1A, RNU1A3, RNU1G4, Rnu1a1, U1, U1A1 "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008870	26872	STEAP1	http://www.ncbi.nlm.nih.gov/gene/?term=26872	"PRSS24, STEAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008871	26872	STEAP1	http://www.ncbi.nlm.nih.gov/gene/?term=26872	"PRSS24, STEAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008872	268749	Rnf31	http://www.ncbi.nlm.nih.gov/gene/?term=268749	"AL033293, BC031509, Flj10111, HOIP, Paul, mFLJ00217 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008873	26878	B3galt2	http://www.ncbi.nlm.nih.gov/gene/?term=26878		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008874	26879	B3galnt1	http://www.ncbi.nlm.nih.gov/gene/?term=26879	"B3galt3, b3GT3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008875	2687	GGT5	http://www.ncbi.nlm.nih.gov/gene/?term=2687	"GGL, GGT 5, GGT-REL, GGTLA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008876	268857	Nlrc3	http://www.ncbi.nlm.nih.gov/gene/?term=268857	"CLR16.2, D230007K08Rik, mFLJ00348 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008877	26893	Cops6	http://www.ncbi.nlm.nih.gov/gene/?term=26893	"Sgn3, VIP/MOV34 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008878	26894	Cops7a	http://www.ncbi.nlm.nih.gov/gene/?term=26894	D6Ertd35e	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008879	268977	Ltbp1	http://www.ncbi.nlm.nih.gov/gene/?term=268977	"9430031G15Rik, 9830146M04, Ltbp-1, Tgfb, b2b1000Clo "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008880	268996	Ss18	http://www.ncbi.nlm.nih.gov/gene/?term=268996	"D130059H17, Ssxt, Syt "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008881	26900	Ddx3y	http://www.ncbi.nlm.nih.gov/gene/?term=26900	"8030469F12Rik, D1Pas1-rs1, Dby "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008882	269033	4930503L19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=269033	"9930107F24, BB148262, Lars, Las2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008883	269053	Gpr152	http://www.ncbi.nlm.nih.gov/gene/?term=269053	"A930009H15Rik, Gm673 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008884	269061	Cpsf7	http://www.ncbi.nlm.nih.gov/gene/?term=269061	"5730453I16Rik, AL022757, C330017N18Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008885	26909	Exo1	http://www.ncbi.nlm.nih.gov/gene/?term=26909	"5730442G03Rik, Msa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008886	2690	GHR	http://www.ncbi.nlm.nih.gov/gene/?term=2690	"GHBP, GHIP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008887	2690	GHR	http://www.ncbi.nlm.nih.gov/gene/?term=2690	"GHBP, GHIP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008888	26912	Gcat	http://www.ncbi.nlm.nih.gov/gene/?term=26912	"AI526977, Kbl "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008889	26921	Map4k4	http://www.ncbi.nlm.nih.gov/gene/?term=26921	"9430080K19Rik, AU043147, AU045934, AW046177, HGK, Nik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008890	26922	Mecr	http://www.ncbi.nlm.nih.gov/gene/?term=26922	"AI195831, Nrbf1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008891	269252	Gtf3c4	http://www.ncbi.nlm.nih.gov/gene/?term=269252	"5330400C03, AI426938, AU014771, AU017413, KAT12, TFIIIC90 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008892	269254	Setx	http://www.ncbi.nlm.nih.gov/gene/?term=269254	"A130090N03, A930037J23Rik, AOA2, AW060766, Als4, SCAR1, Sen1, mKIAA0625 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008893	269261	Rpl12	http://www.ncbi.nlm.nih.gov/gene/?term=269261	E430018F03	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008894	269261	Rpl12	http://www.ncbi.nlm.nih.gov/gene/?term=269261	E430018F03	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008895	269261	Rpl12	http://www.ncbi.nlm.nih.gov/gene/?term=269261	E430018F03	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00008896	26926	Aifm1	http://www.ncbi.nlm.nih.gov/gene/?term=26926	"AIF, AIFsh2, Hq, Pdcd8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008897	26932	Ppp2r5e	http://www.ncbi.nlm.nih.gov/gene/?term=26932	"4633401M22Rik, AI449017, B56beta "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008898	269344	Ell3	http://www.ncbi.nlm.nih.gov/gene/?term=269344	A930015D22Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008899	26934	Racgap1	http://www.ncbi.nlm.nih.gov/gene/?term=26934	"AI227039, AI327394, Band25, GTPase, MgcRacGAP, gtl11, mKIAA1478 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008900	26936	Mprip	http://www.ncbi.nlm.nih.gov/gene/?term=26936	"9530046C02, AA536749, AI647711, C76423, RIP3, Rhoip3, mKIAA0864, p116Rip "	mRNA	Mus musculus	18539120	Synapse	Brain	qRT-PCR	"The mRNA targets reduced in Kif5 association included genes involved in actin remodeling at synapses (cofilin phosphatase (PP2Ac); p116-RIP), synapse-associated signaling (DAG1;RGS5) and synapse structure (SAPAP4; CaMKIIa; MAP1b). Not all mRNAs were significantly reduced in Kif5 IPs, as OCRL1 mRNA was similar in KO brain (P>0.05, n=8). "
RLID00008901	269400	Rtel1	http://www.ncbi.nlm.nih.gov/gene/?term=269400	"AI451565, AW540478, Rtel "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008902	26940	Ecsit	http://www.ncbi.nlm.nih.gov/gene/?term=26940	Sitpec	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008903	26941	Slc9a3r1	http://www.ncbi.nlm.nih.gov/gene/?term=26941	"EBP-50, NHE-RF, NHERF-1, NHERF1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008904	269424	Jade1	http://www.ncbi.nlm.nih.gov/gene/?term=269424	"AU041499, D530048A03Rik, Phf17, mKIAA1807 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008905	26942	Spag1	http://www.ncbi.nlm.nih.gov/gene/?term=26942	tpis	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008906	269470	Wdr3	http://www.ncbi.nlm.nih.gov/gene/?term=269470	"AW546279, D030020G18Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008907	269472	LOC269472	http://www.ncbi.nlm.nih.gov/gene/?term=269472		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008908	269473	Lrig2	http://www.ncbi.nlm.nih.gov/gene/?term=269473	"4632419I10Rik, BB096938, LIG-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008909	26949	Vat1	http://www.ncbi.nlm.nih.gov/gene/?term=26949	VAT-1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008910	26951	Zw10	http://www.ncbi.nlm.nih.gov/gene/?term=26951	"6330566F14Rik, MmZw10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008911	269536	Tex10	http://www.ncbi.nlm.nih.gov/gene/?term=269536	"2610206N19Rik, 2810462N03Rik, BC006867 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008912	26953	RANBP6	http://www.ncbi.nlm.nih.gov/gene/?term=26953		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008913	26953	RANBP6	http://www.ncbi.nlm.nih.gov/gene/?term=26953		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008914	26953	RANBP6	http://www.ncbi.nlm.nih.gov/gene/?term=26953		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008915	269582	Clspn	http://www.ncbi.nlm.nih.gov/gene/?term=269582	"B130025E01, C85083, E130314M08Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008916	26958	COPG2	http://www.ncbi.nlm.nih.gov/gene/?term=26958	"2-COP, gamma-2-COP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008917	269593	Luzp1	http://www.ncbi.nlm.nih.gov/gene/?term=269593	"2700072H04Rik, AI266952, Luzp, mFLJ00226 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008918	26959	HBP1	http://www.ncbi.nlm.nih.gov/gene/?term=26959		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008919	269614	Pank4	http://www.ncbi.nlm.nih.gov/gene/?term=269614	"D030031I12Rik, R75150 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008920	269623	Rbm48	http://www.ncbi.nlm.nih.gov/gene/?term=269623	"AW548102, C030048B08Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008921	26965	Cul1	http://www.ncbi.nlm.nih.gov/gene/?term=26965		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008922	269682	Golga3	http://www.ncbi.nlm.nih.gov/gene/?term=269682	"5330413L04, 5430416E01Rik, AI449376, AW490576, G1-499-14, Mea-2, Mea2, repro27 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008923	269704	Zfp664	http://www.ncbi.nlm.nih.gov/gene/?term=269704	"AW060232, D930038J03Rik, ZFOC1, Znf664 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008924	26970	Pla2g2e	http://www.ncbi.nlm.nih.gov/gene/?term=26970		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008925	26973	CHORDC1	http://www.ncbi.nlm.nih.gov/gene/?term=26973	CHP1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008926	269784	Cntn4	http://www.ncbi.nlm.nih.gov/gene/?term=269784	"9630050B05, Axcam, BIG-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008927	269788	Lhfpl4	http://www.ncbi.nlm.nih.gov/gene/?term=269788	"1190004M23Rik, AI604880, B230384L07, mKIAA4027 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008928	2697	GJA1	http://www.ncbi.nlm.nih.gov/gene/?term=2697	"AVSD3, CMDR, CX43, EKVP, GJAL, HLHS1, HSS, ODDD, PPKCA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008929	2697	GJA1	http://www.ncbi.nlm.nih.gov/gene/?term=2697	"AVSD3, CMDR, CX43, EKVP, GJAL, HLHS1, HSS, ODDD, PPKCA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008930	26984	SEC22A	http://www.ncbi.nlm.nih.gov/gene/?term=26984	SEC22L2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008931	26985	AP3M1	http://www.ncbi.nlm.nih.gov/gene/?term=26985		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008932	26985	AP3M1	http://www.ncbi.nlm.nih.gov/gene/?term=26985		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008933	26985	AP3M1	http://www.ncbi.nlm.nih.gov/gene/?term=26985		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008934	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008935	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008936	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008937	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008938	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008939	269881	Map3k10	http://www.ncbi.nlm.nih.gov/gene/?term=269881	"BC028668, BC046514, MST, Mlk2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008940	269941	Chsy1	http://www.ncbi.nlm.nih.gov/gene/?term=269941	mKIAA0990	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008941	26994	RNF11	http://www.ncbi.nlm.nih.gov/gene/?term=26994	"CGI-123, SID1669 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008942	269955	Rccd1	http://www.ncbi.nlm.nih.gov/gene/?term=269955	"5830436H09, E430018M08Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008943	26995	TRUB2	http://www.ncbi.nlm.nih.gov/gene/?term=26995	CLONE24922	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008944	26996	GPR160	http://www.ncbi.nlm.nih.gov/gene/?term=26996	"GPCR1, GPCR150 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008945	26996	GPR160	http://www.ncbi.nlm.nih.gov/gene/?term=26996	"GPCR1, GPCR150 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008946	26999	CYFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=26999	PIR121	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008947	26999	CYFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=26999	PIR121	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008948	26999	CYFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=26999	PIR121	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008949	27000	DNAJC2	http://www.ncbi.nlm.nih.gov/gene/?term=27000	"MPHOSPH11, MPP11, ZRF1, ZUO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008950	27000	DNAJC2	http://www.ncbi.nlm.nih.gov/gene/?term=27000	"MPHOSPH11, MPP11, ZRF1, ZUO1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008951	27000	DNAJC2	http://www.ncbi.nlm.nih.gov/gene/?term=27000	"MPHOSPH11, MPP11, ZRF1, ZUO1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008952	270028	Fam155a	http://www.ncbi.nlm.nih.gov/gene/?term=270028	"6430500D16, AW121567, Tmem28 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008953	270049	Galntl6	http://www.ncbi.nlm.nih.gov/gene/?term=270049	"1700021K10Rik, 4930431L04Rik, A830023L05 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008954	27004	TCL6	http://www.ncbi.nlm.nih.gov/gene/?term=27004	"TNG1, TNG2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008955	27004	TCL6	http://www.ncbi.nlm.nih.gov/gene/?term=27004	"TNG1, TNG2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008956	270058	Map1s	http://www.ncbi.nlm.nih.gov/gene/?term=270058	"6430517J16Rik, Bpy2ip1, Map8, Mtap1s, VCY2IP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008957	27005	USP21	http://www.ncbi.nlm.nih.gov/gene/?term=27005	"USP16, USP23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008958	270097	Vat1l	http://www.ncbi.nlm.nih.gov/gene/?term=270097	"9430073I07, AI427515, mKIAA1576 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008959	270106	Rpl13	http://www.ncbi.nlm.nih.gov/gene/?term=270106	"A52, L13 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008960	270106	Rpl13	http://www.ncbi.nlm.nih.gov/gene/?term=270106	"A52, L13 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00008961	27010	TPK1	http://www.ncbi.nlm.nih.gov/gene/?term=27010	"HTPK1, PP20, THMD5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008962	27013	CNPPD1	http://www.ncbi.nlm.nih.gov/gene/?term=27013	"C2orf24, CGI-57 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008963	27018	BEX3	http://www.ncbi.nlm.nih.gov/gene/?term=27018	"Bex, DXS6984E, HGR74, NADE, NGFRAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008964	27018	BEX3	http://www.ncbi.nlm.nih.gov/gene/?term=27018	"Bex, DXS6984E, HGR74, NADE, NGFRAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008965	270190	Ephb1	http://www.ncbi.nlm.nih.gov/gene/?term=270190	"9330129L11, AW488255, C130099E04Rik, Cek6, ENSMUSG00000074119, Elk, Elkh, Hek6, Net "	mRNA	Mus musculus	18524895	Axon	Embryo	RT-PCR	"Interestingly, EphB1 mRNA is also localized to the distal axonal compartment (Fig. 3B, lane 6). This result indicates that Zic2 activates transcription of EphB1 mRNA in the cell nucleus and that EphB1 mRNA is transported down to the axon terminus. "
RLID00008966	27020	NPTN	http://www.ncbi.nlm.nih.gov/gene/?term=27020	"GP55, GP65, SDFR1, SDR1, np55, np65 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008967	27030	MLH3	http://www.ncbi.nlm.nih.gov/gene/?term=27030	HNPCC7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008968	27030	MLH3	http://www.ncbi.nlm.nih.gov/gene/?term=27030	HNPCC7	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008969	27032	ATP2C1	http://www.ncbi.nlm.nih.gov/gene/?term=27032	"ATP2C1A, BCPM, HHD, PMR1, SPCA1, hSPCA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008970	27034	ACAD8	http://www.ncbi.nlm.nih.gov/gene/?term=27034	"ACAD-8, ARC42 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008971	27034	ACAD8	http://www.ncbi.nlm.nih.gov/gene/?term=27034	"ACAD-8, ARC42 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008972	27037	TRMT2A	http://www.ncbi.nlm.nih.gov/gene/?term=27037	HTF9C	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008973	27037	TRMT2A	http://www.ncbi.nlm.nih.gov/gene/?term=27037	HTF9C	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008974	27040	LAT	http://www.ncbi.nlm.nih.gov/gene/?term=27040	"LAT1, pp36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008975	27042	DIEXF	http://www.ncbi.nlm.nih.gov/gene/?term=27042	"C1orf107, DEF, DJ434O14.5, UTP25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008976	27042	DIEXF	http://www.ncbi.nlm.nih.gov/gene/?term=27042	"C1orf107, DEF, DJ434O14.5, UTP25 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008977	27042	DIEXF	http://www.ncbi.nlm.nih.gov/gene/?term=27042	"C1orf107, DEF, DJ434O14.5, UTP25 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00008978	27043	PELP1	http://www.ncbi.nlm.nih.gov/gene/?term=27043	"MNAR, P160 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008979	27044	SND1	http://www.ncbi.nlm.nih.gov/gene/?term=27044	"TDRD11, p100 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008980	27044	SND1	http://www.ncbi.nlm.nih.gov/gene/?term=27044	"TDRD11, p100 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008981	27044	SND1	http://www.ncbi.nlm.nih.gov/gene/?term=27044	"TDRD11, p100 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008982	27045	Nit1	http://www.ncbi.nlm.nih.gov/gene/?term=27045	"AI255805, ESTM30, W57327 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008983	27052	Aoah	http://www.ncbi.nlm.nih.gov/gene/?term=27052	4930433E13Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008984	27053	Asns	http://www.ncbi.nlm.nih.gov/gene/?term=27053		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008985	27055	Fkbp9	http://www.ncbi.nlm.nih.gov/gene/?term=27055	"1810014L23, AW549641, FKBP-63, FKBP-9, FKBP60, FKBP63, FKBP65RS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008986	2705	GJB1	http://www.ncbi.nlm.nih.gov/gene/?term=2705	"CMTX, CMTX1, CX32 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008987	27061	Bcap31	http://www.ncbi.nlm.nih.gov/gene/?term=27061	Bap31	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008988	270627	Taf1	http://www.ncbi.nlm.nih.gov/gene/?term=270627	"AU015687, B430306D02Rik, Ccg-1, Ccg1, KAT4, N-TAF1, TAFII250, Taf2a, p250 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008989	27062	Cadps	http://www.ncbi.nlm.nih.gov/gene/?term=27062	"AU067781, CAPS, CAPS1, mKIAA1121 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00008990	27067	STAU2	http://www.ncbi.nlm.nih.gov/gene/?term=27067	"39K2, 39K3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008991	270685	Mthfd1l	http://www.ncbi.nlm.nih.gov/gene/?term=270685	"2410004L15Rik, AI647056, Fthfsdc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00008992	27068	PPA2	http://www.ncbi.nlm.nih.gov/gene/?term=27068	"HSPC124, SID6-306 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008993	27068	PPA2	http://www.ncbi.nlm.nih.gov/gene/?term=27068	"HSPC124, SID6-306 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008994	27068	PPA2	http://www.ncbi.nlm.nih.gov/gene/?term=27068	"HSPC124, SID6-306 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00008995	27069	GHITM	http://www.ncbi.nlm.nih.gov/gene/?term=27069	"DERP2, HSPC282, MICS1, My021, PTD010, TMBIM5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008996	2706	GJB2	http://www.ncbi.nlm.nih.gov/gene/?term=2706	"CX26, DFNA3, DFNA3A, DFNB1, DFNB1A, HID, KID, NSRD1, PPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008997	2706	GJB2	http://www.ncbi.nlm.nih.gov/gene/?term=2706	"CX26, DFNA3, DFNA3A, DFNB1, DFNB1A, HID, KID, NSRD1, PPK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00008998	27072	VPS41	http://www.ncbi.nlm.nih.gov/gene/?term=27072	"HVPS41, HVSP41, hVps41p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00008999	27072	VPS41	http://www.ncbi.nlm.nih.gov/gene/?term=27072	"HVPS41, HVSP41, hVps41p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009000	27075	TSPAN13	http://www.ncbi.nlm.nih.gov/gene/?term=27075	"NET-6, NET6, TM4SF13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009001	27077	B9D1	http://www.ncbi.nlm.nih.gov/gene/?term=27077	"B9, EPPB9, MKS9, MKSR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009002	27077	B9D1	http://www.ncbi.nlm.nih.gov/gene/?term=27077	"B9, EPPB9, MKS9, MKSR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009003	27078	B9d1	http://www.ncbi.nlm.nih.gov/gene/?term=27078	"AW045994, B9, Eppb9 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009004	27079	RPUSD2	http://www.ncbi.nlm.nih.gov/gene/?term=27079	"C15orf19, C18B11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009005	2707	GJB3	http://www.ncbi.nlm.nih.gov/gene/?term=2707	"CX31, DFNA2, DFNA2B, EKV "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009006	27086	FOXP1	http://www.ncbi.nlm.nih.gov/gene/?term=27086	"12CC4, HSPC215, MFH, QRF1, hFKH1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009007	27089	UQCRQ	http://www.ncbi.nlm.nih.gov/gene/?term=27089	"MC3DN4, QCR8, QP-C, QPC, UQCR7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009008	27089	UQCRQ	http://www.ncbi.nlm.nih.gov/gene/?term=27089	"MC3DN4, QCR8, QP-C, QPC, UQCR7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009009	27089	UQCRQ	http://www.ncbi.nlm.nih.gov/gene/?term=27089	"MC3DN4, QCR8, QP-C, QPC, UQCR7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009010	27089	UQCRQ	http://www.ncbi.nlm.nih.gov/gene/?term=27089	"MC3DN4, QCR8, QP-C, QPC, UQCR7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009011	27090	ST6GALNAC4	http://www.ncbi.nlm.nih.gov/gene/?term=27090	"IV, SIAT3-C, SIAT3C, SIAT7-D, SIAT7D, ST6GALNACIV, ST6GalNAc "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009012	27092	CACNG4	http://www.ncbi.nlm.nih.gov/gene/?term=27092		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009013	27095	TRAPPC3	http://www.ncbi.nlm.nih.gov/gene/?term=27095	BET3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009014	27095	TRAPPC3	http://www.ncbi.nlm.nih.gov/gene/?term=27095	BET3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009015	2709	GJB5	http://www.ncbi.nlm.nih.gov/gene/?term=2709	CX31.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009016	27101	CACYBP	http://www.ncbi.nlm.nih.gov/gene/?term=27101	"GIG5, PNAS-107, S100A6BP, SIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009017	27101	CACYBP	http://www.ncbi.nlm.nih.gov/gene/?term=27101	"GIG5, PNAS-107, S100A6BP, SIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009018	27101	CACYBP	http://www.ncbi.nlm.nih.gov/gene/?term=27101	"GIG5, PNAS-107, S100A6BP, SIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009019	27102	EIF2AK1	http://www.ncbi.nlm.nih.gov/gene/?term=27102	"HCR, HRI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009020	27102	EIF2AK1	http://www.ncbi.nlm.nih.gov/gene/?term=27102	"HCR, HRI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009021	271036	Catsperb	http://www.ncbi.nlm.nih.gov/gene/?term=271036	"4931410B03, 4932415G16Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009022	27103	Eif2ak4	http://www.ncbi.nlm.nih.gov/gene/?term=27103	"2610011M03, GCN2, MGCN2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009023	27107	ZBTB11	http://www.ncbi.nlm.nih.gov/gene/?term=27107	"ZNF-U69274, ZNF913 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009024	27109	ATP5S	http://www.ncbi.nlm.nih.gov/gene/?term=27109	"ATPW, FB, HSU79253 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009025	27113	BBC3	http://www.ncbi.nlm.nih.gov/gene/?term=27113	"JFY-1, JFY1, PUMA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009026	27113	BBC3	http://www.ncbi.nlm.nih.gov/gene/?term=27113	"JFY-1, JFY1, PUMA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009027	27124	INPP5J	http://www.ncbi.nlm.nih.gov/gene/?term=27124	"INPP5, PIB5PA, PIPP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009028	27125	AFF4	http://www.ncbi.nlm.nih.gov/gene/?term=27125	"AF5Q31, CHOPS, MCEF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009029	27125	AFF4	http://www.ncbi.nlm.nih.gov/gene/?term=27125	"AF5Q31, CHOPS, MCEF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009030	27131	SNX5	http://www.ncbi.nlm.nih.gov/gene/?term=27131		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009031	27134	TJP3	http://www.ncbi.nlm.nih.gov/gene/?term=27134	"ZO-3, ZO3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009032	271377	Zbtb11	http://www.ncbi.nlm.nih.gov/gene/?term=271377	"9230110G02Rik, ZNF-U69274 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009033	27141	CIDEB	http://www.ncbi.nlm.nih.gov/gene/?term=27141		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009034	27141	CIDEB	http://www.ncbi.nlm.nih.gov/gene/?term=27141		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009035	27143	PALD1	http://www.ncbi.nlm.nih.gov/gene/?term=27143	"KIAA1274, PALD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009036	271564	Vps13a	http://www.ncbi.nlm.nih.gov/gene/?term=271564	"4930425F11, 4930516E05Rik, 4930543C13Rik, 9930023P20, Chac, Chorein, D330038K10Rik, mKIAA0986 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009037	27161	AGO2	http://www.ncbi.nlm.nih.gov/gene/?term=27161	"EIF2C2, Q10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009038	27161	AGO2	http://www.ncbi.nlm.nih.gov/gene/?term=27161	"EIF2C2, Q10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009039	27163	NAAA	http://www.ncbi.nlm.nih.gov/gene/?term=27163	"ASAHL, PLT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009040	27163	NAAA	http://www.ncbi.nlm.nih.gov/gene/?term=27163	"ASAHL, PLT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009041	27166	PRELID1	http://www.ncbi.nlm.nih.gov/gene/?term=27166	"CGI-106, PRELI, PX19, SBBI12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009042	27166	PRELID1	http://www.ncbi.nlm.nih.gov/gene/?term=27166	"CGI-106, PRELI, PX19, SBBI12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009043	27173	SLC39A1	http://www.ncbi.nlm.nih.gov/gene/?term=27173	"ZIP1, ZIRTL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009044	27173	SLC39A1	http://www.ncbi.nlm.nih.gov/gene/?term=27173	"ZIP1, ZIRTL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009045	27175	TUBG2	http://www.ncbi.nlm.nih.gov/gene/?term=27175		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009046	27175	TUBG2	http://www.ncbi.nlm.nih.gov/gene/?term=27175		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009047	27176	Rpl7a	http://www.ncbi.nlm.nih.gov/gene/?term=27176	Surf3	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009048	27176	Rpl7a	http://www.ncbi.nlm.nih.gov/gene/?term=27176	Surf3	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00009049	2717	GLA	http://www.ncbi.nlm.nih.gov/gene/?term=2717	GALA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009050	2717	GLA	http://www.ncbi.nlm.nih.gov/gene/?term=2717	GALA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009051	2717	GLA	http://www.ncbi.nlm.nih.gov/gene/?term=2717	GALA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009052	27181	SIGLEC8	http://www.ncbi.nlm.nih.gov/gene/?term=27181	"SAF2, SIGLEC-8L, SIGLEC8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009053	27181	SIGLEC8	http://www.ncbi.nlm.nih.gov/gene/?term=27181	"SAF2, SIGLEC-8L, SIGLEC8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009054	27183	VPS4A	http://www.ncbi.nlm.nih.gov/gene/?term=27183	"SKD1, SKD1A, SKD2, VPS4, VPS4-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009055	27183	VPS4A	http://www.ncbi.nlm.nih.gov/gene/?term=27183	"SKD1, SKD1A, SKD2, VPS4, VPS4-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009056	27183	VPS4A	http://www.ncbi.nlm.nih.gov/gene/?term=27183	"SKD1, SKD1A, SKD2, VPS4, VPS4-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009057	27185	DISC1	http://www.ncbi.nlm.nih.gov/gene/?term=27185	"C1orf136, SCZD9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009058	27185	DISC1	http://www.ncbi.nlm.nih.gov/gene/?term=27185	"C1orf136, SCZD9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009059	271981	Tbck	http://www.ncbi.nlm.nih.gov/gene/?term=271981	"1700120J03Rik, 9430001M19, A630047E20Rik, C030007I09Rikl, Tbck "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009060	27198	HCAR1	http://www.ncbi.nlm.nih.gov/gene/?term=27198	"FKSG80, GPR104, GPR81, HCA1, LACR1, TA-GPCR, TAGPCR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009061	27198	HCAR1	http://www.ncbi.nlm.nih.gov/gene/?term=27198	"FKSG80, GPR104, GPR81, HCA1, LACR1, TA-GPCR, TAGPCR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009062	2719	GPC3	http://www.ncbi.nlm.nih.gov/gene/?term=2719	"DGSX, GTR2-2, MXR7, OCI-5, SDYS, SGB, SGBS, SGBS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009063	271	AMPD2	http://www.ncbi.nlm.nih.gov/gene/?term=271	"PCH9, SPG63 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009064	27207	Rps11	http://www.ncbi.nlm.nih.gov/gene/?term=27207		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009065	27209	Snord32a	http://www.ncbi.nlm.nih.gov/gene/?term=27209	"Rnu32, Rnu32a, U32, U32A "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00009066	2720	GLB1	http://www.ncbi.nlm.nih.gov/gene/?term=2720	"EBP, ELNR1, MPS4B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009067	2720	GLB1	http://www.ncbi.nlm.nih.gov/gene/?term=2720	"EBP, ELNR1, MPS4B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009068	2720	GLB1	http://www.ncbi.nlm.nih.gov/gene/?term=2720	"EBP, ELNR1, MPS4B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009069	27214	Dbf4	http://www.ncbi.nlm.nih.gov/gene/?term=27214	"AA545217, Ask "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009070	272158	Poln	http://www.ncbi.nlm.nih.gov/gene/?term=272158	POL4P	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009071	27218	Slamf1	http://www.ncbi.nlm.nih.gov/gene/?term=27218	"4933415F16, AA177906, CD150, CDw150, ESTM51, IPO-3, Slam "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009072	27220	Cartpt	http://www.ncbi.nlm.nih.gov/gene/?term=27220	Cart	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009073	27223	Trp53bp1	http://www.ncbi.nlm.nih.gov/gene/?term=27223	"53BP1, Tp53bp1, m53BP1, p53BP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009074	27229	TUBGCP4	http://www.ncbi.nlm.nih.gov/gene/?term=27229	"76P, GCP-4, GCP4, Grip76, MCCRP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009075	27230	SERP1	http://www.ncbi.nlm.nih.gov/gene/?term=27230	RAMP4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009076	27230	SERP1	http://www.ncbi.nlm.nih.gov/gene/?term=27230	RAMP4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009077	27230	SERP1	http://www.ncbi.nlm.nih.gov/gene/?term=27230	RAMP4	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009078	27235	COQ2	http://www.ncbi.nlm.nih.gov/gene/?term=27235	"CL640, COQ10D1, MSA1, PHB:PPT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009079	27236	ARFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=27236	HSU52521	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009080	27237	ARHGEF16	http://www.ncbi.nlm.nih.gov/gene/?term=27237	"GEF16, NBR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009081	27238	GPKOW	http://www.ncbi.nlm.nih.gov/gene/?term=27238	"GPATC5, GPATCH5, Spp2, T54 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009082	27239	GPR162	http://www.ncbi.nlm.nih.gov/gene/?term=27239	"A-2, GRCA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009083	27242	TNFRSF21	http://www.ncbi.nlm.nih.gov/gene/?term=27242	"BM-018, CD358, DR6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009084	27243	CHMP2A	http://www.ncbi.nlm.nih.gov/gene/?term=27243	"BC-2, BC2, CHMP2, VPS2, VPS2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009085	27243	CHMP2A	http://www.ncbi.nlm.nih.gov/gene/?term=27243	"BC-2, BC2, CHMP2, VPS2, VPS2A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009086	27244	SESN1	http://www.ncbi.nlm.nih.gov/gene/?term=27244	"PA26, SEST1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009087	27244	SESN1	http://www.ncbi.nlm.nih.gov/gene/?term=27244	"PA26, SEST1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009088	27245	AHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=27245	MRD25	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009089	27247	NFU1	http://www.ncbi.nlm.nih.gov/gene/?term=27247	"CGI-33, HIRIP, HIRIP5, MMDS1, NIFUC, Nfu, NifU "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009090	27248	ERLEC1	http://www.ncbi.nlm.nih.gov/gene/?term=27248	"C2orf30, CIM, CL24936, CL25084, HEL117, XTP3-B, XTP3TPB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009091	27249	MMADHC	http://www.ncbi.nlm.nih.gov/gene/?term=27249	"C2orf25, CL25022, cblD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009092	27250	PDCD4	http://www.ncbi.nlm.nih.gov/gene/?term=27250	H731	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009093	27250	PDCD4	http://www.ncbi.nlm.nih.gov/gene/?term=27250	H731	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009094	27252	KLHL20	http://www.ncbi.nlm.nih.gov/gene/?term=27252	"KHLHX, KLEIP, KLHLX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009095	27254	CSDC2	http://www.ncbi.nlm.nih.gov/gene/?term=27254	"PIPPIN, dJ347H13.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009096	272551	Gins2	http://www.ncbi.nlm.nih.gov/gene/?term=272551	"2210013I18Rik, 4833427B12Rik, AI323585, Pfs2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009097	27257	LSM1	http://www.ncbi.nlm.nih.gov/gene/?term=27257	"CASM, YJL124C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009098	27257	LSM1	http://www.ncbi.nlm.nih.gov/gene/?term=27257	"CASM, YJL124C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009099	27257	LSM1	http://www.ncbi.nlm.nih.gov/gene/?term=27257	"CASM, YJL124C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009100	272589	Tbcel	http://www.ncbi.nlm.nih.gov/gene/?term=272589	"D330014K23, E130107N23Rik, Lrrc35 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009101	27258	LSM3	http://www.ncbi.nlm.nih.gov/gene/?term=27258	"SMX4, USS2, YLR438C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009102	27258	LSM3	http://www.ncbi.nlm.nih.gov/gene/?term=27258	"SMX4, USS2, YLR438C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009103	27260	Plek2	http://www.ncbi.nlm.nih.gov/gene/?term=27260		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009104	27261	Dok3	http://www.ncbi.nlm.nih.gov/gene/?term=27261	"AI450713, Dokl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009105	27275	Nufip1	http://www.ncbi.nlm.nih.gov/gene/?term=27275	Nufip	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009106	27277	Golga5	http://www.ncbi.nlm.nih.gov/gene/?term=27277	Ret-II	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009107	27280	Phlda3	http://www.ncbi.nlm.nih.gov/gene/?term=27280	Tih1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009108	27287	VENTX	http://www.ncbi.nlm.nih.gov/gene/?term=27287	"HPX42B, NA88A2, VENTX "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009109	27287	VENTX	http://www.ncbi.nlm.nih.gov/gene/?term=27287	"HPX42B, NA88A2, VENTX "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009110	27289	RND1	http://www.ncbi.nlm.nih.gov/gene/?term=27289	"ARHS, RHO6, RHOS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009111	27289	RND1	http://www.ncbi.nlm.nih.gov/gene/?term=27289	"ARHS, RHO6, RHOS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009112	27290	SPINK4	http://www.ncbi.nlm.nih.gov/gene/?term=27290	"HEL136, PEC-60, PEC60 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009113	27290	SPINK4	http://www.ncbi.nlm.nih.gov/gene/?term=27290	"HEL136, PEC-60, PEC60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009114	27291	R3HCC1L	http://www.ncbi.nlm.nih.gov/gene/?term=27291	"C10orf28, GIDRP86, GIDRP88, PSORT "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009115	27291	R3HCC1L	http://www.ncbi.nlm.nih.gov/gene/?term=27291	"C10orf28, GIDRP86, GIDRP88, PSORT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009116	27292	DIMT1	http://www.ncbi.nlm.nih.gov/gene/?term=27292	"DIM1, DIMT1L, HSA9761, HUSSY5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009117	27292	DIMT1	http://www.ncbi.nlm.nih.gov/gene/?term=27292	"DIM1L, HSA9761, HUSSY5, DIMT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009118	27297	CRCP	http://www.ncbi.nlm.nih.gov/gene/?term=27297	"CGRP-RCP, CGRPRCP, RCP, RCP9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009119	2729	GCLC	http://www.ncbi.nlm.nih.gov/gene/?term=2729	"GCL, GCS, GLCL, GLCLC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009120	2729	GCLC	http://www.ncbi.nlm.nih.gov/gene/?term=2729	"GCL, GCS, GLCL, GLCLC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009121	272	AMPD3	http://www.ncbi.nlm.nih.gov/gene/?term=272		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009122	27301	APEX2	http://www.ncbi.nlm.nih.gov/gene/?term=27301	"APE2, APEXL2, XTH2, ZGRF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009123	27303	RBMS3	http://www.ncbi.nlm.nih.gov/gene/?term=27303		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009124	27304	MOCS3	http://www.ncbi.nlm.nih.gov/gene/?term=27304	UBA4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009125	27304	MOCS3	http://www.ncbi.nlm.nih.gov/gene/?term=27304	UBA4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009126	27309	ZNF330	http://www.ncbi.nlm.nih.gov/gene/?term=27309	"HSA6591, NOA36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009127	27309	ZNF330	http://www.ncbi.nlm.nih.gov/gene/?term=27309	"HSA6591, NOA36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009128	2730	GCLM	http://www.ncbi.nlm.nih.gov/gene/?term=2730	GLCLR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009129	2730	GCLM	http://www.ncbi.nlm.nih.gov/gene/?term=2730	GLCLR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009130	27315	PGAP2	http://www.ncbi.nlm.nih.gov/gene/?term=27315	"CWH43-N, FRAG1, HPMRS3, MRT17, MRT21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009131	27316	RBMX	http://www.ncbi.nlm.nih.gov/gene/?term=27316	"HNRNPG, HNRPG, MRXS11, RBMXP1, RBMXRT, RNMX, hnRNP-G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009132	27316	RBMX	http://www.ncbi.nlm.nih.gov/gene/?term=27316	"HNRNPG, HNRPG, MRXS11P1, RBMXRT, RNMX, hnRNP-G, RBMX "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009133	2731	GLDC	http://www.ncbi.nlm.nih.gov/gene/?term=2731	"GCE, GCSP, HYGN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009134	27327	TNRC6A	http://www.ncbi.nlm.nih.gov/gene/?term=27327	"CAGH26, GW1, GW182, TNRC6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009135	27332	ZNF638	http://www.ncbi.nlm.nih.gov/gene/?term=27332	"NP220, ZFML, Zfp638 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009136	27333	GOLIM4	http://www.ncbi.nlm.nih.gov/gene/?term=27333	"GIMPC, GOLPH4, GPP130, P138 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009137	27333	GOLIM4	http://www.ncbi.nlm.nih.gov/gene/?term=27333	"GIMPC, GOLPH4, GPP130, P138 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009138	27333	GOLIM4	http://www.ncbi.nlm.nih.gov/gene/?term=27333	"GIMPC, GOLPH4, GPP130, P138 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009139	27335	EIF3K	http://www.ncbi.nlm.nih.gov/gene/?term=27335	"ARG134, EIF3-p28, EIF3S12, HSPC029, M9, MSTP001, PLAC-24, PLAC24, PRO1474, PTD001 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009140	27335	EIF3K	http://www.ncbi.nlm.nih.gov/gene/?term=27335	"ARG134, EIF3-p28, EIF3S12, HSPC029, M9, MSTP001, PLAC-24, PLAC24, PRO1474, PTD001 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009141	27335	EIF3K	http://www.ncbi.nlm.nih.gov/gene/?term=27335	"ARG134, EIF3-p28, EIF3S12, HSPC029, M9, MSTP001, PLAC-24, PLAC24, PRO1474, PTD001 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009142	27336	HTATSF1	http://www.ncbi.nlm.nih.gov/gene/?term=27336	"TAT-SF1, TATSF1, dJ196E23.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009143	27338	UBE2S	http://www.ncbi.nlm.nih.gov/gene/?term=27338	"E2-EPF, E2EPF, EPF5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009144	27338	UBE2S	http://www.ncbi.nlm.nih.gov/gene/?term=27338	"E2-EPF, E2EPF, EPF5 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00009145	27339	PRPF19	http://www.ncbi.nlm.nih.gov/gene/?term=27339	"NMP200, PRP19, PSO4, SNEV, UBOX4, hPSO4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009146	2733	GLE1	http://www.ncbi.nlm.nih.gov/gene/?term=2733	"GLE1L, LCCS, LCCS1, hGLE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009147	2733	GLE1	http://www.ncbi.nlm.nih.gov/gene/?term=2733	"GLE1L, LCCS, LCCS1, hGLE1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009148	27340	UTP20	http://www.ncbi.nlm.nih.gov/gene/?term=27340	"1A6/DRIM, DRIM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009149	27340	UTP20	http://www.ncbi.nlm.nih.gov/gene/?term=27340	"1A6/DRIM, DRIM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009150	27340	UTP20	http://www.ncbi.nlm.nih.gov/gene/?term=27340	"1A6/DRIM, DRIM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009151	27340	UTP20	http://www.ncbi.nlm.nih.gov/gene/?term=27340	"1A6/DRIM, DRIM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009152	27341	RRP7A	http://www.ncbi.nlm.nih.gov/gene/?term=27341	"BK126B4.3, CGI-96 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009153	27342	RABGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=27342	"RABEX5, RAP1, rabex-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009154	27345	KCNMB4	http://www.ncbi.nlm.nih.gov/gene/?term=27345		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009155	27346	TMEM97	http://www.ncbi.nlm.nih.gov/gene/?term=27346	MAC30	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009156	27346	TMEM97	http://www.ncbi.nlm.nih.gov/gene/?term=27346	MAC30	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009157	27346	TMEM97	http://www.ncbi.nlm.nih.gov/gene/?term=27346	MAC30	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009158	27347	STK39	http://www.ncbi.nlm.nih.gov/gene/?term=27347	"DCHT, PASK, SPAK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009159	27347	STK39	http://www.ncbi.nlm.nih.gov/gene/?term=27347	"DCHT, PASK, SPAK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009160	27348	TOR1B	http://www.ncbi.nlm.nih.gov/gene/?term=27348	DQ1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009161	27348	TOR1B	http://www.ncbi.nlm.nih.gov/gene/?term=27348	DQ1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009162	27348	TOR1B	http://www.ncbi.nlm.nih.gov/gene/?term=27348	DQ1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009163	27348	TOR1B	http://www.ncbi.nlm.nih.gov/gene/?term=27348	DQ1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009164	27349	MCAT	http://www.ncbi.nlm.nih.gov/gene/?term=27349	"FASN2C, MCT, MT, NET62, fabD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009165	2734	GLG1	http://www.ncbi.nlm.nih.gov/gene/?term=2734	"CFR-1, ESL-1, MG-160, MG160 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009166	2734	GLG1	http://www.ncbi.nlm.nih.gov/gene/?term=2734	"CFR-1, ESL-1, MG-160, MG160 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009167	27351	DESI1	http://www.ncbi.nlm.nih.gov/gene/?term=27351	"D15Wsu75e, DESI2, DJ347H13.4, DeSI-1, FAM152B, PPPDE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009168	27352	SGSM3	http://www.ncbi.nlm.nih.gov/gene/?term=27352	"MAP, RABGAP5, RUSC3, RUTBC3, RabGAP-5, rabGAPLP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009169	27352	SGSM3	http://www.ncbi.nlm.nih.gov/gene/?term=27352	"MAP, RABGAP5, RUSC3, RUTBC3, RabGAP-5, rabGAPLP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009170	27361	Msrb1	http://www.ncbi.nlm.nih.gov/gene/?term=27361	"D17Wsu82e, SELX, SelR, Sepr, Sepx1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009171	27362	Dnajb9	http://www.ncbi.nlm.nih.gov/gene/?term=27362	"AA408011, AA673251, AA673481, AW556981, ERdj4, Mdg1, mDj7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009172	27366	Txnl4a	http://www.ncbi.nlm.nih.gov/gene/?term=27366	"D18Wsu98e, Dim1, ENSMUSG00000057130, Txnl4, U5-15kD, U5-15kDa "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009173	27367	Rpl3	http://www.ncbi.nlm.nih.gov/gene/?term=27367	"F2, J1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009174	27367	Rpl3	http://www.ncbi.nlm.nih.gov/gene/?term=27367	"F2, J1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00009175	27368	Tbl2	http://www.ncbi.nlm.nih.gov/gene/?term=27368	"C76179, WS-bTRP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009176	2736	GLI2	http://www.ncbi.nlm.nih.gov/gene/?term=2736	"CJS, HPE9, PHS2, THP1, THP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009177	27370	Rps26	http://www.ncbi.nlm.nih.gov/gene/?term=27370		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009178	27376	Slc25a10	http://www.ncbi.nlm.nih.gov/gene/?term=27376	Dic	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009179	27377	Yme1l1	http://www.ncbi.nlm.nih.gov/gene/?term=27377	"FtsH1, Ftsh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009180	2737	GLI3	http://www.ncbi.nlm.nih.gov/gene/?term=2737	"ACLS, GCPS-190, GLI3FL, PAP-A, PAPA, PAPA1, PAPB, PHS, PPDIV, GLI3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009181	27392	Pign	http://www.ncbi.nlm.nih.gov/gene/?term=27392	"Gm20308, PIG-N "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009182	27398	Mrpl2	http://www.ncbi.nlm.nih.gov/gene/?term=27398	"CGI-22, L2mt, MRP-L14, MRP-L2, Rpml14 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009183	2739	GLO1	http://www.ncbi.nlm.nih.gov/gene/?term=2739	"GLOD1, GLYI, HEL-S-74 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009184	2739	GLO1	http://www.ncbi.nlm.nih.gov/gene/?term=2739	"GLOD1, GLYI, HEL-S-74 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009185	2739	GLO1	http://www.ncbi.nlm.nih.gov/gene/?term=2739	"GLOD1, GLYI, HEL-S-74 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009186	273	AMPH	http://www.ncbi.nlm.nih.gov/gene/?term=273	AMPH1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009187	27401	Skp2	http://www.ncbi.nlm.nih.gov/gene/?term=27401	"4930500A04Rik, FBXL1, FWD1, p45 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009188	27418	Mkln1	http://www.ncbi.nlm.nih.gov/gene/?term=27418	"A130067F06Rik, AU015903, BB154892 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009189	27430	MAT2B	http://www.ncbi.nlm.nih.gov/gene/?term=27430	"MAT-II, MATIIbeta, Nbla02999, SDR23E1, TGR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009190	27430	MAT2B	http://www.ncbi.nlm.nih.gov/gene/?term=27430	"MAT-II, MATIIbeta, Nbla02999, SDR23E1, TGR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009191	27433	TOR2A	http://www.ncbi.nlm.nih.gov/gene/?term=27433	TORP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009192	27436	EML4	http://www.ncbi.nlm.nih.gov/gene/?term=27436	"C2orf2, ELP120, EMAP-4, EMAPL4, ROPP120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009193	27436	EML4	http://www.ncbi.nlm.nih.gov/gene/?term=27436	"C2orf2, ELP120, EMAP-4, EMAPL4, ROPP120 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009194	27436	EML4	http://www.ncbi.nlm.nih.gov/gene/?term=27436	"C2orf2, ELP120, EMAP-4, EMAPL4, ROPP120 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009195	27439	CECR6	http://www.ncbi.nlm.nih.gov/gene/?term=27439		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009196	27440	CECR5	http://www.ncbi.nlm.nih.gov/gene/?term=27440		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009197	2744	GLS	http://www.ncbi.nlm.nih.gov/gene/?term=2744	"AAD20, GAC, GAM, GLS1, KGA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009198	2744	GLS	http://www.ncbi.nlm.nih.gov/gene/?term=2744	"AAD20, GAC, GAM1, KGA, GLS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009199	2744	GLS	http://www.ncbi.nlm.nih.gov/gene/?term=2744	"AAD20, GAC, GAM1, KGA, GLS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009200	2745	GLRX	http://www.ncbi.nlm.nih.gov/gene/?term=2745	"GRX, GRX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009201	2745	GLRX	http://www.ncbi.nlm.nih.gov/gene/?term=2745	"GRX, GRX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009202	2745	GLRX	http://www.ncbi.nlm.nih.gov/gene/?term=2745	"GRX, GRX1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009203	2745	GLRX	http://www.ncbi.nlm.nih.gov/gene/?term=2745	"GRX, GRX1 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00009204	2746	GLUD1	http://www.ncbi.nlm.nih.gov/gene/?term=2746	"GDH, GDH1, GLUD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009205	2746	GLUD1	http://www.ncbi.nlm.nih.gov/gene/?term=2746	"GDH, GDH1, GLUD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009206	2747	GLUD2	http://www.ncbi.nlm.nih.gov/gene/?term=2747	"GDH2, GLUDP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009207	27493	A230006K03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=27493	"CAG-3, CAG8, D0Kist2, Gm7414 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009208	274	BIN1	http://www.ncbi.nlm.nih.gov/gene/?term=274	"AMPH2, AMPHL, SH3P9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009209	274	BIN1	http://www.ncbi.nlm.nih.gov/gene/?term=274	"AMPH2, AMPHL, SH3P9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009210	2752	GLUL	http://www.ncbi.nlm.nih.gov/gene/?term=2752	"GLNS, GS, PIG43, PIG59 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009211	275	AMT	http://www.ncbi.nlm.nih.gov/gene/?term=275	"GCE, GCST, GCVT, NKH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009212	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009213	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009214	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009215	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009216	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009217	2762	GMDS	http://www.ncbi.nlm.nih.gov/gene/?term=2762	"GMD, SDR3E1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009218	2762	GMDS	http://www.ncbi.nlm.nih.gov/gene/?term=2762	"GMD, SDR3E1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009219	2762	GMDS	http://www.ncbi.nlm.nih.gov/gene/?term=2762	"GMD, SDR3E1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009220	27632	Nelfe	http://www.ncbi.nlm.nih.gov/gene/?term=27632	"D17H6S45, NELF-E, RD, Rdbp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009221	2764	GMFB	http://www.ncbi.nlm.nih.gov/gene/?term=2764	GMF	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009222	2766	GMPR	http://www.ncbi.nlm.nih.gov/gene/?term=2766	"GMPR 1, GMPR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009223	276770	Eif5a	http://www.ncbi.nlm.nih.gov/gene/?term=276770	"AA410058, D19Wsu54e, Eif4d1, eIF-4D, eIF-5A, eIF-5A-1, eIF-5A1, Eif5a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009224	2767	GNA11	http://www.ncbi.nlm.nih.gov/gene/?term=2767	"FBH, FBH2, FHH2, GNA-11, HHC2, HYPOC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009225	2767	GNA11	http://www.ncbi.nlm.nih.gov/gene/?term=2767	"FBH, FBH2, FHH2, GNA-11, HHC2, HYPOC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009226	2767	GNA11	http://www.ncbi.nlm.nih.gov/gene/?term=2767	"FBH, FBH2, FHH2, GNA-11, HHC2, HYPOC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009227	2768951	CG33217	http://www.ncbi.nlm.nih.gov/gene/?term=2768951	"Dmel_ BcDNA:RE15216, Dmel\CG33217 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00009228	2768961	CG7369	http://www.ncbi.nlm.nih.gov/gene/?term=2768961	Dmel_ Dmel\CG7369	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00009229	2768996	CG33229	http://www.ncbi.nlm.nih.gov/gene/?term=2768996	"Dmel_ CG16971, CG32492, Dmel\CG33229 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00009230	2768	GNA12	http://www.ncbi.nlm.nih.gov/gene/?term=2768	"NNX3, RMP, gep "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009231	276920	Ccdc42	http://www.ncbi.nlm.nih.gov/gene/?term=276920	A530001H01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009232	2770	GNAI1	http://www.ncbi.nlm.nih.gov/gene/?term=2770	Gi	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009233	2771	GNAI2	http://www.ncbi.nlm.nih.gov/gene/?term=2771	"GIPB, H_LUCA15.1, H_LUCA16.1, GNAI2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009234	277250	Kdm3b	http://www.ncbi.nlm.nih.gov/gene/?term=277250	"5830462I21Rik, JHDM2B, Jmjd1b, mKIAA1082 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009235	277328	Trpa1	http://www.ncbi.nlm.nih.gov/gene/?term=277328	"Anktm1, TRPA1b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009236	2773	GNAI3	http://www.ncbi.nlm.nih.gov/gene/?term=2773	"87U6, ARCND1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009237	2773	GNAI3	http://www.ncbi.nlm.nih.gov/gene/?term=2773	"87U6, ARCND1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009238	2773	GNAI3	http://www.ncbi.nlm.nih.gov/gene/?term=2773	"87U6, ARCND1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009239	2773	GNAI3	http://www.ncbi.nlm.nih.gov/gene/?term=2773	"87U6, ARCND1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009240	2773	GNAI3	http://www.ncbi.nlm.nih.gov/gene/?term=2773	"87U6, ARCND1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009241	277432	Vstm2l	http://www.ncbi.nlm.nih.gov/gene/?term=277432	Gm691	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009242	277463	Gpr107	http://www.ncbi.nlm.nih.gov/gene/?term=277463	"9930033D15Rik, AI790205, C530034M11, mKIAA1624 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009243	2774	GNAL	http://www.ncbi.nlm.nih.gov/gene/?term=2774	DYT25	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009244	27756	Lsm2	http://www.ncbi.nlm.nih.gov/gene/?term=27756	"D17H6S56E-2, D17H6S56E2, Dmapl, Dmpkap, G7b, Sm-X5, SmX5, snRNP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009245	2775	GNAO1	http://www.ncbi.nlm.nih.gov/gene/?term=2775	"EIEE17, G-ALPHA-o, GNAO "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009246	27762	Vwa7	http://www.ncbi.nlm.nih.gov/gene/?term=27762	"C6orf27, D17H6S56E-3, G7c, NG37 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009247	2776	GNAQ	http://www.ncbi.nlm.nih.gov/gene/?term=2776	"CMC1, G-ALPHA-q, GAQ, SWS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009248	2778	GNAS	http://www.ncbi.nlm.nih.gov/gene/?term=2778	"AHO, C20orf45, GNAS1, GPSA, GSA, GSP, NESP, POH, SCG6, SgVI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009249	2778	GNAS	http://www.ncbi.nlm.nih.gov/gene/?term=2778	"AHO, C20orf451, GPSA, GSA, GSP, NESP, POH, SCG6, SgVI, GNAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009250	2778	GNAS	http://www.ncbi.nlm.nih.gov/gene/?term=2778	"AHO, C20orf451, GPSA, GSA, GSP, NESP, POH, SCG6, SgVI, GNAS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009251	2778	GNAS	http://www.ncbi.nlm.nih.gov/gene/?term=2778	"AHO, C20orf451, GPSA, GSA, GSP, NESP, POH, SCG6, SgVI, GNAS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009252	2781	GNAZ	http://www.ncbi.nlm.nih.gov/gene/?term=2781		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009253	278240	Spin2c	http://www.ncbi.nlm.nih.gov/gene/?term=278240	"BC068162, SPIN-2C, Spin2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009254	278279	Tmtc2	http://www.ncbi.nlm.nih.gov/gene/?term=278279	"8430438D04Rik, D330034A10Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009255	2782	GNB1	http://www.ncbi.nlm.nih.gov/gene/?term=2782		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009256	2782	GNB1	http://www.ncbi.nlm.nih.gov/gene/?term=2782		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009257	278304	Zfp385c	http://www.ncbi.nlm.nih.gov/gene/?term=278304	"A930006D11Rik, Znf385c "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009258	2783	GNB2	http://www.ncbi.nlm.nih.gov/gene/?term=2783		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009259	2783	GNB2	http://www.ncbi.nlm.nih.gov/gene/?term=2783		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009260	278507	Wfikkn2	http://www.ncbi.nlm.nih.gov/gene/?term=278507	"2610304F08Rik, AY100450, Gasp1, WFIKKNRP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009261	278725	E130310I04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=278725	A930019C19Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009262	2787	GNG5	http://www.ncbi.nlm.nih.gov/gene/?term=2787		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009263	2787	GNG5	http://www.ncbi.nlm.nih.gov/gene/?term=2787		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009264	27886	Dgcr14	http://www.ncbi.nlm.nih.gov/gene/?term=27886	"AI462402, D16H22S1269E, Dgcr1, Dgsi, ES2, Es2el "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009265	2790	GNG10	http://www.ncbi.nlm.nih.gov/gene/?term=2790		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009266	2794	GNL1	http://www.ncbi.nlm.nih.gov/gene/?term=2794	HSR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009267	2794	GNL1	http://www.ncbi.nlm.nih.gov/gene/?term=2794	HSR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009268	279766	Rhbdd3	http://www.ncbi.nlm.nih.gov/gene/?term=279766	Ptag	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009269	27981	Rsrp1	http://www.ncbi.nlm.nih.gov/gene/?term=27981	"2700043I21Rik, D4Ucla2, D4Wsu53e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009270	27984	Efhd2	http://www.ncbi.nlm.nih.gov/gene/?term=27984	"2600015J22Rik, AA408606, D4Wsu27e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009271	27998	Exosc5	http://www.ncbi.nlm.nih.gov/gene/?term=27998	D7Wsu180e	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009272	27999	Fam3c	http://www.ncbi.nlm.nih.gov/gene/?term=27999	"D6Wsu176e, Ilei "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009273	2799	GNS	http://www.ncbi.nlm.nih.gov/gene/?term=2799	G6S	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009274	2799	GNS	http://www.ncbi.nlm.nih.gov/gene/?term=2799	G6S	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009275	2799	GNS	http://www.ncbi.nlm.nih.gov/gene/?term=2799	G6S	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009276	2799	GNS	http://www.ncbi.nlm.nih.gov/gene/?term=2799	G6S	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009277	2799	GNS	http://www.ncbi.nlm.nih.gov/gene/?term=2799	G6S	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009278	27	ABL2	http://www.ncbi.nlm.nih.gov/gene/?term=27	"ABLL, ARG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009279	28000	Prpf19	http://www.ncbi.nlm.nih.gov/gene/?term=28000	"AA617263, AL024362, D19Wsu55e, NMP200, PSO4, Prp19, Snev "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009280	28000	Prpf19	http://www.ncbi.nlm.nih.gov/gene/?term=28000	"AA617263, AL024362, D19Wsu55e, NMP200, PSO4, Prp19, Snev "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009281	2800	GOLGA1	http://www.ncbi.nlm.nih.gov/gene/?term=2800	golgin-97	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009282	28018	Ubfd1	http://www.ncbi.nlm.nih.gov/gene/?term=28018	"AI467302, D7Wsu105e, D7Wsu128e, Ubph "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009283	2802	GOLGA3	http://www.ncbi.nlm.nih.gov/gene/?term=2802	"GCP170, MEA-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009284	2802	GOLGA3	http://www.ncbi.nlm.nih.gov/gene/?term=2802	"GCP170, MEA-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009285	2802	GOLGA3	http://www.ncbi.nlm.nih.gov/gene/?term=2802	"GCP170, MEA-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009286	2802	GOLGA3	http://www.ncbi.nlm.nih.gov/gene/?term=2802	"GCP170, MEA-2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009287	2802	GOLGA3	http://www.ncbi.nlm.nih.gov/gene/?term=2802	"GCP170, MEA-2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009288	28030	Gfm1	http://www.ncbi.nlm.nih.gov/gene/?term=28030	"AW545374, D3Wsu133e, Gfm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009289	28036	Larp7	http://www.ncbi.nlm.nih.gov/gene/?term=28036	"C330027G06Rik, D3Wsu161e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009290	2803	GOLGA4	http://www.ncbi.nlm.nih.gov/gene/?term=2803	"CRPF46, GCP2, GOLG, MU-RMS-40.18, p230 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009291	2803	GOLGA4	http://www.ncbi.nlm.nih.gov/gene/?term=2803	"CRPF46, GCP2, GOLG, MU-RMS-40.18, p230 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009292	2803	GOLGA4	http://www.ncbi.nlm.nih.gov/gene/?term=2803	"CRPF46, GCP2, GOLG, MU-RMS-40.18, p230 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009293	28040	D6Wsu163e	http://www.ncbi.nlm.nih.gov/gene/?term=28040	C12orf4	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009294	28042	Ept1	http://www.ncbi.nlm.nih.gov/gene/?term=28042	"4933402G07Rik, AI448296, AI452230, C79563, D5Wsu178e, SELI, mKIAA1724 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009295	2804	GOLGB1	http://www.ncbi.nlm.nih.gov/gene/?term=2804	"GCP, GCP372, GOLIM1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009296	2804	GOLGB1	http://www.ncbi.nlm.nih.gov/gene/?term=2804	"GCP, GCP372, GOLIM1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009297	2805	GOT1	http://www.ncbi.nlm.nih.gov/gene/?term=2805	"AST1, ASTQTL1, GIG18, cAspAT, cCAT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009298	2805	GOT1	http://www.ncbi.nlm.nih.gov/gene/?term=2805	"AST1, ASTQTL1, GIG18, cAspAT, cCAT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009299	2805	GOT1	http://www.ncbi.nlm.nih.gov/gene/?term=2805	"AST1, ASTQTL1, GIG18, cAspAT, cCAT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009300	280636	C11orf31	http://www.ncbi.nlm.nih.gov/gene/?term=280636	"C17orf10, SELH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009301	2806	GOT2	http://www.ncbi.nlm.nih.gov/gene/?term=2806	"KAT4, KATIV, mitAAT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009302	2806	GOT2	http://www.ncbi.nlm.nih.gov/gene/?term=2806	"KAT4, KATIV, mitAAT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009303	28071	Twistnb	http://www.ncbi.nlm.nih.gov/gene/?term=28071	"2410173G11, 2810024J17Rik, D16Wsu83e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009304	2810	SFN	http://www.ncbi.nlm.nih.gov/gene/?term=2810	YWHAS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009305	28114	Nsun2	http://www.ncbi.nlm.nih.gov/gene/?term=28114	"D13Wsu123e, Misu "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009306	2812	GP1BB	http://www.ncbi.nlm.nih.gov/gene/?term=2812	"BDPLT1, BS, CD42C, GPIBB, GPIbbeta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009307	28135	Cep63	http://www.ncbi.nlm.nih.gov/gene/?term=28135	"4921501M07, AL450317.13gm1, AW107703, CD20R, D9Mgc41, D9Mgc48e, ET2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009308	2813	GP2	http://www.ncbi.nlm.nih.gov/gene/?term=2813	ZAP75	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009309	2815	GP9	http://www.ncbi.nlm.nih.gov/gene/?term=2815	"CD42a, GPIX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009310	2817	GPC1	http://www.ncbi.nlm.nih.gov/gene/?term=2817	glypican	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009311	2817	GPC1	http://www.ncbi.nlm.nih.gov/gene/?term=2817	glypican	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009312	28185	Tomm70a	http://www.ncbi.nlm.nih.gov/gene/?term=28185	"2610044B22Rik, D16Ium22, D16Ium22e, D16Wsu109e, Tom70, mKIAA0719 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009313	2819	GPD1	http://www.ncbi.nlm.nih.gov/gene/?term=2819	"GPD-C, GPDH-C, HTGTI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009314	2820	GPD2	http://www.ncbi.nlm.nih.gov/gene/?term=2820	"GDH2, GPDM, mGPDH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009315	2820	GPD2	http://www.ncbi.nlm.nih.gov/gene/?term=2820	"GDH2, GPDM, mGPDH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009316	2821	GPI	http://www.ncbi.nlm.nih.gov/gene/?term=2821	"AMF, GNPI, NLK, PGI, PHI, SA-36, SA36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009317	2821	GPI	http://www.ncbi.nlm.nih.gov/gene/?term=2821	"AMF, GNPI, NLK, PGI, PHI, SA-36, SA36 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009318	2821	GPI	http://www.ncbi.nlm.nih.gov/gene/?term=2821	"AMF, GNPI, NLK, PGI, PHI, SA-36, SA36 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00009319	28227	PPP2R3B	http://www.ncbi.nlm.nih.gov/gene/?term=28227	"NYREN8, PPP2R3L, PPP2R3LY, PR48 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009320	2822	GPLD1	http://www.ncbi.nlm.nih.gov/gene/?term=2822	"GPIPLD, GPIPLDM, PIGPLD, PIGPLD1, PLD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009321	28231	SLCO4A1	http://www.ncbi.nlm.nih.gov/gene/?term=28231	"OATP-E, OATP1, OATP4A1, OATPE, OATPRP1, POAT, SLC21A12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009322	28231	SLCO4A1	http://www.ncbi.nlm.nih.gov/gene/?term=28231	"OATP-E, OATP1, OATP4A1, OATPE, OATPRP1, POAT, SLC21A12 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009323	28240	Trpm2	http://www.ncbi.nlm.nih.gov/gene/?term=28240	"9830168K16Rik, C79133, LTRPC2, TRPC7, Trp7, Trrp7 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009324	2824	GPM6B	http://www.ncbi.nlm.nih.gov/gene/?term=2824	M6B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009325	2825	GPR1	http://www.ncbi.nlm.nih.gov/gene/?term=2825		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009326	282679	AQP11	http://www.ncbi.nlm.nih.gov/gene/?term=282679	AQPX1	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00009327	282679	AQP11	http://www.ncbi.nlm.nih.gov/gene/?term=282679	AQPX1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009328	282809	POC1B	http://www.ncbi.nlm.nih.gov/gene/?term=282809	"CORD20, PIX1, TUWD12, WDR51B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009329	28295	D10Jhu81e	http://www.ncbi.nlm.nih.gov/gene/?term=28295	"C21orf33, ES1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009330	282969	FUOM	http://www.ncbi.nlm.nih.gov/gene/?term=282969	"C10orf125, FUCU, FucM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009331	282973	JAKMIP3	http://www.ncbi.nlm.nih.gov/gene/?term=282973	"C10orf14, C10orf39, Jamip3, NECC2, bA140A10.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009332	282974	STK32C	http://www.ncbi.nlm.nih.gov/gene/?term=282974	"PKE, YANK3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009333	282991	BLOC1S2	http://www.ncbi.nlm.nih.gov/gene/?term=282991	"BLOS2, BORCS2, CEAP, CEAP11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009334	2829	XCR1	http://www.ncbi.nlm.nih.gov/gene/?term=2829	"CCXCR1, GPR5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009335	283078	MKX	http://www.ncbi.nlm.nih.gov/gene/?term=283078	"C10orf48, IFRX, IRXL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009336	283104	SBF2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=283104		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009337	283106	CSNK2A3	http://www.ncbi.nlm.nih.gov/gene/?term=283106	CSNK2A1P	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009338	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009339	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	1688465	Cytoplasm	Hepatoma cell	Next generation sequencing	Cellular fractionation showed that H19 RNA is cytoplasmic but not associated with the translational machinery.
RLID00009340	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/H19/
RLID00009341	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	23898077	Circulating	Plasma	RT-PCR	"Analysis showed that samples with pre-amplification had a higher level of linearity in the reverse transcription polymerase chain reaction (RT-PCR) assay than those without pre-amplification. Plasma H19 levels were significantly higher in patients than in healthy controls. Plasma H19 levels were significantly reduced in postoperative samples. Conclusion: Circulating lncRNAs can be detectable in plasma, and the detection of circulating lncRNAs may provide new complementary tumor markers for gastric cancer. "
RLID00009342	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	18794369	Nucleus	Breast cancer cell	qRT-PCR	This activity occurs antisense to the H19 gene and has the potential to produce a single 120-kb transcript that we called the 91H RNA. This nuclear and short-lived RNA is not imprinted in mouse but is expressed predominantly from the maternal allele in both mice and humans within the H19 gene region.
RLID00009343	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/H19/
RLID00009344	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009345	283120	H19	http://www.ncbi.nlm.nih.gov/gene/?term=283120	"ASM, ASM1, BWS, D11S813E, LINC00008, NCRNA00008, WT2 "	lncRNA	Homo sapiens	22955988	Cytoplasm	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00009346	283130	SLC25A45	http://www.ncbi.nlm.nih.gov/gene/?term=283130		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009347	283130	SLC25A45	http://www.ncbi.nlm.nih.gov/gene/?term=283130		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009348	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009349	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	17270048	Nucleus	Fibroblast|Lymphoblast	In situ hybridization	"This screen identified no more than three transcripts; XIST, and two unique noncoding nuclear enriched abundant transcripts (NEAT) RNAs strikingly located less than 70 kb apart on human chromosome 11: NEAT1, a noncoding RNA from the locus encoding for TncRNA, and NEAT2 (also known as MALAT-1). "
RLID00009350	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	21128942	Nucleus	Brain tissue	qRT-PCR|Microarray	Table 2: Long noncoding RNAs represented on Affymetrix U133 arrays that were reliably detected in human nucleus accumbens. An lncRNA was considered reliably detected in human NAcc if at least one probe corresponding to the transcript gave a specific signal in all control subjects. No transcripts undetected in the controls were consistently detected in drug abusers. Data are collected from Talbe 2.
RLID00009351	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	23835137	Nucleus	HeLa cell  	Immunoblotting|RT-PCR	"NEAT1_2 lncRNA may act as a scaffold of RNAs and RNA binding proteins in the nuclei of ALS motor neurons, thereby modulating the functions of ALS-associated RNA-binding proteins during the early phase of ALS. These findings provide the first evidence of a direct association between paraspeckle formation and a neurodegenerative disease, and may shed light on the development of novel therapeutic targets for the treatment of ALS. "
RLID00009352	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009353	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	25415230	Nucleus	Prostate cancer cell	qRT-PCR	NEAT1 was originally identified localized to subnuclear organelles called paraspeckles that are free of chromatin and function as repositories of edited RNA and a number of nuclear RNA-binding proteins5.
RLID00009354	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/NEAT1/
RLID00009355	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	19217333	Nucleus	HeLa cell	In situ hybridization|qRT-PCR	"Unlike other nuclear-retained RNAs, NEAT1 RNA is not A-I edited, consistent with a structural role in paraspeckles. "
RLID00009356	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	19716791	Nucleus	HeLa cell	In situ hybridization|qRT-PCR	"Using in situ hybridization we demonstrated that hNEAT1 localizes to paraspeckles in HeLa cells. As shown in Fig. 3C, hNEAT1 RNA is restricted to a small number of large, distinct nuclear speckles in HeLa cell nuclei. "
RLID00009357	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC "	lncRNA	Homo sapiens	24280234	Nucleus	Placenta	qRT-PCR	One candidate gene identified was the long non-coding RNA NEAT1 (nuclear paraspeckle assembly transcript 1). NEAT1 is the core component of a subnuclear structure called paraspeckle.
RLID00009358	283219	KCTD21	http://www.ncbi.nlm.nih.gov/gene/?term=283219	KCASH2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009359	283229	CRACR2B	http://www.ncbi.nlm.nih.gov/gene/?term=283229	EFCAB4A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009360	283229	CRACR2B	http://www.ncbi.nlm.nih.gov/gene/?term=283229	EFCAB4A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009361	283232	TMEM80	http://www.ncbi.nlm.nih.gov/gene/?term=283232		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009362	283234	CCDC88B	http://www.ncbi.nlm.nih.gov/gene/?term=283234	"BRLZ, CCDC88, HKRP3, gipie "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009363	283237	TTC9C	http://www.ncbi.nlm.nih.gov/gene/?term=283237		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009364	283337	ZNF740	http://www.ncbi.nlm.nih.gov/gene/?term=283337	Zfp740	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009365	283373	ANKRD52	http://www.ncbi.nlm.nih.gov/gene/?term=283373	ANKRD33	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009366	283377	SPRYD4	http://www.ncbi.nlm.nih.gov/gene/?term=283377		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009367	283377	SPRYD4	http://www.ncbi.nlm.nih.gov/gene/?term=283377		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009368	283377	SPRYD4	http://www.ncbi.nlm.nih.gov/gene/?term=283377		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009369	283377	SPRYD4	http://www.ncbi.nlm.nih.gov/gene/?term=283377		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009370	283417	DPY19L2	http://www.ncbi.nlm.nih.gov/gene/?term=283417	"SPATA34, SPGF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009371	283431	GAS2L3	http://www.ncbi.nlm.nih.gov/gene/?term=283431	G2L3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009372	283450	HECTD4	http://www.ncbi.nlm.nih.gov/gene/?term=283450	"C12orf51, POTAGE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009373	283459	GATC	http://www.ncbi.nlm.nih.gov/gene/?term=283459	15E1.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009374	283464	GXYLT1	http://www.ncbi.nlm.nih.gov/gene/?term=283464	GLT8D3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009375	283576	ZDHHC22	http://www.ncbi.nlm.nih.gov/gene/?term=283576	C14orf59	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009376	283578	TMED8	http://www.ncbi.nlm.nih.gov/gene/?term=283578	FAM15B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009377	283578	TMED8	http://www.ncbi.nlm.nih.gov/gene/?term=283578	FAM15B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009378	283578	TMED8	http://www.ncbi.nlm.nih.gov/gene/?term=283578	FAM15B	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009379	283579	C14orf178	http://www.ncbi.nlm.nih.gov/gene/?term=283579		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009380	283579	C14orf178	http://www.ncbi.nlm.nih.gov/gene/?term=283579		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009381	283596	SNHG10	http://www.ncbi.nlm.nih.gov/gene/?term=283596	"C14orf62, LINC00063, NCRNA00063 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009382	283596	SNHG10	http://www.ncbi.nlm.nih.gov/gene/?term=283596	"C14orf62, LINC00063, NCRNA00063 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009383	283635	FAM177A1	http://www.ncbi.nlm.nih.gov/gene/?term=283635	C14orf24	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009384	283635	FAM177A1	http://www.ncbi.nlm.nih.gov/gene/?term=283635	C14orf24	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009385	283638	CEP170B	http://www.ncbi.nlm.nih.gov/gene/?term=283638	"CEP170R, FAM68C, KIAA0284 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009386	283643	C14orf80	http://www.ncbi.nlm.nih.gov/gene/?term=283643		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009387	283673	EWSAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283673	"LINC00277, NCRNA00277, TMEM84 "	lncRNA	Homo sapiens	25401475	Nucleus	Ewing sarcoma cell|osteosarcoma cell	RT-PCR	"Notably, EWSAT1 is expressed both in the nucleus and in the cytoplasm, suggesting that it may have complex roles in gene regulation (Supplemental Figure 4, E and F).  "
RLID00009388	283673	EWSAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283673	"LINC00277, NCRNA00277, TMEM84 "	lncRNA	Homo sapiens	25401475	Cytoplasm	Ewing sarcoma cell|osteosarcoma cell	RT-PCR	"Notably, EWSAT1 is expressed both in the nucleus and in the cytoplasm, suggesting that it may have complex roles in gene regulation (Supplemental Figure 4, E and F).  "
RLID00009389	283677	REC114	http://www.ncbi.nlm.nih.gov/gene/?term=283677	"C15orf60, CT147 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009390	283742	FAM98B	http://www.ncbi.nlm.nih.gov/gene/?term=283742		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009391	283748	PLA2G4D	http://www.ncbi.nlm.nih.gov/gene/?term=283748	cPLA2delta	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009392	283748	PLA2G4D	http://www.ncbi.nlm.nih.gov/gene/?term=283748	cPLA2delta	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009393	283807	FBXL22	http://www.ncbi.nlm.nih.gov/gene/?term=283807	Fbl22	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009394	283807	FBXL22	http://www.ncbi.nlm.nih.gov/gene/?term=283807	Fbl22	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009395	283820	NOMO2	http://www.ncbi.nlm.nih.gov/gene/?term=283820	"Nomo, PM5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009396	283871	PGP	http://www.ncbi.nlm.nih.gov/gene/?term=283871	PGPase	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009397	283871	PGP	http://www.ncbi.nlm.nih.gov/gene/?term=283871	PGPase	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009398	283899	INO80E	http://www.ncbi.nlm.nih.gov/gene/?term=283899	CCDC95	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009399	283899	INO80E	http://www.ncbi.nlm.nih.gov/gene/?term=283899	CCDC95	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009400	283951	C16orf91	http://www.ncbi.nlm.nih.gov/gene/?term=283951	"CCSMST1, URLC5, gs103 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009401	283985	FADS6	http://www.ncbi.nlm.nih.gov/gene/?term=283985	FP18279	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009402	283989	TSEN54	http://www.ncbi.nlm.nih.gov/gene/?term=283989	"PCH2A, PCH4, PCH5, SEN54L, sen54 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009403	283989	TSEN54	http://www.ncbi.nlm.nih.gov/gene/?term=283989	"PCH2A, PCH4, PCH5, SEN54L, sen54 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009404	283991	UBALD2	http://www.ncbi.nlm.nih.gov/gene/?term=283991	FAM100B	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009405	283	ANG	http://www.ncbi.nlm.nih.gov/gene/?term=283	"ALS9, HEL168, RAA1, RNASE4, RNASE5 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00009406	284001	CCDC57	http://www.ncbi.nlm.nih.gov/gene/?term=284001		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009407	284001	CCDC57	http://www.ncbi.nlm.nih.gov/gene/?term=284001		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009408	284004	HEXDC	http://www.ncbi.nlm.nih.gov/gene/?term=284004		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009409	284018	C17orf58	http://www.ncbi.nlm.nih.gov/gene/?term=284018		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009410	284018	C17orf58	http://www.ncbi.nlm.nih.gov/gene/?term=284018		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009411	284029	LINC00324	http://www.ncbi.nlm.nih.gov/gene/?term=284029	"C17orf44, NCRNA00324 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009412	284058	KANSL1	http://www.ncbi.nlm.nih.gov/gene/?term=284058	"CENP-36, KDVS, KIAA1267, MSL1v1, NSL1, hMSL1v1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009413	284058	KANSL1	http://www.ncbi.nlm.nih.gov/gene/?term=284058	"CENP-36, KDVS, KIAA1267, MSL1v1, NSL1, hMSL1v1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009414	284058	KANSL1	http://www.ncbi.nlm.nih.gov/gene/?term=284058	"CENP-36, KDVS, KIAA1267, MSL1v1, NSL1, hMSL1v1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009415	284086	NEK8	http://www.ncbi.nlm.nih.gov/gene/?term=284086	"JCK, NEK12A, NPHP9, RHPD2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009416	284086	NEK8	http://www.ncbi.nlm.nih.gov/gene/?term=284086	"JCK, NEK12A, NPHP9, RHPD2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009417	284098	PIGW	http://www.ncbi.nlm.nih.gov/gene/?term=284098	"Gwt1, HPMRS5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009418	284098	PIGW	http://www.ncbi.nlm.nih.gov/gene/?term=284098	"Gwt1, HPMRS5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009419	284098	PIGW	http://www.ncbi.nlm.nih.gov/gene/?term=284098	"Gwt1, HPMRS5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009420	2840	GPR17	http://www.ncbi.nlm.nih.gov/gene/?term=2840		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009421	284106	CISD3	http://www.ncbi.nlm.nih.gov/gene/?term=284106	Miner2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009422	284110	GSDMA	http://www.ncbi.nlm.nih.gov/gene/?term=284110	"FKSG9, GSDM, GSDM1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009423	284110	GSDMA	http://www.ncbi.nlm.nih.gov/gene/?term=284110	"FKSG9, GSDM, GSDM1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009424	284111	SLC13A5	http://www.ncbi.nlm.nih.gov/gene/?term=284111	"EIEE25, NACT, mIndy "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009425	284119	PTRF	http://www.ncbi.nlm.nih.gov/gene/?term=284119	"CAVIN, CAVIN1, CGL4, FKSG13, cavin-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009426	284119	PTRF	http://www.ncbi.nlm.nih.gov/gene/?term=284119	"CAVIN, CAVIN1, CGL4, FKSG13, cavin-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009427	284131	ENDOV	http://www.ncbi.nlm.nih.gov/gene/?term=284131		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009428	284184	C17orf89	http://www.ncbi.nlm.nih.gov/gene/?term=284184		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009429	284184	C17orf89	http://www.ncbi.nlm.nih.gov/gene/?term=284184		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009430	284186	TMEM105	http://www.ncbi.nlm.nih.gov/gene/?term=284186		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009431	284186	TMEM105	http://www.ncbi.nlm.nih.gov/gene/?term=284186		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009432	284207	METRNL	http://www.ncbi.nlm.nih.gov/gene/?term=284207		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009433	284257	BOD1L2	http://www.ncbi.nlm.nih.gov/gene/?term=284257	"BOD1P, FAM44C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009434	284273	ZADH2	http://www.ncbi.nlm.nih.gov/gene/?term=284273		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009435	284293	HMSD	http://www.ncbi.nlm.nih.gov/gene/?term=284293	"ACC-6, ACC6, C18orf53, HSMD-v "	mRNA	Homo sapiens	17409267	Dendrite	B-LCLs	RT-PCR	"Both HMSD-v and HMSD transcripts were selectively expressed at higher levels in mature dendritic cells and primary leukemia cells, especially those of myeloid lineage. "
RLID00009436	2842	GPR19	http://www.ncbi.nlm.nih.gov/gene/?term=2842		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009437	284325	C19orf54	http://www.ncbi.nlm.nih.gov/gene/?term=284325		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009438	284325	C19orf54	http://www.ncbi.nlm.nih.gov/gene/?term=284325		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009439	284325	C19orf54	http://www.ncbi.nlm.nih.gov/gene/?term=284325		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009440	284349	ZNF283	http://www.ncbi.nlm.nih.gov/gene/?term=284349	"HZF19, HZF41 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009441	284349	ZNF283	http://www.ncbi.nlm.nih.gov/gene/?term=284349	"HZF19, HZF41 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009442	284352	PPP1R37	http://www.ncbi.nlm.nih.gov/gene/?term=284352	LRRC68	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009443	284361	EMC10	http://www.ncbi.nlm.nih.gov/gene/?term=284361	"C19orf63, HSM1, HSS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009444	284361	EMC10	http://www.ncbi.nlm.nih.gov/gene/?term=284361	"C19orf63, HSM1, HSS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009445	284403	WDR62	http://www.ncbi.nlm.nih.gov/gene/?term=284403	"C19orf14, MCPH2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009446	284439	SLC25A42	http://www.ncbi.nlm.nih.gov/gene/?term=284439		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009447	284565	NBPF15	http://www.ncbi.nlm.nih.gov/gene/?term=284565	"AB14, AG3, NBPF16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009448	284565	NBPF15	http://www.ncbi.nlm.nih.gov/gene/?term=284565	"AB14, AG3, NBPF16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009449	284611	FAM102B	http://www.ncbi.nlm.nih.gov/gene/?term=284611	SYM-3B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009450	284613	CYB561D1	http://www.ncbi.nlm.nih.gov/gene/?term=284613		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009451	284613	CYB561D1	http://www.ncbi.nlm.nih.gov/gene/?term=284613		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009452	284613	CYB561D1	http://www.ncbi.nlm.nih.gov/gene/?term=284613		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009453	284656	EPHA10	http://www.ncbi.nlm.nih.gov/gene/?term=284656		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009454	284695	ZNF326	http://www.ncbi.nlm.nih.gov/gene/?term=284695	"ZAN75, ZIRD, Zfp326, dJ871E2.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009455	284716	RIMKLA	http://www.ncbi.nlm.nih.gov/gene/?term=284716	"FAM80A, NAAGS, NAAGS-II "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009456	284801	MIR663AHG	http://www.ncbi.nlm.nih.gov/gene/?term=284801		lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009457	284802	FRG1BP	http://www.ncbi.nlm.nih.gov/gene/?term=284802	"C20orf80, FRG1B, bA348I14.2 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009458	284942	RPL23AP82	http://www.ncbi.nlm.nih.gov/gene/?term=284942	RPL23A_43_1761	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009459	284992	CCDC150	http://www.ncbi.nlm.nih.gov/gene/?term=284992		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009460	284996	RNF149	http://www.ncbi.nlm.nih.gov/gene/?term=284996	DNAPTP2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009461	284996	RNF149	http://www.ncbi.nlm.nih.gov/gene/?term=284996	DNAPTP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009462	284	ANGPT1	http://www.ncbi.nlm.nih.gov/gene/?term=284	"AGP1, AGPT, ANG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009463	285074	LOC285074	http://www.ncbi.nlm.nih.gov/gene/?term=285074		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009464	285095	LOC285095	http://www.ncbi.nlm.nih.gov/gene/?term=285095		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009465	28511	NKIRAS2	http://www.ncbi.nlm.nih.gov/gene/?term=28511	"KBRAS2, kappaB-Ras2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009466	28511	NKIRAS2	http://www.ncbi.nlm.nih.gov/gene/?term=28511	"KBRAS2, kappaB-Ras2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009467	28513	CDH19	http://www.ncbi.nlm.nih.gov/gene/?term=28513	"CDH7, CDH7L2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009468	285148	IAH1	http://www.ncbi.nlm.nih.gov/gene/?term=285148		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009469	28514	DLL1	http://www.ncbi.nlm.nih.gov/gene/?term=28514	"DELTA1, DL1, Delta "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009470	285194	TUSC7	http://www.ncbi.nlm.nih.gov/gene/?term=285194	"LINC00902, LSAMP-AS1, LSAMP-AS3, LSAMPAS3, NCRNA00295 "	lncRNA	Homo sapiens	23558749	Cytoplasm	Colon cancer cell	In situ hybridization	"Moreover, we performed in situ hybridization to detect the level of loc285194 in the cells after doxo treatment. We observed a substantial increase of loc285194 in the doxo-treated cells compared with no doxo control (Figure 1D). Of note, we found that a majority signal came from the cytoplasm.  "
RLID00009471	285195	SLC9A9	http://www.ncbi.nlm.nih.gov/gene/?term=285195	"AUTS16, NHE9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009472	285203	EOGT	http://www.ncbi.nlm.nih.gov/gene/?term=285203	"AER61, AOS4, C3orf64, EOGT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009473	285203	EOGT	http://www.ncbi.nlm.nih.gov/gene/?term=285203	"AER61, AOS4, C3orf641, EOGT "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009474	285203	EOGT	http://www.ncbi.nlm.nih.gov/gene/?term=285203	"AER61, AOS4, C3orf641, EOGT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009475	285268	ZNF621	http://www.ncbi.nlm.nih.gov/gene/?term=285268		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009476	285268	ZNF621	http://www.ncbi.nlm.nih.gov/gene/?term=285268		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009477	285282	RABL3	http://www.ncbi.nlm.nih.gov/gene/?term=285282		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009478	2852	GPER1	http://www.ncbi.nlm.nih.gov/gene/?term=2852	"CEPR, CMKRL2, DRY12, FEG-1, GPCR-Br, GPER, GPR30, LERGU, LERGU2, LyGPR, mER "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009479	2852	GPER1	http://www.ncbi.nlm.nih.gov/gene/?term=2852	"CEPR, CMKRL2, DRY12, FEG-1, GPCR-Br, GPER, GPR30, LERGU, LERGU2, LyGPR, mER "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009480	285315	C3orf33	http://www.ncbi.nlm.nih.gov/gene/?term=285315	AC3-33	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009481	285315	C3orf33	http://www.ncbi.nlm.nih.gov/gene/?term=285315	AC3-33	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009482	285343	TCAIM	http://www.ncbi.nlm.nih.gov/gene/?term=285343	"C3orf23, TOAG-1, TOAG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009483	285362	SUMF1	http://www.ncbi.nlm.nih.gov/gene/?term=285362	"AAPA3037, FGE, UNQ3037 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009484	285362	SUMF1	http://www.ncbi.nlm.nih.gov/gene/?term=285362	"AAPA3037, FGE, UNQ3037 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009485	285367	RPUSD3	http://www.ncbi.nlm.nih.gov/gene/?term=285367		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009486	285367	RPUSD3	http://www.ncbi.nlm.nih.gov/gene/?term=285367		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009487	285381	DPH3	http://www.ncbi.nlm.nih.gov/gene/?term=285381	"DELGIP, DELGIP1, DESR1, DPH3A, KTI11, ZCSL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009488	285381	DPH3	http://www.ncbi.nlm.nih.gov/gene/?term=285381	"DELGIP, DELGIP1, DESR1A, KTI11, ZCSL2, DPH3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009489	285381	DPH3	http://www.ncbi.nlm.nih.gov/gene/?term=285381	"DELGIP, DELGIP1, DESR1A, KTI11, ZCSL2, DPH3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009490	285382	C3orf70	http://www.ncbi.nlm.nih.gov/gene/?term=285382		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009491	285382	C3orf70	http://www.ncbi.nlm.nih.gov/gene/?term=285382		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009492	285429	DCAF4L1	http://www.ncbi.nlm.nih.gov/gene/?term=285429	WDR21B	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009493	285429	DCAF4L1	http://www.ncbi.nlm.nih.gov/gene/?term=285429	WDR21B	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009494	285440	CYP4V2	http://www.ncbi.nlm.nih.gov/gene/?term=285440	"BCD, CYP4AH1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009495	285440	CYP4V2	http://www.ncbi.nlm.nih.gov/gene/?term=285440	"BCD, CYP4AH1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009496	285513	GPRIN3	http://www.ncbi.nlm.nih.gov/gene/?term=285513	GRIN3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009497	285521	COX18	http://www.ncbi.nlm.nih.gov/gene/?term=285521	COX18HS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009498	285521	COX18	http://www.ncbi.nlm.nih.gov/gene/?term=285521	COX18HS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009499	285521	COX18	http://www.ncbi.nlm.nih.gov/gene/?term=285521	COX18HS	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009500	285521	COX18	http://www.ncbi.nlm.nih.gov/gene/?term=285521	COX18HS	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009501	285527	FRYL	http://www.ncbi.nlm.nih.gov/gene/?term=285527	"AF4p12, KIAA0826, MOR2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009502	285533	RNF175	http://www.ncbi.nlm.nih.gov/gene/?term=285533		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009503	285550	FAM200B	http://www.ncbi.nlm.nih.gov/gene/?term=285550		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009504	285550	FAM200B	http://www.ncbi.nlm.nih.gov/gene/?term=285550		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009505	285605	DTWD2	http://www.ncbi.nlm.nih.gov/gene/?term=285605		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009506	285605	DTWD2	http://www.ncbi.nlm.nih.gov/gene/?term=285605		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009507	285605	DTWD2	http://www.ncbi.nlm.nih.gov/gene/?term=285605		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009508	285668	C5orf64	http://www.ncbi.nlm.nih.gov/gene/?term=285668		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009509	285668	C5orf64	http://www.ncbi.nlm.nih.gov/gene/?term=285668		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009510	285672	SREK1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=285672	"P18SRP, SFRS12IP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009511	285755	PPIL6	http://www.ncbi.nlm.nih.gov/gene/?term=285755	"PPIase, RSPH12, bA425D10.6, dJ919F19.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009512	285755	PPIL6	http://www.ncbi.nlm.nih.gov/gene/?term=285755	"PPIase, RSPH12, bA425D10.6, dJ919F19.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009513	285761	DCBLD1	http://www.ncbi.nlm.nih.gov/gene/?term=285761	dJ94G16.1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009514	285761	DCBLD1	http://www.ncbi.nlm.nih.gov/gene/?term=285761	dJ94G16.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009515	285780	LY86-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=285780	"LY86-AS, LY86AS "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009516	285812	LOC285812	http://www.ncbi.nlm.nih.gov/gene/?term=285812		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009517	285835	LOC285835	http://www.ncbi.nlm.nih.gov/gene/?term=285835		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009518	285849	COX6A1P2	http://www.ncbi.nlm.nih.gov/gene/?term=285849		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009519	285855	RPL7L1	http://www.ncbi.nlm.nih.gov/gene/?term=285855	dJ475N16.4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009520	285958	SNHG15	http://www.ncbi.nlm.nih.gov/gene/?term=285958	"C7orf40, Linc-Myo1g, MYO1GUT "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009521	285958	SNHG15	http://www.ncbi.nlm.nih.gov/gene/?term=285958	"C7orf40, Linc-Myo1g, MYO1GUT "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009522	285961	SEPT7P9	http://www.ncbi.nlm.nih.gov/gene/?term=285961	"CDC10L, SEPT7L, bA291L22.2 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009523	285971	ZNF775	http://www.ncbi.nlm.nih.gov/gene/?term=285971		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009524	285973	ATG9B	http://www.ncbi.nlm.nih.gov/gene/?term=285973	"APG9L2, NOS3AS, SONE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009525	2859	GPR35	http://www.ncbi.nlm.nih.gov/gene/?term=2859		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009526	285	ANGPT2	http://www.ncbi.nlm.nih.gov/gene/?term=285	"AGPT2, ANG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009527	286053	NSMCE2	http://www.ncbi.nlm.nih.gov/gene/?term=286053	"C8orf36, MMS21, NSE2, ZMIZ7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009528	286075	ZNF707	http://www.ncbi.nlm.nih.gov/gene/?term=286075		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009529	286075	ZNF707	http://www.ncbi.nlm.nih.gov/gene/?term=286075		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009530	286077	FAM83H	http://www.ncbi.nlm.nih.gov/gene/?term=286077	AI3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009531	286077	FAM83H	http://www.ncbi.nlm.nih.gov/gene/?term=286077	AI3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009532	286101	ZNF252P	http://www.ncbi.nlm.nih.gov/gene/?term=286101	ZNF252	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009533	286109	CASC7	http://www.ncbi.nlm.nih.gov/gene/?term=286109	LINC00980	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009534	286144	TRIQK	http://www.ncbi.nlm.nih.gov/gene/?term=286144	"C8orf83, PRO0845, UPF0599 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009535	286148	DPY19L4	http://www.ncbi.nlm.nih.gov/gene/?term=286148		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009536	286207	CFAP157	http://www.ncbi.nlm.nih.gov/gene/?term=286207	C9orf117	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009537	286223	C9orf47	http://www.ncbi.nlm.nih.gov/gene/?term=286223	"C9orf108, bA791O21.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009538	286257	C9orf142	http://www.ncbi.nlm.nih.gov/gene/?term=286257	PAXX	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009539	286262	TPRN	http://www.ncbi.nlm.nih.gov/gene/?term=286262	"C9orf75, DFNB79 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009540	286262	TPRN	http://www.ncbi.nlm.nih.gov/gene/?term=286262	"C9orf75, DFNB79 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009541	286451	YIPF6	http://www.ncbi.nlm.nih.gov/gene/?term=286451	FinGER6	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009542	286451	YIPF6	http://www.ncbi.nlm.nih.gov/gene/?term=286451	FinGER6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009543	286827	TRIM59	http://www.ncbi.nlm.nih.gov/gene/?term=286827	"IFT80L, MRF1, RNF104, TRIM57, TSBF1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009544	286827	TRIM59	http://www.ncbi.nlm.nih.gov/gene/?term=286827	"IFT80L, MRF1, RNF104, TRIM57, TSBF1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009545	286827	TRIM59	http://www.ncbi.nlm.nih.gov/gene/?term=286827	"IFT80L, MRF1, RNF104, TRIM57, TSBF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009546	286827	TRIM59	http://www.ncbi.nlm.nih.gov/gene/?term=286827	"IFT80L, MRF1, RNF104, TRIM57, TSBF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009547	2868	GRK4	http://www.ncbi.nlm.nih.gov/gene/?term=2868	"GPRK2L, GPRK4, GRK4a, IT11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009548	286923	Dlgap3	http://www.ncbi.nlm.nih.gov/gene/?term=286923	"DAP-3, Dap3, SAPAP3 "	mRNA	Rattus norvegicus	15207911	Dendrite	Hippocampus	In situ hybridization	"Dendritic localization of SAPAP3 transcripts in the hippocampus is observed throughout postnatal development (Fig. 6A, P3-adult).  In horizontal sections of P21 rat brain, both SAPAP3(+) and SAPAP3(-) transcripts are localized into dendrites (Fig. 6B).  Two mRNAs encoding distinct SAPAP3 isoforms exhibit basically identical postnatal expression patterns and are both localized into dendrites of hippocampal neurons. "
RLID00009549	2869	GRK5	http://www.ncbi.nlm.nih.gov/gene/?term=2869	GPRK5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009550	286	ANK1	http://www.ncbi.nlm.nih.gov/gene/?term=286	"ANK, SPH1, SPH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009551	287004	LOC287004	http://www.ncbi.nlm.nih.gov/gene/?term=287004	"GB.7, Pinc "	lncRNA	Rattus norvegicus	16574773	Cytoplasm	Mammary gland	In situ hybridization|RT-PCR	Here we report that PINC expression is temporally and spatially regulated in response to developmental stimuli in vivo and that PINC RNA is localized to distinct foci in either the nucleus or the cytoplasm in a cell-cycle-specific manner. 
RLID00009552	287004	LOC287004	http://www.ncbi.nlm.nih.gov/gene/?term=287004	"GB.7, Pinc "	lncRNA	Rattus norvegicus	16574773	Nucleus	Mammary gland	In situ hybridization|RT-PCR	Here we report that PINC expression is temporally and spatially regulated in response to developmental stimuli in vivo and that PINC RNA is localized to distinct foci in either the nucleus or the cytoplasm in a cell-cycle-specific manner. 
RLID00009553	2870	GRK6	http://www.ncbi.nlm.nih.gov/gene/?term=2870	GPRK6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009554	2870	GRK6	http://www.ncbi.nlm.nih.gov/gene/?term=2870	GPRK6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009555	2872	MKNK2	http://www.ncbi.nlm.nih.gov/gene/?term=2872	"GPRK7, MNK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009556	2872	MKNK2	http://www.ncbi.nlm.nih.gov/gene/?term=2872	"GPRK7, MNK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009557	28738	TRAJ17	http://www.ncbi.nlm.nih.gov/gene/?term=28738		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009558	2873	GPS1	http://www.ncbi.nlm.nih.gov/gene/?term=2873	"COPS1, CSN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009559	2873	GPS1	http://www.ncbi.nlm.nih.gov/gene/?term=2873	"COPS1, CSN1, SGN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009560	2873	GPS1	http://www.ncbi.nlm.nih.gov/gene/?term=2873	"COPS1, CSN1, SGN1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009561	2875	GPT	http://www.ncbi.nlm.nih.gov/gene/?term=2875	"AAT1, ALT1, GPT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009562	2876	GPX1	http://www.ncbi.nlm.nih.gov/gene/?term=2876	"GPXD, GSHPX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009563	2876	GPX1	http://www.ncbi.nlm.nih.gov/gene/?term=2876	"GPXD, GSHPX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009564	2876	GPX1	http://www.ncbi.nlm.nih.gov/gene/?term=2876	"GPXD, GSHPX1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009565	2877	GPX2	http://www.ncbi.nlm.nih.gov/gene/?term=2877	"GI-GPx, GPRP, GPRP-2, GPx-2, GPx-GI, GSHPX-GI, GSHPx-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009566	2877	GPX2	http://www.ncbi.nlm.nih.gov/gene/?term=2877	"GI-GPx, GPRP, GPRP-2, GPx-2, GPx-GI, GSHPX-GI, GSHPx-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009567	2878	GPX3	http://www.ncbi.nlm.nih.gov/gene/?term=2878	"GPx-P, GSHPx-3, GSHPx-P "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009568	2879	GPX4	http://www.ncbi.nlm.nih.gov/gene/?term=2879	"GPx-4, GSHPx-4, MCSP, PHGPx, SMDS, snGPx, snPHGPx "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009569	2879	GPX4	http://www.ncbi.nlm.nih.gov/gene/?term=2879	"GPx-4, GSHPx-4, MCSP, PHGPx, SMDS, snGPx, snPHGPx "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009570	2879	GPX4	http://www.ncbi.nlm.nih.gov/gene/?term=2879	"GPx-4, GSHPx-4, MCSP, PHGPx, SMDS, snGPx, snPHGPx "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009571	287	ANK2	http://www.ncbi.nlm.nih.gov/gene/?term=287	"ANK-2, LQT4, brank-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009572	288064	Kpna1	http://www.ncbi.nlm.nih.gov/gene/?term=288064		mRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"By quantitative fluorescent in situ hybridization combined with immunofluorescence to unambiguously distinguish intra-axonal mRNAs, we show that regenerating spinal cord axons contain β-actin, GAP-43, Neuritin, Reg3a, Hamp, and Importin β1 mRNAs.  "
RLID00009573	288064	Kpna1	http://www.ncbi.nlm.nih.gov/gene/?term=288064		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009574	2885	GRB2	http://www.ncbi.nlm.nih.gov/gene/?term=2885	"ASH, EGFRBP-GRB2, Grb3-3, MST084, MSTP084, NCKAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009575	2885	GRB2	http://www.ncbi.nlm.nih.gov/gene/?term=2885	"ASH, EGFRBP-GRB2, Grb3-3, MST084, MSTP084, NCKAP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009576	2886	GRB7	http://www.ncbi.nlm.nih.gov/gene/?term=2886		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009577	2887	GRB10	http://www.ncbi.nlm.nih.gov/gene/?term=2887	"GRB-IR, Grb-10, IRBP, MEG1, RSS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009578	2887	GRB10	http://www.ncbi.nlm.nih.gov/gene/?term=2887	"GRB-IR, Grb-10, IRBP, MEG1, RSS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009579	2887	GRB10	http://www.ncbi.nlm.nih.gov/gene/?term=2887	"GRB-IR, Grb-10, IRBP, MEG1, RSS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009580	288	ANK3	http://www.ncbi.nlm.nih.gov/gene/?term=288	"ANKYRIN-G, MRT37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009581	28951	TRIB2	http://www.ncbi.nlm.nih.gov/gene/?term=28951	"C5FW, GS3955, TRB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009582	28951	TRIB2	http://www.ncbi.nlm.nih.gov/gene/?term=28951	"C5FW, GS3955, TRB2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009583	28952	CCDC22	http://www.ncbi.nlm.nih.gov/gene/?term=28952	"CXorf37, JM1, RTSC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009584	28955	DEXI	http://www.ncbi.nlm.nih.gov/gene/?term=28955	MYLE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009585	28955	DEXI	http://www.ncbi.nlm.nih.gov/gene/?term=28955	MYLE	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009586	28956	LAMTOR2	http://www.ncbi.nlm.nih.gov/gene/?term=28956	"ENDAP, HSPC003, MAPBPIP, MAPKSP1AP, ROBLD3, Ragulator2, p14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009587	28957	MRPS28	http://www.ncbi.nlm.nih.gov/gene/?term=28957	"HSPC007, MRP-S28, MRP-S35, MRPS35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009588	28957	MRPS28	http://www.ncbi.nlm.nih.gov/gene/?term=28957	"HSPC007, MRP-S28, MRP-S35, MRPS35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009589	28958	COA3	http://www.ncbi.nlm.nih.gov/gene/?term=28958	"CCDC56, HSPC009, MITRAC12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009590	28960	DCPS	http://www.ncbi.nlm.nih.gov/gene/?term=28960	"ARS, DCS1, HINT-5, HINT5, HSL1, HSPC015 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009591	28962	OSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=28962	"GIPN, GL, HSPC019, OPTB5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009592	28962	OSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=28962	"GIPN, GL, HSPC019, OPTB5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009593	28965	SLC27A6	http://www.ncbi.nlm.nih.gov/gene/?term=28965	"ACSVL2, FACVL2, FATP6, VLCS-H1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009594	28966	SNX24	http://www.ncbi.nlm.nih.gov/gene/?term=28966	"PRO1284, SBBI31 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009595	28969	BZW2	http://www.ncbi.nlm.nih.gov/gene/?term=28969	"HSPC028, MST017, MSTP017 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009596	2896	GRN	http://www.ncbi.nlm.nih.gov/gene/?term=2896	"CLN11, GEP, GP88, PCDGF, PEPI, PGRN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009597	2896	GRN	http://www.ncbi.nlm.nih.gov/gene/?term=2896	"CLN11, GEP, GP88, PCDGF, PEPI, PGRN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009598	2896	GRN	http://www.ncbi.nlm.nih.gov/gene/?term=2896	"CLN11, GEP, GP88, PCDGF, PEPI, PGRN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009599	28970	C11orf54	http://www.ncbi.nlm.nih.gov/gene/?term=28970	"PTD012, PTOD012 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009600	28971	AAMDC	http://www.ncbi.nlm.nih.gov/gene/?term=28971	"C11orf67, CK067, PTD015 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009601	28972	SPCS1	http://www.ncbi.nlm.nih.gov/gene/?term=28972	"HSPC033, SPC1, SPC12, YJR010C-A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009602	28973	MRPS18B	http://www.ncbi.nlm.nih.gov/gene/?term=28973	"C6orf14, HSPC183, HumanS18a, MRP-S18-2, MRPS18-2, PTD017, S18amt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009603	28973	MRPS18B	http://www.ncbi.nlm.nih.gov/gene/?term=28973	"C6orf14, HSPC183, HumanS18a, MRP-S18-2, MRPS18-2, PTD017, S18amt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009604	28974	C19orf53	http://www.ncbi.nlm.nih.gov/gene/?term=28974	"HSPC023, LYDG10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009605	28974	C19orf53	http://www.ncbi.nlm.nih.gov/gene/?term=28974	"HSPC023, LYDG10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009606	28976	ACAD9	http://www.ncbi.nlm.nih.gov/gene/?term=28976	NPD002	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009607	28976	ACAD9	http://www.ncbi.nlm.nih.gov/gene/?term=28976	NPD002	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009608	28977	MRPL42	http://www.ncbi.nlm.nih.gov/gene/?term=28977	"HSPC204, L31MT, L42MT, MRP-L31, MRP-L42, MRP-S32, MRPL31, MRPS32, PTD007, RPML31, S32MT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009609	28978	TMEM14A	http://www.ncbi.nlm.nih.gov/gene/?term=28978	"C6orf73, PTD011 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009610	28981	IFT81	http://www.ncbi.nlm.nih.gov/gene/?term=28981	"CDV-1, CDV-1R, CDV1, CDV1R, DV1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009611	28982	FLVCR1	http://www.ncbi.nlm.nih.gov/gene/?term=28982	"AXPC1, FLVCR, MFSD7B, PCA, PCARP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009612	28985	MCTS1	http://www.ncbi.nlm.nih.gov/gene/?term=28985	"MCT-1, MCT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009613	28985	MCTS1	http://www.ncbi.nlm.nih.gov/gene/?term=28985	"MCT-1, MCT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009614	28985	MCTS1	http://www.ncbi.nlm.nih.gov/gene/?term=28985	"MCT-1, MCT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009615	28987	NOB1	http://www.ncbi.nlm.nih.gov/gene/?term=28987	"ART-4, MST158, MSTP158P, PSMD8BP1, NOB1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009616	28988	DBNL	http://www.ncbi.nlm.nih.gov/gene/?term=28988	"ABP1, HIP-55, HIP55, SH3P7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009617	28989	NTMT1	http://www.ncbi.nlm.nih.gov/gene/?term=28989	"AD-003, C9orf32, HOMT1A, METTL11A, NRMT, NTM1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009618	28991	COMMD5	http://www.ncbi.nlm.nih.gov/gene/?term=28991	"HCARG, HT002 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009619	28991	COMMD5	http://www.ncbi.nlm.nih.gov/gene/?term=28991	"HCARG, HT002 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009620	28992	MACROD1	http://www.ncbi.nlm.nih.gov/gene/?term=28992	LRP16	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009621	28992	MACROD1	http://www.ncbi.nlm.nih.gov/gene/?term=28992	LRP16	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009622	28996	HIPK2	http://www.ncbi.nlm.nih.gov/gene/?term=28996	PRO0593	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009623	28996	HIPK2	http://www.ncbi.nlm.nih.gov/gene/?term=28996	PRO0593	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009624	28996	HIPK2	http://www.ncbi.nlm.nih.gov/gene/?term=28996	PRO0593	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009625	28998	MRPL13	http://www.ncbi.nlm.nih.gov/gene/?term=28998	"L13, L13A, L13mt, RPL13, RPML13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009626	2899	GRIK3	http://www.ncbi.nlm.nih.gov/gene/?term=2899	"EAA5, GLR7, GLUR7, GluK3, GluR7a "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009627	29015	SLC43A3	http://www.ncbi.nlm.nih.gov/gene/?term=29015	"EEG1, FOAP-13, PRO1659, SEEEG-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009628	29028	ATAD2	http://www.ncbi.nlm.nih.gov/gene/?term=29028	"ANCCA, CT137, PRO2000 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009629	29028	ATAD2	http://www.ncbi.nlm.nih.gov/gene/?term=29028	"ANCCA, CT137, PRO2000 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009630	29035	C16orf72	http://www.ncbi.nlm.nih.gov/gene/?term=29035	PRO0149	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009631	29035	C16orf72	http://www.ncbi.nlm.nih.gov/gene/?term=29035	PRO0149	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009632	2903	GRIN2A	http://www.ncbi.nlm.nih.gov/gene/?term=2903	"EPND, FESD, GluN2A, LKS, NMDAR2A, NR2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009633	29058	TMEM230	http://www.ncbi.nlm.nih.gov/gene/?term=29058	"C20orf30, HSPC274, dJ1116H23.2.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009634	29058	TMEM230	http://www.ncbi.nlm.nih.gov/gene/?term=29058	"C20orf30, HSPC274, dJ1116H23.2.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009635	2905	GRIN2C	http://www.ncbi.nlm.nih.gov/gene/?term=2905	"GluN2C, NMDAR2C, NR2C "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009636	29066	ZC3H7A	http://www.ncbi.nlm.nih.gov/gene/?term=29066	"HSPC055, ZC3H7, ZC3HDC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009637	29068	ZBTB44	http://www.ncbi.nlm.nih.gov/gene/?term=29068	"BTBD15, HSPC063, ZNF851 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009638	29070	CCDC113	http://www.ncbi.nlm.nih.gov/gene/?term=29070	HSPC065	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009639	29070	CCDC113	http://www.ncbi.nlm.nih.gov/gene/?term=29070	HSPC065	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009640	29072	SETD2	http://www.ncbi.nlm.nih.gov/gene/?term=29072	"HBP231, HIF-1, HIP-1, HSPC069, HYPB, KMT3A, SET2, p231HBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009641	29072	SETD2	http://www.ncbi.nlm.nih.gov/gene/?term=29072	"HBP231, HIF-1, HIP-1, HSPC069, HYPB, KMT3A, LLS, SET2, p231HBP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009642	29072	SETD2	http://www.ncbi.nlm.nih.gov/gene/?term=29072	"HBP231, HIF-1, HIP-1, HSPC069, HYPB, KMT3A, LLS, SET2, p231HBP "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00009643	29074	MRPL18	http://www.ncbi.nlm.nih.gov/gene/?term=29074	"HSPC071, L18mt, MRP-L18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009644	29074	MRPL18	http://www.ncbi.nlm.nih.gov/gene/?term=29074	"HSPC071, L18mt, MRP-L18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009645	29078	NDUFAF4	http://www.ncbi.nlm.nih.gov/gene/?term=29078	"C6orf66, HRPAP20, HSPC125, My013, bA22L21.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009646	29078	NDUFAF4	http://www.ncbi.nlm.nih.gov/gene/?term=29078	"C6orf66, HRPAP20, HSPC125, My013, bA22L21.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009647	29079	MED4	http://www.ncbi.nlm.nih.gov/gene/?term=29079	"ARC36, DRIP36, HSPC126, TRAP36, VDRIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009648	29079	MED4	http://www.ncbi.nlm.nih.gov/gene/?term=29079	"ARC36, DRIP36, HSPC126, TRAP36, VDRIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009649	29079	MED4	http://www.ncbi.nlm.nih.gov/gene/?term=29079	"ARC36, DRIP36, HSPC126, TRAP36, VDRIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009650	2907	GRINA	http://www.ncbi.nlm.nih.gov/gene/?term=2907	"HNRGW, LFG1, NMDARA1, TMBIM3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009651	2907	GRINA	http://www.ncbi.nlm.nih.gov/gene/?term=2907	"HNRGW, LFG1, NMDARA1, TMBIM3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009652	29080	CCDC59	http://www.ncbi.nlm.nih.gov/gene/?term=29080	"BR22, HSPC128, TAP26 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009653	29080	CCDC59	http://www.ncbi.nlm.nih.gov/gene/?term=29080	"BR22, HSPC128, TAP26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009654	29081	METTL5	http://www.ncbi.nlm.nih.gov/gene/?term=29081	HSPC133	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009655	29083	GTPBP8	http://www.ncbi.nlm.nih.gov/gene/?term=29083	HSPC135	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009656	29085	PHPT1	http://www.ncbi.nlm.nih.gov/gene/?term=29085	"CGI-202, HEL-S-132P, HSPC141, PHP14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009657	29086	BABAM1	http://www.ncbi.nlm.nih.gov/gene/?term=29086	"C19orf62, HSPC142, MERIT40, NBA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009658	29087	THYN1	http://www.ncbi.nlm.nih.gov/gene/?term=29087	"HSPC144, MDS012, MY105, THY28, THY28KD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009659	29087	THYN1	http://www.ncbi.nlm.nih.gov/gene/?term=29087	"HSPC144, MDS012, MY105, THY28, THY28KD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009660	29088	MRPL15	http://www.ncbi.nlm.nih.gov/gene/?term=29088	"HSPC145, L15mt, MRP-L15, MRP-L7, RPML7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009661	29088	MRPL15	http://www.ncbi.nlm.nih.gov/gene/?term=29088	"HSPC145, L15mt, MRP-L15, MRP-L7, RPML7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009662	29089	UBE2T	http://www.ncbi.nlm.nih.gov/gene/?term=29089	"FANCT, HSPC150, PIG50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009663	29089	UBE2T	http://www.ncbi.nlm.nih.gov/gene/?term=29089	"FANCT, HSPC150, PIG50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009664	29089	UBE2T	http://www.ncbi.nlm.nih.gov/gene/?term=29089	"FANCT, HSPC150, PIG50 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009665	2908	NR3C1	http://www.ncbi.nlm.nih.gov/gene/?term=2908	"GCCR, GCR, GCRST, GR, GRL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009666	29090	TIMM21	http://www.ncbi.nlm.nih.gov/gene/?term=29090	"C18orf55, HSPC154, TIM21 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009667	29090	TIMM21	http://www.ncbi.nlm.nih.gov/gene/?term=29090	"C18orf55, HSPC154, TIM21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009668	29090	TIMM21	http://www.ncbi.nlm.nih.gov/gene/?term=29090	"C18orf55, HSPC154, TIM21 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009669	29090	TIMM21	http://www.ncbi.nlm.nih.gov/gene/?term=29090	"C18orf55, HSPC154, TIM21 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009670	29092	LINC00339	http://www.ncbi.nlm.nih.gov/gene/?term=29092	"HSPC157, NCRNA00339 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009671	29092	LINC00339	http://www.ncbi.nlm.nih.gov/gene/?term=29092	"HSPC157, NCRNA00339 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009672	29093	MRPL22	http://www.ncbi.nlm.nih.gov/gene/?term=29093	"HSPC158, L22mt, MRP-L22, MRP-L25, RPML25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009673	29094	LGALSL	http://www.ncbi.nlm.nih.gov/gene/?term=29094	"GRP, HSPC159 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009674	29095	ORMDL2	http://www.ncbi.nlm.nih.gov/gene/?term=29095	"HSPC160, MST095, MSTP095, adoplin-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009675	29097	CNIH4	http://www.ncbi.nlm.nih.gov/gene/?term=29097	"CNIH-4, HSPC163 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009676	29097	CNIH4	http://www.ncbi.nlm.nih.gov/gene/?term=29097	"CNIH-4, HSPC163 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009677	29098	RANGRF	http://www.ncbi.nlm.nih.gov/gene/?term=29098	"HSPC165, HSPC236, MOG1, RANGNRF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009678	29099	COMMD9	http://www.ncbi.nlm.nih.gov/gene/?term=29099	HSPC166	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009679	29099	COMMD9	http://www.ncbi.nlm.nih.gov/gene/?term=29099	HSPC166	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009680	29099	COMMD9	http://www.ncbi.nlm.nih.gov/gene/?term=29099	HSPC166	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009681	2909	ARHGAP35	http://www.ncbi.nlm.nih.gov/gene/?term=2909	"GRF-1, GRLF1, P190-A, P190A, p190ARhoGAP, p190RhoGAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009682	29100	TMEM208	http://www.ncbi.nlm.nih.gov/gene/?term=29100	HSPC171	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009683	29101	SSU72	http://www.ncbi.nlm.nih.gov/gene/?term=29101	"HSPC182, PNAS-120 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009684	29102	DROSHA	http://www.ncbi.nlm.nih.gov/gene/?term=29102	"ETOHI2, HSA242976, RANSE3L, RN3, RNASE3L, RNASEN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009685	29103	DNAJC15	http://www.ncbi.nlm.nih.gov/gene/?term=29103	"DNAJD1, HSD18, MCJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009686	29105	CFAP20	http://www.ncbi.nlm.nih.gov/gene/?term=29105	"C16orf80, EVORF, GTL3, fSAP23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009687	29105	CFAP20	http://www.ncbi.nlm.nih.gov/gene/?term=29105	"C16orf80, EVORF, GTL3, fSAP23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009688	29107	NXT1	http://www.ncbi.nlm.nih.gov/gene/?term=29107	"MTR2, P15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009689	29108	PYCARD	http://www.ncbi.nlm.nih.gov/gene/?term=29108	"ASC, CARD5, TMS, TMS-1, TMS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009690	29109	FHOD1	http://www.ncbi.nlm.nih.gov/gene/?term=29109	FHOS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009691	29114	TAGLN3	http://www.ncbi.nlm.nih.gov/gene/?term=29114	"NP22, NP24, NP25 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009692	29115	SAP30BP	http://www.ncbi.nlm.nih.gov/gene/?term=29115	"HCNGP, HTRG, HTRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009693	29115	SAP30BP	http://www.ncbi.nlm.nih.gov/gene/?term=29115	"HCNGP, HTRG, HTRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009694	29116	MYLIP	http://www.ncbi.nlm.nih.gov/gene/?term=29116	"IDOL, MIR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009695	29116	MYLIP	http://www.ncbi.nlm.nih.gov/gene/?term=29116	"IDOL, MIR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009696	29117	BRD7	http://www.ncbi.nlm.nih.gov/gene/?term=29117	"BP75, CELTIX1, NAG4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009697	29117	BRD7	http://www.ncbi.nlm.nih.gov/gene/?term=29117	"BP75, CELTIX1, NAG4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009698	29123	ANKRD11	http://www.ncbi.nlm.nih.gov/gene/?term=29123	"ANCO-1, ANCO1, LZ16, T13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009699	29123	ANKRD11	http://www.ncbi.nlm.nih.gov/gene/?term=29123	"ANCO-1, ANCO1, LZ16, T13 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009700	29127	RACGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=29127	"CYK4, HsCYK-4, ID-GAP, MgcRacGAP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009701	2912	GRM2	http://www.ncbi.nlm.nih.gov/gene/?term=2912	"GLUR2, GPRC1B, MGLUR2, mGlu2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009702	291339	Commd3	http://www.ncbi.nlm.nih.gov/gene/?term=291339		mRNA	Rattus norvegicus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00009703	2913	GRM3	http://www.ncbi.nlm.nih.gov/gene/?term=2913	"GLUR3, GPRC1C, MGLUR3, mGlu3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009704	29141	Gal	http://www.ncbi.nlm.nih.gov/gene/?term=29141	Galn	mRNA	Rattus norvegicus	9579792	Dendrite	Neuron	In situ hybridization	Preprogalanin messenger RNA was also clustered in dendrites containing rough endoplasmic reticulum.
RLID00009705	29141	Gal	http://www.ncbi.nlm.nih.gov/gene/?term=29141	Galn	mRNA	Rattus norvegicus	9579792	Axon	Neuron	In situ hybridization	"In the present study, using non-radioactive in situ hybridization and immunohistochemistry at the light and electron microscope levels, preprogalanin messenger RNA and galanin-like immunoreactivity were localized in the hypothalamo-posthypophyseal system. After salt loading, preprogalanin transcripts were found throughout the perikaryal cytoplasm, especially in the peripheral cytoplasm and in the perinuclear area. Preprogalanin messenger RNA was also clustered in dendrites containing rough endoplasmic reticulum. Thus, preprogalanin messenger RNA was segregated in the axons. "
RLID00009706	29141	Gal	http://www.ncbi.nlm.nih.gov/gene/?term=29141	Galn	mRNA	Rattus norvegicus	9579792	Cytoplasm	Neuron	In situ hybridization	"In the present study, using non-radioactive in situ hybridization and immunohistochemistry at the light and electron microscope levels, preprogalanin messenger RNA and galanin-like immunoreactivity were localized in the hypothalamo-posthypophyseal system. After salt loading, preprogalanin transcripts were found throughout the perikaryal cytoplasm, especially in the peripheral cytoplasm and in the perinuclear area. Preprogalanin messenger RNA was also clustered in dendrites containing rough endoplasmic reticulum. Thus, preprogalanin messenger RNA was segregated in the axons. "
RLID00009707	29141	Gal	http://www.ncbi.nlm.nih.gov/gene/?term=29141	Galn	mRNA	Rattus norvegicus	12814355	Cytoplasm	Neuron	In situ hybridization	"Furthermore, galanin and vasopressin messenger RNAs were detected at different domains of the endoplasmic reticulum, suggesting that translation might also occur at different locations, thus leading to partial segregation of galanin and vasopressin cargoes between two populations of secretory granules. In contrast, galanin mRNA was detected in a perinuclear area and in patches scattered in peripheral cytoplasm. In processes, vasopressin mRNA signal was clearly detected(Fig.1B) but labelling remained weak for galanin mRNA. "
RLID00009708	29141	Gal	http://www.ncbi.nlm.nih.gov/gene/?term=29141	Galn	mRNA	Rattus norvegicus	12814355	Endoplasmic reticulum	Neuron	In situ hybridization	"Furthermore, galanin and vasopressin messenger RNAs were detected at different domains of the endoplasmic reticulum, suggesting that translation might also occur at different locations, thus leading to partial segregation of galanin and vasopressin cargoes between two populations of secretory granules. In contrast, galanin mRNA was detected in a perinuclear area and in patches scattered in peripheral cytoplasm. In processes, vasopressin mRNA signal was clearly detected(Fig.1B) but labelling remained weak for galanin mRNA. "
RLID00009709	2915	GRM5	http://www.ncbi.nlm.nih.gov/gene/?term=2915	"GPRC1E, MGLUR5, PPP1R86, mGlu5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009710	291671	Hspa9	http://www.ncbi.nlm.nih.gov/gene/?term=291671	"Crp40, GRP-75a, PBP74, Hspa9 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009711	291671	Hspa9	http://www.ncbi.nlm.nih.gov/gene/?term=291671	"Crp40, GRP-75a, PBP74, Hspa9 "	mRNA	Rattus norvegicus	15673657	Cell body	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00009712	2916	GRM6	http://www.ncbi.nlm.nih.gov/gene/?term=2916	"CSNB1B, GPRC1F, MGLUR6, mGlu6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009713	2916	GRM6	http://www.ncbi.nlm.nih.gov/gene/?term=2916	"CSNB1B, GPRC1F, MGLUR6, mGlu6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009714	2919	CXCL1	http://www.ncbi.nlm.nih.gov/gene/?term=2919	"FSP, GRO1, GROa, MGSA, MGSA-a, NAP-3, SCYB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009715	291	SLC25A4	http://www.ncbi.nlm.nih.gov/gene/?term=291	"AAC1, ANT, ANT 1, ANT1, MTDPS12, PEO2, PEO3, PEOA2, T1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009716	291	SLC25A4	http://www.ncbi.nlm.nih.gov/gene/?term=291	"AAC1, ANT, ANT 1, ANT1, MTDPS12, PEO2, PEO3, PEOA2, T1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009717	291	SLC25A4	http://www.ncbi.nlm.nih.gov/gene/?term=291	"AAC1, ANT, ANT 1, ANT1, MTDPS12, PEO2, PEO3, PEOA2, T1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009718	2920	CXCL2	http://www.ncbi.nlm.nih.gov/gene/?term=2920	"CINC-2a, GRO2, GROb, MGSA-b, MIP-2a, MIP2, MIP2A, SCYB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009719	29219	Snca	http://www.ncbi.nlm.nih.gov/gene/?term=29219		mRNA	Rattus norvegicus	25896939	Synapse	Nerve cell	qRT-PCR|Immunocytochemistry	"Physiologically, a-syn is located at the presynapse and might be involved in regulating of neurotransmission.  "
RLID00009720	2923	PDIA3	http://www.ncbi.nlm.nih.gov/gene/?term=2923	"ER60, ERp57, ERp60, ERp61, GRP57, GRP58, HEL-S-269, HEL-S-93n, HsT17083, P58, PI-PLC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009721	2923	PDIA3	http://www.ncbi.nlm.nih.gov/gene/?term=2923	"ER60, ERp57, ERp60, ERp61, GRP57, GRP58, HEL-S-269, HEL-S-93n, HsT17083, P58, PI-PLC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009722	2926	GRSF1	http://www.ncbi.nlm.nih.gov/gene/?term=2926		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009723	2926	GRSF1	http://www.ncbi.nlm.nih.gov/gene/?term=2926		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009724	2926	GRSF1	http://www.ncbi.nlm.nih.gov/gene/?term=2926		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009725	29271	Cfl1	http://www.ncbi.nlm.nih.gov/gene/?term=29271		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009726	29271	Cfl1	http://www.ncbi.nlm.nih.gov/gene/?term=29271		mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00009727	29286	Rps17	http://www.ncbi.nlm.nih.gov/gene/?term=29286		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009728	29292	Ftl1	http://www.ncbi.nlm.nih.gov/gene/?term=29292	Ftl	mRNA	Rattus norvegicus	9888989	Cell body	Hippocampus	In situ hybridization	"Using nonisotopic in situ hybridization, ferritin mRNA is found restricted to the cell body of cultured rat hippocampal neurons.  "
RLID00009729	29294	Bc1	http://www.ncbi.nlm.nih.gov/gene/?term=29294		lncRNA	Rattus norvegicus	7692010	Axon	Neuron	In situ hybridization	"In this report, we identify BC1 RNA, a small RNA polymerase III transcript that is specifically expressed in neurons, in hypothalamo-neurohypophyseal axons. Here we present evidence that BC1 RNA is transported along the hypothalamo-neurohypopjyscal tract to axonal nervel endings in the posterior pituitary. While these data indicate that hypothalamo-neurohypophyscal axons contain BC1 RNA, they do not rule out possibility that other, non- neuronal elements in the neurohypophysis may also contrabute to the labeling signal. "
RLID00009730	29294	Bc1	http://www.ncbi.nlm.nih.gov/gene/?term=29294		lncRNA	Rattus norvegicus	21807882	Dendrite	Sympathetic neuron	In situ hybridization	"We first performed in situ hybridization experiments to confirm that endogenous BC1 RNA is located to somato-dendritic domains of sympathetic neurons in culture (Fig. 4, A and B), which is analogous to the previously reported localization in hippocampal neurons in culture (Muslimov et al., 1998).  "
RLID00009731	29294	Bc1	http://www.ncbi.nlm.nih.gov/gene/?term=29294		lncRNA	Rattus norvegicus	1706516	Dendrite	Spinal cord neuron	In situ hybridization	"In adult rats as well as in immature rats in late developmental stages, BC1 RNA has been located in the dendrites and somata of a subset of neurons in the central and peripheral nervous system. "
RLID00009732	29294	Bc1	http://www.ncbi.nlm.nih.gov/gene/?term=29294		lncRNA	Rattus norvegicus	9169532	Dendrite	Neuron	Microinjection	"After cytoplasmic microinjection, full-length BC1 RNA was selectively transported to dendrites; in contrast, control RNAs such as nuclear RNAs and random-sequence irrelevant RNAs remained restricted to cytoplasmic areas proximal to the injection sites.  We report here that BC1 RNA is selectively transported to dendrites, and that it is competent to direct dendritic targeting of normally nondendritic mRNAs. In summary, the data show that BC1 RNA is transported selectively and specifically to dendrites of sympathetic neurons in culture.  "
RLID00009733	292	SLC25A5	http://www.ncbi.nlm.nih.gov/gene/?term=292	"2F1, AAC2, ANT2, T2, T3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009734	292	SLC25A5	http://www.ncbi.nlm.nih.gov/gene/?term=292	"2F1, AAC2, ANT2, T2, T3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009735	292	SLC25A5	http://www.ncbi.nlm.nih.gov/gene/?term=292	"2F1, AAC2, ANT2, T2, T3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009736	2931	GSK3A	http://www.ncbi.nlm.nih.gov/gene/?term=2931		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009737	2932	GSK3B	http://www.ncbi.nlm.nih.gov/gene/?term=2932		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009738	2932	GSK3B	http://www.ncbi.nlm.nih.gov/gene/?term=2932		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009739	29335	Oprk1	http://www.ncbi.nlm.nih.gov/gene/?term=29335		mRNA	Rattus norvegicus	17167054	Axon	Dorsal root ganglia	In situ hybridization	In situ hybridization detected axonal distribution of kor mRNA in primary neurons of dorsal root ganglia (DRG).
RLID00009740	2934	GSN	http://www.ncbi.nlm.nih.gov/gene/?term=2934	"ADF, AGEL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009741	2934	GSN	http://www.ncbi.nlm.nih.gov/gene/?term=2934	"ADF, AGEL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009742	2934	GSN	http://www.ncbi.nlm.nih.gov/gene/?term=2934	"ADF, AGEL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009743	2935	GSPT1	http://www.ncbi.nlm.nih.gov/gene/?term=2935	"551G9.2, ETF3A, GST1, eRF3a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009744	2935	GSPT1	http://www.ncbi.nlm.nih.gov/gene/?term=2935	"551G9.2, ETF3A, GST1, eRF3a "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009745	2936	GSR	http://www.ncbi.nlm.nih.gov/gene/?term=2936	"HEL-75, HEL-S-122m "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009746	2936	GSR	http://www.ncbi.nlm.nih.gov/gene/?term=2936	"HEL-75, HEL-S-122m "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009747	2936	GSR	http://www.ncbi.nlm.nih.gov/gene/?term=2936	"HEL-75, HEL-S-122m "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009748	2937	GSS	http://www.ncbi.nlm.nih.gov/gene/?term=2937	"GSHS, HEL-S-64p, HEL-S-88n "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009749	2937	GSS	http://www.ncbi.nlm.nih.gov/gene/?term=2937	"GSHS, HEL-S-64p, HEL-S-88n "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009750	2938	GSTA1	http://www.ncbi.nlm.nih.gov/gene/?term=2938	"GST2, GTH1, GSTA1-1, GST-epsilon "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00009751	2938	GSTA1	http://www.ncbi.nlm.nih.gov/gene/?term=2938	"GST-epsilon, GST2-1, GTH1, GSTA1 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00009752	293	SLC25A6	http://www.ncbi.nlm.nih.gov/gene/?term=293	"AAC3, ANT, ANT 2, ANT 3, ANT3, ANT3Y "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009753	293	SLC25A6	http://www.ncbi.nlm.nih.gov/gene/?term=293	"AAC3, ANT, ANT 2, ANT 3, ANT3, ANT3Y "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009754	293	SLC25A6	http://www.ncbi.nlm.nih.gov/gene/?term=293	"AAC3, ANT, ANT 2, ANT 3, ANT3, ANT3Y "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009755	293	SLC25A6	http://www.ncbi.nlm.nih.gov/gene/?term=293	"AAC3, ANT, ANT 2, ANT 3, ANT3, ANT3Y "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009756	294239	Ddah2	http://www.ncbi.nlm.nih.gov/gene/?term=294239		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009757	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	2148487	Cell body	Neuron	In situ hybridization	"In contrast, mRNAs encoding GAP-43 and alpha-tubulin were restricted to the cell body and largely excluded from dendrites as well as axons. "
RLID00009758	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	7773006	Dendrite	Neuron	In situ hybridization	"Table 1. As of 1994, mRNAs that have been localized within dendrites by in situ hybridization.  Data are collected from Table 1. "
RLID00009759	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	7877439	Dendrite	Neuron	In situ hybridization	"Similarly, although stain corresponding to GAP-43 mRNA was found primarily within the soma of pyramidal neurons of hippocampus, it was also evident within the proximal regions of some apical dendrites (arrowheads in Fig. 1D).  "
RLID00009760	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	9322162	Dendrite	Cerebral cortex	In situ hybridization	"The mRNAs for b-tubulin, neurofilament 68, and F1/GAP43 were restricted to the region of the cell body and very proximal dendrites in most neurons.  In the cerebral cortex, labeling for F1/GAP43 mRNA extended into the dendrites of large pyramidal neurons, but the distribution was limited to proximal dendritic segments and appeared comparable to the distribution of labeling for NF-68 and b-tubulin mRNAs. "
RLID00009761	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	9322162	Cell body	Cerebral cortex	In situ hybridization	"The mRNAs for b-tubulin, neurofilament 68, and F1/GAP43 were restricted to the region of the cell body and very proximal dendrites in most neurons.  In the cerebral cortex, labeling for F1/GAP43 mRNA extended into the dendrites of large pyramidal neurons, but the distribution was limited to proximal dendritic segments and appeared comparable to the distribution of labeling for NF-68 and b-tubulin mRNAs. "
RLID00009762	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	23586486	Axon	Sciatic nerve	Fluorescence in situ hybridization	"The cell bodies of these cultured DRG neurons showed a more robust signal for GAP-43 mRNA (Fig. 1A), suggesting that only a fraction of the GAP-43 mRNA localizes into the axonal compartment as previously shown for β-actin mRNA. "
RLID00009763	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"By quantitative fluorescent in situ hybridization combined with immunofluorescence to unambiguously distinguish intra-axonal mRNAs, we show that regenerating spinal cord axons contain β-actin, GAP-43, Neuritin, Reg3a, Hamp, and Importin β1 mRNAs.  "
RLID00009764	29423	Gap43	http://www.ncbi.nlm.nih.gov/gene/?term=29423	Basp2	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009765	29445	Cox4i1	http://www.ncbi.nlm.nih.gov/gene/?term=29445	"Cox4, Cox4a "	mRNA	Rattus norvegicus	20144716	Axon	Neuron	qRT-PCR	"In this report, we studied cytochrome c oxidase subunit IV (COXIV) mRNA trafficking into distal axons of primary superior cervical ganglia (SCG) neurons. "
RLID00009766	2946	GSTM2	http://www.ncbi.nlm.nih.gov/gene/?term=2946	"GST4, GSTM, GSTM2-2, GTHMUS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009767	29477	Mapt	http://www.ncbi.nlm.nih.gov/gene/?term=29477	"Mtapt, RNPTAU, Tau, pTau "	mRNA	Rattus norvegicus	7639096	Axon	Neuron	Transfection assay	"Our results support a novel model in which cis-acting signals, together with RNA-binding proteins are involved in the targeting of tau mRNA, that may ultimately lead to its axonal localization. "
RLID00009768	2947	GSTM3	http://www.ncbi.nlm.nih.gov/gene/?term=2947	"GST5, GSTB, GSTM3-3, GTM3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009769	2947	GSTM3	http://www.ncbi.nlm.nih.gov/gene/?term=2947	"GST5, GSTB-3, GTM3, GSTM3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009770	2948	GSTM4	http://www.ncbi.nlm.nih.gov/gene/?term=2948	"GSTM4-4, GTM4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009771	2949	GSTM5	http://www.ncbi.nlm.nih.gov/gene/?term=2949	"GSTM5-5, GTM5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009772	2950	GSTP1	http://www.ncbi.nlm.nih.gov/gene/?term=2950	"DFN7, FAEES3, GST3, GSTP, HEL-S-22, PI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009773	2950	GSTP1	http://www.ncbi.nlm.nih.gov/gene/?term=2950	"DFN7, FAEES3, GST3, GSTP, HEL-S-22, PI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009774	2950	GSTP1	http://www.ncbi.nlm.nih.gov/gene/?term=2950	"DFN7, FAEES3, GST3, GSTP, HEL-S-22, PI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009775	2952	GSTT1	http://www.ncbi.nlm.nih.gov/gene/?term=2952		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009776	29542	Pebp1	http://www.ncbi.nlm.nih.gov/gene/?term=29542	"HCNP, Pbp, Rkip "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009777	29545	Uchl1	http://www.ncbi.nlm.nih.gov/gene/?term=29545		mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00009778	29545	Uchl1	http://www.ncbi.nlm.nih.gov/gene/?term=29545		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009779	2954	GSTZ1	http://www.ncbi.nlm.nih.gov/gene/?term=2954	"GSTZ1-1, MAAI, MAI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009780	2954	GSTZ1	http://www.ncbi.nlm.nih.gov/gene/?term=2954	"GSTZ1-1, MAAI, MAI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009781	29565	Eef2	http://www.ncbi.nlm.nih.gov/gene/?term=29565	Ef-2	mRNA	Rattus norvegicus	19073915	Dendrite	Hippocampus	In situ hybridization	"We found that RARa protein co-immunoprecipitated with GluR1 mRNA as well as mRNAs encoding GluR2 and eukaryotic elongation factor 2 (eEF2), all of which have been shown to be dendritically localized by in situ hybridization "
RLID00009782	2956	MSH6	http://www.ncbi.nlm.nih.gov/gene/?term=2956	"GTBP, GTMBP, HNPCC5, HSAP, p160 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009783	2957	GTF2A1	http://www.ncbi.nlm.nih.gov/gene/?term=2957	"TF2A1, TFIIA, TFIIA-42, TFIIAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009784	2958	GTF2A2	http://www.ncbi.nlm.nih.gov/gene/?term=2958	"HsT18745, TF2A2, TFIIA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009785	2958	GTF2A2	http://www.ncbi.nlm.nih.gov/gene/?term=2958	"HsT18745, T18745, TF2A2, TFIIA, TFIIA-12, TFIIA-gamma, TFIIAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009786	29597	P2ry2	http://www.ncbi.nlm.nih.gov/gene/?term=29597	P2Y2	mRNA	Rattus norvegicus	12566628	Cytoplasm	Thymus|T cell|Endothelial cell	In situ hybridization	"In the T cells, transcripts for the P2Y(2 )receptor were localised in the cytoplasm as well as on the smooth endoplasmic reticulum and cell membrane. Dividing T cells also expressed P2Y(2 )receptor mRNA, mostly in the cytoplasm around chromosomal material. Endothelial cells displaying labels for P2Y(2 )receptor transcripts were of cortical arteries/arterioles and capillaries and of postcapillary venules in the corticomedullary junction. P2Y(2) mRNA transcripts were localised in the cytoplasm of endothelial cells, although they did not appear to be specifically associated with subcellular organelles or structures.  "
RLID00009787	29597	P2ry2	http://www.ncbi.nlm.nih.gov/gene/?term=29597	P2Y2	mRNA	Rattus norvegicus	12566628	Endoplasmic reticulum	Thymus|T cell|Endothelial cell	In situ hybridization	"In the T cells, transcripts for the P2Y(2 )receptor were localised in the cytoplasm as well as on the smooth endoplasmic reticulum and cell membrane. Dividing T cells also expressed P2Y(2 )receptor mRNA, mostly in the cytoplasm around chromosomal material. Endothelial cells displaying labels for P2Y(2 )receptor transcripts were of cortical arteries/arterioles and capillaries and of postcapillary venules in the corticomedullary junction. P2Y(2) mRNA transcripts were localised in the cytoplasm of endothelial cells, although they did not appear to be specifically associated with subcellular organelles or structures.  "
RLID00009788	29597	P2ry2	http://www.ncbi.nlm.nih.gov/gene/?term=29597	P2Y2	mRNA	Rattus norvegicus	16780199	Cytoplasm	Cerebellum	In situ hybridization	This chapter describes a pre-embedding in situ hybridization method utilizing an immunogold-silver intensification step to identify P2Y2 receptor mRNA transcripts in the adult rat cerebellum. Transcripts were essentially localized in the cytoplasm although they also appeared to be specifically associated with granular endoplasmic reticulum.
RLID00009789	29597	P2ry2	http://www.ncbi.nlm.nih.gov/gene/?term=29597	P2Y2	mRNA	Rattus norvegicus	16780199	Endoplasmic reticulum	Cerebellum	In situ hybridization	This chapter describes a pre-embedding in situ hybridization method utilizing an immunogold-silver intensification step to identify P2Y2 receptor mRNA transcripts in the adult rat cerebellum. Transcripts were essentially localized in the cytoplasm although they also appeared to be specifically associated with granular endoplasmic reticulum.
RLID00009790	2959	GTF2B	http://www.ncbi.nlm.nih.gov/gene/?term=2959	"TF2B, TFIIB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009791	2959	GTF2B	http://www.ncbi.nlm.nih.gov/gene/?term=2959	"TF2B, TFIIB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009792	2960	GTF2E1	http://www.ncbi.nlm.nih.gov/gene/?term=2960	"FE, TF2E1, TFIIE-A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009793	2960	GTF2E1	http://www.ncbi.nlm.nih.gov/gene/?term=2960	"FE, TF2E1, TFIIE-A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009794	2960	GTF2E1	http://www.ncbi.nlm.nih.gov/gene/?term=2960	"FE, TF2E1, TFIIE-A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009795	2961	GTF2E2	http://www.ncbi.nlm.nih.gov/gene/?term=2961	"FE, TF2E2, TFIIE-B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009796	2961	GTF2E2	http://www.ncbi.nlm.nih.gov/gene/?term=2961	"FE, TF2E2, TFIIE-B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009797	29627	Gria2	http://www.ncbi.nlm.nih.gov/gene/?term=29627	"GluA2, GluR-K2, GluR2, gluR-B "	mRNA	Rattus norvegicus	19073915	Dendrite	Hippocampus	In situ hybridization	"We found that RARa protein co-immunoprecipitated with GluR1 mRNA as well as mRNAs encoding GluR2 and eukaryotic elongation factor 2 (eEF2), all of which have been shown to be dendritically localized by in situ hybridization "
RLID00009798	29627	Gria2	http://www.ncbi.nlm.nih.gov/gene/?term=29627	"GluA2, GluR-K2, GluR2, gluR-B "	mRNA	Rattus norvegicus	23166306	Dendrite	Cortical cultures	In situ hybridization	The hybridization signals of GluA1 and GluA2 mRNAs were present in both the cell soma and dendrites of cultured cortical cells immunolabeled with a specific marker for Microtubule-Associated Protein-2 a (MAP2a).
RLID00009799	29627	Gria2	http://www.ncbi.nlm.nih.gov/gene/?term=29627	"GluA2, GluR-K2, GluR2, gluR-B "	mRNA	Rattus norvegicus	23296627	Dendrite	Pyramidal cell	Fluorescence in situ hybridization	"GluA1-4 subunit mRNAs were highly localized to the apical dendrites of pyramidal cells, whereas in interneurons they were present in multiple dendrites. In contrast, in the dentate gyrus, GluA1-4 subunit mRNAs were virtually restricted to the somata and were absent from the dendrites of granule cells. "
RLID00009800	29627	Gria2	http://www.ncbi.nlm.nih.gov/gene/?term=29627	"GluA2, GluR-K2, GluR2, gluR-B "	mRNA	Rattus norvegicus	23166306	Cell body	Cortical cultures	In situ hybridization	"In vivo, GluA1 and GluA2 mRNAs showed a strong signal in the cell bodies across hippocampal and cortical regions, together with the presence of a clear signal in the proximal dendrites. "
RLID00009801	29628	Gria3	http://www.ncbi.nlm.nih.gov/gene/?term=29628	"GLUR3, GluA3, GluR-3, GluR-C, GluR-K3 "	mRNA	Rattus norvegicus	23296627	Dendrite	Pyramidal cell	Fluorescence in situ hybridization	"GluA1-4 subunit mRNAs were highly localized to the apical dendrites of pyramidal cells, whereas in interneurons they were present in multiple dendrites. In contrast, in the dentate gyrus, GluA1-4 subunit mRNAs were virtually restricted to the somata and were absent from the dendrites of granule cells. "
RLID00009802	29629	Gria4	http://www.ncbi.nlm.nih.gov/gene/?term=29629	"GluA4, GluR-D, GluR4 "	mRNA	Rattus norvegicus	23296627	Dendrite	Pyramidal cell	Fluorescence in situ hybridization	"GluA1-4 subunit mRNAs were highly localized to the apical dendrites of pyramidal cells, whereas in interneurons they were present in multiple dendrites. In contrast, in the dentate gyrus, GluA1-4 subunit mRNAs were virtually restricted to the somata and were absent from the dendrites of granule cells. "
RLID00009803	2962	GTF2F1	http://www.ncbi.nlm.nih.gov/gene/?term=2962	"BTF4, RAP74, TF2F1, TFIIF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009804	2962	GTF2F1	http://www.ncbi.nlm.nih.gov/gene/?term=2962	"BTF4, RAP74, TF2F1, TFIIF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009805	2963	GTF2F2	http://www.ncbi.nlm.nih.gov/gene/?term=2963	"BTF4, RAP30, TF2F2, TFIIF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009806	2963	GTF2F2	http://www.ncbi.nlm.nih.gov/gene/?term=2963	"BTF4, RAP30, TF2F2, TFIIF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009807	2965	GTF2H1	http://www.ncbi.nlm.nih.gov/gene/?term=2965	"BTF2, P62, TFB1, TFIIH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009808	2966	GTF2H2	http://www.ncbi.nlm.nih.gov/gene/?term=2966	"BTF2, BTF2P44, T-BTF2P44, TFIIH, p44 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009809	2967	GTF2H3	http://www.ncbi.nlm.nih.gov/gene/?term=2967	"BTF2, P34, TFB4, TFIIH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009810	2967	GTF2H3	http://www.ncbi.nlm.nih.gov/gene/?term=2967	"BTF2, P34, TFB4, TFIIH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009811	2969	GTF2I	http://www.ncbi.nlm.nih.gov/gene/?term=2969	"BAP135, BTKAP1, DIWS, GTFII-I, IB291, SPIN, TFII-I, WBS, WBSCR6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009812	2969	GTF2I	http://www.ncbi.nlm.nih.gov/gene/?term=2969	"BAP135, BTKAP1, DIWS, GTFII-I, IB291, SPIN, TFII-I, WBS, WBSCR6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009813	29705	Gabra1	http://www.ncbi.nlm.nih.gov/gene/?term=29705		mRNA	Rattus norvegicus	9030628	Dendrite	Neuron	In situ hybridization	"With light nonradioactive in situ hybridization (ISH), we observe that GlyR alpha subunit mRNAs are present in both somata and dendrites of most neurons of the ventral horn of rat spinal cord, whereas the beta subunit and gephyrin mRNAs are predominantly in somata. Using a specific monoclonal antibody against α and β subunits of GlyR (mAb 4a) (Pfeiffer et al., 1984), we demonstrated that GlyR α1  "
RLID00009814	2970	GTF2IP1	http://www.ncbi.nlm.nih.gov/gene/?term=2970	WBSCR7	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00009815	2970	GTF2IP1	http://www.ncbi.nlm.nih.gov/gene/?term=2970	WBSCR7	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00009816	2971	GTF3A	http://www.ncbi.nlm.nih.gov/gene/?term=2971	"AP2, TFIIIA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009817	2971	GTF3A	http://www.ncbi.nlm.nih.gov/gene/?term=2971	"AP2, TFIIIA "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009818	2971	GTF3A	http://www.ncbi.nlm.nih.gov/gene/?term=2971	"AP2, TFIIIA "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00009819	2971	GTF3A	http://www.ncbi.nlm.nih.gov/gene/?term=2971	"AP2, TFIIIA "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. "
RLID00009820	2972	BRF1	http://www.ncbi.nlm.nih.gov/gene/?term=2972	"BRF, BRF-1, CFDS, GTF3B, HEL-S-76p, TAF3B2, TAF3C, TAFIII90, TF3B90, TFIIIB90, hBRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009821	2972	BRF1	http://www.ncbi.nlm.nih.gov/gene/?term=2972	"BRF, BRF-1, CFDS, GTF3B, HEL-S-76p, TAF3B2, TAF3C, TAFIII90, TF3B90, TFIIIB90, hBRF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009822	2975	GTF3C1	http://www.ncbi.nlm.nih.gov/gene/?term=2975	"TFIIIC, TFIIIC220, TFIIICalpha "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009823	29761	USP25	http://www.ncbi.nlm.nih.gov/gene/?term=29761	USP21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009824	29761	USP25	http://www.ncbi.nlm.nih.gov/gene/?term=29761	USP21	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009825	29763	PACSIN3	http://www.ncbi.nlm.nih.gov/gene/?term=29763	SDPIII	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009826	29766	TMOD3	http://www.ncbi.nlm.nih.gov/gene/?term=29766	UTMOD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009827	29766	TMOD3	http://www.ncbi.nlm.nih.gov/gene/?term=29766	UTMOD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009828	29766	TMOD3	http://www.ncbi.nlm.nih.gov/gene/?term=29766	UTMOD	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009829	29767	TMOD2	http://www.ncbi.nlm.nih.gov/gene/?term=29767	"N-TMOD, NTMOD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009830	29767	TMOD2	http://www.ncbi.nlm.nih.gov/gene/?term=29767	"N-TMOD, NTMOD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009831	2976	GTF3C2	http://www.ncbi.nlm.nih.gov/gene/?term=2976	"TFIIIC-BETA, TFIIIC110 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009832	29775	CARD10	http://www.ncbi.nlm.nih.gov/gene/?term=29775	"BIMP1, CARMA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009833	29777	ABT1	http://www.ncbi.nlm.nih.gov/gene/?term=29777	hABT1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009834	29780	PARVB	http://www.ncbi.nlm.nih.gov/gene/?term=29780	CGI-56	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009835	29781	NCAPH2	http://www.ncbi.nlm.nih.gov/gene/?term=29781	CAPH2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009836	29781	NCAPH2	http://www.ncbi.nlm.nih.gov/gene/?term=29781	CAPH2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009837	29785	CYP2S1	http://www.ncbi.nlm.nih.gov/gene/?term=29785	CYPIIS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009838	29789	OLA1	http://www.ncbi.nlm.nih.gov/gene/?term=29789	"DOC45, GBP45, GTBP9, GTPBP9, PTD004 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009839	29789	OLA1	http://www.ncbi.nlm.nih.gov/gene/?term=29789	"DOC45, GBP45, GTBP9, GTPBP9, PTD004 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009840	29789	OLA1	http://www.ncbi.nlm.nih.gov/gene/?term=29789	"DOC45, GBP45, GTBP9, GTPBP9, PTD004 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009841	2978	GUCA1A	http://www.ncbi.nlm.nih.gov/gene/?term=2978	"C6orf131, COD3, CORD14, GCAP, GCAP1, GUCA, GUCA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009842	29796	UQCR10	http://www.ncbi.nlm.nih.gov/gene/?term=29796	"HSPC051, HSPC119, HSPC151, QCR9, UCCR7.2, UCRC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009843	29796	UQCR10	http://www.ncbi.nlm.nih.gov/gene/?term=29796	"HSPC051, HSPC119, HSPC151, QCR9, UCCR7.2, UCRC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009844	29798	C2orf27A	http://www.ncbi.nlm.nih.gov/gene/?term=29798	"C2orf27, C2orf27B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009845	29799	YPEL1	http://www.ncbi.nlm.nih.gov/gene/?term=29799	FKSG3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009846	2979	GUCA1B	http://www.ncbi.nlm.nih.gov/gene/?term=2979	"GCAP2, GUCA2, RP48 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009847	2979	GUCA1B	http://www.ncbi.nlm.nih.gov/gene/?term=2979	"GCAP2, GUCA2, RP48 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009848	29801	ZDHHC8	http://www.ncbi.nlm.nih.gov/gene/?term=29801	"DHHC8, ZDHHCL1, ZNF378 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009849	29801	ZDHHC8	http://www.ncbi.nlm.nih.gov/gene/?term=29801	"DHHC8, ZDHHCL1, ZNF378 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009850	29803	REPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=29803	"AP4, RIP60, ZNF464, Zfp464 "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00009851	29803	REPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=29803	"AP4, RIP60, ZNF464, Zfp464 "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00009852	29805	Znhit2	http://www.ncbi.nlm.nih.gov/gene/?term=29805	"C11orf5, Fon, ORF6-ps, Znhit2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009853	29809	Rabgap1l	http://www.ncbi.nlm.nih.gov/gene/?term=29809	"5830411O09Rik, 8430421H08Rik, 9630005B12Rik, AW049894, HHL, Hh1, mKIAA0471 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009854	29813	Zfp385a	http://www.ncbi.nlm.nih.gov/gene/?term=29813	"Hzf, Zfp385, Znf385a "	mRNA	Mus musculus	25821909	Dendrite	Neuron	Fluorescence in situ hybridization	"DISC1 colocalizes with HZF and ITPR1 mRNA in hippocampal dendrites and directly associates with neuronal mRNAs, including ITPR1 mRNA.  DISC1 colocalized with HZF and Itpr1 mRNA in hippocampal dendrites. "
RLID00009855	29817	Igfbp7	http://www.ncbi.nlm.nih.gov/gene/?term=29817	"AGM, Fstl2, Mac25 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00009856	29819	Stau2	http://www.ncbi.nlm.nih.gov/gene/?term=29819		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00009857	2983	GUCY1B3	http://www.ncbi.nlm.nih.gov/gene/?term=2983	"GC-S-beta-1, GC-SB3, GUC1B3, GUCB3, GUCSB3, GUCY1B1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009858	29841	GRHL1	http://www.ncbi.nlm.nih.gov/gene/?term=29841	"LBP32, MGR, NH32, TFCP2L2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009859	29841	GRHL1	http://www.ncbi.nlm.nih.gov/gene/?term=29841	"LBP32, MGR, NH32, TFCP2L2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009860	29842	TFCP2L1	http://www.ncbi.nlm.nih.gov/gene/?term=29842	"CRTR1, LBP-9, LBP9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009861	29843	SENP1	http://www.ncbi.nlm.nih.gov/gene/?term=29843	SuPr-2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009862	29845	Olfr155	http://www.ncbi.nlm.nih.gov/gene/?term=29845	"GA_x5J8B7W5BNN-979337-980296, MOR262-14, OR37A, Olfr37a, mOR37a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009863	29846	Olfr156	http://www.ncbi.nlm.nih.gov/gene/?term=29846	"MOR262-6, OR37B, Olfr37b, mOR37b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009864	2984	GUCY2C	http://www.ncbi.nlm.nih.gov/gene/?term=2984	"DIAR6, GUC2C, MECIL, MUCIL, STAR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009865	29855	UBN1	http://www.ncbi.nlm.nih.gov/gene/?term=29855	"VT, VT4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009866	29859	Sult4a1	http://www.ncbi.nlm.nih.gov/gene/?term=29859	"2400007A17Rik, AI853543, BR-STL-1, ST4A1, Sultx3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009867	29861	Dpf1	http://www.ncbi.nlm.nih.gov/gene/?term=29861	Neud4	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009868	29875	Iqgap1	http://www.ncbi.nlm.nih.gov/gene/?term=29875	"AA682088, D7Ertd237e, D7Ertd257e, mKIAA0051 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009869	29877	Hdgfrp3	http://www.ncbi.nlm.nih.gov/gene/?term=29877	"2700022B06Rik, HRP-3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009870	2987	GUK1	http://www.ncbi.nlm.nih.gov/gene/?term=2987	GMK	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009871	2987	GUK1	http://www.ncbi.nlm.nih.gov/gene/?term=2987	GMK	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009872	29880	ALG5	http://www.ncbi.nlm.nih.gov/gene/?term=29880	bA421P11.2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009873	29880	ALG5	http://www.ncbi.nlm.nih.gov/gene/?term=29880	bA421P11.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009874	29880	ALG5	http://www.ncbi.nlm.nih.gov/gene/?term=29880	bA421P11.2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009875	29881	NPC1L1	http://www.ncbi.nlm.nih.gov/gene/?term=29881	NPC11L1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009876	29881	NPC1L1	http://www.ncbi.nlm.nih.gov/gene/?term=29881	NPC11L1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009877	29882	ANAPC2	http://www.ncbi.nlm.nih.gov/gene/?term=29882	APC2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009878	29883	CNOT7	http://www.ncbi.nlm.nih.gov/gene/?term=29883	"CAF1, Caf1a, hCAF-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009879	29883	CNOT7	http://www.ncbi.nlm.nih.gov/gene/?term=29883	"CAF-1, CAF1, Caf1a, hCAF-1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009880	29886	SNX8	http://www.ncbi.nlm.nih.gov/gene/?term=29886	Mvp1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009881	29888	STRN4	http://www.ncbi.nlm.nih.gov/gene/?term=29888	"ZIN, zinedin "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009882	29888	STRN4	http://www.ncbi.nlm.nih.gov/gene/?term=29888	"ZIN, zinedin "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009883	29889	GNL2	http://www.ncbi.nlm.nih.gov/gene/?term=29889	"HUMAUANTIG, NGP1, Ngp-1, Nog2, Nug2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009884	29889	GNL2	http://www.ncbi.nlm.nih.gov/gene/?term=29889	"HUMAUANTIG, NGP1, Ngp-1, Nog2, Nug2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009885	29890	RBM15B	http://www.ncbi.nlm.nih.gov/gene/?term=29890	"HUMAGCGB, OTT3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009886	29894	CPSF1	http://www.ncbi.nlm.nih.gov/gene/?term=29894	"CPSF160, HSU37012, P/cl.18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009887	29894	CPSF1	http://www.ncbi.nlm.nih.gov/gene/?term=29894	"CPSF160, HSU37012, P/cl.18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009888	29896	TRA2A	http://www.ncbi.nlm.nih.gov/gene/?term=29896	"AWMS1, HSU53209 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009889	29899	GPSM2	http://www.ncbi.nlm.nih.gov/gene/?term=29899	"CMCS, DFNB82, LGN, PINS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009890	29899	GPSM2	http://www.ncbi.nlm.nih.gov/gene/?term=29899	"CMCS, DFNB82, LGN, PINS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009891	29899	GPSM2	http://www.ncbi.nlm.nih.gov/gene/?term=29899	"CMCS, DFNB82, LGN, PINS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009892	29901	SAC3D1	http://www.ncbi.nlm.nih.gov/gene/?term=29901	"HSU79266, SHD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009893	29901	SAC3D1	http://www.ncbi.nlm.nih.gov/gene/?term=29901	"HSU79266, SHD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009894	29902	FAM216A	http://www.ncbi.nlm.nih.gov/gene/?term=29902	"C12orf24, HSU79274 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009895	29902	FAM216A	http://www.ncbi.nlm.nih.gov/gene/?term=29902	"C12orf24, HSU79274 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009896	29903	CCDC106	http://www.ncbi.nlm.nih.gov/gene/?term=29903	"HSU79303, ZNF581 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009897	29904	EEF2K	http://www.ncbi.nlm.nih.gov/gene/?term=29904	"HSU93850, eEF-2K "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009898	29904	EEF2K	http://www.ncbi.nlm.nih.gov/gene/?term=29904	"HSU93850, eEF-2K "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009899	29907	SNX15	http://www.ncbi.nlm.nih.gov/gene/?term=29907	HSAF001435	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009900	29907	SNX15	http://www.ncbi.nlm.nih.gov/gene/?term=29907	HSAF001435	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009901	29907	SNX15	http://www.ncbi.nlm.nih.gov/gene/?term=29907	HSAF001435	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009902	2990	GUSB	http://www.ncbi.nlm.nih.gov/gene/?term=2990	"BG, MPS7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009903	2990	GUSB	http://www.ncbi.nlm.nih.gov/gene/?term=2990	"BG, MPS7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009904	29911	HOOK2	http://www.ncbi.nlm.nih.gov/gene/?term=29911	HK2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009905	29914	UBIAD1	http://www.ncbi.nlm.nih.gov/gene/?term=29914	"SCCD, TERE1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009906	29915	HCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=29915	"HCF-2, HCF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009907	29915	HCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=29915	"HCF-2, HCF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009908	29916	SNX11	http://www.ncbi.nlm.nih.gov/gene/?term=29916		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009909	29916	SNX11	http://www.ncbi.nlm.nih.gov/gene/?term=29916		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009910	29919	C18orf8	http://www.ncbi.nlm.nih.gov/gene/?term=29919	"HsT2591, MIC1, Mic-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009911	29920	PYCR2	http://www.ncbi.nlm.nih.gov/gene/?term=29920	"HLD10, P5CR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009912	29923	HILPDA	http://www.ncbi.nlm.nih.gov/gene/?term=29923	"C7orf68, HIG-2, HIG2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009913	29926	GMPPA	http://www.ncbi.nlm.nih.gov/gene/?term=29926	AAMR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009914	29927	SEC61A1	http://www.ncbi.nlm.nih.gov/gene/?term=29927	"SEC61, HSEC61, SEC61A "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00009915	29927	SEC61A1	http://www.ncbi.nlm.nih.gov/gene/?term=29927	"HSEC61, SEC61, SEC61A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009916	29927	SEC61A1	http://www.ncbi.nlm.nih.gov/gene/?term=29927	"HSEC61, SEC61, SEC61A "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. As depicted in Figure 4, Sec61u and calnexin were highly enriched in the membrane-bound fraction, as may be predicted for those mRNAs encoding signal sequences. "
RLID00009917	29927	SEC61A1	http://www.ncbi.nlm.nih.gov/gene/?term=29927	"HSEC61, SEC61, SEC61A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009918	29927	SEC61A1	http://www.ncbi.nlm.nih.gov/gene/?term=29927	"HSEC61, SEC61, SEC61A "	mRNA	Homo sapiens	22679391	Cytoplasm	U2OS cell	RT-PCR	"Figure 3A: The levels of Sec61a and b-actin transcripts isolated from unbound (i.e., non-ER) cytoplasmic and ER fractions from either cycloheximide treated (“Control� or puromycin treated EDTA extracted (“Puromycin+EDTA� U2OS cells were assessed by quantitative RT-PCR analysis. "
RLID00009919	29927	SEC61A1	http://www.ncbi.nlm.nih.gov/gene/?term=29927	"HSEC61, SEC61, SEC61A "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00009920	29928	TIMM22	http://www.ncbi.nlm.nih.gov/gene/?term=29928	"TEX4, TIM22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009921	29928	TIMM22	http://www.ncbi.nlm.nih.gov/gene/?term=29928	"TEX4, TIM22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009922	29929	ALG6	http://www.ncbi.nlm.nih.gov/gene/?term=29929	CDG1C	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009923	29929	ALG6	http://www.ncbi.nlm.nih.gov/gene/?term=29929	CDG1C	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009924	2992	GYG1	http://www.ncbi.nlm.nih.gov/gene/?term=2992	"GSD15, GYG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009925	299331	Hsp90aa1	http://www.ncbi.nlm.nih.gov/gene/?term=299331	"Hsp86, Hsp90, Hspca "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00009926	299331	Hsp90aa1	http://www.ncbi.nlm.nih.gov/gene/?term=299331	"Hsp86, Hsp90, Hspca "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00009927	29933	GPR132	http://www.ncbi.nlm.nih.gov/gene/?term=29933	G2A	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009928	29934	SNX12	http://www.ncbi.nlm.nih.gov/gene/?term=29934		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009929	29934	SNX12	http://www.ncbi.nlm.nih.gov/gene/?term=29934		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009930	29937	NENF	http://www.ncbi.nlm.nih.gov/gene/?term=29937	"CIR2, SCIRP10, SPUF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009931	29937	NENF	http://www.ncbi.nlm.nih.gov/gene/?term=29937	"CIR2, SCIRP10, SPUF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009932	29937	NENF	http://www.ncbi.nlm.nih.gov/gene/?term=29937	"CIR2, SCIRP10, SPUF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009933	2993	GYPA	http://www.ncbi.nlm.nih.gov/gene/?term=2993	"CD235a, GPA, GPErik, GPSAT, HGpMiV, HGpMiXI, HGpSta(C), MN, MNS, PAS-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009934	2994	GYPB	http://www.ncbi.nlm.nih.gov/gene/?term=2994	"CD235b, GPB, GYP, MNS, PAS-3, SS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009935	29950	SERTAD1	http://www.ncbi.nlm.nih.gov/gene/?term=29950	"SEI1, TRIP-Br1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009936	29952	DPP7	http://www.ncbi.nlm.nih.gov/gene/?term=29952	"DPP2, DPPII, QPP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009937	29954	POMT2	http://www.ncbi.nlm.nih.gov/gene/?term=29954	"LGMD2N, MDDGA2, MDDGB2, MDDGC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009938	29956	CERS2	http://www.ncbi.nlm.nih.gov/gene/?term=29956	"L3, LASS2, SP260, TMSG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009939	29956	CERS2	http://www.ncbi.nlm.nih.gov/gene/?term=29956	"L3, LASS2, SP260, TMSG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009940	29957	SLC25A24	http://www.ncbi.nlm.nih.gov/gene/?term=29957	"APC1, SCAMC-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009941	29959	NRBP1	http://www.ncbi.nlm.nih.gov/gene/?term=29959	"BCON3, MADM, MUDPNP, NRBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009942	29959	NRBP1	http://www.ncbi.nlm.nih.gov/gene/?term=29959	"BCON3, MADM, MUDPNP, NRBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009943	29959	NRBP1	http://www.ncbi.nlm.nih.gov/gene/?term=29959	"BCON3, MADM, MUDPNP, NRBP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009944	2995	GYPC	http://www.ncbi.nlm.nih.gov/gene/?term=2995	"CD236, CD236R, GE, GPC, GPD, GYPD, PAS-2, PAS-2' "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009945	29960	FTSJ2	http://www.ncbi.nlm.nih.gov/gene/?term=29960	"FJH1, HEL97, MRM2, RRMJ2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009946	29965	CDIP1	http://www.ncbi.nlm.nih.gov/gene/?term=29965	"C16orf5, CDIP, I1, LITAFL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009947	29966	STRN3	http://www.ncbi.nlm.nih.gov/gene/?term=29966	SG2NA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009948	29966	STRN3	http://www.ncbi.nlm.nih.gov/gene/?term=29966	SG2NA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009949	29966	STRN3	http://www.ncbi.nlm.nih.gov/gene/?term=29966	SG2NA	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009950	29967	LRP12	http://www.ncbi.nlm.nih.gov/gene/?term=29967	ST7	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009951	29968	PSAT1	http://www.ncbi.nlm.nih.gov/gene/?term=29968	"EPIP, NLS2, PSA, PSAT, PSATD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009952	29969	MDFIC	http://www.ncbi.nlm.nih.gov/gene/?term=29969	HIC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009953	29969	MDFIC	http://www.ncbi.nlm.nih.gov/gene/?term=29969	HIC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009954	29969	MDFIC	http://www.ncbi.nlm.nih.gov/gene/?term=29969	HIC	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009955	2996	GYPE	http://www.ncbi.nlm.nih.gov/gene/?term=2996	"GPE, MNS, MiIX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009956	29974	A1CF	http://www.ncbi.nlm.nih.gov/gene/?term=29974	"ACF, ACF64, ACF65, APOBEC1CF, ASP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009957	29979	UBQLN1	http://www.ncbi.nlm.nih.gov/gene/?term=29979	"DA41, DSK2, PLIC-1, UBQN, XDRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009958	29979	UBQLN1	http://www.ncbi.nlm.nih.gov/gene/?term=29979	"DA41, DSK2, PLIC-1, UBQN, XDRP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009959	29979	UBQLN1	http://www.ncbi.nlm.nih.gov/gene/?term=29979	"DA41, DSK2, PLIC-1, UBQN, XDRP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009960	2997	GYS1	http://www.ncbi.nlm.nih.gov/gene/?term=2997	"GSY, GYS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009961	29980	DONSON	http://www.ncbi.nlm.nih.gov/gene/?term=29980	"B17, C21orf60 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009962	29980	DONSON	http://www.ncbi.nlm.nih.gov/gene/?term=29980	"B17, C21orf60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009963	29982	NRBF2	http://www.ncbi.nlm.nih.gov/gene/?term=29982	"COPR, COPR1, COPR2, NRBF-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009964	29982	NRBF2	http://www.ncbi.nlm.nih.gov/gene/?term=29982	"COPR, COPR1, COPR2, NRBF-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009965	29982	NRBF2	http://www.ncbi.nlm.nih.gov/gene/?term=29982	"COPR, COPR1, COPR2, NRBF-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00009966	29984	RHOD	http://www.ncbi.nlm.nih.gov/gene/?term=29984	"ARHD, RHOHP1, RHOM, Rho "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009967	29984	RHOD	http://www.ncbi.nlm.nih.gov/gene/?term=29984	"ARHD, RHOHP1, RHOM, Rho "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009968	29985	SLC39A3	http://www.ncbi.nlm.nih.gov/gene/?term=29985	"ZIP-3, ZIP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009969	29985	SLC39A3	http://www.ncbi.nlm.nih.gov/gene/?term=29985	"ZIP-3, ZIP3 "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00009970	29988	SLC2A8	http://www.ncbi.nlm.nih.gov/gene/?term=29988	"GLUT8, GLUTX1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009971	29990	PILRB	http://www.ncbi.nlm.nih.gov/gene/?term=29990	"FDFACT1, FDFACT2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009972	29990	PILRB	http://www.ncbi.nlm.nih.gov/gene/?term=29990	"FDFACT1, FDFACT2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009973	29994	BAZ2B	http://www.ncbi.nlm.nih.gov/gene/?term=29994	WALp4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009974	29994	BAZ2B	http://www.ncbi.nlm.nih.gov/gene/?term=29994	WALp4	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009975	29997	GLTSCR2	http://www.ncbi.nlm.nih.gov/gene/?term=29997	"PICT-1, PICT1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009976	29	ABR	http://www.ncbi.nlm.nih.gov/gene/?term=29	MDB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009977	30000	TNPO2	http://www.ncbi.nlm.nih.gov/gene/?term=30000	"IPO3, KPNB2B, TRN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009978	30000	TNPO2	http://www.ncbi.nlm.nih.gov/gene/?term=30000	"IPO3, KPNB2B, TRN2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009979	30001	ERO1A	http://www.ncbi.nlm.nih.gov/gene/?term=30001	"ERO1-L, ERO1-L-alpha, ERO1-alpha, ERO1L, ERO1LA, Ero1alpha "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009980	30001	ERO1A	http://www.ncbi.nlm.nih.gov/gene/?term=30001	"ERO1-L, ERO1-L-alpha, ERO1-alpha, ERO1L, ERO1LA, Ero1alpha "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009981	30001	ERO1A	http://www.ncbi.nlm.nih.gov/gene/?term=30001	"ERO1-L, ERO1-L-alpha, ERO1-alpha, ERO1L, ERO1LA, Ero1alpha "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00009982	30046	Zfp292	http://www.ncbi.nlm.nih.gov/gene/?term=30046	"5730450D02Rik, 5830493J20Rik, 9430062L07Rik, AI449016, Krox-10, Zfp-15, Zfp15, Zn-15, Zn-16, mKIAA0530 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00009983	3005	H1F0	http://www.ncbi.nlm.nih.gov/gene/?term=3005	"H10, H1FV "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009984	30061	SLC40A1	http://www.ncbi.nlm.nih.gov/gene/?term=30061	"FPN1, HFE4, IREG1, MST079, MSTP079, MTP1, SLC11A3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009985	3006	HIST1H1C	http://www.ncbi.nlm.nih.gov/gene/?term=3006	"H1.2, H1C, H1F2, H1s-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009986	3006	HIST1H1C	http://www.ncbi.nlm.nih.gov/gene/?term=3006	"H1.2, H1C, H1F2, H1s-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009987	3008	HIST1H1E	http://www.ncbi.nlm.nih.gov/gene/?term=3008	"H1.4, H1E, H1F4, H1s-4, dJ221C16.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009988	30122	wnt8a	http://www.ncbi.nlm.nih.gov/gene/?term=30122	"wnt-8, wnt8, wnt8.1, wu:fa20e02, wu:fe05d07 "	mRNA	Danio rerio	22949618	Vegetal	Embryo	Fluorescence in situ hybridization	"Injected fluorescent wnt8a RNA localizes asymmetrically to the vegetal lateral cortex (yellow arrowheads in I) and to the blastoderm (red asterisk in I), similar to endogenous wnt8a transcripts. "
RLID00009989	30122	wnt8a	http://www.ncbi.nlm.nih.gov/gene/?term=30122	"wnt-8, wnt8, wnt8.1, wu:fa20e02, wu:fe05d07 "	mRNA	Danio rerio	26528729	Vegetal	Embryo	Whole mount in situ hybridization	Whole mount in situ hybridization shows that grip2a and wnt8a mRNA are localized at the base of the vegetal cortex and experience an off-cen-ter shift in control (DMSO-treated) embryos 
RLID00009990	30122	wnt8a	http://www.ncbi.nlm.nih.gov/gene/?term=30122	"wnt-8, wnt8, wnt8.1, wu:fa20e02, wu:fe05d07 "	mRNA	Danio rerio	26528729	Vegetal	Embryo	Fluorescence in situ hybridization	"FIGURE 2. Dual label FISH of pairwise comparisons of wnt8a, grip2a and dazl mRNA localization at the vegetal cortex. (A-C) dazl (green) and wnt8a (red). (D-F) grip2a (green) and dazl (red). (G-I) grip2a (green) and wnt8a (red). In all cases mRNAs localize to discrete units, which do not overlap between different RNAs. Embryos are wild type fixed at 20mpf. Panels are 2-D projections of imaged vegetal cortex samples. Scale bar in (I) represents 5mm for all images. (Color figure available online.) "
RLID00009991	3012	HIST1H2AE	http://www.ncbi.nlm.nih.gov/gene/?term=3012	"H2A.1, H2A.2, H2A/a, H2AFA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009992	3012	HIST1H2AE	http://www.ncbi.nlm.nih.gov/gene/?term=3012	"H2A.1, H2A.2, H2A/a, H2AFA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00009993	3014	H2AFX	http://www.ncbi.nlm.nih.gov/gene/?term=3014	"H2A.X, H2A/X, H2AX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009994	3014	H2AFX	http://www.ncbi.nlm.nih.gov/gene/?term=3014	"H2A.X, H2A/X, H2AX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009995	3015	H2AFZ	http://www.ncbi.nlm.nih.gov/gene/?term=3015	"H2A.Z-1, H2A.z, H2A/z, H2AZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009996	3017	HIST1H2BD	http://www.ncbi.nlm.nih.gov/gene/?term=3017	"H2B.1B, H2B/b, H2BFB, HIRIP2, dJ221C16.6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009997	3017	HIST1H2BD	http://www.ncbi.nlm.nih.gov/gene/?term=3017	"H2B.1B, H2B/b, H2BFB, HIRIP2, dJ221C16.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00009998	301	ANXA1	http://www.ncbi.nlm.nih.gov/gene/?term=301	"ANX1, LPC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00009999	301	ANXA1	http://www.ncbi.nlm.nih.gov/gene/?term=301	"ANX1, LPC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010000	301	ANXA1	http://www.ncbi.nlm.nih.gov/gene/?term=301	"ANX1, LPC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010001	3020	H3F3A	http://www.ncbi.nlm.nih.gov/gene/?term=3020	"H3.3A, H3F3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010002	3020	H3F3A	http://www.ncbi.nlm.nih.gov/gene/?term=3020	"H3.3A, H3F3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010003	3020	H3F3A	http://www.ncbi.nlm.nih.gov/gene/?term=3020	"H3.3A, H3F3 "	mRNA	Homo sapiens	21431749	Cytosol	HEK293 cell	Northern blot	"Similarly, Northern blot analysis of the mRNA composition of the cytosol and membrane fractions show that the cytosol fraction is enriched for mRNAs encoding histone (H3F3A) and GAPDH, whereas the membrane fraction is enriched in mRNAs encoding ER resident proteins, such as GRP94 and calreticulin (Fig. 2 B). "
RLID00010004	3021	H3F3B	http://www.ncbi.nlm.nih.gov/gene/?term=3021	H3.3B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010005	30263	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=30263	"vas, vasa, vlg, wu:fi24g05, zgc:109812, zgc:158535 "	mRNA	Danio rerio	10811828	Germ plasm	Embryo	In situ hybridization	"To understand the structural nature of localized vasa RNA aggregates in zebrafish embryogenesis, we performed transmission electron microscopy on four-cell embryos that are labeled for vasa RNA using in situ hybridization and an electron-dense substrate (see Materials and Methods)..Based on the presence of the vasa RNA, which is embedded in electron-dense material that resembles nuage, we conclude that this structure is the zebrafish germ plasm. "
RLID00010006	30263	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=30263	"vas, vasa, vlg, wu:fi24g05, zgc:109812, zgc:158535 "	mRNA	Danio rerio	16457796	Germ plasm	Embryo	Fluorescence in situ hybridization	"Fig. 1. Endogenous patterns of RNA localization of dnd, nos1, vas, and dazl RNAs during the first cell cycle. Animal views of embryos fixed at progressively older stages of development (A-D: 15 min p.f.; E-H: 30 min. p.f.; I-L: 45 min p.f.) and labeled using FISH to detect germ plasm RNAs (dnd (A, E, I); nos1 (B, F, J); vas(C,G, K); dazl (D, H, L). (A-D) Immediately after fertilization, dnd, nos1, and vas RNA aggregates can be observed as a band at the animal pole, while dazl RNA aggregates are not initially present in the animal pole. (E-H) During the initiation of furrow formation, RNA aggregates fordnd, nos1, and vas begin to be recruited as a rod at the forming furrow (arrows in E-G). At this stage, dazl RNA is not yet detectable at the furrows (H). (I-L) As the furrow matures, there is an increase in the amount of dnd, nos1, and vasRNAs recruited at the furrow, and dazlRNA becomes detectable at the furrow (arrows in I-L). Scale bar in panel (L) represents 100 μmThus, although all four RNAs are recruited to the forming furrow, RNAs for dnd, nos1, and vas are already present in the animal pole in the freshly laid egg, while dazlRNA arrives to the animal pole from the vegetal region at a later stage. Based on their different times of appearance at the animal region, we refer to the dnd, nos1, and vas RNAs as the early animal germ plasm RNAs, while dazl is also referred to as a vegetally localized germ plasm RNA. "
RLID00010007	30263	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=30263	"vas, vasa, vlg, wu:fi24g05, zgc:109812, zgc:158535 "	mRNA	Danio rerio	17217535	Germ plasm	Embryo	In situ hybridization	"This finding, coupled with the fact that vasa mRNA, which is localized to the germ plasm of zebrafish but does not label a similar structure in medaka opened the possibility of fundamentally different mechanisms governing PGC specification in these two fish species. "
RLID00010008	30263	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=30263	"vas, vasa, vlg, wu:fi24g05, zgc:109812, zgc:158535 "	mRNA	Danio rerio	17293094	Germ plasm	Oocyte	In situ hybridization	"Here we report that the germ plasm RNAs vasa, nanos1, and dazl co-localize with the mitochondrial cloud (MC) and are transported to the vegetal cortex during early oogenesis. "
RLID00010009	30263	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=30263	"vas, vasa, vlg, wu:fi24g05, zgc:109812, zgc:158535 "	mRNA	Danio rerio	17293094	Mitochondrion	Oocyte	In situ hybridization	"Here we report that the germ plasm RNAs vasa, nanos1, and dazl co-localize with the mitochondrial cloud (MC) and are transported to the vegetal cortex during early oogenesis. "
RLID00010010	30263	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=30263	"vas, vasa, vlg, wu:fi24g05, zgc:109812, zgc:158535 "	mRNA	Danio rerio	24967891	Germ plasm	Embryo	In situ hybridization	"The localization patterns of dazl mRNA, a germ plasm component initially localized to the vegetal pole of the egg ([36,46,47]; Figure 8A), is not affected in these mutants (Figure 8D). During the first two cell cycles, dazl mRNA localizes normally to the furrows in hec mutants (Figure 8B, 8E), as does vasa mRNA (Figure 8C, 8F), an animal germ plasm component already present in the animal cortical region during egg activation. "
RLID00010011	3028	HSD17B10	http://www.ncbi.nlm.nih.gov/gene/?term=3028	"17b-HSD10, ABAD, CAMR, DUPXp11.22, ERAB, HADH2, HCD2, MHBD, MRPP2, MRX17, MRX31, MRXS10, SCHAD, SDR5C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010012	3028	HSD17B10	http://www.ncbi.nlm.nih.gov/gene/?term=3028	"17b-HSD10, ABAD, CAMR, DUPXp11.22, ERAB, HADH2, HCD2, MHBD, MRPP2, MRX17, MRX31, MRXS10, SCHAD, SDR5C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010013	3028	HSD17B10	http://www.ncbi.nlm.nih.gov/gene/?term=3028	"17b-HSD10, ABAD, CAMR, DUPXp11.22, ERAB, HADH2, HCD2, MHBD, MRPP2, MRX17, MRX31, MRXS10, SCHAD, SDR5C1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010014	3029	HAGH	http://www.ncbi.nlm.nih.gov/gene/?term=3029	"GLO2, GLX2, GLXII1, HAGH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010015	302	ANXA2	http://www.ncbi.nlm.nih.gov/gene/?term=302	"ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2, LPC2D, P36, PAP-IV "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010016	302	ANXA2	http://www.ncbi.nlm.nih.gov/gene/?term=302	"ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2, LPC2D, P36, PAP-IV "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010017	302	ANXA2	http://www.ncbi.nlm.nih.gov/gene/?term=302	"ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2, LPC2D, P36, PAP-IV "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010018	3030	HADHA	http://www.ncbi.nlm.nih.gov/gene/?term=3030	"ECHA, GBP, HADH, LCEH, LCHAD, MTPA, TP-ALPHA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010019	3030	HADHA	http://www.ncbi.nlm.nih.gov/gene/?term=3030	"ECHA, GBP, HADH, LCEH, LCHAD, MTPA, TP-ALPHA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010020	3032	HADHB	http://www.ncbi.nlm.nih.gov/gene/?term=3032	"ECHB, MSTP029, MTPB, TP-BETA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010021	3033	HADH	http://www.ncbi.nlm.nih.gov/gene/?term=3033	"HAD, HADH1, HADHSC, HCDH, HHF4, MSCHAD, SCHAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010022	3033	HADH	http://www.ncbi.nlm.nih.gov/gene/?term=3033	"HAD1, HADHSC, HCDH, HHF4, MSCHAD, SCHAD, HADH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010023	3033	HADH	http://www.ncbi.nlm.nih.gov/gene/?term=3033	"HAD1, HADHSC, HCDH, HHF4, MSCHAD, SCHAD, HADH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010024	3035	HARS	http://www.ncbi.nlm.nih.gov/gene/?term=3035	"CMT2W, HRS, USH3B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010025	3039	HBA1	http://www.ncbi.nlm.nih.gov/gene/?term=3039	"HBA-T3, HBH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010026	3040	HBA2	http://www.ncbi.nlm.nih.gov/gene/?term=3040	"HBA-T2, HBH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010027	3040	HBA2	http://www.ncbi.nlm.nih.gov/gene/?term=3040	"HBA-T2, HBH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010028	3043	HBB	http://www.ncbi.nlm.nih.gov/gene/?term=3043	"CD113t-C, beta-globin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010029	3046	HBE1	http://www.ncbi.nlm.nih.gov/gene/?term=3046	HBE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010030	3052	HCCS	http://www.ncbi.nlm.nih.gov/gene/?term=3052	"CCHL, LSDMCA1, MCOPS7, MLS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010031	3052	HCCS	http://www.ncbi.nlm.nih.gov/gene/?term=3052	"CCHL, LSDMCA1, MCOPS7, MLS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010032	3054	HCFC1	http://www.ncbi.nlm.nih.gov/gene/?term=3054	"CFF, HCF, HCF-1, HCF1, HFC1, MRX3, PPP1R89, VCAF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010033	3054	HCFC1	http://www.ncbi.nlm.nih.gov/gene/?term=3054	"CFF, HCF, HCF-1, HCF1, HFC1, MRX3, PPP1R89, VCAF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010034	3059	HCLS1	http://www.ncbi.nlm.nih.gov/gene/?term=3059	"CTTNL, HS1, lckBP1, p75 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010035	3061	HCRTR1	http://www.ncbi.nlm.nih.gov/gene/?term=3061	OX1R	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010036	3064	HTT	http://www.ncbi.nlm.nih.gov/gene/?term=3064	"HD, IT15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010037	3064	HTT	http://www.ncbi.nlm.nih.gov/gene/?term=3064	"HD, IT15 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010038	3064	HTT	http://www.ncbi.nlm.nih.gov/gene/?term=3064	"HD, IT15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010039	3065	HDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=3065	"GON-10, HD1, RPD3, RPD3L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010040	3065	HDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=3065	"HD1, RPD3, GON-10, RPD3L1 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00010041	3065	HDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=3065	"GON-10, HD1, RPD3, RPD3L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010042	3065	HDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=3065	"GON-10, HD1, RPD3, RPD3L1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010043	3066	HDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=3066	"HD2, RPD3, YAF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010044	3066	HDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=3066	"HD2, RPD3, YAF1 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00010045	3066	HDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=3066	"HD2, RPD3, YAF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010046	3066	HDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=3066	"HD2, RPD3, YAF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010047	3066	HDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=3066	"HD2, RPD3, YAF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010048	3066	HDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=3066	"HD2, RPD3, YAF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010049	3068	HDGF	http://www.ncbi.nlm.nih.gov/gene/?term=3068	HMG1L2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010050	3068	HDGF	http://www.ncbi.nlm.nih.gov/gene/?term=3068	HMG1L2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010051	3068	HDGF	http://www.ncbi.nlm.nih.gov/gene/?term=3068	HMG1L2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010052	3069	HDLBP	http://www.ncbi.nlm.nih.gov/gene/?term=3069	"HBP, PRO2900, VGL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010053	3069	HDLBP	http://www.ncbi.nlm.nih.gov/gene/?term=3069	"HBP, PRO2900, VGL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010054	3070	HELLS	http://www.ncbi.nlm.nih.gov/gene/?term=3070	"LSH, Nbla10143, PASG, SMARCA6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010055	3071	NCKAP1L	http://www.ncbi.nlm.nih.gov/gene/?term=3071	HEM1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010056	3073	HEXA	http://www.ncbi.nlm.nih.gov/gene/?term=3073	TSD	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010057	3073	HEXA	http://www.ncbi.nlm.nih.gov/gene/?term=3073	TSD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010058	3073	HEXA	http://www.ncbi.nlm.nih.gov/gene/?term=3073	TSD	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010059	3074	HEXB	http://www.ncbi.nlm.nih.gov/gene/?term=3074	"ENC-1AS, HEL-248, HEL-S-111 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010060	3074	HEXB	http://www.ncbi.nlm.nih.gov/gene/?term=3074	"ENC-1AS, HEL-248, HEL-S-111 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010061	3074	HEXB	http://www.ncbi.nlm.nih.gov/gene/?term=3074	"ENC-1AS, HEL-248, HEL-S-111 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010062	3077	HFE	http://www.ncbi.nlm.nih.gov/gene/?term=3077	"HFE1, HH, HLA-H, MVCD7, TFQTL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010063	3078	CFHR1	http://www.ncbi.nlm.nih.gov/gene/?term=3078	"CFHL, CFHL1, CFHL1P, CFHR1P, FHR1, H36-1, H36-2, HFL1, HFL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010064	30795	Fkbp3	http://www.ncbi.nlm.nih.gov/gene/?term=30795	"25kDa, FKBP-3, FKBP25 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010065	307	ANXA4	http://www.ncbi.nlm.nih.gov/gene/?term=307	"ANX4, HEL-S-274, PIG28, ZAP36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010066	307	ANXA4	http://www.ncbi.nlm.nih.gov/gene/?term=307	"ANX4, HEL-S-274, P32.5, PAP-II, PIG28, PP4-X, ZAP36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010067	307	ANXA4	http://www.ncbi.nlm.nih.gov/gene/?term=307	"ANX4, HEL-S-274, P32.5, PAP-II, PIG28, PP4-X, ZAP36 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010068	30811	HUNK	http://www.ncbi.nlm.nih.gov/gene/?term=30811		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010069	30811	HUNK	http://www.ncbi.nlm.nih.gov/gene/?term=30811		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010070	30815	ST6GALNAC6	http://www.ncbi.nlm.nih.gov/gene/?term=30815	"SIAT7-F, SIAT7F, ST6GALNACVI "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010071	30818	KCNIP3	http://www.ncbi.nlm.nih.gov/gene/?term=30818	"CSEN, DREAM, KCHIP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010072	30827	CXXC1	http://www.ncbi.nlm.nih.gov/gene/?term=30827	"2410002I16Rik, 5830420C16Rik, CFP1, CGBP, HsT2645, PCCX1, PHF18, SPP1, ZCGPC1, hCGBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010073	30827	CXXC1	http://www.ncbi.nlm.nih.gov/gene/?term=30827	"2410002I16Rik, 5830420C16Rik, CFP1, CGBP, HsT2645, PCCX1, PHF18, SPP1, ZCGPC1, hCGBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010074	3082	HGF	http://www.ncbi.nlm.nih.gov/gene/?term=3082	"DFNB39, F-TCF, HGFB, HPTA, SF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010075	30833	NT5C	http://www.ncbi.nlm.nih.gov/gene/?term=30833	"DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010076	30833	NT5C	http://www.ncbi.nlm.nih.gov/gene/?term=30833	"DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010077	30833	NT5C	http://www.ncbi.nlm.nih.gov/gene/?term=30833	"DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010078	30834	ZNRD1	http://www.ncbi.nlm.nih.gov/gene/?term=30834	"HTEX-6, HTEX6, Rpa12, TCTEX6, TEX6, ZR14, hZR14, tctex-6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010079	30834	ZNRD1	http://www.ncbi.nlm.nih.gov/gene/?term=30834	"HTEX-6, HTEX6, Rpa12, TCTEX6, TEX6, ZR14, hZR14, tctex-6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010080	30835	CD209	http://www.ncbi.nlm.nih.gov/gene/?term=30835	"CDSIGN, CLEC4L, DC-SIGN, DC-SIGN1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010081	30835	CD209	http://www.ncbi.nlm.nih.gov/gene/?term=30835	"CDSIGN, CLEC4L, DC-SIGN, DC-SIGN1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010082	30836	DNTTIP2	http://www.ncbi.nlm.nih.gov/gene/?term=30836	"ERBP, FCF2, HSU15552, LPTS-RP2, TdIF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010083	30836	DNTTIP2	http://www.ncbi.nlm.nih.gov/gene/?term=30836	"ERBP, FCF2, HSU15552, LPTS-RP2, TdIF2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010084	30837	SOCS7	http://www.ncbi.nlm.nih.gov/gene/?term=30837	"NAP4, NCKAP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010085	30837	SOCS7	http://www.ncbi.nlm.nih.gov/gene/?term=30837	"NAP4, NCKAP4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010086	30838	Fbxw4	http://www.ncbi.nlm.nih.gov/gene/?term=30838	"Dac, Fbw4, SHFM3, SHSF3, dactylin, dactylyn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010087	30839	Fbxw5	http://www.ncbi.nlm.nih.gov/gene/?term=30839	"AI159739, Fbw5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010088	30841	Kdm2b	http://www.ncbi.nlm.nih.gov/gene/?term=30841	"Cxxc2, Fbl10, Fbxl10, Jhdm1b, PCCX2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010089	30844	EHD4	http://www.ncbi.nlm.nih.gov/gene/?term=30844	PAST4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010090	30844	EHD4	http://www.ncbi.nlm.nih.gov/gene/?term=30844	PAST4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010091	30846	EHD2	http://www.ncbi.nlm.nih.gov/gene/?term=30846	PAST2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010092	30846	EHD2	http://www.ncbi.nlm.nih.gov/gene/?term=30846	PAST2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010093	30849	PIK3R4	http://www.ncbi.nlm.nih.gov/gene/?term=30849	"VPS15, p150 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010094	30849	PIK3R4	http://www.ncbi.nlm.nih.gov/gene/?term=30849	"VPS15, p150 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010095	3084	NRG1	http://www.ncbi.nlm.nih.gov/gene/?term=3084	"ARIA, GGF, GGF2, HGL, HRG, HRG1, HRGA, MST131, MSTP131, NDF, NRG1-IT2, SMDF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010096	30851	TAX1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=30851	"TIP-1, TIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010097	30851	TAX1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=30851	"TIP-1, TIP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010098	30851	TAX1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=30851	"TIP-1, TIP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010099	30877	Gnl3	http://www.ncbi.nlm.nih.gov/gene/?term=30877	Ns	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010100	30878	Apln	http://www.ncbi.nlm.nih.gov/gene/?term=30878	"6030430G11Rik, Apel "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010101	308	ANXA5	http://www.ncbi.nlm.nih.gov/gene/?term=308	"ANX5, ENX2, HEL-S-7, PP4, RPRGL3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010102	309122	H19	http://www.ncbi.nlm.nih.gov/gene/?term=309122	"ASM, ASM1, D11S813E "	lncRNA	Rattus norvegicus	15094229	Cytoplasm	Hepatocyte	In situ hybridization	"Similar to albumin mRNA, H19 mRNA appeared to be localized mainly in the cytoplasm. "
RLID00010103	3091	HIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=3091	"HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1, PASD8, bHLHe78 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010104	3091	HIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=3091	"HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1, PASD8, bHLHe78 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010105	3091	HIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=3091	"HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1, PASD8, bHLHe78 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010106	3091	HIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=3091	"HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1, PASD8, bHLHe78 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00010107	3091	HIF1A	http://www.ncbi.nlm.nih.gov/gene/?term=3091	"HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1, PASD8, bHLHe78 "	mRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	qRT-PCR	Figure S1: Polysomal gradient analysis. HT1080 cells were incubated under control (21% oxygen) or hypoxic (1% oxygen) conditions for up to 36 h as described in Figure 1. Shown are representative original RT-PCR data (30 cycles for beta-Actin and the external standard [extSt]; 35 cycles for the other genes) from pooled samples to visualize mRNA distribution following fractionation of sucrose gradients at control conditions (C) and 36 h of hypoxia (Hy). The external standard (a synthetic in vitro transcript) was diluted to appropriate concentration for qPCR and added directly after gradient fractionation and prior to RNA isolation as a technical control. The external standard served for fraction dependent normalization.
RLID00010108	3092	HIP1	http://www.ncbi.nlm.nih.gov/gene/?term=3092	"HIP-I, ILWEQ, SHON, SHONbeta, SHONgamma "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010109	3092	HIP1	http://www.ncbi.nlm.nih.gov/gene/?term=3092	"HIP-I, ILWEQ, SHON, SHONbeta, SHONgamma "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010110	3092	HIP1	http://www.ncbi.nlm.nih.gov/gene/?term=3092	"HIP-I, ILWEQ, SHON, SHONbeta, SHONgamma "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010111	30930	Vps26a	http://www.ncbi.nlm.nih.gov/gene/?term=30930	"AA407240, HB58, Vps26 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010112	30931	Tor1a	http://www.ncbi.nlm.nih.gov/gene/?term=30931	"DQ2, Dyt1, torsinA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010113	30934	Tor1b	http://www.ncbi.nlm.nih.gov/gene/?term=30934	"2610016F05Rik, DQ1, torsinB "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010114	3093	UBE2K	http://www.ncbi.nlm.nih.gov/gene/?term=3093	"E2-25K, HIP2, HYPG, LIG, UBC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010115	3093	UBE2K	http://www.ncbi.nlm.nih.gov/gene/?term=3093	"E2-25K, HIP2, HYPG, LIG, UBC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010116	30940	Usp25	http://www.ncbi.nlm.nih.gov/gene/?term=30940		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010117	30940	Usp25	http://www.ncbi.nlm.nih.gov/gene/?term=30940		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010118	30944	Zfp354c	http://www.ncbi.nlm.nih.gov/gene/?term=30944	"5330421P20Rik, AJ18, AW743325, Kid3, Tcf17l2, Znf354c, mKIAA4218 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010119	30947	Adat1	http://www.ncbi.nlm.nih.gov/gene/?term=30947	"MMADAT1, mADAT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010120	3094	HINT1	http://www.ncbi.nlm.nih.gov/gene/?term=3094	"HINT, NMAN, PKCI-1, PRKCNH1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010121	3094	HINT1	http://www.ncbi.nlm.nih.gov/gene/?term=3094	"HINT, NMAN, PKCI-1, PRKCNH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010122	3094	HINT1	http://www.ncbi.nlm.nih.gov/gene/?term=3094	"HINT, NMAN, PKCI-1, PRKCNH1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010123	30957	Mapk8ip3	http://www.ncbi.nlm.nih.gov/gene/?term=30957	"BB120594, D17Wsu15e, JIP-3, JSAP1, JSAP1a, JSAP1b, JSAP1c, JSAP1d, Jip3, Syd2, mKIAA1066 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010124	30960	Vapa	http://www.ncbi.nlm.nih.gov/gene/?term=30960	"33kDa, VAP33 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010125	30968	STOML2	http://www.ncbi.nlm.nih.gov/gene/?term=30968	"HSPC108, SLP-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010126	3096	HIVEP1	http://www.ncbi.nlm.nih.gov/gene/?term=3096	"CIRIP, CRYBP1, GAAP, MBP-1, PRDII-BF1, Schnurri-1, ZAS1, ZNF40, ZNF40A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010127	3099	HK2	http://www.ncbi.nlm.nih.gov/gene/?term=3099	"HKII, HXK2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010128	3099	HK2	http://www.ncbi.nlm.nih.gov/gene/?term=3099	"HKII, HXK2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010129	3099	HK2	http://www.ncbi.nlm.nih.gov/gene/?term=3099	"HKII, HXK2 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00010130	309	ANXA6	http://www.ncbi.nlm.nih.gov/gene/?term=309	"ANX6, CBP68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010131	309	ANXA6	http://www.ncbi.nlm.nih.gov/gene/?term=309	"ANX6, CBP68 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010132	30	ACAA1	http://www.ncbi.nlm.nih.gov/gene/?term=30	"ACAA, PTHIO, THIO "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010133	31011	Dredd	http://www.ncbi.nlm.nih.gov/gene/?term=31011	"Dmel_CG7486, CASP8_DROME, CG7486, DCP-2, DCP-2/DREDD, DCP2, DREDD, Dcp-2, Dcp-2/Dredd, Dcp2, Dedd, Dmel\CG7486/DCP-2, EG:115C2.9, Redd, anon-1BCa, dDredd, dcp-2/dredd, dredd, Dredd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010134	31017	sdk	http://www.ncbi.nlm.nih.gov/gene/?term=31017	"Dmel_CG5227, BcDNA:LD22322, BcDNA:RE63453, CG5227, CT16627, Dmel\CG5227, EG:BACR19J1.1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010135	31017	sdk	http://www.ncbi.nlm.nih.gov/gene/?term=31017	"Dmel_CG5227, BcDNA:LD22322, BcDNA:RE63453, CG5227, CT16627, Dmel\CG5227, EG:BACR19J1.1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010136	31026	CG16989	http://www.ncbi.nlm.nih.gov/gene/?term=31026	"Dmel_ Dmel\CG16989, EG:34F3.4 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010137	31027	Rbf	http://www.ncbi.nlm.nih.gov/gene/?term=31027	"Dmel_CG7413, CG7413, Dmel\CG7413, EG:34F3.3, FBF, RB, RBF, RBF1, Rb, Rb1, RbF1, dRBF, pRb, rb, rbf, rbf1, Rbf "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010138	31043	CG3704	http://www.ncbi.nlm.nih.gov/gene/?term=31043	"Dmel_ Dmel\CG3704, EG:BACR7A4.17, XAB1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010139	31043	CG3704	http://www.ncbi.nlm.nih.gov/gene/?term=31043	"Dmel_ Dmel\CG3704, EG:BACR7A4.17, XAB1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010140	31055	CG14629	http://www.ncbi.nlm.nih.gov/gene/?term=31055	"Dmel_ Dmel\CG14629, EG:103E12.2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010141	3105	HLA-A	http://www.ncbi.nlm.nih.gov/gene/?term=3105	HLAA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010142	3105	HLA-A	http://www.ncbi.nlm.nih.gov/gene/?term=3105	"Aw-33, Aw-74, HLAA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010143	3105	HLA-A	http://www.ncbi.nlm.nih.gov/gene/?term=3105	"Aw-33, Aw-74, HLAA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010144	31065	CG11380	http://www.ncbi.nlm.nih.gov/gene/?term=31065	"Dmel_ Dmel\CG11380, EG:BACR42I17.7 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010145	31065	CG11380	http://www.ncbi.nlm.nih.gov/gene/?term=31065	"Dmel_ Dmel\CG11380, EG:BACR42I17.7 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010146	3106	HLA-B	http://www.ncbi.nlm.nih.gov/gene/?term=3106	"AS, Bw-47, Bw-50, HLAB, SPDA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010147	3106	HLA-B	http://www.ncbi.nlm.nih.gov/gene/?term=3106	"AS, Bw-47, Bw-50, HLAB, SPDA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010148	31072	CG11403	http://www.ncbi.nlm.nih.gov/gene/?term=31072	"Dmel_ Dmel\CG11403, EG:33C11.2, cg11403 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010149	3107	HLA-C	http://www.ncbi.nlm.nih.gov/gene/?term=3107	"D6S204, HLA-JY3, HLC-C, PSORS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010150	3107	HLA-C	http://www.ncbi.nlm.nih.gov/gene/?term=3107	"D6S204, HLA-JY3, HLAC, HLC-C, PSORS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010151	31085	CG14770	http://www.ncbi.nlm.nih.gov/gene/?term=31085	Dmel_ Dmel\CG14770	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010152	310	ANXA7	http://www.ncbi.nlm.nih.gov/gene/?term=310	"ANX7, SNX, SYNEXIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010153	310	ANXA7	http://www.ncbi.nlm.nih.gov/gene/?term=310	"ANX7, SNX, SYNEXIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010154	31102	CG14780	http://www.ncbi.nlm.nih.gov/gene/?term=31102	"Dmel_ Dmel\CG14780, EG:80H7.3, SP95 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010155	31104	mei-38	http://www.ncbi.nlm.nih.gov/gene/?term=31104	"Dmel_CG14781, CG14781, D-TPX2, Dmel\CG14781, EG:80H7.11, Mei-38, Ssp1, ssp1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010156	31115	CG11509	http://www.ncbi.nlm.nih.gov/gene/?term=31115	Dmel_ Dmel\CG11509	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010157	3111	HLA-DOA	http://www.ncbi.nlm.nih.gov/gene/?term=3111	"HLA-DNA, HLA-DZA, HLADZ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010158	3111	HLA-DOA	http://www.ncbi.nlm.nih.gov/gene/?term=3111	"HLA-DNA, HLA-DZA, HLADZ "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010159	31136	CG42666	http://www.ncbi.nlm.nih.gov/gene/?term=31136	"Dmel_ CG14799, CG14800, CG14801, CG17968, Dmel\CG42666, Dmel_CG14799, Dmel_CG14801, EG:131F2.2, EG:137E7.1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010160	31139	CG14814	http://www.ncbi.nlm.nih.gov/gene/?term=31139	"Dmel_ Dmel\CG14814, EG:63B12.6 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010161	3113	HLA-DPA1	http://www.ncbi.nlm.nih.gov/gene/?term=3113	"DP(W3), DP(W4), HLA-DP1A, HLADP, HLASB, PLT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010162	31166	Actn	http://www.ncbi.nlm.nih.gov/gene/?term=31166	"Dmel_CG4376, ACTN, CG4376, CT14163, CT14232, Dmel\CG4376, EG:133E12.1, GA17, HM-29, actn, alpha-actinin, alphaActn, fliA, l(1)2Cb, l(1)EA82, y "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010163	31173	CG4194	http://www.ncbi.nlm.nih.gov/gene/?term=31173	"Dmel_ Dmel\CG4194, EG:22E5.6 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010164	31179	Unc-76	http://www.ncbi.nlm.nih.gov/gene/?term=31179	"Dmel_CG3981, BcDNA:GH10260, CG18851, CG3981, Dmel\CG3981, Dunc-76, EG:67A9.1, UNC-76, l(1)G0066, l(1)G0158, l(1)G0310, l(1)G0333, l(1)G0360, unc-76 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010165	31198	Mct1	http://www.ncbi.nlm.nih.gov/gene/?term=31198	"Dmel_CG3456, CG3456, Dmel\CG3456, EG:103B4.3 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010166	3119	HLA-DQB1	http://www.ncbi.nlm.nih.gov/gene/?term=3119	"CELIAC1, HLA-DQB, IDDM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010167	311	ANXA11	http://www.ncbi.nlm.nih.gov/gene/?term=311	"ANX11, CAP50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010168	311	ANXA11	http://www.ncbi.nlm.nih.gov/gene/?term=311	"ANX11, CAP50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010169	311	ANXA11	http://www.ncbi.nlm.nih.gov/gene/?term=311	"ANX11, CAP50 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010170	31221	Raf	http://www.ncbi.nlm.nih.gov/gene/?term=31221	"Dmel_CG2845, 11-29, C110, CG2845, D-RAF, D-Raf, D-raf, D-raf1, DRaf, DRaf1, Dmel\CG2845, Draf, Draf-1, Draf1, EG:BACH48C10.3, Phl, RAF/phl, Raf1, dRaf, draf, l(1)2Fe, l(1)G0475, l(1)ph, l(1)phl, l(1)pole hole, l(1)polehole, l(1)polehole/draf, l(1)raf, lincRNA.937, ph, ph1, phl, raf, raf-1, raf1, rafl, Raf "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010171	3122	HLA-DRA	http://www.ncbi.nlm.nih.gov/gene/?term=3122	"HLA-DRA1, MLRW "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010172	3123	HLA-DRB1	http://www.ncbi.nlm.nih.gov/gene/?term=3123	"DRB1, DRw10, HLA-DR1B, HLA-DRB, SS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010173	31284	CG14420	http://www.ncbi.nlm.nih.gov/gene/?term=31284	Dmel_ Dmel\CG14420	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010174	31287	CG14423	http://www.ncbi.nlm.nih.gov/gene/?term=31287	Dmel_ Dmel\CG14423	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010175	31289	CG3603	http://www.ncbi.nlm.nih.gov/gene/?term=31289	"Dmel_ BcDNA:RH09070, Dmel\CG3603 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010176	31295	CG3939	http://www.ncbi.nlm.nih.gov/gene/?term=31295	"Dmel_ BEST:SD07039, Dmel\CG3939, EG:140G11.5 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010177	31309	dnc	http://www.ncbi.nlm.nih.gov/gene/?term=31309	"Dmel_CG32498, CG10791, CG10792, CG10797, CG14267, CG14268, CG32498, Dmel\CG32498, EG:140G11.4, EG:96G10.7, EG:BACN05I09.3, EG:BACN5I9.2, PDE4, PDEII, fs(1)M42 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010178	31310	Myc	http://www.ncbi.nlm.nih.gov/gene/?term=31310	"Dmel_CG10798, CG10798, D- DM, DMYc, Dm, Dmel\CG10798, Dmyc, EG:BACN5I9.1, MYC, anon-WO03040301.171, bHLHe57, c-MYC, c-Myc, c-myc, d-myc, dMYC, dMyc, dMyc1, dm, dm/dMyc, dm/myc, dmyc, dmyc1, l(1)G0139, l(1)G0354, l(1)G0359, myc "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010179	31310	Myc	http://www.ncbi.nlm.nih.gov/gene/?term=31310	"Dmel_CG10798, CG10798, D- DM, DMYc, Dm, Dmel\CG10798, Dmyc, EG:BACN5I9.1, MYC, anon-WO03040301.171, bHLHe57, c-MYC, c-Myc, c-myc, d-myc, dMYC, dMyc, dMyc1, dm, dm/dMyc, dm/myc, dmyc, dmyc1, l(1)G0139, l(1)G0354, l(1)G0359, myc "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010180	31310	Myc	http://www.ncbi.nlm.nih.gov/gene/?term=31310	"Dmel_CG10798, CG10798, D- DM, DMYc, Dm, Dmel\CG10798, Dmyc, EG:BACN5I9.1, MYC, anon-WO03040301.171, bHLHe57, c-MYC, c-Myc, c-myc, d-myc, dMYC, dMyc, dMyc1, dm, dm/dMyc, dm/myc, dmyc, dmyc1, l(1)G0139, l(1)G0354, l(1)G0359, myc "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010181	31310	Myc	http://www.ncbi.nlm.nih.gov/gene/?term=31310	"Dmel_CG10798, CG10798, D- DM, DMYc, Dm, Dmel\CG10798, Dmyc, EG:BACN5I9.1, MYC, anon-WO03040301.171, bHLHe57, c-MYC, c-Myc, c-myc, d-myc, dMYC, dMyc, dMyc1, dm, dm/dMyc, dm/myc, dmyc, dmyc1, l(1)G0139, l(1)G0354, l(1)G0359, myc "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010182	31310	Myc	http://www.ncbi.nlm.nih.gov/gene/?term=31310	"Dmel_CG10798, CG10798, D- DM, DMYc, Dm, Dmel\CG10798, Dmyc, EG:BACN5I9.1, MYC, anon-WO03040301.171, bHLHe57, c-MYC, c-Myc, c-myc, d-myc, dMYC, dMyc, dMyc1, dm, dm/dMyc, dm/myc, dmyc, dmyc1, l(1)G0139, l(1)G0354, l(1)G0359, myc "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010183	31318	CG10802	http://www.ncbi.nlm.nih.gov/gene/?term=31318	"Dmel_ Dmel\CG10802, anon-EST:Posey113 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010184	31320	CG10803	http://www.ncbi.nlm.nih.gov/gene/?term=31320	Dmel_ Dmel\CG10803	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010185	31322	DIP-alpha	http://www.ncbi.nlm.nih.gov/gene/?term=31322	"Dmel_CG32791, 32791, CG13019, CG13020, CG32791, Dmel\CG32791 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010186	3133	HLA-E	http://www.ncbi.nlm.nih.gov/gene/?term=3133	"EA1.2, EA2.1, HLA-6.2, MHC, QA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010187	3133	HLA-E	http://www.ncbi.nlm.nih.gov/gene/?term=3133	"EA1.2, EA2.1, HLA-6.2, MHC, QA1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010188	31348	CG2941	http://www.ncbi.nlm.nih.gov/gene/?term=31348	Dmel_ Dmel\CG2941	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010189	31348	CG2941	http://www.ncbi.nlm.nih.gov/gene/?term=31348	Dmel_ Dmel\CG2941	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010190	3134	HLA-F	http://www.ncbi.nlm.nih.gov/gene/?term=3134	"CDA12, HLA-5.4, HLA-CDA12, HLAF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010191	3136	HLA-H	http://www.ncbi.nlm.nih.gov/gene/?term=3136	HLAHP	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010192	31381	rb	http://www.ncbi.nlm.nih.gov/gene/?term=31381	"Dmel_CG11427, AP-3beta, CG11427, Dmel\CG11427, Rb, apl6, beta3, cg11427 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010193	31384	Usf	http://www.ncbi.nlm.nih.gov/gene/?term=31384	"Dmel_CG17592, CG17592, Dm  DmUsf, Dmel\CG17592, bHLHb13, dUSF, dUSF2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010194	31384	Usf	http://www.ncbi.nlm.nih.gov/gene/?term=31384	"Dmel_CG17592, CG17592, Dm  DmUsf, Dmel\CG17592, bHLHb13, dUSF, dUSF2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010195	31386	CG11436	http://www.ncbi.nlm.nih.gov/gene/?term=31386	Dmel_ Dmel\CG11436	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010196	31388	CG11444	http://www.ncbi.nlm.nih.gov/gene/?term=31388	Dmel_ Dmel\CG11444	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010197	3140	MR1	http://www.ncbi.nlm.nih.gov/gene/?term=3140	HLALS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010198	3141	HLCS	http://www.ncbi.nlm.nih.gov/gene/?term=3141	HCS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010199	3141	HLCS	http://www.ncbi.nlm.nih.gov/gene/?term=3141	HCS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010200	3141	HLCS	http://www.ncbi.nlm.nih.gov/gene/?term=3141	HCS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010201	31426	CG15468	http://www.ncbi.nlm.nih.gov/gene/?term=31426	"Dmel_ Dmel\CG15468, SIP3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010202	31429	ovo	http://www.ncbi.nlm.nih.gov/gene/?term=31429	"Dmel_CG6824, CG15467, CG6824, Dmel\CG6824, Fs(1)K1103, Fs(1)K1237, Fs(1)K155, OVO, Ovo, Ovo-D, Shv, Svb, Svb/Ovo, fs(1)K1237, fs(1)M1, fs(1)M38/shavenbaby, ovo/svb, ovoD, svb "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00010203	314310	Zfp410	http://www.ncbi.nlm.nih.gov/gene/?term=314310	Znf410	mRNA	Rattus norvegicus	25301173	Dendrite	Hippocampus	In situ hybridization	"Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). Probes Zfp410, Commd3, and Rps6 showed lower dendrite soma ratios for mouse vs rat at 0.085 vs 0.174 (p < 0.09), 0.101 vs 0.215 (p < 0.001), and 0.034 vs 0.097 (p < 0.008), respectively.  "
RLID00010204	31444	dhd	http://www.ncbi.nlm.nih.gov/gene/?term=31444	"Dmel_CG4193, 4193, CG4193, Dhd, DmTrx-1, Dmdhd, Dmel\CG4193, Dmeldhd, Trx-1 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010205	31448	Rnp4F	http://www.ncbi.nlm.nih.gov/gene/?term=31448	"Dmel_CG3312, 4F-rnp, 4f-rnp, CG3312, Dmel\CG3312, RNP-4F, Rnp-4F, rnp-4f "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010206	31459	spoon	http://www.ncbi.nlm.nih.gov/gene/?term=31459	"Dmel_CG3249, BcDNA:GM04319, CG3249, DAKAP550, Dmel\CG3249, PKAAP, Yu, yu "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010207	31459	spoon	http://www.ncbi.nlm.nih.gov/gene/?term=31459	"Dmel_CG3249, BcDNA:GM04319, CG3249, DAKAP550, Dmel\CG3249, PKAAP, Yu, yu "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010208	3145	HMBS	http://www.ncbi.nlm.nih.gov/gene/?term=3145	"PBG-D, PBGD, PORC, UPS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010209	3145	HMBS	http://www.ncbi.nlm.nih.gov/gene/3145	"UPS, PBGD, PORC, PBG-D "	mRNA	Homo sapiens	19175411	Ribosome	T-cell|SeAx	qRT-PCR	"Using quantitative real-time RT-PCR we evaluated, whether mRNAs coding for differently located proteins are selectively enriched in one of the two analysed compartments, namely free versus membrane-associated polysomes. We selected genes coding for proteins located in the plasma membrane (GPR137B), secreted proteins (TIC2, IBP2, PAI) and cytosolic proteins (the house keeping genes GAPDH and HMBS). In fact, the distribution of the specific mRNA was as predicted ( Fig. 1): The average ratio of specific mRNA at bound ribosomes versus free ribosomes was 1 ? 4.4 for the housekeeping genes (GAPDH and HMBS) and 13.3 ? 1 for genes coding for membrane-bound or secreted proteins. Ratios for genes coding for cytosolic proteins were always below 0.6 and those for membrane or secreted genes were always above 1. The highest values were observed for PAI in MyLa (57 ? 1) and GPR137B in SeAx (34 ? 1), while the lowest ratios were detected for HMBS (1 ? 55) and GAPDH (1 ? 12) in HuT78. "
RLID00010210	3145	HMBS	http://www.ncbi.nlm.nih.gov/gene/?term=3145	"PBG-D, PBGD, PORC, UPS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010211	3146	HMGB1	http://www.ncbi.nlm.nih.gov/gene/?term=3146	"HMG-1, HMG1, HMG3, SBP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010212	3146	HMGB1	http://www.ncbi.nlm.nih.gov/gene/?term=3146	"HMG-1, HMG1, HMG3, SBP-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010213	3148	HMGB2	http://www.ncbi.nlm.nih.gov/gene/?term=3148	HMG2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010214	31491	CG33080	http://www.ncbi.nlm.nih.gov/gene/?term=31491	"Dmel_ CG15774, CG15775, CG3141, Dmel\CG33080 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010215	31498	CG15772	http://www.ncbi.nlm.nih.gov/gene/?term=31498	Dmel_ Dmel\CG15772	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010216	3149	HMGB3	http://www.ncbi.nlm.nih.gov/gene/?term=3149	"HMG-2a, HMG-4, HMG2A, HMG4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010217	3150	HMGN1	http://www.ncbi.nlm.nih.gov/gene/?term=3150	HMG14	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010218	31513	CG15765	http://www.ncbi.nlm.nih.gov/gene/?term=31513	Dmel_ Dmel\CG15765	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010219	3151	HMGN2	http://www.ncbi.nlm.nih.gov/gene/?term=3151	HMG17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010220	3151	HMGN2	http://www.ncbi.nlm.nih.gov/gene/?term=3151	HMG17	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010221	3151	HMGN2	http://www.ncbi.nlm.nih.gov/gene/?term=3151	HMG17	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010222	3155	HMGCL	http://www.ncbi.nlm.nih.gov/gene/?term=3155	HL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010223	3155	HMGCL	http://www.ncbi.nlm.nih.gov/gene/?term=3155	HL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010224	3156	HMGCR	http://www.ncbi.nlm.nih.gov/gene/?term=3156	LDLCQ3	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010225	3156	HMGCR	http://www.ncbi.nlm.nih.gov/gene/?term=3156	LDLCQ3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010226	3157	HMGCS1	http://www.ncbi.nlm.nih.gov/gene/?term=3157	HMGCS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010227	3157	HMGCS1	http://www.ncbi.nlm.nih.gov/gene/?term=3157	HMGCS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010228	31585	CG3918	http://www.ncbi.nlm.nih.gov/gene/?term=31585	Dmel_ Dmel\CG3918	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010229	3158	HMGCS2	http://www.ncbi.nlm.nih.gov/gene/?term=3158		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010230	3159	HMGA1	http://www.ncbi.nlm.nih.gov/gene/?term=3159	"HMG-R, HMGA1A, HMGIY "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010231	3159	HMGA1	http://www.ncbi.nlm.nih.gov/gene/?term=3159	"HMG-RA, HMGIY, HMGA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010232	31602	CG3198	http://www.ncbi.nlm.nih.gov/gene/?term=31602	Dmel_ Dmel\CG3198	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010233	31617	shf	http://www.ncbi.nlm.nih.gov/gene/?term=31617	"Dmel_CG3135, CG3134, CG3135, CT10514, D-Wif, DmWIF, DmWif, Dmel\CG3135, Shf-ov, shf "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010234	31618	C3G	http://www.ncbi.nlm.nih.gov/gene/?term=31618	"Dmel_CG42328, C(3)G, CG14436, CG3126, CG42328, DC3-G, DC3G, Dmel\CG42328, Dmel_CG14436, Dmel_CG3126, c(3)G "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010235	3161	HMMR	http://www.ncbi.nlm.nih.gov/gene/?term=3161	"CD168, IHABP, RHAMM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010236	3161	HMMR	http://www.ncbi.nlm.nih.gov/gene/?term=3161	"CD168, IHABP, RHAMM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010237	3161	HMMR	http://www.ncbi.nlm.nih.gov/gene/?term=3161	"CD168, IHABP, RHAMM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010238	31628	CG14435	http://www.ncbi.nlm.nih.gov/gene/?term=31628	Dmel_ Dmel\CG14435	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010239	3163	HMOX2	http://www.ncbi.nlm.nih.gov/gene/?term=3163	HO-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010240	3163	HMOX2	http://www.ncbi.nlm.nih.gov/gene/?term=3163	HO-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010241	31646	Inx2	http://www.ncbi.nlm.nih.gov/gene/?term=31646	"Dmel_CG4590, CG4590, D-inx-2, Dm-inx, Dm-inx2, Dmel\CG4590, FBpp0291074, INX-2, Ix2, inx-2, inx2, kropf, l(1)G0035, l(1)G0036, l(1)G0043, l(1)G0059, l(1)G0118, l(1)G0157, l(1)G0317, l(1)G0364, prp33 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010242	3164	NR4A1	http://www.ncbi.nlm.nih.gov/gene/?term=3164	"GFRP1, HMR, N10, NAK-1, NGFIB, NP10, NUR77, TR3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010243	31651	CG14427	http://www.ncbi.nlm.nih.gov/gene/?term=31651	Dmel_ Dmel\CG14427	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010244	31658	CG8300	http://www.ncbi.nlm.nih.gov/gene/?term=31658	Dmel_ Dmel\CG8300	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010245	31658	CG8300	http://www.ncbi.nlm.nih.gov/gene/?term=31658	Dmel_ Dmel\CG8300	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010246	31665	brk	http://www.ncbi.nlm.nih.gov/gene/?term=31665	"Dmel_CG9653, Brk, CG9653, Dm brk, Dmel\CG9653, ssg-1 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010247	31665	brk	http://www.ncbi.nlm.nih.gov/gene/?term=31665	"Dmel_CG9653, Brk, CG9653, Dm brk, Dmel\CG9653, ssg-1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010248	31667	Dok	http://www.ncbi.nlm.nih.gov/gene/?term=31667	"Dmel_CG2079, CG2079, Ddok, Dmel\CG2079, l(1)G0331 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010249	31667	Dok	http://www.ncbi.nlm.nih.gov/gene/?term=31667	"Dmel_CG2079, CG2079, Ddok, Dmel\CG2079, l(1)G0331 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010250	31667	Dok	http://www.ncbi.nlm.nih.gov/gene/?term=31667	"Dmel_CG2079, CG2079, Ddok, Dmel\CG2079, l(1)G0331 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010251	31667	Dok	http://www.ncbi.nlm.nih.gov/gene/?term=31667	"Dmel_CG2079, CG2079, Ddok, Dmel\CG2079, l(1)G0331 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010252	31696	Nek2	http://www.ncbi.nlm.nih.gov/gene/?term=31696	"Dmel_CG17256, CG17256, Dm  DmNek2, Dmel\CG17256, NEK2, dNek2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010253	316	AOX1	http://www.ncbi.nlm.nih.gov/gene/?term=316	"AO, AOH1 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00010254	31704	snz	http://www.ncbi.nlm.nih.gov/gene/?term=31704	"Dmel_CG1514, CG1514, DmSNX25, Dmel\CG1514, Snz "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010255	31704	snz	http://www.ncbi.nlm.nih.gov/gene/?term=31704	"Dmel_CG1514, CG1514, DmSNX25, Dmel\CG1514, Snz "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010256	31712	l(1)G0193	http://www.ncbi.nlm.nih.gov/gene/?term=31712	"Dmel_CG2206, CG2206, Dmel\CG2206, l(1)G0327 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010257	31717	sn	http://www.ncbi.nlm.nih.gov/gene/?term=31717	"Dmel_CG32858, CG15331, CG1536, CG32858, Dmel\CG32858, SN, Sn, fs(1)A1057, fs(1)K1421, fs(1)K418, fs(1)K473, fs(1)K743, fs(1)M45 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010258	31717	sn	http://www.ncbi.nlm.nih.gov/gene/?term=31717	"Dmel_CG32858, CG15331, CG1536, CG32858, Dmel\CG32858, SN, Sn, fs(1)A1057, fs(1)K1421, fs(1)K418, fs(1)K473, fs(1)K743, fs(1)M45 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010259	31717	sn	http://www.ncbi.nlm.nih.gov/gene/?term=31717	"Dmel_CG32858, CG15331, CG1536, CG32858, Dmel\CG32858, SN, Sn, fs(1)A1057, fs(1)K1421, fs(1)K418, fs(1)K473, fs(1)K743, fs(1)M45 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010260	3171	FOXA3	http://www.ncbi.nlm.nih.gov/gene/?term=3171	"FKHH3, HNF3G, TCF3G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010261	3172	HNF4A	http://www.ncbi.nlm.nih.gov/gene/?term=3172	"FRTS4, HNF4, HNF4a7, HNF4a8, HNF4a9, HNF4alpha, MODY, MODY1, NR2A1, NR2A21, TCF, TCF14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010262	31733	cyr	http://www.ncbi.nlm.nih.gov/gene/?term=31733	"Dmel_CG15335, CG15335, CG15338, Dmel\CG15335 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010263	31738	Smox	http://www.ncbi.nlm.nih.gov/gene/?term=31738	"Dmel_CG2262, CG2262, DSMAD2, DSmad2, Dmel\CG2262, SMAD2, SMOX, Sad, Smad, Smad2, SmoX, dSMAD2, dSmad2, dsmad2, l(1)G0348, sad, smad2, smox, ted, tmp "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00010264	31744	Gbeta5	http://www.ncbi.nlm.nih.gov/gene/?term=31744	"Dmel_CG10763, CG10763, Dmel\CG10763, G[[beta5]], G[[beta]], Gbeta, Gbeta 5, Gbetagamma "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010265	317646	Rpl13a	http://www.ncbi.nlm.nih.gov/gene/?term=317646		snoRNA	Rattus norvegicus	25792744	Nucleus	Myocardium	Next-generation sequencing|qRT-PCR	"Our data showing that 99% of Rpl13a snoRNAs are nuclear in unstressed cells are consistent with this (Fig. 1F). However, by using the high sensitivity methods of qPCR and RNA-seq, we show for the first time that a broad range of snoRNAs are easily detectable in the cytoplasm. The accumulation of Rpl13a snoRNAs in the cytoplasm after oxidative stress is rapid and significant. "
RLID00010266	317646	Rpl13a	http://www.ncbi.nlm.nih.gov/gene/?term=317646		snoRNA	Rattus norvegicus	25792744	Cytoplasm	Myocardium	Next-generation sequencing|qRT-PCR	"Our data showing that 99% of Rpl13a snoRNAs are nuclear in unstressed cells are consistent with this (Fig. 1F). However, by using the high sensitivity methods of qPCR and RNA-seq, we show for the first time that a broad range of snoRNAs are easily detectable in the cytoplasm. The accumulation of Rpl13a snoRNAs in the cytoplasm after oxidative stress is rapid and significant. "
RLID00010267	317648	NOP14-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=317648	"C4orf10, RES4-24 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010268	317662	FAM149B1	http://www.ncbi.nlm.nih.gov/gene/?term=317662	KIAA0974	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010269	3176	HNMT	http://www.ncbi.nlm.nih.gov/gene/?term=3176	"HMT, HNMT-S1, HNMT-S2, MRT51 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010270	3176	HNMT	http://www.ncbi.nlm.nih.gov/gene/?term=3176	"HMT-S1, HNMT-S2, MRT51, HNMT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010271	31773	Trf2	http://www.ncbi.nlm.nih.gov/gene/?term=31773	"Dmel_CG18009, CG11195, CG18009, Dmel\CG18009, TLF, TRF2, dTRF2, dTRF2L, dTRF2S, dTrf2, l(1)G0039, l(1)G0071, l(1)G0295, l(1)G0425, p79/TRF2, trf2 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00010272	317758	Gimap9	http://www.ncbi.nlm.nih.gov/gene/?term=317758	"A630002K24, BB145400 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010273	31775	CG12125	http://www.ncbi.nlm.nih.gov/gene/?term=31775	Dmel_ Dmel\CG12125	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010274	317762	CCDC85C	http://www.ncbi.nlm.nih.gov/gene/?term=317762		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010275	317772	HIST2H2AB	http://www.ncbi.nlm.nih.gov/gene/?term=317772	H2AB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010276	317781	DDX51	http://www.ncbi.nlm.nih.gov/gene/?term=317781		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010277	3177	SLC29A2	http://www.ncbi.nlm.nih.gov/gene/?term=3177	"DER12, ENT2, HNP36 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010278	317824	Zyx	http://www.ncbi.nlm.nih.gov/gene/?term=317824	"Dmel_CG32018, BcDNA:LD06023, CG32018, DLim-1, DmLIM-1, Dmel\CG32018, Lim102EF, ZYX102102, Zyx102EF, lim, zyx, zyx102, zyxin, Zyx "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00010279	317824	Zyx	http://www.ncbi.nlm.nih.gov/gene/?term=317824	"Dmel_CG32018, BcDNA:LD06023, CG32018, DLim-1, DmLIM-1, Dmel\CG32018, Lim102EF, ZYX102102, Zyx102EF, lim, zyx, zyx102, zyxin, Zyx "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010280	317829	CG32026	http://www.ncbi.nlm.nih.gov/gene/?term=317829	"Dmel_ BcDNA:GH12815, Dmel\CG32026, anon-WO0140519.202 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010281	317894	CG32170	http://www.ncbi.nlm.nih.gov/gene/?term=317894	"Dmel_ BcDNA:RE28470, CT12913, Dmel\CG32170 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010282	317894	CG32170	http://www.ncbi.nlm.nih.gov/gene/?term=317894	"Dmel_ BcDNA:RE28470, CT12913, Dmel\CG32170 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010283	3178	HNRNPA1	http://www.ncbi.nlm.nih.gov/gene/?term=3178	"ALS19, ALS20, HNRPA1, HNRPA1L3, IBMPFD3, UP 1, hnRNP A1, hnRNP-A1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010284	3178	HNRNPA1	http://www.ncbi.nlm.nih.gov/gene/?term=3178	"ALS19, ALS20, HNRPA1, HNRPA1L3, IBMPFD3, UP 1, hnRNP A1, hnRNP-A1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010285	3178	HNRNPA1	http://www.ncbi.nlm.nih.gov/gene/?term=3178	"ALS19, ALS20, HNRPA1, HNRPA1L3, IBMPFD3, UP 1, hnRNP A1, hnRNP-A1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010286	317	APAF1	http://www.ncbi.nlm.nih.gov/gene/?term=317	"APAF-1, CED4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010287	317	APAF1	http://www.ncbi.nlm.nih.gov/gene/?term=317	"APAF-1, CED4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010288	318000	CG32373	http://www.ncbi.nlm.nih.gov/gene/?term=318000	"Dmel_ BcDNA:RE64043, CG3237, Dmel\CG32373 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010289	318000	CG32373	http://www.ncbi.nlm.nih.gov/gene/?term=318000	"Dmel_ BcDNA:RE64043, CG3237, Dmel\CG32373 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010290	31808	Hexo2	http://www.ncbi.nlm.nih.gov/gene/?term=31808	"Dmel_CG1787, CG1787, DmHex2, Dmel\CG1787, HEX 2, HEX2, HEXO2 "	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010291	31813	Lim1	http://www.ncbi.nlm.nih.gov/gene/?term=31813	"Dmel_CG11354, BcDNA:GH04929, CG10760, CG11354, Dlim1, Dmel\CG11354, Lim, d dlim-1, dlim1, lim1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010292	31813	Lim1	http://www.ncbi.nlm.nih.gov/gene/?term=31813	"Dmel_CG11354, BcDNA:GH04929, CG10760, CG11354, Dlim1, Dmel\CG11354, Lim, d dlim-1, dlim1, lim1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010293	31816	Moe	http://www.ncbi.nlm.nih.gov/gene/?term=31816	"Dmel_CG10701, CG10701, D17, Dmel\CG10701, Dmoe, EMR1, ERM, Emr1s, anon-WO03040301.155, anon-WO03040301.157, anon-WO03040301.159, anon-WO03040301.161, dMoe, gma, l(1)G0067, l(1)G0323, l(1)G0404, l(1)G0415, moe, moesin/ezrin/radixin homolog mRNA, Moe "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010294	3181	HNRNPA2B1	http://www.ncbi.nlm.nih.gov/gene/?term=3181	"HNRNPA2, HNRNPB1, HNRPA2, HNRPA2B1, HNRPB1, IBMPFD2, RNPA2, SNRPB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010295	3181	HNRNPA2B1	http://www.ncbi.nlm.nih.gov/gene/?term=3181	"HNRNPA2, HNRNPB1, HNRPA2, HNRPA2B1, HNRPB1, IBMPFD2, RNPA2, SNRPB1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010296	3181	HNRNPA2B1	http://www.ncbi.nlm.nih.gov/gene/?term=3181	"HNRNPA2, HNRNPB1, HNRPA2, HNRPA2B1, HNRPB1, IBMPFD2, RNPA2, SNRPB1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010297	31824	CG10962	http://www.ncbi.nlm.nih.gov/gene/?term=31824	"Dmel_ BcDNA:RE29909, CG7090, Dmel\CG10962, EP(X)1565, EP1565 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010298	3182	HNRNPAB	http://www.ncbi.nlm.nih.gov/gene/?term=3182	"ABBP1, HNRPAB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010299	3182	HNRNPAB	http://www.ncbi.nlm.nih.gov/gene/?term=3182	"ABBP1, HNRPAB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010300	3182	HNRNPAB	http://www.ncbi.nlm.nih.gov/gene/?term=3182	"ABBP1, HNRPAB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010301	31833	CG7246	http://www.ncbi.nlm.nih.gov/gene/?term=31833	"Dmel_ Dmel\CG7246, dUTP6 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010302	31833	CG7246	http://www.ncbi.nlm.nih.gov/gene/?term=31833	"Dmel_ Dmel\CG7246, dUTP6 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010303	3183	HNRNPC	http://www.ncbi.nlm.nih.gov/gene/?term=3183	"C1, C2, HNRNP, HNRPC, SNRPC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010304	3183	HNRNPC	http://www.ncbi.nlm.nih.gov/gene/?term=3183	"C1, C2, HNRNP, HNRPC, SNRPC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010305	3183	HNRNPC	http://www.ncbi.nlm.nih.gov/gene/?term=3183	"C1, C2, HNRNP, HNRPC, SNRPC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010306	318566	CG34133	http://www.ncbi.nlm.nih.gov/gene/?term=318566	"Dmel_ CG31035, CG7814, Dmel\CG34133, anon-WO0118547.417 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010307	3185	HNRNPF	http://www.ncbi.nlm.nih.gov/gene/?term=3185	"HNRPF, OK/SW-cl.23, mcs94-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010308	3185	HNRNPF	http://www.ncbi.nlm.nih.gov/gene/?term=3185	"HNRPF, OK/SW-cl.23, mcs94-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010309	3185	HNRNPF	http://www.ncbi.nlm.nih.gov/gene/?term=3185	"HNRPF, OK/SW-cl.23, mcs94-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010310	3187	HNRNPH1	http://www.ncbi.nlm.nih.gov/gene/?term=3187	"HNRPH, HNRPH1, hnRNPH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010311	3187	HNRNPH1	http://www.ncbi.nlm.nih.gov/gene/?term=3187	"HNRPH, HNRPH1, hnRNPH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010312	318841	Bsg	http://www.ncbi.nlm.nih.gov/gene/?term=318841	"Dmel_CG31605, 135/10, BcDNA:GH21853, CG31605, Dmel\CG31605, NP6293, bsg, gel, l(2)06243, l(2)SH1217, l(2)SH2 1217, l(2)k06338, l(2)k09030, l(2)k13638, l(2)k14308, ms(2)08318 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010313	3188	HNRNPH2	http://www.ncbi.nlm.nih.gov/gene/?term=3188	"FTP3, HNRPH', HNRPH2, hnRNPH' "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010314	3188	HNRNPH2	http://www.ncbi.nlm.nih.gov/gene/?term=3188	"FTP3, HNRPH', HNRPH2, hnRNPH' "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010315	3189	HNRNPH3	http://www.ncbi.nlm.nih.gov/gene/?term=3189	"2H9, HNRPH3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010316	318	NUDT2	http://www.ncbi.nlm.nih.gov/gene/?term=318	APAH1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010317	3190	HNRNPK	http://www.ncbi.nlm.nih.gov/gene/?term=3190	"AUKS, CSBP, HNRPK, TUNP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010318	3190	HNRNPK	http://www.ncbi.nlm.nih.gov/gene/?term=3190	"AUKS, CSBP, HNRPK, TUNP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010319	3190	HNRNPK	http://www.ncbi.nlm.nih.gov/gene/?term=3190	"AUKS, CSBP, HNRPK, TUNP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010320	319103	SNORD8	http://www.ncbi.nlm.nih.gov/gene/?term=319103	"RNU6C, mgU6-53 "	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010321	319103	SNORD8	http://www.ncbi.nlm.nih.gov/gene/?term=319103	"RNU6C, mgU6-53 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00010322	319146	Ifnz	http://www.ncbi.nlm.nih.gov/gene/?term=319146	"6030405N23Rik, BGIF, ENSMUSG00000073810, Lmtn "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010323	319172	Hist1h2ab	http://www.ncbi.nlm.nih.gov/gene/?term=319172	"H2A.1, H2a-53 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010324	319178	Hist1h2bb	http://www.ncbi.nlm.nih.gov/gene/?term=319178	H2b-143	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010325	319181	Hist1h2bg	http://www.ncbi.nlm.nih.gov/gene/?term=319181		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010326	319190	Hist2h2be	http://www.ncbi.nlm.nih.gov/gene/?term=319190	"AV127319, H2b-613, T25626 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010327	319195	Rpl17	http://www.ncbi.nlm.nih.gov/gene/?term=319195		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010328	319195	Rpl17	http://www.ncbi.nlm.nih.gov/gene/?term=319195		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00010329	3191	HNRNPL	http://www.ncbi.nlm.nih.gov/gene/?term=3191	"HNRPL, P/OKcl.14, hnRNP-L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010330	319211	Nol4	http://www.ncbi.nlm.nih.gov/gene/?term=319211	"1700013J13Rik, 4930568N03Rik, Gm1262 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010331	319243	9430062P05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319243		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010332	319269	A130040M12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319269	"CA782090, H3053C11, VL30 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010333	319269	A130040M12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319269	"CA782090, H3053C11, VL30 "	mRNA	Mus musculus	16730676	Ribosome	Brain	In situ hybridization	"These VL30 transcripts remained associated with polyribosomes in the presence of 0.5 M KCl, indicating that VL30 mRNA was tightly associated with ribosomal subunits.  "
RLID00010334	319269	A130040M12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319269	"CA782090, H3053C11, VL30 "	mRNA	Mus musculus	25847616	Mitochondrion	Liver	Next-generation sequencing|qRT-PCR	"Several nuclear transcribed RNAs were found within mitochondrial RNA (mtRNA) samples, including nuclear ribosomal RNAs, gamma satellite RNA and VL30 retroelement RNA. Additionally, our improved mitochondrial localization interrogation technique supported the localization of VL30 retroelement RNA within mitochondria. Maintenance of VL30 RNA was observed until mitochondrial rupture, where it was destroyed by nuclease activity. "
RLID00010335	3192	HNRNPU	http://www.ncbi.nlm.nih.gov/gene/?term=3192	"HNRNPU-AS1, HNRPU, SAF-A, SAFA, U21.1, hnRNP U "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010336	3192	HNRNPU	http://www.ncbi.nlm.nih.gov/gene/?term=3192	"HNRNPU-AS1, HNRPU, SAF-A, SAFA, U21.1, hnRNP U "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010337	319301	A730027B03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319301		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010338	319352	Pianp	http://www.ncbi.nlm.nih.gov/gene/?term=319352	"AI255183, AU067746, C530028O21Rik, Panp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010339	319377	D130012P04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319377		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010340	319430	C5ar2	http://www.ncbi.nlm.nih.gov/gene/?term=319430	"C5L2, E030029A11Rik, Gpr77 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010341	319448	Fndc3a	http://www.ncbi.nlm.nih.gov/gene/?term=319448	"1700094E19Rik, D14Ertd453e, F730017H24Rik, Fndc3, sys "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010342	31945	RhoU	http://www.ncbi.nlm.nih.gov/gene/?term=31945	"Dmel_CG34104, CG12094, CG12102, CG34104, Dmel\CG34104 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010343	31945	RhoU	http://www.ncbi.nlm.nih.gov/gene/?term=31945	"Dmel_CG34104, CG12094, CG12102, CG34104, Dmel\CG34104 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010344	31945	RhoU	http://www.ncbi.nlm.nih.gov/gene/?term=31945	"Dmel_CG34104, CG12094, CG12102, CG34104, Dmel\CG34104 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010345	319460	A130094D17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319460		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010346	319475	Zfp672	http://www.ncbi.nlm.nih.gov/gene/?term=319475	"4930488P06Rik, 4930511N19Rik, Znf672 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010347	31949	CG15309	http://www.ncbi.nlm.nih.gov/gene/?term=31949	"Dmel_ BcDNA:GH10478, Dmel\CG15309 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010348	319552	Spx	http://www.ncbi.nlm.nih.gov/gene/?term=319552	"B230216G23Rik, Npq "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010349	319556	A330041J22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319556		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010350	319560	9630002D21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319560		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010351	319564	C230012O17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319564		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010352	319583	Lig4	http://www.ncbi.nlm.nih.gov/gene/?term=319583	"5830471N16Rik, tiny "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010353	319604	Fam168a	http://www.ncbi.nlm.nih.gov/gene/?term=319604	"2610030B18Rik, B930006L02Rik, mKIAA0280 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010354	319615	Zfp944	http://www.ncbi.nlm.nih.gov/gene/?term=319615	6330416L07Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010355	319626	9530059O14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319626		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010356	319637	A430072C10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319637		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010357	319651	Usp37	http://www.ncbi.nlm.nih.gov/gene/?term=319651	"4932415L06Rik, C330008N13Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010358	319664	E230012J19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319664		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010359	319665	A430010J10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319665		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010360	319670	Eml5	http://www.ncbi.nlm.nih.gov/gene/?term=319670	"BC027154, C130068M19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010361	319675	Cep295	http://www.ncbi.nlm.nih.gov/gene/?term=319675	"5830418K08Rik, 5832426L23Rik, Gm1131, Kiaa1731 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010362	319675	Cep295	http://www.ncbi.nlm.nih.gov/gene/?term=319675	"5830418K08Rik, 5832426L23Rik, Gm1131, Kiaa1731 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010363	319710	Frmd6	http://www.ncbi.nlm.nih.gov/gene/?term=319710	"2610019M19Rik, 4930488L10Rik, AW212977, Willin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010364	319719	Simc1	http://www.ncbi.nlm.nih.gov/gene/?term=319719	4732471D19Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010365	319739	B230303O12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319739		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010366	319747	C130023A14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319747		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010367	319758	Rfx7	http://www.ncbi.nlm.nih.gov/gene/?term=319758	"2510005N23Rik, 9930116O05Rik, D130086K05Rik, Rfxdc2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010368	319765	Igf2bp2	http://www.ncbi.nlm.nih.gov/gene/?term=319765	"C330012H03Rik, IMP-2, Imp2, Neilsen "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010369	319806	D630022N01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319806		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010370	319807	Nwd2	http://www.ncbi.nlm.nih.gov/gene/?term=319807	"3110047P20Rik, B830017A01Rik, Hn1-ps2, mKIAA1239 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010371	319817	Rc3h2	http://www.ncbi.nlm.nih.gov/gene/?term=319817	"2900024N03Rik, 9430019J22Rik, D930043C02Rik, Mnab, Rnf164 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010372	319819	4932435O22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319819		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010373	319829	9330154K18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319829		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010374	31986	CG15296	http://www.ncbi.nlm.nih.gov/gene/?term=31986	"Dmel_ BcDNA:AT26906, Dmel\CG15296 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010375	31986	CG15296	http://www.ncbi.nlm.nih.gov/gene/?term=31986	"Dmel_ BcDNA:AT26906, Dmel\CG15296 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010376	319876	Cobll1	http://www.ncbi.nlm.nih.gov/gene/?term=319876	"1810047P18Rik, Coblr1, D430044D16Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010377	319876	Cobll1	http://www.ncbi.nlm.nih.gov/gene/?term=319876	"1810047P18Rik, Coblr1, D430044D16Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010378	31987	spri	http://www.ncbi.nlm.nih.gov/gene/?term=31987	"Dmel_CG34414, CG12638, CG15297, CG15298, CG15299, CG15300, CG15301, CG32674, CG32680, CG33175, CG34414, Dmel\CG34414, Dmel_CG32680, Dmel_CG33175, Rin1, Spri, anon-WO03040301.275 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010379	319885	Zcchc7	http://www.ncbi.nlm.nih.gov/gene/?term=319885	"4930572I07Rik, D4Wsu132e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010380	319929	A630076J17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319929		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010381	319945	Flad1	http://www.ncbi.nlm.nih.gov/gene/?term=319945	"A930017E24Rik, Pp591 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010382	319951	A230001M10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319951		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010383	319965	Cc2d1b	http://www.ncbi.nlm.nih.gov/gene/?term=319965	"A830039B04Rik, Freud2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010384	319982	5930430L01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319982		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010385	319996	Casc4	http://www.ncbi.nlm.nih.gov/gene/?term=319996	"D130060C09Rik, VGFG2573 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010386	319997	A630001G21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319997		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010387	319998	Tmem198	http://www.ncbi.nlm.nih.gov/gene/?term=319998	"A230078I05Rik-1, Tmem198a, Tmem198 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010388	31	ACACA	http://www.ncbi.nlm.nih.gov/gene/?term=31	"ACAC, ACACAD, ACC, ACC1, ACCA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010389	31	ACACA	http://www.ncbi.nlm.nih.gov/gene/?term=31	"ACACD, ACC, ACC1, ACCA, ACACA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010390	31	ACACA	http://www.ncbi.nlm.nih.gov/gene/?term=31	"ACACD, ACC, ACC1, ACCA, ACACA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010391	31	ACACA	http://www.ncbi.nlm.nih.gov/gene/?term=31	"ACACD, ACC, ACC1, ACCA, ACACA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010392	320011	Uggt1	http://www.ncbi.nlm.nih.gov/gene/?term=320011	"0910001L17Rik, A930007H10Rik, AA589501, AI414429, AI448372, C820010P03Rik, GT, UGT1, Ugcgl1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010393	320020	6330415G19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320020		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010394	32005	CG32676	http://www.ncbi.nlm.nih.gov/gene/?term=32005	"Dmel_ CG9725, CG9732, Dmel\CG32676 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010395	32005	CG32676	http://www.ncbi.nlm.nih.gov/gene/?term=32005	"Dmel_ CG9725, CG9732, Dmel\CG32676 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010396	32005	CG32676	http://www.ncbi.nlm.nih.gov/gene/?term=32005	"Dmel_ CG9725, CG9732, Dmel\CG32676 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010397	32007	sesB	http://www.ncbi.nlm.nih.gov/gene/?term=32007	"Dmel_CG16944, A/A-T, A/A-T/sesB, ADP/ATP translocase, ADT2, ANT, ANT1, CG16944, Dmel\CG16944, EM12, Hmr, S12, SesB, anon-WO02059370.55, dANT, jive, l(1)9Ed, l(1)9Fa, l(1)DC701, l(1)EM31, l(1)G0126, l(1)G0247, l(1)G0386, l(1)S12, orangi, ses B "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010398	32007	sesB	http://www.ncbi.nlm.nih.gov/gene/?term=32007	"Dmel_CG16944, A/A-T, A/A-T/sesB, ADP/ATP translocase, ADT2, ANT, ANT1, CG16944, Dmel\CG16944, EM12, Hmr, S12, SesB, anon-WO02059370.55, dANT, jive, l(1)9Ed, l(1)9Fa, l(1)DC701, l(1)EM31, l(1)G0126, l(1)G0247, l(1)G0386, l(1)S12, orangi, ses B "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010399	320082	Fbxw21	http://www.ncbi.nlm.nih.gov/gene/?term=320082	E330009P21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010400	320092	E030003E18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320092	1700127G21Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010401	320095	6430550D23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320095		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010402	32009	Imp	http://www.ncbi.nlm.nih.gov/gene/?term=32009	"Dmel_CG1691, CG1691, Dmel\CG1691, IGF-II, IGF2BP1, IMP, IMP-1, MRE11, ORE-9, anon-EST:fe2B3, anon-WO0140519.39, cg1691, dIMP, imp, l(1)G0072, mre11 "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010403	32009	Imp	http://www.ncbi.nlm.nih.gov/gene/?term=32009	"Dmel_CG1691, CG1691, Dmel\CG1691, IGF-II, IGF2BP1, IMP, IMP-1, MRE11, ORE-9, anon-EST:fe2B3, anon-WO0140519.39, cg1691, dIMP, imp, l(1)G0072, mre11 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010404	32009	Imp	http://www.ncbi.nlm.nih.gov/gene/?term=32009	"Dmel_CG1691, CG1691, Dmel\CG1691, IGF-II, IGF2BP1, IMP, IMP-1, MRE11, ORE-9, anon-EST:fe2B3, anon-WO0140519.39, cg1691, dIMP, imp, l(1)G0072, mre11 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010405	320100	Relt	http://www.ncbi.nlm.nih.gov/gene/?term=320100	"E430021K24Rik, Tnfrsf19l "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010406	320117	C730049O14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320117		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010407	320129	Adrbk2	http://www.ncbi.nlm.nih.gov/gene/?term=320129	"4833444A01Rik, AI851927, AW551196, Adrbk-2, Bark-2, GRK3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010408	320150	Zdhhc17	http://www.ncbi.nlm.nih.gov/gene/?term=320150	"A230053P19Rik, BB187739, D130071N24Rik, Hip14 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010409	320162	Cep95	http://www.ncbi.nlm.nih.gov/gene/?term=320162	"4732496G21Rik, AI118346, AI448335, Ccdc45, D330027A14Rik, F630025I20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010410	320165	Tacc1	http://www.ncbi.nlm.nih.gov/gene/?term=320165	"4833447E04Rik, AA960202, B230378H13Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010411	320168	9630050E16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320168		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010412	320172	E230016M11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320172		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010413	320203	C130071C03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320203	2810449C10Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010414	320206	A730028G07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320206		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010415	320226	Ccdc171	http://www.ncbi.nlm.nih.gov/gene/?term=320226	"4930418J05Rik, 4930473A06Rik, A330015D16Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010416	320260	A230059L01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320260		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010417	320266	D130060J02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320266		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010418	320267	Fubp3	http://www.ncbi.nlm.nih.gov/gene/?term=320267	"A330051M14Rik, AV006371, FBP3, Marta2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010419	320271	Scai	http://www.ncbi.nlm.nih.gov/gene/?term=320271	"9330112M16, A930041I02Rik, AI662729 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010420	320271	Scai	http://www.ncbi.nlm.nih.gov/gene/?term=320271	"9330112M16, A930041I02Rik, AI662729 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010421	320274	9330209N08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320274		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010422	320289	B830004H01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320289		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010423	320299	Iqcb1	http://www.ncbi.nlm.nih.gov/gene/?term=320299	"6820449I09Rik, AV128382, NPHP5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010424	320302	Glt28d2	http://www.ncbi.nlm.nih.gov/gene/?term=320302	"4732486J07Rik, Glt28d1l "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010425	320316	9330164J24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320316		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010426	320321	9430077A04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320321		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010427	320331	D230015J17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320331		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010428	320391	D930017J03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320391		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010429	320394	Cenpt	http://www.ncbi.nlm.nih.gov/gene/?term=320394	G630055P03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010430	320406	A630009H07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320406		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010431	320411	A730089K16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320411		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010432	320415	Gchfr	http://www.ncbi.nlm.nih.gov/gene/?term=320415	"2010323F13Rik, GFRP, P35 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010433	320430	C230073G13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320430		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010434	320435	Rinl	http://www.ncbi.nlm.nih.gov/gene/?term=320435	"5830482F20Rik, 9930116N10Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010435	320438	Alg6	http://www.ncbi.nlm.nih.gov/gene/?term=320438	E230028F23Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010436	320460	Vwc2l	http://www.ncbi.nlm.nih.gov/gene/?term=320460	"A830006F12Rik, Brl "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010437	320471	D230022J07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320471		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010438	320473	Heatr5b	http://www.ncbi.nlm.nih.gov/gene/?term=320473	"2010013B10Rik, A230048G03Rik, AV071430, D330050P16Rik, mKIAA1414 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010439	320478	Sox2ot	http://www.ncbi.nlm.nih.gov/gene/?term=320478	B230215L15Rik	lncRNA	Mus musculus	19767420	Nucleus	Embryonic stem cell	In situ hybridization|qRT-PCR	"SOX2OT was originally reported as a spliced ncRNA mapping to human chromosome 3q26.3-q27, with an intron overlapping the SOX2 gene in the same transcriptional orientation (Fantes et al. 2003). "
RLID00010440	320478	Sox2ot	http://www.ncbi.nlm.nih.gov/gene/?term=320478	B230215L15Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010441	320487	Heatr5a	http://www.ncbi.nlm.nih.gov/gene/?term=320487	"C230081H03Rik, D930036F22Rik, mKIAA1316 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010442	320492	A830018L16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320492		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010443	320502	Lmod3	http://www.ncbi.nlm.nih.gov/gene/?term=320502	5430424A14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010444	320506	Lmbrd2	http://www.ncbi.nlm.nih.gov/gene/?term=320506	9930036E21Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010445	320512	D930014O13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320512		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010446	320556	C230085N15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320556		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010447	32057	Dlic	http://www.ncbi.nlm.nih.gov/gene/?term=32057	"Dmel_CG1938, CG1938, D-LIC, DLIC, DLIC22, Dmel\CG1938, dlic, dlic2, l(1)G0065, l(1)G0190, Dlic "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010448	320581	Idi2	http://www.ncbi.nlm.nih.gov/gene/?term=320581	"4833405L16Rik, IPPI2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010449	320587	Tmem88b	http://www.ncbi.nlm.nih.gov/gene/?term=320587	A230069A22Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010450	320589	9530020O07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320589		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010451	3205	HOXA9	http://www.ncbi.nlm.nih.gov/gene/?term=3205	"ABD-B, HOX1, HOX1.7, HOX1G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010452	3205	HOXA9	http://www.ncbi.nlm.nih.gov/gene/?term=3205	"ABD-B, HOX1, HOX1.7, HOX1G "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010453	320604	Ccdc169	http://www.ncbi.nlm.nih.gov/gene/?term=320604	A730037C10Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010454	320615	Dopey1	http://www.ncbi.nlm.nih.gov/gene/?term=320615	"B130005I07Rik, BC035275, C130028L17, D9Ertd809e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010455	320621	D830044D21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320621		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010456	320632	Snrnp200	http://www.ncbi.nlm.nih.gov/gene/?term=320632	"A330064G03Rik, Ascc3l1, BC011390, HELIC2, U5-200-KD, U5-200KD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010457	320633	Zbtb26	http://www.ncbi.nlm.nih.gov/gene/?term=320633	A630026F21Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010458	320642	A630066F11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320642		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010459	320675	4921513D23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320675	BC031575	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010460	320698	C530042K13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320698		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010461	320701	Fam19a4	http://www.ncbi.nlm.nih.gov/gene/?term=320701	"C130034I18Rik Tafa-4, Tafa-4, Fam19a4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010462	320706	Soga1	http://www.ncbi.nlm.nih.gov/gene/?term=320706	"9830001H06Rik, AI426038, D430036N24Rik, Soga "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010463	320714	Trappc11	http://www.ncbi.nlm.nih.gov/gene/?term=320714	"AW558465, D030016E14Rik, R75422 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010464	320717	Pptc7	http://www.ncbi.nlm.nih.gov/gene/?term=320717	"9130017A15Rik, AA672638, AI848390, TA-PP2C "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010465	320720	Fastkd1	http://www.ncbi.nlm.nih.gov/gene/?term=320720	"5330408N05Rik, mKIAA1800 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010466	320746	5330437M03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320746		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010467	32075	CG1738	http://www.ncbi.nlm.nih.gov/gene/?term=32075	"Dmel_ BcDNA:RE11532, Dmel\CG1738 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010468	320766	E030022I16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320766		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010469	320772	Mdga2	http://www.ncbi.nlm.nih.gov/gene/?term=320772	"6720489L24Rik, 9330209L04Rik, Adp, Mamdc1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010470	320787	9130221L21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320787		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010471	320790	Chd7	http://www.ncbi.nlm.nih.gov/gene/?term=320790	"A730019I05Rik, Cycn, Cyn, Dz, Edy, Flo, GENA 47, GENA 60, Gena 52, Lda, Mt, Obt, Todo, WBE1, Whi, metis "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010472	320790	Chd7	http://www.ncbi.nlm.nih.gov/gene/?term=320790	"A730019I05Rik, Cycn, Cyn, Dz, Edy, Flo, GENA 47, GENA 60, Gena 52, Lda, Mt, Obt, Todo, WBE1, Whi, metis "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010473	320799	Zhx3	http://www.ncbi.nlm.nih.gov/gene/?term=320799	"1810059C13Rik, 4932418O04Rik, 9530010N21Rik, Tix1, mKIAA0395 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010474	3207	HOXA11	http://www.ncbi.nlm.nih.gov/gene/?term=3207	"HOX1, HOX1I, RUSAT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010475	320806	Gfm2	http://www.ncbi.nlm.nih.gov/gene/?term=320806	"6530419G12Rik, A930009M04Rik, EF-G2mt, EFG2, MST027, RRF2mt "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010476	320816	Ankrd16	http://www.ncbi.nlm.nih.gov/gene/?term=320816	"2810455F06Rik, AI646698, D430029B21Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010477	320822	4732417M03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320822		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010478	320825	Samd5	http://www.ncbi.nlm.nih.gov/gene/?term=320825	E130306M17Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010479	320829	C430014B12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320829		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010480	32083	dlg1	http://www.ncbi.nlm.nih.gov/gene/?term=32083	"Dmel_CG1725, 11, CG1725, CG1730, CPD, DLG, DLG-A, DLG1, Discs-large, Dlg, Dlg-A, Dlg1, DlgA, DlgS97, Dmel\CG1725, Drodlg, PSD95, SAP97, anon-EST:Posey93, anon-WO03040301.258, anon-WO03040301.260, anon-WO03040301.268, d. lg.-1, dlg, dlg-1, dlg-A, dlgA, dlgS97, l(1)10Bf, l(1)G0276, l(1)G0342, l(1)G0456, l(1)G19, l(1)L11, l(1)bwn, l(1)d.lg-1, l(1)d.lg.-1, l(1)discs large, l(1)dlg, l(1)dlg-1, l(1)dlg1, l(1)l.pr.-2, l(1)lpr-2, misb "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010481	320841	9230115F04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320841		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010482	320864	Krt26	http://www.ncbi.nlm.nih.gov/gene/?term=320864	"4732407F15Rik, Krt25b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010483	320873	Cdh10	http://www.ncbi.nlm.nih.gov/gene/?term=320873	"A830016G23Rik, C030003B10Rik, C030011H18Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010484	320873	Cdh10	http://www.ncbi.nlm.nih.gov/gene/?term=320873	"A830016G23Rik, C030003B10Rik, C030011H18Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010485	320893	6430562O15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320893		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010486	3208	HPCA	http://www.ncbi.nlm.nih.gov/gene/?term=3208	"BDR2, DYT2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010487	320910	Itgb8	http://www.ncbi.nlm.nih.gov/gene/?term=320910	4832412O06Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010488	320929	4732460I02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320929		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010489	320938	Tnpo3	http://www.ncbi.nlm.nih.gov/gene/?term=320938	"5730544L10Rik, C430013M08Rik, C81142, D6Ertd313e, Trn-SR, mKIAA4133 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010490	32093	Cyp4g15	http://www.ncbi.nlm.nih.gov/gene/?term=32093	"Dmel_CG11715, 152658_at, 4g15, CG11715, Dmel\CG11715 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010491	320949	D830039M14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320949		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010492	320951	Pisd	http://www.ncbi.nlm.nih.gov/gene/?term=320951	9030221M09Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010493	320975	D330050G23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320975		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010494	320999	9530019H20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320999		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010495	320	APBA1	http://www.ncbi.nlm.nih.gov/gene/?term=320	"D9S411E, LIN10, MINT1, X11, X11A, X11ALPHA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010496	321000	Lrif1	http://www.ncbi.nlm.nih.gov/gene/?term=321000	"2010012G17Rik, 4933421E11Rik, AI450568 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010497	321006	Vprbp	http://www.ncbi.nlm.nih.gov/gene/?term=321006	"AI447437, B930007L02Rik, mKIAA0800 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010498	321015	5330439B14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=321015		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010499	321022	Cdv3	http://www.ncbi.nlm.nih.gov/gene/?term=321022	"2510010F10Rik, C230084J24Rik, C79446, TPP36 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010500	321022	Cdv3	http://www.ncbi.nlm.nih.gov/gene/?term=321022	"2510010F10Rik, C230084J24Rik, C79446, TPP36 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010501	32102	Kmn1	http://www.ncbi.nlm.nih.gov/gene/?term=32102	"Dmel_CG1558, CG1558, CT4038, Dmel\CG1558, Nsl1, anon-WO03040301.201, dmNsl1R, l(1)G0237, nsl1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010502	32124	prtp	http://www.ncbi.nlm.nih.gov/gene/?term=32124	"Dmel_CG1837, CG1837, Dmel\CG1837, anon-EST:Posey253, p47 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010503	32140	p24-1	http://www.ncbi.nlm.nih.gov/gene/?term=32140	"Dmel_CG1967, CG1967, Dmel\CG1967, anon-EST:Liang-1.45, clone 1.45, p24, p24.1, p26/p24gamma4 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010504	3215	HOXB5	http://www.ncbi.nlm.nih.gov/gene/?term=3215	"HHO.C10, HOX2, HOX2A, HU-1, Hox2.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010505	3216	HOXB6	http://www.ncbi.nlm.nih.gov/gene/?term=3216	"HOX2, HOX2B, HU-2, Hox-2.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010506	32174	Muc11A	http://www.ncbi.nlm.nih.gov/gene/?term=32174	"Dmel_CG32656, CG2779, CG32656, Dmel\CG32656 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010507	32174	Muc11A	http://www.ncbi.nlm.nih.gov/gene/?term=32174	"Dmel_CG32656, CG2779, CG32656, Dmel\CG32656 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010508	32179	CG2750	http://www.ncbi.nlm.nih.gov/gene/?term=32179	"Dmel_ Dmel\CG2750, anon-WO0140519.124 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010509	3217	HOXB7	http://www.ncbi.nlm.nih.gov/gene/?term=3217	"HHO.C1, HOX2, HOX2C, Hox-2.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010510	3217	HOXB7	http://www.ncbi.nlm.nih.gov/gene/?term=3217	"HHO.C1, HOX2, HOX2C, Hox-2.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010511	32194	CG15731	http://www.ncbi.nlm.nih.gov/gene/?term=32194	Dmel_ Dmel\CG15731	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010512	321	APBA2	http://www.ncbi.nlm.nih.gov/gene/?term=321	"D15S1518E, HsT16821, LIN-10, MGC:14091, MINT2, X11-BETA, X11L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010513	32273	sno	http://www.ncbi.nlm.nih.gov/gene/?term=32273	"Dmel_CG44436, CG1903, CG44436, Dmel\CG44436, Dmel_CG1903, Sno, g-l, l(1)11Ea "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010514	32275	mew	http://www.ncbi.nlm.nih.gov/gene/?term=32275	"Dmel_CG1771, CG1771, CT5254, Dmel\CG1771, ItgaPS1, PS1, PS1alpha, PSalpha1, aPS1, alpha-PS1, alpha1Int, alphaPS1, alpha[[PS1]], l(1)G0429, l(1)G0443 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010515	32285	IP3K2	http://www.ncbi.nlm.nih.gov/gene/?term=32285	"Dmel_CG45017, CG12724, CG15745, CG1630, CG34359, CG4501, CG45017, D-IP3K2, DIP3K2, Dmel\CG45017, Dmel_CG12724, Dmel_CG15745, Dmel_CG1630, Dmel_CG34359, IP[[3]]K-2, IP[[3]]K2, NP2758, dmIP3K2, dmIP3Kbeta, dmIP[[3]]beta, ip3k2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010516	32285	IP3K2	http://www.ncbi.nlm.nih.gov/gene/?term=32285	"Dmel_CG45017, CG12724, CG15745, CG1630, CG34359, CG4501, CG45017, D-IP3K2, DIP3K2, Dmel\CG45017, Dmel_CG12724, Dmel_CG15745, Dmel_CG1630, Dmel_CG34359, IP[[3]]K-2, IP[[3]]K2, NP2758, dmIP3K2, dmIP3Kbeta, dmIP[[3]]beta, ip3k2 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010517	322903	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=322903	"fb76c12, wu:fb76c12, wu:fb93h11, wu:fb98e07, wu:fq21a10 "	mRNA	Danio rerio	17293094	Germ plasm	Oocyte	In situ hybridization	"Here we report that the germ plasm RNAs vasa, nanos1, and dazl co-localize with the mitochondrial cloud (MC) and are transported to the vegetal cortex during early oogenesis. "
RLID00010518	322903	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=322903	"fb76c12, wu:fb76c12, wu:fb93h11, wu:fb98e07, wu:fq21a10 "	mRNA	Danio rerio	17293094	Mitochondrion	Oocyte	In situ hybridization	"Here we report that the germ plasm RNAs vasa, nanos1, and dazl co-localize with the mitochondrial cloud (MC) and are transported to the vegetal cortex during early oogenesis. "
RLID00010519	32312	Tango13	http://www.ncbi.nlm.nih.gov/gene/?term=32312	"Dmel_CG32632, CG1573, CG15758, CG15759, CG32629, CG32629/CG32632, CG32632, Dmel\CG32632, Dmel_CG15758, Dmel_CG32629, TANGO13 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010520	32312	Tango13	http://www.ncbi.nlm.nih.gov/gene/?term=32312	"Dmel_CG32632, CG1573, CG15758, CG15759, CG32629, CG32629/CG32632, CG32632, Dmel\CG32632, Dmel_CG15758, Dmel_CG32629, TANGO13 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010521	32312	Tango13	http://www.ncbi.nlm.nih.gov/gene/?term=32312	"Dmel_CG32632, CG1573, CG15758, CG15759, CG32629, CG32629/CG32632, CG32632, Dmel\CG32632, Dmel_CG15758, Dmel_CG32629, TANGO13 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010522	32327	CG11158	http://www.ncbi.nlm.nih.gov/gene/?term=32327	Dmel_ Dmel\CG11158	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010523	32348	CG11095	http://www.ncbi.nlm.nih.gov/gene/?term=32348	Dmel_ Dmel\CG11095	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010524	32348	CG11095	http://www.ncbi.nlm.nih.gov/gene/?term=32348	Dmel_ Dmel\CG11095	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010525	32348	CG11095	http://www.ncbi.nlm.nih.gov/gene/?term=32348	Dmel_ Dmel\CG11095	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010526	3234	HOXD8	http://www.ncbi.nlm.nih.gov/gene/?term=3234	"HOX4, HOX4E, HOX5.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010527	32352	AMPdeam	http://www.ncbi.nlm.nih.gov/gene/?term=32352	"Dmel_CG32626, AMP deam, CG11058, CG11065, CG15762, CG32626, Dmel\CG32626 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010528	3235	HOXD9	http://www.ncbi.nlm.nih.gov/gene/?term=3235	"HOX4, HOX4C, Hox-4.3, Hox-5.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010529	32392	CG9411	http://www.ncbi.nlm.nih.gov/gene/?term=32392	Dmel_ Dmel\CG9411	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010530	32398	NetA	http://www.ncbi.nlm.nih.gov/gene/?term=32398	"Dmel_CG18657, CG18657, CT27014, Dmel\CG18657, NetrinA, net, netA, netrin, netrin A "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010531	323	APBB2	http://www.ncbi.nlm.nih.gov/gene/?term=323	"FE65L, FE65L1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010532	323	APBB2	http://www.ncbi.nlm.nih.gov/gene/?term=323	"FE65L, FE65L1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010533	32400	NetB	http://www.ncbi.nlm.nih.gov/gene/?term=32400	"Dmel_CG10521, CG10521, CT29512, Dmel\CG10521, NETB, net, netB, netrin, netrin B "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010534	32407	CG14408	http://www.ncbi.nlm.nih.gov/gene/?term=32407	Dmel_ Dmel\CG14408	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010535	3241	HPCAL1	http://www.ncbi.nlm.nih.gov/gene/?term=3241	"BDR1, HLP2, VILIP-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010536	32488	CG7860	http://www.ncbi.nlm.nih.gov/gene/?term=32488	Dmel_ Dmel\CG7860	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010537	32490	CG9213	http://www.ncbi.nlm.nih.gov/gene/?term=32490	"Dmel_ CG32585, Dmel\CG9213 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010538	32498	sog	http://www.ncbi.nlm.nih.gov/gene/?term=32498	"Dmel_CG9224, CG9224, Dm sog, Dmel\CG9224, SOG, Sog, l(1)G0160, l(1)G0395, l(1)G0479 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010539	324	APC	http://www.ncbi.nlm.nih.gov/gene/?term=324	"BTPS2, DP2, DP2.5, DP3, GS, PPP1R46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010540	324	APC	http://www.ncbi.nlm.nih.gov/gene/?term=324	"BTPS2, DP2, DP2.5, DP3, GS, PPP1R46 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010541	324	APC	http://www.ncbi.nlm.nih.gov/gene/?term=324	"BTPS2, DP2, DP2.5, DP3, GS, PPP1R46 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010542	3251	HPRT1	http://www.ncbi.nlm.nih.gov/gene/?term=3251	"HGPRT, HPRT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010543	3251	HPRT1	http://www.ncbi.nlm.nih.gov/gene/?term=3251	"HGPRT, HPRT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010544	3251	HPRT1	http://www.ncbi.nlm.nih.gov/gene/?term=3251	"HGPRT, HPRT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010545	32530	mRpS30	http://www.ncbi.nlm.nih.gov/gene/?term=32530	"Dmel_CG8470, CG8470, Dmel\CG8470, MRP-S30, mRSp30 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010546	32535	CG8509	http://www.ncbi.nlm.nih.gov/gene/?term=32535	Dmel_ Dmel\CG8509	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010547	32536	sd	http://www.ncbi.nlm.nih.gov/gene/?term=32536	"Dmel_CG8544, CG8544, DROEXO, DROEXO2, Dmel\CG8544, EP(X)1088, EP1088, SD, Sd, TEAD, anon-EST:Liang-2.14, clone 2.14, l(1)G0239, l(1)G0262, l(1)G0309, l(1)G0315, l(1)G0483, l(1)HF394, l(1)III, sp "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00010548	32544	Gbeta13F	http://www.ncbi.nlm.nih.gov/gene/?term=32544	"Dmel_CG10545, CG10545, Dmel\CG10545, G b13F, G-beta, G-betab, G[[beta13F]], G[[beta]], Gb13F, Gbb, Gbeta, anon-EST:Liang-1.22, clone 1.22, dgbeta, gbeta13F "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010549	32548	MSBP	http://www.ncbi.nlm.nih.gov/gene/?term=32548	"Dmel_CG9066, CG9066, Dmel\CG9066, dm_MSBP "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010550	32566	eIF5	http://www.ncbi.nlm.nih.gov/gene/?term=32566	"Dmel_CG9177, CG9177, Dmel\CG9177, EIf5, anon-EST:fe3C6 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010551	3257	HPS1	http://www.ncbi.nlm.nih.gov/gene/?term=3257	"BLOC3S1, HPS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010552	32587	caz	http://www.ncbi.nlm.nih.gov/gene/?term=32587	"Dmel_CG3606, BcDNA:GM09207, CG3606, Caz, Dmel\CG3606, EWSR1, P19, Pen19, SARFH, Sarfh, TFIID, anon-Pen19, cas, p19, pen19 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010553	32599	CG9921	http://www.ncbi.nlm.nih.gov/gene/?term=32599	Dmel_ Dmel\CG9921	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010554	325	APCS	http://www.ncbi.nlm.nih.gov/gene/?term=325	"HEL-S-92n, PTX2, SAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010555	32602	U2af50	http://www.ncbi.nlm.nih.gov/gene/?term=32602	"Dmel_CG9998, 9-21, CG9998, DU2AF50, DmU2AF[50], Dmel\CG9998, U2AF, U2AF 50, U2AF-50, U2AF50, U2af, dU2AF50, dU2AF[50], dUTAf[50], l(1)14Ca, l(1)14Cc, l(1)9-21 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010556	326148	CG31523	http://www.ncbi.nlm.nih.gov/gene/?term=326148	"Dmel_ CG9798, Dmel\CG31523 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010557	326255	4EHP	http://www.ncbi.nlm.nih.gov/gene/?term=326255	"Dmel_CG33100, 4E-HP, CG10716, CG33100, CT30033, Dmel\CG33100, d4EHP, eIF4E-8 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010558	326255	4EHP	http://www.ncbi.nlm.nih.gov/gene/?term=326255	"Dmel_CG33100, 4E-HP, CG10716, CG33100, CT30033, Dmel\CG33100, d4EHP, eIF4E-8 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010559	32629	CG9784	http://www.ncbi.nlm.nih.gov/gene/?term=32629	"Dmel_ Dmel\CG9784, IPP, lincRNA.S9473 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010560	32651	CG9672	http://www.ncbi.nlm.nih.gov/gene/?term=32651	"Dmel_ BcDNA:GH16384, Dmel\CG9672, SPH161 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010561	3265	HRAS	http://www.ncbi.nlm.nih.gov/gene/?term=3265	"C-BAS/HAS, C-H-RAS, C-HA-RAS1, CTLO, H-RASIDX, HAMSV, HRAS1, RASH1, p21ras "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010562	3265	HRAS	http://www.ncbi.nlm.nih.gov/gene/?term=3265	"C-BAS/HAS, C-H-RAS, C-HA-RAS1, CTLO, H-RASIDX, HAMSV1, RASH1, p21ras, HRAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010563	326623	Tnfsf15	http://www.ncbi.nlm.nih.gov/gene/?term=326623	"Tl1, Tl1a, Tnlg1b, Vegi "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010564	326625	MMAB	http://www.ncbi.nlm.nih.gov/gene/?term=326625	"ATR, CFAP23, cblB, cob "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010565	32663	CG9609	http://www.ncbi.nlm.nih.gov/gene/?term=32663	Dmel_ Dmel\CG9609	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010566	32675	CG13003	http://www.ncbi.nlm.nih.gov/gene/?term=32675	Dmel_ Dmel\CG13003	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010567	3267	AGFG1	http://www.ncbi.nlm.nih.gov/gene/?term=3267	"HRB, RAB, RIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010568	3267	AGFG1	http://www.ncbi.nlm.nih.gov/gene/?term=3267	"HRB, RAB, RIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010569	3267	AGFG1	http://www.ncbi.nlm.nih.gov/gene/?term=3267	"HRB, RAB, RIP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010570	3267	AGFG1	http://www.ncbi.nlm.nih.gov/gene/?term=3267	"HRB, RAB, RIP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010571	32691	CG4949	http://www.ncbi.nlm.nih.gov/gene/?term=32691	Dmel_ Dmel\CG4949	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010572	32691	CG4949	http://www.ncbi.nlm.nih.gov/gene/?term=32691	Dmel_ Dmel\CG4949	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010573	327216	ofd1	http://www.ncbi.nlm.nih.gov/gene/?term=327216	"wu:fa07a10, wu:fd17e11, zgc:92562 "	mRNA	Danio rerio	18971206	Centrosome	Embryo	qRT-PCR	"In wild-type embryos, ofd1 mRNA is widely expressed and Ofd1-green fluorescent protein (GFP) fusion localizes to the centrosome/basal body. "
RLID00010574	32724	B-H1	http://www.ncbi.nlm.nih.gov/gene/?term=32724	"Dmel_CG5529, BH1, Bar, Bar H1, Bar-H1, BarH, BarHI, Barh1, CG5529, Dmel\CG5529, bar-h1, barH1, barh1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010575	32727	p-cup	http://www.ncbi.nlm.nih.gov/gene/?term=32727	"Dmel_CG12993, CG12993, Dmel\CG12993 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010576	327368	rgs14a	http://www.ncbi.nlm.nih.gov/gene/?term=327368	"rgs14, wu:fi04g12 "	mRNA	Danio rerio	25049415	Germ plasm	Embryo	In situ hybridization	"Rgs14a RNA is a previously unidentified component of the germ plasm strongly expressed in premigratory PGCs. Fig. 1. Zebrafish regulator of G-protein signaling 14a (rgs14a) RNA expression and Rgs14a protein localization. (A) A schematic representation of the Rgs14a protein structure showing the N-terminal RGS domain, the two Raf-like Ras-binding domains (RBD), and the C-terminal GoLoco domain. (B) Wholemount in situ RNA hybridization using rgs14a (Left) and nanos (Right) antisense RNA probes at the indicated embryonic stages; 5.3- and 10-hpf embryos were overstained in the case of rgs14a in situ hybridization to detect the weak expression in the PGCs. "
RLID00010577	32737	stas	http://www.ncbi.nlm.nih.gov/gene/?term=32737	"Dmel_CG8408, CG8408, Dmel\CG8408, Tmem41b "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010578	32739	corolla	http://www.ncbi.nlm.nih.gov/gene/?term=32739	"Dmel_CG8316, CG8316, Dmel\CG8316, mei-39 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010579	32739	corolla	http://www.ncbi.nlm.nih.gov/gene/?term=32739	"Dmel_CG8316, CG8316, Dmel\CG8316, mei-39 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010580	32739	corolla	http://www.ncbi.nlm.nih.gov/gene/?term=32739	"Dmel_CG8316, CG8316, Dmel\CG8316, mei-39 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010581	32748	chas	http://www.ncbi.nlm.nih.gov/gene/?term=32748	"Dmel_CG32556, CG12987, CG12988, CG12989, CG32556, Dmel\CG32556, EP-631 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010582	32752	par-6	http://www.ncbi.nlm.nih.gov/gene/?term=32752	"Dmel_CG5884, CG5884, DPar-6, DPar6, Dm-Par-6, Dm-Par6, DmPAR-6, DmPar-6, DmPar6, Dmel\CG5884, Dmpar6, PAR-6, PAR6, Par, Par-6, Par6, dPAR-6, dPar-6, dmPar-6, par, par6 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010583	32757	unc-4	http://www.ncbi.nlm.nih.gov/gene/?term=32757	"Dmel_CG6269, CG6269, DPHD-1, Dmel\CG6269, D Unc4 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010584	3275	PRMT2	http://www.ncbi.nlm.nih.gov/gene/?term=3275	HRMT1L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010585	3275	PRMT2	http://www.ncbi.nlm.nih.gov/gene/?term=3275	HRMT1L1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010586	3276	PRMT1	http://www.ncbi.nlm.nih.gov/gene/?term=3276	"ANM1, HCP1, HRMT1L2, IR1B4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010587	3276	PRMT1	http://www.ncbi.nlm.nih.gov/gene/?term=3276	"ANM1, HCP1, HRMT1L2, IR1B4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010588	3276	PRMT1	http://www.ncbi.nlm.nih.gov/gene/?term=3276	"ANM1, HCP1, HRMT1L2, IR1B4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010589	327762	Dna2	http://www.ncbi.nlm.nih.gov/gene/?term=327762	"Dna2l, E130315B21Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010590	327781	A130033P14	http://www.ncbi.nlm.nih.gov/gene/?term=327781		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010591	327857	A330087I24	http://www.ncbi.nlm.nih.gov/gene/?term=327857		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010592	32786	CG7536	http://www.ncbi.nlm.nih.gov/gene/?term=32786	Dmel_ Dmel\CG7536	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010593	327987	Med13	http://www.ncbi.nlm.nih.gov/gene/?term=327987	"1110067M05Rik, D030023K18, Thrap1, Trap240 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010594	327988	Gm9975	http://www.ncbi.nlm.nih.gov/gene/?term=327988	"C730049P21, ENSMUSG00000055697 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010595	32799	Frq2	http://www.ncbi.nlm.nih.gov/gene/?term=32799	"Dmel_CG5907, CG5907, Dmel\CG5907, Frq, frq, frq2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010596	327	APEH	http://www.ncbi.nlm.nih.gov/gene/?term=327	"AARE, ACPH, APH, D3F15S2, D3S48E, DNF15S2, OPH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010597	327	APEH	http://www.ncbi.nlm.nih.gov/gene/?term=327	"AARE, ACPH, APH, D3F15S2, D3S48E, DNF15S2, OPH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010598	327	APEH	http://www.ncbi.nlm.nih.gov/gene/?term=327	"AARE, ACPH, APH, D3F15S2, D3S48E, DNF15S2, OPH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010599	327	APEH	http://www.ncbi.nlm.nih.gov/gene/?term=327	"AARE, ACPH, APH, D3F15S2, D3S48E, DNF15S2, OPH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010600	328099	Prps1l3	http://www.ncbi.nlm.nih.gov/gene/?term=328099	"AU021838, AW536152, Gm5081 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010601	3280	HES1	http://www.ncbi.nlm.nih.gov/gene/?term=3280	"HES-1, HHL, HRY, bHLHb39 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010602	328110	Prpf39	http://www.ncbi.nlm.nih.gov/gene/?term=328110	Srcs1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010603	328172	LOC328172	http://www.ncbi.nlm.nih.gov/gene/?term=328172		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010604	3281	HSBP1	http://www.ncbi.nlm.nih.gov/gene/?term=3281	NPC-A-13	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010605	32820	betaCOP	http://www.ncbi.nlm.nih.gov/gene/?term=32820	"Dmel_CG6223, BcDNA.GH09317, BcDNA:GH09317, Beta Cop, BetaCop, CG6223, COPI, Dmel\CG6223, bcop, beta-COP, beta-Cop, beta-CopII, betaCop "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010606	32826	CG32548	http://www.ncbi.nlm.nih.gov/gene/?term=32826	"Dmel_ CG15051, CG6306, Dmel\CG32548, anon-WO0140519.88 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010607	32826	CG32548	http://www.ncbi.nlm.nih.gov/gene/?term=32826	"Dmel_ CG15051, CG6306, Dmel\CG32548, anon-WO0140519.88 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010608	328417	Parp4	http://www.ncbi.nlm.nih.gov/gene/?term=328417	"Adprtl1, C030027K23Rik, E230037B21Rik, Gm743, PARPL, PH5P, VAULT3, VPARP, p193 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010609	328572	Ep300	http://www.ncbi.nlm.nih.gov/gene/?term=328572	"A430090G16, A730011L11, KAT3B, p300, p300 HAT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010610	32871	Atg101	http://www.ncbi.nlm.nih.gov/gene/?term=32871	"Dmel_CG7053, CG7053, Dmel\CG7053 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010611	32871	Atg101	http://www.ncbi.nlm.nih.gov/gene/?term=32871	"Dmel_CG7053, CG7053, Dmel\CG7053 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010612	328801	Zfp414	http://www.ncbi.nlm.nih.gov/gene/?term=328801	"0610030H11Rik, Znf414 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010613	328953	Gm5095	http://www.ncbi.nlm.nih.gov/gene/?term=328953	A730092B10	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010614	328963	G630071F17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=328963	G630071F17	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010615	328	APEX1	http://www.ncbi.nlm.nih.gov/gene/?term=328	"APE, APE1, APEN, APEX, APX, HAP1, REF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010616	328	APEX1	http://www.ncbi.nlm.nih.gov/gene/?term=328	"APE, APE1, APEN, APEX, APX, HAP1, REF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010617	328	APEX1	http://www.ncbi.nlm.nih.gov/gene/?term=328	"APE, APE1, APEN, APEX, APX, HAP1, REF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010618	3290	HSD11B1	http://www.ncbi.nlm.nih.gov/gene/?term=3290	"11-DH, 11-beta-HSD1, CORTRD2, HDL, HSD11, HSD11B, HSD11L, SDR26C1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010619	329122	4932436B18	http://www.ncbi.nlm.nih.gov/gene/?term=329122		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010620	3291	HSD11B2	http://www.ncbi.nlm.nih.gov/gene/?term=3291	"AME, AME1, HSD11K, HSD2, SDR9C3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010621	329260	Dennd1b	http://www.ncbi.nlm.nih.gov/gene/?term=329260	"4632404N19Rik, 4930467M19Rik, 6820401H01Rik, F730008N07Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010622	329260	Dennd1b	http://www.ncbi.nlm.nih.gov/gene/?term=329260	"4632404N19Rik, 4930467M19Rik, 6820401H01Rik, F730008N07Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010623	32926	out	http://www.ncbi.nlm.nih.gov/gene/?term=32926	"Dmel_CG8062, BcDNA:LD28120, CG8062, Dmel\CG8062 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010624	32926	out	http://www.ncbi.nlm.nih.gov/gene/?term=32926	"Dmel_CG8062, BcDNA:LD28120, CG8062, Dmel\CG8062 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010625	329271	C230024C17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=329271	C230024C17	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010626	329274	Fam163a	http://www.ncbi.nlm.nih.gov/gene/?term=329274	A230106N23Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010627	32938	Pfrx	http://www.ncbi.nlm.nih.gov/gene/?term=32938	"Dmel_CG3400, CG3400, Dmel\CG3400, PFK2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010628	3293	HSD17B3	http://www.ncbi.nlm.nih.gov/gene/?term=3293	"EDH17B3, SDR12C2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010629	3295	HSD17B4	http://www.ncbi.nlm.nih.gov/gene/?term=3295	"DBP, MFE-2, MPF-2, PRLTS1, SDR8C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010630	3295	HSD17B4	http://www.ncbi.nlm.nih.gov/gene/?term=3295	"DBP, MFE-2, MPF-2, PRLTS1, SDR8C1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010631	329716	BC107364	http://www.ncbi.nlm.nih.gov/gene/?term=329716	D730018G16	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010632	329739	Fam102b	http://www.ncbi.nlm.nih.gov/gene/?term=329739	"1600010D10Rik, B430201A12Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010633	32976	dome	http://www.ncbi.nlm.nih.gov/gene/?term=32976	"Dmel_CG14226, 142932_at, CG14226, CT33841, DOME, Dmel\CG14226, Dome, anon-18DEb, l(1)G0217, l(1)G0218, l(1)G0264, l(1)G0282, l(1)G0321, l(1)G0367, l(1)G0405, l(1)G0441, l(1)G0468, mom, vsp "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010634	32976	dome	http://www.ncbi.nlm.nih.gov/gene/?term=32976	"Dmel_CG14226, 142932_at, CG14226, CT33841, DOME, Dmel\CG14226, Dome, anon-18DEb, l(1)G0217, l(1)G0218, l(1)G0264, l(1)G0282, l(1)G0321, l(1)G0367, l(1)G0405, l(1)G0441, l(1)G0468, mom, vsp "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010635	329777	Pigk	http://www.ncbi.nlm.nih.gov/gene/?term=329777	3000001O05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010636	329795	Tmem67	http://www.ncbi.nlm.nih.gov/gene/?term=329795	"5330408M12Rik, B230117O07, b2b1163.1Clo, b2b1291.1Clo "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010637	32981	Cdc42	http://www.ncbi.nlm.nih.gov/gene/?term=32981	"Dmel_CG12530, CDC42, CG12530Dm, D-CDC42, D-Cdc42, D-cdc42, DCDC42, DCdc42, Dcdc42, Dm Cdc42, DmCDC42, Dmcdc42, Dmel\CG12530, P40793, cdc42 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010638	3298	HSF2	http://www.ncbi.nlm.nih.gov/gene/?term=3298	"HSF 2, HSTF 2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010639	3298	HSF2	http://www.ncbi.nlm.nih.gov/gene/?term=3298	"HSF 2, HSTF 2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010640	329975	LOC329975	http://www.ncbi.nlm.nih.gov/gene/?term=329975		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010641	3299	HSF4	http://www.ncbi.nlm.nih.gov/gene/?term=3299	"CTM, CTRCT5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010642	329	BIRC2	http://www.ncbi.nlm.nih.gov/gene/?term=329	"API1, HIAP2, Hiap-2, MIHB, RNF48, c-IAP1, cIAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010643	329	BIRC2	http://www.ncbi.nlm.nih.gov/gene/?term=329	"API1, HIAP2, Hiap-2, MIHB, RNF48, c-IAP1, cIAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010644	32	ACACB	http://www.ncbi.nlm.nih.gov/gene/?term=32	"ACC2, ACCB, HACC275 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010645	32	ACACB	http://www.ncbi.nlm.nih.gov/gene/?term=32	"ACC2, ACCB, HACC275 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010646	330050	Fam185a	http://www.ncbi.nlm.nih.gov/gene/?term=330050	"4631428I10, AI847670 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010647	33007	Dop2R	http://www.ncbi.nlm.nih.gov/gene/?term=33007	"Dmel_CG33517, CG17004, CG33517, CG9569, D2R, DD2R, Dmel\CG33517, anon-WO0170980.130, anon-WO0170980.131, anon-WO0170980.31, anon-WO0170980.32, dD2R "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010648	330096	Shisa3	http://www.ncbi.nlm.nih.gov/gene/?term=330096	D830007B15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010649	3300	DNAJB2	http://www.ncbi.nlm.nih.gov/gene/?term=3300	"CMT2T, DSMA5, HSJ-1, HSJ1, HSPF3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010650	330166	Miat	http://www.ncbi.nlm.nih.gov/gene/?term=330166	"3632434I06, A230057G18Rik, Rncr2, gomafu "	lncRNA	Mus musculus	17623775	Nucleus	Brain	In situ hybridization|RT-PCR	"Interestingly, spliced mature Gomafu RNA is localized to the nucleus despite its mRNA-like characteristics, which usually act as potent export signals to the cytoplasm.  "
RLID00010651	330166	Miat	http://www.ncbi.nlm.nih.gov/gene/?term=330166	"3632434I06, A230057G18Rik, Rncr2, gomafu "	lncRNA	Mus musculus	20459797	Nucleus	Retina cell	In situ hybridization	"We further report that RNCR2 RNA, which is normally nuclear-retained, can be exported from the nucleus when fused to an IRES-GFP sequence.  "
RLID00010652	330166	Miat	http://www.ncbi.nlm.nih.gov/gene/?term=330166	"3632434I06, A230057G18Rik, Rncr2, gomafu "	lncRNA	Mus musculus	22070123	Nucleus	Retinas cell	In situ hybridization	"Here, we discuss the functions of a distinct group of vertebrate-specific lncRNAs, NEAT1/MENε/β/VINC, MALAT1/NEAT2, and Gomafu/RNCR2/MIAT, which accumulate abundantly within the nucleus as RNA components of specific nuclear bodies. "
RLID00010653	330166	Miat	http://www.ncbi.nlm.nih.gov/gene/?term=330166	"3632434I06, A230057G18Rik, Rncr2, gomafu "	lncRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"We then analyzed the abundance of several lncRNAs, namely Malat1, Meg3, Rmst, Xist and Miat. All of these lncRNAs were present in the axonal compartment.  "
RLID00010654	330173	2610524H06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=330173		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010655	330177	Taok3	http://www.ncbi.nlm.nih.gov/gene/?term=330177	"2900006A08Rik, A130052D22, A430105I05Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010656	330192	Vps37b	http://www.ncbi.nlm.nih.gov/gene/?term=330192	"2300007F24Rik, AI415429, BC026744 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010657	3301	DNAJA1	http://www.ncbi.nlm.nih.gov/gene/?term=3301	"DJ-2, DjA1, HDJ2, HSDJ, HSJ-2, HSJ2, HSPF4, NEDD7, hDJ-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010658	3301	DNAJA1	http://www.ncbi.nlm.nih.gov/gene/?term=3301	"DJ-2, DjA1, HDJ2, HSDJ, HSJ-2, HSJ2, HSPF4, NEDD7, hDJ-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010659	330286	D630045J12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=330286	"Kiaa1549, mKIAA1549 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010660	3303	HSPA1A	http://www.ncbi.nlm.nih.gov/gene/?term=3303	"HEL-S-103, HSP70-1, HSP70-1A, HSP70.1, HSP70I, HSP72, HSPA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010661	330401	Tmcc1	http://www.ncbi.nlm.nih.gov/gene/?term=330401	"3632431M01Rik, mKIAA0779 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010662	33040	Obp19d	http://www.ncbi.nlm.nih.gov/gene/?term=33040	"Dmel_CG1668, 19d, BcDNA:HL07789, BcDNA:RH68082, CG1668, DmelObp19d, Dmel\CG1668, PB-PRP2, PBP2, PBPRP-2, PBPRP2, Pbprp2, pbprp-2, pbprp2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010663	330414	Gm5112	http://www.ncbi.nlm.nih.gov/gene/?term=330414	D530008I22	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010664	33045	mal	http://www.ncbi.nlm.nih.gov/gene/?term=33045	"Dmel_CG1692, 5, CG1692, Dmel\CG1692, SRF, bz, ma-l "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010665	3304	HSPA1B	http://www.ncbi.nlm.nih.gov/gene/?term=3304	"HSP70-1B, HSP70-2, HSP70.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010666	330599	Gm16938	http://www.ncbi.nlm.nih.gov/gene/?term=330599		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010667	33059	run	http://www.ncbi.nlm.nih.gov/gene/?term=33059	"Dmel_CG1849, 1, 2, AA33, CG1849, Dmel\CG1849, LB5, P235, RUN, Rnt, Run, Runt, l(1)19Ea, l(1)AA33, l(1)B2/13.1, l(1)LB9, lLB5, leg "	mRNA	Drosophila melanogaster	15280214	Basal	Embryo	In situ hybridization	"Whereas embryos laid by wild-type mothers have an almost exclusively apical distribution of pair-rule mRNAs such as eve, ftz, h and runt (run), those laid by egl3e/eglWU50 mothers accumulate a large proportion of these transcripts in the basal cytoplasm (Fig. 5A). "
RLID00010668	33059	run	http://www.ncbi.nlm.nih.gov/gene/?term=33059	"Dmel_CG1849, 1, 2, AA33, CG1849, Dmel\CG1849, LB5, P235, RUN, Rnt, Run, Runt, l(1)19Ea, l(1)AA33, l(1)B2/13.1, l(1)LB9, lLB5, leg "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010669	3305	HSPA1L	http://www.ncbi.nlm.nih.gov/gene/?term=3305	"HSP70-1L, HSP70-HOM, HSP70T, hum70t "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010670	330695	Ctxn1	http://www.ncbi.nlm.nih.gov/gene/?term=330695	"BC028881, Ctxn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010671	3306	HSPA2	http://www.ncbi.nlm.nih.gov/gene/?term=3306	"HSP70-2, HSP70-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010672	330766	LOC330766	http://www.ncbi.nlm.nih.gov/gene/?term=330766		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010673	330817	Dhps	http://www.ncbi.nlm.nih.gov/gene/?term=330817	Dhs	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010674	33081	Cbs	http://www.ncbi.nlm.nih.gov/gene/?term=33081	"Dmel_CG1753, CBS, CG1753, DmCBS, Dmel\CG1753, dCBS "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010675	330836	Slc7a6	http://www.ncbi.nlm.nih.gov/gene/?term=330836	"AI643885, LAT-2, LAT3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010676	33085	CG32512	http://www.ncbi.nlm.nih.gov/gene/?term=33085	"Dmel_ CG15447, CG1739, Dmel\CG32512 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010677	33085	CG32512	http://www.ncbi.nlm.nih.gov/gene/?term=33085	"Dmel_ CG15447, CG1739, Dmel\CG32512 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010678	3308	HSPA4	http://www.ncbi.nlm.nih.gov/gene/?term=3308	"APG-2, HEL-S-5a, HS24/P52, HSPH2, RY, hsp70, hsp70RY "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010679	3308	HSPA4	http://www.ncbi.nlm.nih.gov/gene/?term=3308	"APG-2, HEL-S-5a, HS24/P52, HSPH2, RY, hsp70, hsp70RY "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010680	3308	HSPA4	http://www.ncbi.nlm.nih.gov/gene/?term=3308	"APG-2, HEL-S-5a, HS24/P52, HSPH2, RY, hsp70, hsp70RY "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010681	330938	Dixdc1	http://www.ncbi.nlm.nih.gov/gene/?term=330938	"4930563F16Rik, BC048182, Ccd1, Ccd1Aalpha1L, Ccd1Abeta1L, Ccd1BalphaL, Ccd1BbetaL, Ccd1CL, mKIAA1735 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010682	330958	A730043L09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=330958	A730043L09	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010683	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, MIF2, GRP78, HEL-S-89n "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00010684	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, GRP78, HEL-S-89n, MIF2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010685	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, GRP78, HEL-S-89n, MIF2 "	mRNA	Homo sapiens	12923260	Endoplasmic reticulum	T-cell line Jurkat	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00010686	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, GRP78, HEL-S-89n, MIF2 "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. mRNAs for resident proteins of the ER lumen, including BiP, calreticulin, and GRP94, were also highly enriched on membrane-bound polysomes. "
RLID00010687	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, GRP78, HEL-S-89n, MIF2 "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00010688	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, GRP78, HEL-S-89n, MIF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010689	3309	HSPA5	http://www.ncbi.nlm.nih.gov/gene/?term=3309	"BIP, GRP78, HEL-S-89n, MIF2 "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00010690	330	BIRC3	http://www.ncbi.nlm.nih.gov/gene/?term=330	"AIP1, API2, CIAP2, HAIP1, HIAP1, MALT2, MIHC, RNF49, c-IAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010691	331003	4933400C23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=331003	4933400C23	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010692	331021	9630017O17	http://www.ncbi.nlm.nih.gov/gene/?term=331021		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010693	331026	Gmppb	http://www.ncbi.nlm.nih.gov/gene/?term=331026	"AI317178, E430010H19 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010694	33127	Cyp6t1	http://www.ncbi.nlm.nih.gov/gene/?term=33127	"Dmel_CG1644, 6t1, CG1644, Dmel\CG1644 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010695	33128	CG14621	http://www.ncbi.nlm.nih.gov/gene/?term=33128	"Dmel_ Dmel\CG14621, Slc35e1, lincRNA.1043 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010696	33128	CG14621	http://www.ncbi.nlm.nih.gov/gene/?term=33128	"Dmel_ Dmel\CG14621, Slc35e1, lincRNA.1043 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010697	33129	CG14615	http://www.ncbi.nlm.nih.gov/gene/?term=33129	Dmel_ Dmel\CG14615	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010698	3312	HSPA8	http://www.ncbi.nlm.nih.gov/gene/?term=3312	"HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP-1, LAP1, NIP71 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010699	3312	HSPA8	http://www.ncbi.nlm.nih.gov/gene/?term=3312	"HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP-1, LAP1, NIP71 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010700	3312	HSPA8	http://www.ncbi.nlm.nih.gov/gene/?term=3312	"HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP-1, LAP1, NIP71 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010701	3312	HSPA8	http://www.ncbi.nlm.nih.gov/gene/?term=3312	"HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP-1, LAP1, NIP71 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010702	3312	HSPA8	http://www.ncbi.nlm.nih.gov/gene/?term=3312	"HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP-1, LAP1, NIP71 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010703	33132	Usp2	http://www.ncbi.nlm.nih.gov/gene/?term=33132	"Dmel_CG14619, CG14619, Dmel\CG14619, Q9VR54 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010704	33132	Usp2	http://www.ncbi.nlm.nih.gov/gene/?term=33132	"Dmel_CG14619, CG14619, Dmel\CG14619, Q9VR54 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010705	33134	CG14618	http://www.ncbi.nlm.nih.gov/gene/?term=33134	Dmel_ Dmel\CG14618	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010706	33135	CG12576	http://www.ncbi.nlm.nih.gov/gene/?term=33135	"Dmel_ Dmel\CG12576, anon-WO0140519.40 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010707	33135	CG12576	http://www.ncbi.nlm.nih.gov/gene/?term=33135	"Dmel_ Dmel\CG12576, anon-WO0140519.40 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010708	33135	CG12576	http://www.ncbi.nlm.nih.gov/gene/?term=33135	"Dmel_ Dmel\CG12576, anon-WO0140519.40 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010709	33136	Cp110	http://www.ncbi.nlm.nih.gov/gene/?term=33136	"Dmel_CG14617, CG14617, CG32501, CP110, DCP110, Dmel\CG14617 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010710	3313	HSPA9	http://www.ncbi.nlm.nih.gov/gene/?term=3313	"CRP40, CSA, EVPLS, GRP-75, GRP75, HEL-S-124mB, MOT, MOT2, MTHSP75, PBP74, SAAN, SIDBA4, HSPA9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010711	331401	Thoc2	http://www.ncbi.nlm.nih.gov/gene/?term=331401	"6330441O12Rik, D130005M13Rik, Gm1139, Gm1793, Tho2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010712	331416	Gm773	http://www.ncbi.nlm.nih.gov/gene/?term=331416		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010713	331480	Gm5126	http://www.ncbi.nlm.nih.gov/gene/?term=331480	EG331480	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010714	3315	HSPB1	http://www.ncbi.nlm.nih.gov/gene/?term=3315	"CMT2F, HEL-S-102, HMN2B, HS.76067, HSP27, HSP28, Hsp25, SRP27 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010715	3315	HSPB1	http://www.ncbi.nlm.nih.gov/gene/?term=3315	"CMT2F, HEL-S-102, HMN2B, HS.76067, HSP27, HSP28, Hsp25, SRP27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010716	3315	HSPB1	http://www.ncbi.nlm.nih.gov/gene/?term=3315	"CMT2F, HEL-S-102, HMN2B, HS.76067, HSP27, HSP28, Hsp25, SRP27 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010717	33162	galectin	http://www.ncbi.nlm.nih.gov/gene/?term=33162	"Dmel_CG11372, CG11372, Dmel\CG11372, Dmgal "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010718	33172	Gs1	http://www.ncbi.nlm.nih.gov/gene/?term=33172	"Dmel_CG2718, CG2718, Dmel\CG2718, GS1, GSI, GsI, fs(2)P52, fs(2)throng, gs-m, gsI, l(2)21Bc, mt-gs, thg "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010719	33180	CG3436	http://www.ncbi.nlm.nih.gov/gene/?term=33180	Dmel_ Dmel\CG3436	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010720	33196	smo	http://www.ncbi.nlm.nih.gov/gene/?term=33196	"Dmel_CG11561, CG11561, Dmel\CG11561, SMO, Smo, dSmo "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010721	331	XIAP	http://www.ncbi.nlm.nih.gov/gene/?term=331	"API3, BIRC4, IAP-3, ILP1, MIHA, XLP2, hIAP-3, hIAP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010722	331	XIAP	http://www.ncbi.nlm.nih.gov/gene/?term=331	"API3, BIRC4, IAP-3, ILP1, MIHA, XLP2, hIAP-3, hIAP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010723	331	XIAP	http://www.ncbi.nlm.nih.gov/gene/?term=331	"API3, BIRC4, IAP-3, ILP1, MIHA, XLP2, hIAP-3, hIAP3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010724	331	XIAP	http://www.ncbi.nlm.nih.gov/gene/?term=331	"API3, BIRC4, IAP-3, ILP1, MIHA, XLP2, hIAP-3, hIAP3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010725	331	XIAP	http://www.ncbi.nlm.nih.gov/gene/?term=331	"API3, BIRC4, IAP-3, ILP1, MIHA, XLP2, hIAP-3, hIAP3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010726	33203	Pi3K21B	http://www.ncbi.nlm.nih.gov/gene/?term=33203	"Dmel_CG2699, CG2699, Dmel\CG2699, Dp60, PI(3)K, PI3K, PI3K-p60, PI3K21B, PI[[3]]K|p60, Pi3Kp60, dP60, dPI3K, droPIK57, p60 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010727	3320	HSP90AA1	http://www.ncbi.nlm.nih.gov/gene/?term=3320	"EL52, HSPN, LAP2, HSP86, HSPC1, HSPCA, Hsp89, Hsp90, LAP-2, HSP89A, HSP90A, HSP90N, HSPCAL1, HSPCAL4, HEL-S-65p "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00010728	3320	HSP90AA1	http://www.ncbi.nlm.nih.gov/gene/?term=3320	"EL52, HEL-S-65p, HSP86, HSP89A, HSP90A, HSP90N, HSPC1, HSPCA, HSPCAL1, HSPCAL4, HSPN, Hsp89, Hsp90, LAP-2, LAP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010729	3320	HSP90AA1	http://www.ncbi.nlm.nih.gov/gene/?term=3320	"EL52, HEL-S-65p, HSP86, HSP89A, HSP90A, HSP90N, HSPC1, HSPCA, HSPCAL1, HSPCAL4, HSPN, Hsp89, Hsp90, LAP-2, LAP2 "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00010730	3320	HSP90AA1	http://www.ncbi.nlm.nih.gov/gene/?term=3320	"EL52, HEL-S-65p, HSP86, HSP89A, HSP90A, HSP90N, HSPC1, HSPCA, HSPCAL1, HSPCAL4, HSPN, Hsp89, Hsp90, LAP-2, LAP2 "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00010731	33211	AP-2alpha	http://www.ncbi.nlm.nih.gov/gene/?term=33211	"Dmel_CG4260, AP-2, AP2, Alpha-Adaptin, CG31654, CG4260, D-Ada, D-alphaAda, Dmel\CG4260, MENE (2L)-A, MENE(2L)-A, ada, alpha, alpha-Ada, alpha-Adaptin, alpha-ada, alpha-adaptin, apl3, cg4260, dAP-2a, l(2)06694, l(2)SH0460, l(2)SH2 0460 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010732	33218	ex	http://www.ncbi.nlm.nih.gov/gene/?term=33218	"Dmel_CG4114, 1270, CG4114, Dmel\CG4114, Ex, Expanded, brl, l(2)01270, l(2)ey "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010733	3321	IGSF3	http://www.ncbi.nlm.nih.gov/gene/?term=3321	"EWI-3, LCDD, V8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010734	33224	cbt	http://www.ncbi.nlm.nih.gov/gene/?term=33224	"Dmel_CG4427, CG4427, Cabot, Cabut, Dmel\CG4427, EP(2)2237, EP2237, dTIEG "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00010735	33234	Nle	http://www.ncbi.nlm.nih.gov/gene/?term=33234	"Dmel_CG2863, CG2863, Dmel\CG2863, anon-WO0026364, l(2)k13714 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010736	33248	GABA-B-R3	http://www.ncbi.nlm.nih.gov/gene/?term=33248	"Dmel_CG3022, CG3022, D-GABA[[B]]R3, D-Gaba3, Dmel\CG3022, GABA B R3, GABA[[B]]-R3, GABA[[B]]R3, GB3, anon-WO0170980.13, anon-WO0170980.14 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010737	33252	CG3544	http://www.ncbi.nlm.nih.gov/gene/?term=33252	Dmel_ Dmel\CG3544	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010738	33262	dock	http://www.ncbi.nlm.nih.gov/gene/?term=33262	"Dmel_CG3727, CG3727, DOCK, Dm0447, Dmel\CG3727, Dock, Nck, dck, doc, l(2)04723 "	mRNA	Drosophila melanogaster	17923096	Nucleus	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010739	3326	HSP90AB1	http://www.ncbi.nlm.nih.gov/gene/?term=3326	"D6S182, HSP84, HSP90B, HSPC2, HSPCB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010740	3326	HSP90AB1	http://www.ncbi.nlm.nih.gov/gene/?term=3326	"D6S182, HSP84, HSP90B, HSPC2, HSPCB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010741	33277	IA-2	http://www.ncbi.nlm.nih.gov/gene/?term=33277	"Dmel_CG31795, CG11344, CG31795, CG4355, Dmel\CG31795, R-PTPX/1A2, anon-WO0153538.69, ia2 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010742	33284	CG4629	http://www.ncbi.nlm.nih.gov/gene/?term=33284	"Dmel_ Dmel\CG4629, anon-WO0257455.15 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010743	33288	Pino	http://www.ncbi.nlm.nih.gov/gene/?term=33288	"Dmel_CG4710, CG4710, Dmel\CG4710, anon-WO0118547.131, smi21F "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010744	3329	HSPD1	http://www.ncbi.nlm.nih.gov/gene/?term=3329	"CPN60, GROEL, HLD4, HSP-60, HSP60, HSP65, HuCHA60, SPG13 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010745	332	BIRC5	http://www.ncbi.nlm.nih.gov/gene/?term=332	"API4, EPR-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010746	332	BIRC5	http://www.ncbi.nlm.nih.gov/gene/?term=332	"API4, EPR-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010747	333329	Cngb1	http://www.ncbi.nlm.nih.gov/gene/?term=333329	"Cngb1b, Gm1959 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010748	3336	HSPE1	http://www.ncbi.nlm.nih.gov/gene/?term=3336	"CPN10, EPF, GROES, HSP10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010749	333789	N4bp2	http://www.ncbi.nlm.nih.gov/gene/?term=333789	"B3bp, E430014I16, Gm1791, Gm868 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010750	3337	DNAJB1	http://www.ncbi.nlm.nih.gov/gene/?term=3337	"HSPF1, Hdj1, Hsp40, RSPH16B, Sis1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010751	3337	DNAJB1	http://www.ncbi.nlm.nih.gov/gene/?term=3337	"HSPF1, Hdj1, Hsp40, RSPH16B, Sis1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010752	3337	DNAJB1	http://www.ncbi.nlm.nih.gov/gene/?term=3337	"HSPF1, Hdj1, Hsp40, RSPH16B, Sis1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010753	3338	DNAJC4	http://www.ncbi.nlm.nih.gov/gene/?term=3338	"DANJC4, HSPF2, MCG18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010754	333926	PPM1J	http://www.ncbi.nlm.nih.gov/gene/?term=333926	"PP2CZ, PP2Czeta, PPP2CZ "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010755	33392	aop	http://www.ncbi.nlm.nih.gov/gene/?term=33392	"Dmel_CG3166, AOP, Aop, Aop/Yan, CG3166, DROYANET, DROYANETSB, Dmel\CG3166, SK2-1, YAN, Yan/yan, fus6, pok, yan, yan/pok, aop "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010756	333932	HIST2H3A	http://www.ncbi.nlm.nih.gov/gene/?term=333932	"H3/n, H3/o "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010757	333932	HIST2H3A	http://www.ncbi.nlm.nih.gov/gene/?term=333932	"H3/n, H3/o "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010758	3339	HSPG2	http://www.ncbi.nlm.nih.gov/gene/?term=3339	"HSPG, PLC, PRCAN, SJA, SJS, SJS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010759	3339	HSPG2	http://www.ncbi.nlm.nih.gov/gene/?term=3339	"HSPG, PLC, PRCAN, SJA, SJS, SJS1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010760	333	APLP1	http://www.ncbi.nlm.nih.gov/gene/?term=333	APLP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010761	3340	NDST1	http://www.ncbi.nlm.nih.gov/gene/?term=3340	"HSST, MRT46, NST1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010762	33418	Rab5	http://www.ncbi.nlm.nih.gov/gene/?term=33418	"Dmel_CG3664, AAF51265, BAA88244, CG3664, D Dm Rab5, DmRab5, Dmel\CG3664, Drab5, RAB5, RAB5a, Rab, Rab-5, dRab5, drab5, l(2)k08232, rab5 "	mRNA	Drosophila melanogaster	18272590	Germ plasm	Oocyte	-	"Here we show that Rabenosyn-5 (Rbsn-5), a Rab5 effector protein required for the early endocytic pathway, is crucial for pole plasm assembly. rbsn-5(-) oocytes fail to maintain microtubule polarity, which secondarily disrupts osk RNA localization. "
RLID00010763	33423	Atxn7	http://www.ncbi.nlm.nih.gov/gene/?term=33423	"Dmel_CG9866, CG9866, Dmel\CG9866 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010764	33432	dpp	http://www.ncbi.nlm.nih.gov/gene/?term=33432	"Dmel_CG9885, BMP, CG9885, DPP, DPP-C, Dm-DPP, Dmel\CG9885, Dpp, Hin-d, M(2)23AB, M(2)LS1, TGF-b, TGF-beta, TGFbeta, Tg, blk, ho, l(2)10638, l(2)22Fa, l(2)k17036, shv "	mRNA	Drosophila melanogaster	15852043	Centrosome	Neuroblasts	-	"Dpp mRNA (red) localization to the centrosome in the MACROMERES of an eight-cell Ilyanassa obsoleta embryo (microtubules, green; DNA, blue). The mRNA moves from the centrosome to the adjacent cortex during prophase, and is asymmetrically segregated into the second quartet of MICROMERES. "
RLID00010765	334375	buc	http://www.ncbi.nlm.nih.gov/gene/?term=334375	"fi43g04, wu:fi43g04 "	mRNA	Danio rerio	23626739	Mitochondrion	Oocyte	Microscopy	"In contrast to Xenopus Xvelo1, buc RNA is localised to the Balbiani body at early stages and to the animal pole at late stages, before becoming unlocalised in later oogenesis. "
RLID00010766	3344	FOXN2	http://www.ncbi.nlm.nih.gov/gene/?term=3344	HTLF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010767	3344	FOXN2	http://www.ncbi.nlm.nih.gov/gene/?term=3344	HTLF	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010768	33460	Cwc25	http://www.ncbi.nlm.nih.gov/gene/?term=33460	"Dmel_CG2843, CG2843, CWC25, Dmel\CG2843 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010769	3346167	btsz	http://www.ncbi.nlm.nih.gov/gene/?term=3346167	"Dmel_CG44012, BcDNA:GH06647, Btsz, CG14858, CG17304, CG18280, CG31306, CG33555, CG44012, CG7343, Dmel\CG44012, Dmel_CG17304, Dmel_CG33555, Granulophilin, l(3)10418 "	mRNA	Drosophila melanogaster	14581614	Apical	Epithelial cell	In situ hybridization	"In epithelial cells large enough to discern cell polarity, btsz mRNA clearly localizes to the apical plasma membrane.  "
RLID00010770	33466	CG3077	http://www.ncbi.nlm.nih.gov/gene/?term=33466	"Dmel_ DmSNX21, Dmel\CG3077 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010771	334	APLP2	http://www.ncbi.nlm.nih.gov/gene/?term=334	"APLP-2, APPH, APPL2, CDEBP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010772	334	APLP2	http://www.ncbi.nlm.nih.gov/gene/?term=334	"APLP-2, APPH, APPL2, CDEBP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010773	33507	okr	http://www.ncbi.nlm.nih.gov/gene/?term=33507	"Dmel_CG3736, CG3736, DhR54, DmRAD54, DmRad54, Dmel\CG3736, Dmrad54, Okr, RAD54, RAD54L, Rad54, Ras54, rad54 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010774	33526	toc	http://www.ncbi.nlm.nih.gov/gene/?term=33526	"Dmel_CG9660, BA34, BcDNA:LD27161, CG9660, Dmel\CG9660, Toc, l(2)01361, l(2)05527, l(2)K08224, l(2)k08224 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010775	33526	toc	http://www.ncbi.nlm.nih.gov/gene/?term=33526	"Dmel_CG9660, BA34, BcDNA:LD27161, CG9660, Dmel\CG9660, Toc, l(2)01361, l(2)05527, l(2)K08224, l(2)k08224 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010776	33526	toc	http://www.ncbi.nlm.nih.gov/gene/?term=33526	"Dmel_CG9660, BA34, BcDNA:LD27161, CG9660, Dmel\CG9660, Toc, l(2)01361, l(2)05527, l(2)K08224, l(2)k08224 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010777	3354888	rl	http://www.ncbi.nlm.nih.gov/gene/?term=3354888	"Dmel_CG12559, 12559, BcDNA:RE08694, CG12559, CG18732, CT34260, CT39192, D-ERK, DERK, DERK-A, DmERK-A, DmERKA, DmErk, DmMAPK, Dmel\CG12559, DpERK, DpErk, Dsor2, E(sina)7, EC2-1, EK2-1, ERK, ERK-A, ERKA, ERKa, EY2-2, Erk, Erk/Map kinase, Erk1, ErkA, GroupII, MAP-k, MAPK, MapK, Mapk, RL, Rl, SEM, SR2-1, Sem, Su(Raf)2B, dERK, dm-dpERK, dp-ERK, dpERK, dpERK1, dpERk, dpErk, dpMAPK, erk, l(2)41Ac, l(2R)EMS45-39, mapk, pERK, pMAPK, pMapK/ERK, rl/MAPK, rll, sem, rl "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010778	3354896	vtd	http://www.ncbi.nlm.nih.gov/gene/?term=3354896	"Dmel_CG17436, 80Fh, CG17436, CG40222, DRAD21, DRad21, DmRAD21, Dmel\CG17436, Drad21, RAD21, Rad21, Rad21/Scc1, Scc1, VTD, dRad21, drad21, l(3)80Fh, l(3)Lh3, l3, lethal 3, rad21, scc1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010779	3354919	Dbp80	http://www.ncbi.nlm.nih.gov/gene/?term=3354919	"Dmel_CG17023, BcDNA:RE44177, CG17023, DBP80, DmDbp80, Dmel\CG17023, HEL80, Hel40, Hel80, hel-40, mdcds_36124 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010780	3354919	Dbp80	http://www.ncbi.nlm.nih.gov/gene/?term=3354919	"Dmel_CG17023, BcDNA:RE44177, CG17023, DBP80, DmDbp80, Dmel\CG17023, HEL80, Hel40, Hel80, hel-40, mdcds_36124 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010781	3354977	MED21	http://www.ncbi.nlm.nih.gov/gene/?term=3354977	"Dmel_CG17397, CG17397, CG40364, Dmel\CG17397, Med21, Trap19, dSRB7, dTRAP19, p18 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010782	3354988	CG17163	http://www.ncbi.nlm.nih.gov/gene/?term=3354988	Dmel_ Dmel\CG17163	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010783	3354992	zyd	http://www.ncbi.nlm.nih.gov/gene/?term=3354992	"Dmel_CG2893, BEST:CK02262, CG2893, CG40147, CK02262, Dmel\CG2893 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010784	3354996	CG17168	http://www.ncbi.nlm.nih.gov/gene/?term=3354996	Dmel_ Dmel\CG17168	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010785	3355011	CG17683	http://www.ncbi.nlm.nih.gov/gene/?term=3355011	"Dmel_ Dmel\CG17683, NAR1p, NC37, NC38, NC70, l(2)NC37, l(2)NC38, l(2)NC70 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010786	3355041	eIF-4B	http://www.ncbi.nlm.nih.gov/gene/?term=3355041	"Dmel_CG10837, CG10837, Dm-eIF4B, Dmel\CG10837, EIF-4B, Eif4B-L, eIF-4B-S, eIF-4b, eIF4B, eIF4B-L, eIF4B-S, eIf4b, eIF-4B "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010787	3355072	CG41099	http://www.ncbi.nlm.nih.gov/gene/?term=3355072	"Dmel_ BEST:GM10035, CG17416, CG17419, Dmel\CG41099, GM10035 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010788	3355079	CG40045	http://www.ncbi.nlm.nih.gov/gene/?term=3355079	"Dmel_ BcDNA:RE63412, Dmel\CG40045 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010789	3355094	CG12567	http://www.ncbi.nlm.nih.gov/gene/?term=3355094	Dmel_ Dmel\CG12567	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010790	3355109	Parp	http://www.ncbi.nlm.nih.gov/gene/?term=3355109	"Dmel_CG40411, BEST:LD21673, CG17685, CG17696, CG17718, CG40411, D.PARP, Dm.pARTa, Dmel\CG40411, LD21673.3prime, PARP, PARP-1, PARP11, dPARP, dmparp, parp, Parp "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010791	3355123	CG40006	http://www.ncbi.nlm.nih.gov/gene/?term=3355123	"Dmel_ BcDNA:RE68569, Dmel\CG40006 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010792	3355123	CG40006	http://www.ncbi.nlm.nih.gov/gene/?term=3355123	"Dmel_ BcDNA:RE68569, Dmel\CG40006 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010793	3355125	CG17490	http://www.ncbi.nlm.nih.gov/gene/?term=3355125	Dmel_ Dmel\CG17490	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010794	3355127	Slmap	http://www.ncbi.nlm.nih.gov/gene/?term=3355127	"Dmel_CG17494, CG17494, Dmel\CG17494 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010795	3355129	CG17715	http://www.ncbi.nlm.nih.gov/gene/?term=3355129	"Dmel_ BcDNA:RE07178, BcDNA:RE63764, CG18603, Dmel\CG17715 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010796	3355130	lt	http://www.ncbi.nlm.nih.gov/gene/?term=3355130	"Dmel_CG18028, CG18028, Dm-lt(het), Dmel\CG18028, Lt, Vps41, l(2)40Fb, vps41 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010797	3355145	CG12547	http://www.ncbi.nlm.nih.gov/gene/?term=3355145	"Dmel_ CG40277, Dmel\CG12547, anon-EST:Posey268 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010798	3356	HTR2A	http://www.ncbi.nlm.nih.gov/gene/?term=3356	"5-HT2A, HTR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010799	33583	odd	http://www.ncbi.nlm.nih.gov/gene/?term=33583	"Dmel_CG3851, CG3851, Dmel\CG3851, ODD, Odd, l(2)01863, ods "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010800	3359	HTR3A	http://www.ncbi.nlm.nih.gov/gene/?term=3359	"5-HT-3, 5-HT3A, 5-HT3R, 5HT3R, HTR3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010801	335	APOA1	http://www.ncbi.nlm.nih.gov/gene/?term=335	apo(a)	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010802	3361053	SPCTRNAILE.09	http://www.ncbi.nlm.nih.gov/gene/?term=3361053	SPCTRNAILE.09	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPCTRNAILE.09
RLID00010803	3361065	SPCTRNAALA.12	http://www.ncbi.nlm.nih.gov/gene/?term=3361065	SPCTRNAALA.12	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPCTRNAALA.12
RLID00010804	3361195	SPBTRNAGLN.01	http://www.ncbi.nlm.nih.gov/gene/?term=3361195	SPBTRNAGLN.01	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLN.01
RLID00010805	3361196	SPBTRNAGLN.02	http://www.ncbi.nlm.nih.gov/gene/?term=3361196	SPBTRNAGLN.02	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLN.02
RLID00010806	3361200	snu4	http://www.ncbi.nlm.nih.gov/gene/?term=3361200	SPSNRNA.04	snRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.04
RLID00010807	3361228	SPBTRNAVAL.08	http://www.ncbi.nlm.nih.gov/gene/?term=3361228	SPBTRNAVAL.08	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAVAL.08
RLID00010808	3361229	SPBTRNAGLU.07	http://www.ncbi.nlm.nih.gov/gene/?term=3361229	SPBTRNAGLU.07	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLU.07
RLID00010809	3361236	SPBTRNALEU.07	http://www.ncbi.nlm.nih.gov/gene/?term=3361236	SPBTRNALEU.07	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNALEU.07
RLID00010810	3361238	SPBTRNAVAL.07	http://www.ncbi.nlm.nih.gov/gene/?term=3361238	SPBTRNAVAL.07	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAVAL.07
RLID00010811	3361240	SPBTRNAVAL.06	http://www.ncbi.nlm.nih.gov/gene/?term=3361240	SPBTRNAVAL.06	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAVAL.06
RLID00010812	3361244	SPBTRNAGLU.06	http://www.ncbi.nlm.nih.gov/gene/?term=3361244	SPBTRNAGLU.06	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLU.06
RLID00010813	3361246	SPBTRNAVAL.05	http://www.ncbi.nlm.nih.gov/gene/?term=3361246	SPBTRNAVAL.05	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAVAL.05
RLID00010814	3361251	SPBTRNALEU.06	http://www.ncbi.nlm.nih.gov/gene/?term=3361251	SPBTRNALEU.06	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNALEU.06
RLID00010815	3361264	SPBTRNALEU.05	http://www.ncbi.nlm.nih.gov/gene/?term=3361264	SPBTRNALEU.05	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNALEU.05
RLID00010816	3361279	SPBTRNAGLN.03	http://www.ncbi.nlm.nih.gov/gene/?term=3361279	SPBTRNAGLN.03	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLN.03
RLID00010817	3361280	SPBTRNAGLN.04	http://www.ncbi.nlm.nih.gov/gene/?term=3361280	SPBTRNAGLN.04	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLN.04
RLID00010818	3361282	SPBTRNAGLU.05	http://www.ncbi.nlm.nih.gov/gene/?term=3361282	SPBTRNAGLU.05	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLU.05
RLID00010819	3361302	SPBTRNAPHE.03	http://www.ncbi.nlm.nih.gov/gene/?term=3361302	SPBTRNAPHE.03	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAPHE.03
RLID00010820	3361311	SPBTRNALEU.08	http://www.ncbi.nlm.nih.gov/gene/?term=3361311	SPBTRNALEU.08	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNALEU.08
RLID00010821	3361317	snu1	http://www.ncbi.nlm.nih.gov/gene/?term=3361317	SPSNRNA.01	snRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.01
RLID00010822	3361326	SPBTRNALEU.09	http://www.ncbi.nlm.nih.gov/gene/?term=3361326	SPBTRNALEU.09	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNALEU.09
RLID00010823	3361328	snu5	http://www.ncbi.nlm.nih.gov/gene/?term=3361328	SPSNRNA.05	snRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.05
RLID00010824	3361347	SPBTRNALEU.10	http://www.ncbi.nlm.nih.gov/gene/?term=3361347	SPBTRNALEU.10	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNALEU.10
RLID00010825	3361355	SPBTRNAGLU.08	http://www.ncbi.nlm.nih.gov/gene/?term=3361355	SPBTRNAGLU.08	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPBTRNAGLU.08
RLID00010826	3361379	SPATRNAPRO.01	http://www.ncbi.nlm.nih.gov/gene/?term=3361379	SPATRNAPRO.01	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAPRO.01
RLID00010827	3361382	sno52	http://www.ncbi.nlm.nih.gov/gene/?term=3361382	SPSNORNA.29	snoRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNORNA.29
RLID00010828	3361404	SPATRNAASP.01	http://www.ncbi.nlm.nih.gov/gene/?term=3361404	SPATRNAASP.01	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAASP.01
RLID00010829	3361447	SPATRNAARG.02	http://www.ncbi.nlm.nih.gov/gene/?term=3361447	SPATRNAARG.02	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAARG.02
RLID00010830	3361463	SPATRNAARG.01	http://www.ncbi.nlm.nih.gov/gene/?term=3361463	SPATRNAARG.01	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAARG.01
RLID00010831	3361522	snu3	http://www.ncbi.nlm.nih.gov/gene/?term=3361522	SPSNRNA.03	snoRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.03
RLID00010832	3361546	SPATRNAPRO.03	http://www.ncbi.nlm.nih.gov/gene/?term=3361546	SPATRNAPRO.03	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAPRO.03
RLID00010833	3361551	SPATRNAARG.03	http://www.ncbi.nlm.nih.gov/gene/?term=3361551	SPATRNAARG.03	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAARG.03
RLID00010834	3361559	SPATRNAASP.02	http://www.ncbi.nlm.nih.gov/gene/?term=3361559	SPATRNAASP.02	tRNA	Saccharomyces cerevisiae	25361970	Cytoplasm	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPATRNAASP.02
RLID00010835	3361571	snu2	http://www.ncbi.nlm.nih.gov/gene/?term=3361571	SPSNRNA.02	snRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.02
RLID00010836	3361572	snu6	http://www.ncbi.nlm.nih.gov/gene/?term=3361572	SPSNRNA.06	snRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.06
RLID00010837	33628	CG3702	http://www.ncbi.nlm.nih.gov/gene/?term=33628	"Dmel_ Dmel\CG3702, cg3702 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010838	33628	CG3702	http://www.ncbi.nlm.nih.gov/gene/?term=33628	"Dmel_ Dmel\CG3702, cg3702 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010839	33629	RpL40	http://www.ncbi.nlm.nih.gov/gene/?term=33629	"Dmel_CG2960, BcDNA:RE10554, CEP52, CG2960, DUb52, Dmel\CG2960, Dub52, Rpl40, Ub52, Ubi-f, Ubi-f52, Ubiq "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010840	33629	RpL40	http://www.ncbi.nlm.nih.gov/gene/?term=33629	"Dmel_CG2960, BcDNA:RE10554, CEP52, CG2960, DUb52, Dmel\CG2960, Dub52, Rpl40, Ub52, Ubi-f, Ubi-f52, Ubiq "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010841	3362	HTR6	http://www.ncbi.nlm.nih.gov/gene/?term=3362	"5-HT6, 5-HT6R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010842	33635	bdl	http://www.ncbi.nlm.nih.gov/gene/?term=33635	"Dmel_CG16857, BcDNA:GH11322, CG16857, CT35491, Dmel\CG16857, GH11322 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010843	33638	Traf4	http://www.ncbi.nlm.nih.gov/gene/?term=33638	"Dmel_CG3048, CG3048, DTRAF, DTRAF1, Dmel\CG3048, TRAF, TRAF1, TRAF4, Traf1, dTRAF, dTRAF1, dTraf1, dTraf4, dtraf1, traf-4, traf1, traf4 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010844	33652	CG15440	http://www.ncbi.nlm.nih.gov/gene/?term=33652	"Dmel_ Dmel\CG15440, Secp43, cg15440 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010845	33710	Trip1	http://www.ncbi.nlm.nih.gov/gene/?term=33710	"Dmel_CG8882, CG8882, DmTRIP, Dmel\CG8882, eIF-3beta, eIF3-S2, eIF3i "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010846	33710	Trip1	http://www.ncbi.nlm.nih.gov/gene/?term=33710	"Dmel_CG8882, CG8882, DmTRIP, Dmel\CG8882, eIF-3beta, eIF3-S2, eIF3i "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010847	3371	TNC	http://www.ncbi.nlm.nih.gov/gene/?term=3371	"150-225, DFNA56, GMEM, GP, HXB, JI, TN, TN-C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010848	3371	TNC	http://www.ncbi.nlm.nih.gov/gene/?term=3371	"150-225, DFNA56, GMEM, GP, HXB, JI, TN, TN-C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010849	33721	Rtnl1	http://www.ncbi.nlm.nih.gov/gene/?term=33721	"Dmel_CG33113, 142893_at, CG18623, CG33113, CG8895, Dmel\CG33113, G9, Retl1, Rtnl-1, rtnl1 "	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010850	33726	vkg	http://www.ncbi.nlm.nih.gov/gene/?term=33726	"Dmel_CG16858, 1209, 6072, CG16858, CT25584, Coll IValpha2, DmColA2, Dmel\CG16858, Vkg, VkgC, alpha(IV)2/vkg, col4a2, coll-IV, coll. IV, collagen-IV, l(2)01209 "	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010851	33726	vkg	http://www.ncbi.nlm.nih.gov/gene/?term=33726	"Dmel_CG16858, 1209, 6072, CG16858, CT25584, Coll IValpha2, DmColA2, Dmel\CG16858, Vkg, VkgC, alpha(IV)2/vkg, col4a2, coll-IV, coll. IV, collagen-IV, l(2)01209 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010852	33726	vkg	http://www.ncbi.nlm.nih.gov/gene/?term=33726	"Dmel_CG16858, 1209, 6072, CG16858, CT25584, Coll IValpha2, DmColA2, Dmel\CG16858, Vkg, VkgC, alpha(IV)2/vkg, col4a2, coll-IV, coll. IV, collagen-IV, l(2)01209 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010853	33739	qtc	http://www.ncbi.nlm.nih.gov/gene/?term=33739	"Dmel_CG14039, CG14039, Dmel\CG14039 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010854	3373	HYAL1	http://www.ncbi.nlm.nih.gov/gene/?term=3373	"HYAL-1, LUCA1, MPS9, NAT6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010855	33757	Bsg25D	http://www.ncbi.nlm.nih.gov/gene/?term=33757	"Dmel_CG14025, CG14025, Dmel\CG14025, brg25D, bsg25D, bsq25D "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010856	33757	Bsg25D	http://www.ncbi.nlm.nih.gov/gene/?term=33757	"Dmel_CG14025, CG14025, Dmel\CG14025, brg25D, bsg25D, bsq25D "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010857	33758	Bub1	http://www.ncbi.nlm.nih.gov/gene/?term=33758	"Dmel_CG14030, BUB1, BUB1-like, BubR1, BubRI, CG14030, CG14030/Bub1, Dmel\CG14030, bub1 "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010858	3375	IAPP	http://www.ncbi.nlm.nih.gov/gene/?term=3375	"DAP, IAP "	mRNA	Homo sapiens	21525359	Cytoplasm	293 cell	qRT-PCR	"Rather, the removal of P bodies shifted IAP mRNA from nonpolysomal to polysomal fractions. Although IAP mRNA localized to P bodies, Gag was targeted to the endoplasmic reticulum (ER), from which IAP buds. Indeed, we observed increased levels of IAP mRNA and Gag upon P-body disruption. "
RLID00010859	3375	IAPP	http://www.ncbi.nlm.nih.gov/gene/?term=3375	"DAP, IAP "	mRNA	Homo sapiens	21525359	Ribosome	293 cell	qRT-PCR	"Rather, the removal of P bodies shifted IAP mRNA from nonpolysomal to polysomal fractions. Although IAP mRNA localized to P bodies, Gag was targeted to the endoplasmic reticulum (ER), from which IAP buds. Indeed, we observed increased levels of IAP mRNA and Gag upon P-body disruption. "
RLID00010860	3376	IARS	http://www.ncbi.nlm.nih.gov/gene/?term=3376	"IARS1, ILERS, ILRS, IRS, PRO0785 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010861	3376	IARS	http://www.ncbi.nlm.nih.gov/gene/?term=3376	"IARS1, ILERS, ILRS, IRS, PRO0785 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010862	3376	IARS	http://www.ncbi.nlm.nih.gov/gene/?term=3376	"IARS1, ILERS, ILRS, IRS, PRO0785 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010863	33770	mid	http://www.ncbi.nlm.nih.gov/gene/?term=33770	"Dmel_CG6634, CG6634, Dmel\CG6634, H15r, H15r/nmr2, Mid(H15), TBX20, extra, los, nmr2 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010864	33770	mid	http://www.ncbi.nlm.nih.gov/gene/?term=33770	"Dmel_CG6634, CG6634, Dmel\CG6634, H15r, H15r/nmr2, Mid(H15), TBX20, extra, los, nmr2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010865	33778	Cap-D3	http://www.ncbi.nlm.nih.gov/gene/?term=33778	"Dmel_CG31989, BcDNA:RE74832, CAP-D2, CAP-D3, CG14019, CG31989, CG6922, CapD3, Dmel\CG31989, cap-D3, dCap-D3 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010866	337867	UBAC2	http://www.ncbi.nlm.nih.gov/gene/?term=337867	PHGDHL1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010867	337	APOA4	http://www.ncbi.nlm.nih.gov/gene/?term=337		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010868	33803	CG11147	http://www.ncbi.nlm.nih.gov/gene/?term=33803	Dmel_ Dmel\CG11147	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010869	33803	CG11147	http://www.ncbi.nlm.nih.gov/gene/?term=33803	Dmel_ Dmel\CG11147	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010870	33814	rau	http://www.ncbi.nlm.nih.gov/gene/?term=33814	"Dmel_CG8965, CG8965, Dmel\CG8965 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010871	33814	rau	http://www.ncbi.nlm.nih.gov/gene/?term=33814	"Dmel_CG8965, CG8965, Dmel\CG8965 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010872	3382	ICA1	http://www.ncbi.nlm.nih.gov/gene/?term=3382	"ICA69, ICAp69 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010873	338337	Cog3	http://www.ncbi.nlm.nih.gov/gene/?term=338337	E430004N23	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010874	33834	chic	http://www.ncbi.nlm.nih.gov/gene/?term=33834	"Dmel_CG9553, CG9553, Chi, Chic, D88, Dmel\CG9553, GH4, chi, l(2)27/7, profilin, sand "	mRNA	Drosophila melanogaster	24656828	Axon	Neuron	In situ hybridization	"Finally, we demonstrate that profilin mRNA is a direct and functional target of Imp that localizes to axons and controls axonal regrowth. "
RLID00010875	33834	chic	http://www.ncbi.nlm.nih.gov/gene/?term=33834	"Dmel_CG9553, CG9553, Chi, Chic, D88, Dmel\CG9553, GH4, chi, l(2)27/7, profilin, sand "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010876	33834	chic	http://www.ncbi.nlm.nih.gov/gene/?term=33834	"Dmel_CG9553, CG9553, Chi, Chic, D88, Dmel\CG9553, GH4, chi, l(2)27/7, profilin, sand "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010877	338350	Acad12	http://www.ncbi.nlm.nih.gov/gene/?term=338350	9330129D05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010878	338352	Nell1	http://www.ncbi.nlm.nih.gov/gene/?term=338352	"B230343H07Rik, l7R6 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010879	338364	Trim65	http://www.ncbi.nlm.nih.gov/gene/?term=338364	4732463G12Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00010880	338372	Map3k9	http://www.ncbi.nlm.nih.gov/gene/?term=338372	"E130314H24Rik, Mlk1, Prke1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010881	3383	ICAM1	http://www.ncbi.nlm.nih.gov/gene/?term=3383	"BB2, CD54, P3.58 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010882	3383	ICAM1	http://www.ncbi.nlm.nih.gov/gene/?term=3383	"BB2, CD54, P3.58 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010883	338428	SNORD109A	http://www.ncbi.nlm.nih.gov/gene/?term=338428	HBII-438A	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00010884	338429	SNORD109B	http://www.ncbi.nlm.nih.gov/gene/?term=338429	HBII-438B	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00010885	338440	ANO9	http://www.ncbi.nlm.nih.gov/gene/?term=338440	"PIG5, TMEM16J, TP53I5 "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00010886	338448	GTF2IP2	http://www.ncbi.nlm.nih.gov/gene/?term=338448		lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00010887	338467	Morc3	http://www.ncbi.nlm.nih.gov/gene/?term=338467	"1110051N18Rik, AI452146, BF318192, D16Jhu32e, NXP2, Zcwcc3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00010888	3384	ICAM2	http://www.ncbi.nlm.nih.gov/gene/?term=3384	CD102	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010889	3385	ICAM3	http://www.ncbi.nlm.nih.gov/gene/?term=3385	"CD50, CDW50, ICAM-R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010890	3385	ICAM3	http://www.ncbi.nlm.nih.gov/gene/?term=3385	"CD50, CDW50, ICAM-R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010891	33861	Kr-h1	http://www.ncbi.nlm.nih.gov/gene/?term=33861	"Dmel_CG45074, 44/11, CG18783, CG45074, CG9167, Dmel\CG45074, Dmel_CG18783, Kr h, Kr-H1, Kr-h, P381, Pow, l(2)05208, l(2)10642 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010892	33863	stai	http://www.ncbi.nlm.nih.gov/gene/?term=33863	"Dmel_CG31641, BEST:LD33989, CG31641, CG5981, D-stat, Dmel\CG31641, LD33989, SCG10-like, rdt, rdtp "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010893	33863	stai	http://www.ncbi.nlm.nih.gov/gene/?term=33863	"Dmel_CG31641, BEST:LD33989, CG31641, CG5981, D-stat, Dmel\CG31641, LD33989, SCG10-like, rdt, rdtp "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010894	338657	CCDC84	http://www.ncbi.nlm.nih.gov/gene/?term=338657	DLNB14	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010895	338657	CCDC84	http://www.ncbi.nlm.nih.gov/gene/?term=338657	DLNB14	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010896	338692	ANKRD13D	http://www.ncbi.nlm.nih.gov/gene/?term=338692		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010897	3386	ICAM4	http://www.ncbi.nlm.nih.gov/gene/?term=3386	"CD242, LW "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010898	338773	TMEM119	http://www.ncbi.nlm.nih.gov/gene/?term=338773	OBIF	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010899	338773	TMEM119	http://www.ncbi.nlm.nih.gov/gene/?term=338773	OBIF	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010900	33881	PDZ-GEF	http://www.ncbi.nlm.nih.gov/gene/?term=33881	"Dmel_CG9491, CG9491, D-PDZGEF, DGEF, Dmel\CG9491, Dzy, EC2-8, GEF, Gef26, PDF-GEF Dizzy, dPDZ-GEF, dizzy, dzy, l(2)k13720 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010901	33904	CG9536	http://www.ncbi.nlm.nih.gov/gene/?term=33904	Dmel_ Dmel\CG9536	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010902	33916	eya	http://www.ncbi.nlm.nih.gov/gene/?term=33916	"Dmel_CG9554, 24582246, BcDNA:LD16029, CG9554, CLI, CLIFT, Dmel\CG9554, EY2-1, EYA, Eya, cli, cli/eya, dEYA, del1, eay, ey-2 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010903	339175	METTL2A	http://www.ncbi.nlm.nih.gov/gene/?term=339175	METTL2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010904	339201	ASB16-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=339201	C17orf65	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010905	339201	ASB16-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=339201	C17orf65	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010906	339229	OXLD1	http://www.ncbi.nlm.nih.gov/gene/?term=339229	C17orf90	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010907	339230	CCDC137	http://www.ncbi.nlm.nih.gov/gene/?term=339230	RaRF	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010908	339231	ARL16	http://www.ncbi.nlm.nih.gov/gene/?term=339231		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010909	339263	C17orf51	http://www.ncbi.nlm.nih.gov/gene/?term=339263		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010910	339287	MSL1	http://www.ncbi.nlm.nih.gov/gene/?term=339287	"MSL-1, hMSL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010911	339324	ZNF260	http://www.ncbi.nlm.nih.gov/gene/?term=339324	"OZRF1, PEX1, ZFP260 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010912	339324	ZNF260	http://www.ncbi.nlm.nih.gov/gene/?term=339324	"OZRF1, PEX1, ZFP260 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010913	33934	cup	http://www.ncbi.nlm.nih.gov/gene/?term=33934	"Dmel_CG11181, CG11181, CUP, Cup, DmCup, Dmel\CG11181, fs(1) fs(2)cup, i239 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010914	339366	ADAMTSL5	http://www.ncbi.nlm.nih.gov/gene/?term=339366	THSD6	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010915	339448	C1orf174	http://www.ncbi.nlm.nih.gov/gene/?term=339448		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010916	339448	C1orf174	http://www.ncbi.nlm.nih.gov/gene/?term=339448		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010917	339448	C1orf174	http://www.ncbi.nlm.nih.gov/gene/?term=339448		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010918	339448	C1orf174	http://www.ncbi.nlm.nih.gov/gene/?term=339448		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010919	339451	KLHL17	http://www.ncbi.nlm.nih.gov/gene/?term=339451		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010920	339451	KLHL17	http://www.ncbi.nlm.nih.gov/gene/?term=339451		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010921	339456	TMEM52	http://www.ncbi.nlm.nih.gov/gene/?term=339456		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010922	339483	MTMR9LP	http://www.ncbi.nlm.nih.gov/gene/?term=339483	MTMR9L	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010923	339487	ZBTB8OS	http://www.ncbi.nlm.nih.gov/gene/?term=339487	"ARCH, ARCH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010924	3394	IRF8	http://www.ncbi.nlm.nih.gov/gene/?term=3394	"H-ICSBP, ICSBP, ICSBP1, IMD32A, IMD32B, IRF-8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010925	3394	IRF8	http://www.ncbi.nlm.nih.gov/gene/?term=3394	"H-ICSBP, ICSBP, ICSBP1, IMD32A, IMD32B, IRF-8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010926	33966	nop5	http://www.ncbi.nlm.nih.gov/gene/?term=33966	"Dmel_CG10206, 2/30, CG10206, DNOP5, Dmel\CG10206, D FBgn0026196, NOP5, Nop5 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010927	3396	ICT1	http://www.ncbi.nlm.nih.gov/gene/?term=3396	"DS-1, DS1, MRP-L58 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010928	33974	SA	http://www.ncbi.nlm.nih.gov/gene/?term=33974	"Dmel_CG3423, CG3423, DSA, DSA1, DmSA, Dmel\CG3423, ESTS:92H2T, SCC3, Scc3 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010929	33974	SA	http://www.ncbi.nlm.nih.gov/gene/?term=33974	"Dmel_CG3423, CG3423, DSA, DSA1, DmSA, Dmel\CG3423, ESTS:92H2T, SCC3, Scc3 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010930	3397	ID1	http://www.ncbi.nlm.nih.gov/gene/?term=3397	"ID, bHLHb24 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010931	3397	ID1	http://www.ncbi.nlm.nih.gov/gene/?term=3397	"ID, bHLHb24 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010932	33981	smt3	http://www.ncbi.nlm.nih.gov/gene/?term=33981	"Dmel_CG4494, CG4494, Dm0342, DmSUMO-1, DmSmt3, Dmel\CG4494, Dm SMT3, SUMO, Smt3, Sumo, anon-EST:Posey240, dSmt3, dsmt3, l(2)04493, l(2)SH0182, l(2)SH2 0182, sumo "	mRNA	Drosophila melanogaster	24058701	Cytosol	S2 cell	qRT-PCR	"As predicted from its sequence and the known cytosolic/nuclear functions of the sumo protein, sumo mRNA was highly enriched in the cytosolic fraction, along with the mRNA encoding actin (Figure 1D). "
RLID00010933	33982	snRNP-U1-70K	http://www.ncbi.nlm.nih.gov/gene/?term=33982	"Dmel_CG8749, 70K, CG8749, Dm70K, Dmel\CG8749, U1, U1 70K, U1 70K snRNP, U1 70k, U1 snRNP, U1-70K, U1-70k, U170K, U1snRNP-70K, dU1-70K, l(2)02107, snRNP, snRNP27D, snRNP70K "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010934	339834	CCDC36	http://www.ncbi.nlm.nih.gov/gene/?term=339834	CT74	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010935	339834	CCDC36	http://www.ncbi.nlm.nih.gov/gene/?term=339834	CT74	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010936	3398	ID2	http://www.ncbi.nlm.nih.gov/gene/?term=3398	"GIG8, ID2A, ID2H, bHLHb26 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010937	3398	ID2	http://www.ncbi.nlm.nih.gov/gene/?term=3398	"GIG8A, ID2H, bHLHb26, ID2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010938	3398	ID2	http://www.ncbi.nlm.nih.gov/gene/?term=3398	"GIG8A, ID2H, bHLHb26, ID2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010939	339983	NAT8L	http://www.ncbi.nlm.nih.gov/gene/?term=339983	"CML3, NACED, NAT8-LIKE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010940	3399	ID3	http://www.ncbi.nlm.nih.gov/gene/?term=3399	"HEIR-1, bHLHb25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010941	3399	ID3	http://www.ncbi.nlm.nih.gov/gene/?term=3399	"HEIR-1, bHLHb25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010942	340061	TMEM173	http://www.ncbi.nlm.nih.gov/gene/?term=340061	"ERIS, MITA, MPYS, NET23, SAVI, STING, hMITA, hSTING "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010943	340075	ARSI	http://www.ncbi.nlm.nih.gov/gene/?term=340075	SPG66	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010944	34009	wg	http://www.ncbi.nlm.nih.gov/gene/?term=34009	"Dmel_CG4889, Br, CG4889, DWint-1, DWnt-1, Dint-1, Dm Wg, Dm-1, Dmel\CG4889, Gla, I, Sp, WG, WNT, Wg, Wnt, Wnt-1, Wnt/Wg, Wnt1, dWnt, fg, int-1, l(2)02657, l(2)rO727, l(2)wg, spdl, wnt, wnt1, wg "	mRNA	Drosophila melanogaster	18045835	Apical	Embryo	Fluorescence in situ hybridization	"Wilkie and Davis (Wilkie and Davis, 2001) have shown that wg mRNA localizes apically in a Dynein-dependent fashion when injected into syncitial stage Drosophila embryos. Consistent with their findings, we found that reporter RNA containing the wg 3UTR is localized to apical cytoplasm within 8 minutes after injection, in 97% of embryos (construct FL, Fig. 1B, Table 2). "
RLID00010945	34009	wg	http://www.ncbi.nlm.nih.gov/gene/?term=34009	"Dmel_CG4889, Br, CG4889, DWint-1, DWnt-1, Dint-1, Dm Wg, Dm-1, Dmel\CG4889, Gla, I, Sp, WG, WNT, Wg, Wnt, Wnt-1, Wnt/Wg, Wnt1, dWnt, fg, int-1, l(2)02657, l(2)rO727, l(2)wg, spdl, wnt, wnt1, wg "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00010946	340206	TREML3P	http://www.ncbi.nlm.nih.gov/gene/?term=340206	"TLT3, TREML3 "	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010947	340252	ZNF680	http://www.ncbi.nlm.nih.gov/gene/?term=340252		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010948	34032	RapGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=34032	"Dmel_CG44086, CG13789, CG13790, CG13791, CG33529, CG34374, CG44086, CG6682, Dmel\CG44086, Dmel_CG13790, Dmel_CG13791, Dmel_CG33529, Dmel_CG34374, Q9VM02_DROME, RapGap1, Rapgap1, rapgap1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010949	34032	RapGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=34032	"Dmel_CG44086, CG13789, CG13790, CG13791, CG33529, CG34374, CG44086, CG6682, Dmel\CG44086, Dmel_CG13790, Dmel_CG13791, Dmel_CG33529, Dmel_CG34374, Q9VM02_DROME, RapGap1, Rapgap1, rapgap1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010950	34032	RapGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=34032	"Dmel_CG44086, CG13789, CG13790, CG13791, CG33529, CG34374, CG44086, CG6682, Dmel\CG44086, Dmel_CG13790, Dmel_CG13791, Dmel_CG33529, Dmel_CG34374, Q9VM02_DROME, RapGap1, Rapgap1, rapgap1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010951	340348	TSPAN33	http://www.ncbi.nlm.nih.gov/gene/?term=340348	"PEN, PEN., TSPAN-33 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010952	34037	CG6739	http://www.ncbi.nlm.nih.gov/gene/?term=34037	Dmel_ Dmel\CG6739	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010953	34037	CG6739	http://www.ncbi.nlm.nih.gov/gene/?term=34037	Dmel_ Dmel\CG6739	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010954	34044	Tep2	http://www.ncbi.nlm.nih.gov/gene/?term=34044	"Dmel_CG7052, 145970_at, 145971_at, CG18589, CG7052, Dmel\CG7052, T13, TEP II, TEP2, TEP2mel, Tep 2, Tep II, TepII, dTEPII, tepII "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010955	340481	ZDHHC21	http://www.ncbi.nlm.nih.gov/gene/?term=340481	"9130404H11Rik, DHHC-21, DHHC21, DNZ1, HSPC097 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010956	340485	ACER2	http://www.ncbi.nlm.nih.gov/gene/?term=340485	"ALKCDase2, ASAH3L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010957	340485	ACER2	http://www.ncbi.nlm.nih.gov/gene/?term=340485	"ALKCDase2, ASAH3L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010958	340542	BEX5	http://www.ncbi.nlm.nih.gov/gene/?term=340542	NGFRAP1L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010959	340547	VSIG1	http://www.ncbi.nlm.nih.gov/gene/?term=340547	"1700062D20Rik, GPA34, dJ889N15.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010960	340547	VSIG1	http://www.ncbi.nlm.nih.gov/gene/?term=340547	"1700062D20Rik, GPA34, dJ889N15.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010961	340554	ZC3H12B	http://www.ncbi.nlm.nih.gov/gene/?term=340554	"CXorf32, MCPIP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010962	340554	ZC3H12B	http://www.ncbi.nlm.nih.gov/gene/?term=340554	"CXorf32, MCPIP2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010963	340554	ZC3H12B	http://www.ncbi.nlm.nih.gov/gene/?term=340554	"CXorf32, MCPIP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010964	340591	CA5BP1	http://www.ncbi.nlm.nih.gov/gene/?term=340591	"CA5BL, CA5BP, PRO2325 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010965	34087	pes	http://www.ncbi.nlm.nih.gov/gene/?term=34087	"Dmel_CG7228, CG7228, Dmel\CG7228, Pes "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010966	340895	MALRD1	http://www.ncbi.nlm.nih.gov/gene/?term=340895	"C10orf112, DIET1, bA265G8.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010967	341032	C11orf53	http://www.ncbi.nlm.nih.gov/gene/?term=341032		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010968	341116	MS4A10	http://www.ncbi.nlm.nih.gov/gene/?term=341116	"CD20L7, MS4A9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010969	341116	MS4A10	http://www.ncbi.nlm.nih.gov/gene/?term=341116	"CD20L7, MS4A9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00010970	34134	wol	http://www.ncbi.nlm.nih.gov/gene/?term=34134	"Dmel_CG7870, ALG5, CG7870, Dmel\CG7870, Wol, alg5, dAlg5 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010971	34136	CG7840	http://www.ncbi.nlm.nih.gov/gene/?term=34136	"Dmel_ Dmel\CG7840, cg7840 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010972	34137	Ostgamma	http://www.ncbi.nlm.nih.gov/gene/?term=34137	"Dmel_CG7830, CG7830, Dmel\CG7830, MagT1, OST, dMagT1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010973	34137	Ostgamma	http://www.ncbi.nlm.nih.gov/gene/?term=34137	"Dmel_CG7830, CG7830, Dmel\CG7830, MagT1, OST, dMagT1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010974	3416	IDE	http://www.ncbi.nlm.nih.gov/gene/?term=3416	INSULYSIN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010975	3416	IDE	http://www.ncbi.nlm.nih.gov/gene/?term=3416	INSULYSIN	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010976	3416	IDE	http://www.ncbi.nlm.nih.gov/gene/?term=3416	INSULYSIN	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00010977	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	10024878	Nucleus	Oocyte	In situ hybridization	"The requirement for microtubules is most clearly seen by confocal microscopy of oocytes nuclear antigen scripts are detected in the oocytes (arrowheads) but are not lolamin. In the absence of microtubules,grkm RNA aggregates into one or a few larg clumps on the surfaceof the oocyte nucleus (Figure 2A). "
RLID00010978	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	10024878	Anterior	Oocyte	In situ hybridization	"During nuclear migration, about 50% of the grk mRNA is closely associated with the ER (Figures 3D-3F). Toward the end of midoogenesis, the ER and grk mRNA are both concentrated along the anterior cortex and again are closely associated with each other (data not shown). During late oogenesis, all of the grk mRNA is associated with the ER, although the ER remains distributed over the entire anterior cortex (Figures 3E-3F). "
RLID00010979	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	10024878	Endoplasmic reticulum	Oocyte	In situ hybridization	"During nuclear migration, about 50% of the grk mRNA is closely associated with the ER (Figures 3D-3F). Toward the end of midoogenesis, the ER and grk mRNA are both concentrated along the anterior cortex and again are closely associated with each other (data not shown). During late oogenesis, all of the grk mRNA is associated with the ER, although the ER remains distributed over the entire anterior cortex (Figures 3E-3F). "
RLID00010980	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	11131516	Posterior	Embryo	In situ hybridization	"For its assembly, localization of gurken mRNA and its translation at the posterior pole of early oogenic stages is essential for establishing the posterior pole of the oocyte. Subsequently, oskar mRNA becomes localized to the posterior pole where its translation leads to the assembly of a functional germ plasm "
RLID00010981	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	15385627	Golgi apparatus	Oocyte|Neuron cell	In situ hybridization	"And we show, by using three Drosophila mutants in which gurken mRNA is mislocalized, that what controls the choice of the tER-Golgi units involved in Gurken transport, among the thousand present, is the localization of gurken mRNA. This pretranslational mechanism is coupled to posttranslational sorting events involving Cornichon and the transmembrane domain of Gurken that prevent its diffusion in the ER away from the D/A corner and ensure its efficient sorting to the tER-Golgi units at that same corner. "
RLID00010982	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	15385627	Endoplasmic reticulum	Oocyte|Neuron cell	In situ hybridization	"Using Drosophila mutants, we show that it is the localization of gurken mRNA coupled to efficient sorting of Gurken out of the ER that determines which of the numerous equivalent tER-Golgi units are used for the protein transport and processing. The choice of tER-Golgi units by mRNA localization makes them independent of each other and represents a nonconventional way, by which the oocyte implements polarized deposition of transmembrane/secreted proteins. "
RLID00010983	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	16319114	Dorsal	Oocyte	In situ hybridization	"Oskar (osk) mRNA is transported to the posterior pole and gurken (grk) mRNA is localized to an antero-dorsal cap near the oocyte nucleus (reviewed by Riechmann and Ephrussi, 2001). The localization of these axes determining transcripts occurs in several steps and is dependent on MTs, cytoplasmic Dynein and Kinesin I.  "
RLID00010984	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	19217894	Cell cortex	Oocyte	In situ hybridization	"The grk mRNA adopts a position at the junction between anterior and lateral cortex of the oocyte, adjacent to the nucleus and at the site destined to become the dorsal surface of the embryo. "
RLID00010985	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Anterior	Oocyte	In situ hybridization	Figure 6: Anterior-central grk mRNA localization in saturn is due to joint inactivation of klc and piRNA pathway.
RLID00010986	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Cell cortex	Oocyte	In situ hybridization	"Grk mRNA is normally tightly associated with the oocyte cortex but, in stage 9 klcsat oocytes, approximately one-half of the grk mRNA is somewhat internally localized (Figure 6C), a phenotype that is evident from as early as stage 2 (Figure 6I). A similar phenotype is seen in klc8ex94 germline clones. "
RLID00010987	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Dorsal	Oocyte	In situ hybridization	"Like other piRNA pathway mutations, armi oocytes show phenotypes associated with the response to DNA damage caused by excessive transposon expression, including failure to restrict anterior grk mRNA localization to a dorsal corner (Figure 5A) due to a misorganized MT cytoskeleton, silencing of Grk translation, and disruption of the karyosome. "
RLID00010988	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Dorsal	Oocyte	In situ hybridization	"In klc oocytes, a population of grk mRNA still localizes to the dorsal cortex, away from the centrosomes, which now lie ventral to the nucleus (Figure 7E). "
RLID00010989	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Dorsal	Oocyte	In situ hybridization	"We also show that initiation of the dorsoanterior localization of grk mRNA precedes centrosome localization, suggesting that microtubule self-organization contributes to breaking axial symmetry to generate a unique dorsoventral axis. "
RLID00010990	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Cytoskeleton	Oocyte	In situ hybridization	"We also show that initiation of the dorsoanterior localization of grk mRNA precedes centrosome localization, suggesting that microtubule self-organization contributes to breaking axial symmetry to generate a unique dorsoventral axis.We also show that initiation of the dorsoanterior localization of grk mRNA precedes centrosome localization, suggesting that microtubule self-organization contributes to breaking axial symmetry to generate a unique dorsoventral axis. "
RLID00010991	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24531791	Posterior	Oocyte	In situ hybridization	"A particularly significant target of dynein-mediated transport is gurken (grk) whose transcript localization is key to establishing the prospective body axes of the future embryo. grk mRNA localizes posteriorly in early oocytes and is translated during stage 5 into a transforming growth factor-a like protein that signals to overlying, somatic follicle cells to specify their posterior character. During this stage, the minus-ends of MTs are orientated predominantly toward the oocyte posterior. "
RLID00010992	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	24718986	Nucleus	Oocyte	In situ hybridization	"Fig. 6. osk mRNA localization is affected in Chcnull germline clones. ChcGF23 germline clones marked by the absence of nuclear GFP signal (green). (A) grk mRNA (red) is enriched at the posterior in stage 6 egg chambers in wild-type and mutant clones. At stage 7-8, grk mRNA is found at the anterior dorsal side of the nucleus. (B) osk mRNA (red) is enriched in the oocyte and at the posterior during early oogenesis (up to stage 6). "
RLID00010993	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	26214278	Cytoplasm	Oocyte	-	This is achieved through the cytoplasmic localization of grk mRNA and regulation of its translation.
RLID00010994	34171	grk	http://www.ncbi.nlm.nih.gov/gene/?term=34171	"Dmel_CG17610, CG17610, CT32746, Dmel\CG17610, GRK, Grk, s-Grk "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010995	3417	IDH1	http://www.ncbi.nlm.nih.gov/gene/?term=3417	"HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC, PICD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010996	3418	IDH2	http://www.ncbi.nlm.nih.gov/gene/?term=3418	"D2HGA2, ICD-M, IDH, IDHM, IDP, IDPM, mNADP-IDH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00010997	3418	IDH2	http://www.ncbi.nlm.nih.gov/gene/?term=3418	"D2HGA2, ICD-M, IDH, IDHM, IDP, IDPM, mNADP-IDH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00010998	34191	CG17834	http://www.ncbi.nlm.nih.gov/gene/?term=34191	"Dmel_ BcDNA:LP07538, Dmel\CG17834, anon-290a, anon-29Da "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00010999	3419	IDH3A	http://www.ncbi.nlm.nih.gov/gene/?term=3419		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011000	3419	IDH3A	http://www.ncbi.nlm.nih.gov/gene/?term=3419		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011001	341	APOC1	http://www.ncbi.nlm.nih.gov/gene/?term=341	"Apo-CI, ApoC-I "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011002	3420	IDH3B	http://www.ncbi.nlm.nih.gov/gene/?term=3420	"H-IDHB, RP46 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011003	3421	IDH3G	http://www.ncbi.nlm.nih.gov/gene/?term=3421	H-IDHG	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011004	3421	IDH3G	http://www.ncbi.nlm.nih.gov/gene/?term=3421	H-IDHG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011005	3422	IDI1	http://www.ncbi.nlm.nih.gov/gene/?term=3422	"IPP1, IPPI1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011006	3422	IDI1	http://www.ncbi.nlm.nih.gov/gene/?term=3422	"IPP1, IPPI1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011007	34237	CG32982	http://www.ncbi.nlm.nih.gov/gene/?term=34237	"Dmel_ CG18566, CG9584, CG9585, Dmel\CG32982 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011008	3423	IDS	http://www.ncbi.nlm.nih.gov/gene/?term=3423	"MPS2, SIDS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011009	3423	IDS	http://www.ncbi.nlm.nih.gov/gene/?term=3423	"MPS2, SIDS "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011010	3423	IDS	http://www.ncbi.nlm.nih.gov/gene/?term=3423	"MPS2, SIDS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011011	34245	borr	http://www.ncbi.nlm.nih.gov/gene/?term=34245	"Dmel_CG4454, BORR, Bor, Borr, CG4454, Dmel\CG4454, dBor "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011012	34245	borr	http://www.ncbi.nlm.nih.gov/gene/?term=34245	"Dmel_CG4454, BORR, Bor, Borr, CG4454, Dmel\CG4454, dBor "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011013	34263	numb	http://www.ncbi.nlm.nih.gov/gene/?term=34263	"Dmel_CG3779, CG3779, Dmel\CG3779, N7-1, Nb, Numb, d-numb, dNumb, l(2)03235, l(2)3235, l(2)s2201, nbs "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011014	3426	CFI	http://www.ncbi.nlm.nih.gov/gene/?term=3426	"AHUS3, ARMD13, C3BINA, C3b-INA, FI, IF, KAF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011015	34286	pelo	http://www.ncbi.nlm.nih.gov/gene/?term=34286	"Dmel_CG3959, CG3959, Dmel\CG3959, ms(2)01559 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011016	34286	pelo	http://www.ncbi.nlm.nih.gov/gene/?term=34286	"Dmel_CG3959, CG3959, Dmel\CG3959, ms(2)01559 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011017	342926	ZNF677	http://www.ncbi.nlm.nih.gov/gene/?term=342926		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011018	342926	ZNF677	http://www.ncbi.nlm.nih.gov/gene/?term=342926		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011019	34292	zf30C	http://www.ncbi.nlm.nih.gov/gene/?term=34292	"Dmel_CG3998, C282, CG3998, Dmel\CG3998, Zf30c, Zn30C, anon-EST:Liang-1.52, clone 1.52, l(2)k02506, zf30c "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011020	342945	ZSCAN22	http://www.ncbi.nlm.nih.gov/gene/?term=342945	"HKR2, ZNF50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011021	342945	ZSCAN22	http://www.ncbi.nlm.nih.gov/gene/?term=342945	"HKR2, ZNF50 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011022	342945	ZSCAN22	http://www.ncbi.nlm.nih.gov/gene/?term=342945	"HKR2, ZNF50 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011023	3429	IFI27	http://www.ncbi.nlm.nih.gov/gene/?term=3429	"FAM14D, ISG12, ISG12A, P27 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011024	3429	IFI27	http://www.ncbi.nlm.nih.gov/gene/?term=3429	"FAM14D, ISG12, ISG12A, P27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011025	34309	RpS2	http://www.ncbi.nlm.nih.gov/gene/?term=34309	"Dmel_CG5920, CG5920, Dm01335, Dmel\CG5920, Rp S2, S2, anon-EST:Posey202, dS2, l(2)03848, l(2)k04603, sop "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011026	3430	IFI35	http://www.ncbi.nlm.nih.gov/gene/?term=3430	IFP35	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011027	3430	IFI35	http://www.ncbi.nlm.nih.gov/gene/?term=3430	IFP35	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011028	3431	SP110	http://www.ncbi.nlm.nih.gov/gene/?term=3431	"IFI41, IFI75, IPR1, VODI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011029	34321	CG4619	http://www.ncbi.nlm.nih.gov/gene/?term=34321	"Dmel_ CG31879, Dmel\CG4619 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011030	34330	bib	http://www.ncbi.nlm.nih.gov/gene/?term=34330	"Dmel_CG4722, BIB_DROME, Bib, CG4722, Dmel\CG4722, EP(2)2278, l(2)neo66, l(2)neo91, m-bib "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011031	34330	bib	http://www.ncbi.nlm.nih.gov/gene/?term=34330	"Dmel_CG4722, BIB_DROME, Bib, CG4722, Dmel\CG4722, EP(2)2278, l(2)neo66, l(2)neo91, m-bib "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011032	34338	Pen	http://www.ncbi.nlm.nih.gov/gene/?term=34338	"Dmel_CG4799, 2.1, CG4799, DPend, Dalpha2, Dimp-alpha2, Dmel\CG4799, IMPalpha2, Imp-alpha2, Kap alpha2, Kap-alpha2, Kpna2, OHO31, Oho31, Rch1, alpha2, alpha2A-Kap, alphaKap2, anon-WO0140519.258, bs29g06.y1, imp alpha2, imp-alpha2, impalpha2, importin alpha2/pendulin, l(2)144/1, l(2)k06324, l(2)k14401, oho-31, oho31, pen, pen-2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011033	343450	KCNT2	http://www.ncbi.nlm.nih.gov/gene/?term=343450	"KCa4.2, SLICK, SLO2.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011034	3434	IFIT1	http://www.ncbi.nlm.nih.gov/gene/?term=3434	"C56, G10P1, IFI-56, IFI-56K, IFI56, IFIT-1, IFNAI1, ISG56, P56, RNM561 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011035	3434	IFIT1	http://www.ncbi.nlm.nih.gov/gene/?term=3434	"C56, G10P1, IFI-56, IFI-56K, IFI56, IFIT-1, IFNAI1, ISG56, P56, RNM561 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011036	3434	IFIT1	http://www.ncbi.nlm.nih.gov/gene/?term=3434	"C56, G10P1, IFI-56, IFI-56K, IFI56, IFIT-1, IFNAI1, ISG56, P56, RNM561 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011037	34377	Utx	http://www.ncbi.nlm.nih.gov/gene/?term=34377	"Dmel_CG5640, CG5640, Dmel\CG5640, UTX, anon-31BCa, dUTX, dUtx, utx "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011038	343990	KIAA1211L	http://www.ncbi.nlm.nih.gov/gene/?term=343990	C2orf55	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011039	343	AQP8	http://www.ncbi.nlm.nih.gov/gene/?term=343	AQP-8	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011040	34416	Cnot4	http://www.ncbi.nlm.nih.gov/gene/?term=34416	"Dmel_CG31716, CG31716, CG5244, CG5251, Cont4, Dmel\CG31716, NOT4, Not4, Q8IPB9_DROME, cg5251, not4 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011041	34419	Ip259	http://www.ncbi.nlm.nih.gov/gene/?term=34419	"Dmel_CG5277, CG5277, Dmel\CG5277, IP259 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011042	34419	Ip259	http://www.ncbi.nlm.nih.gov/gene/?term=34419	"Dmel_CG5277, CG5277, Dmel\CG5277, IP259 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011043	34449	Lrr47	http://www.ncbi.nlm.nih.gov/gene/?term=34449	"Dmel_CG6098, CG6098, CT19173, Dmel\CG6098, LRR47, Lrr-47 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011044	34450	Lip4	http://www.ncbi.nlm.nih.gov/gene/?term=34450	"Dmel_CG6113, CG6113, Dmel\CG6113, dLip4, dlip4 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011045	34450	Lip4	http://www.ncbi.nlm.nih.gov/gene/?term=34450	"Dmel_CG6113, CG6113, Dmel\CG6113, dLip4, dlip4 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011046	34450	Lip4	http://www.ncbi.nlm.nih.gov/gene/?term=34450	"Dmel_CG6113, CG6113, Dmel\CG6113, dLip4, dlip4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011047	34465	CG17104	http://www.ncbi.nlm.nih.gov/gene/?term=34465	"Dmel_ BEST:LD16579, Dmel\CG17104 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011048	34465	CG17104	http://www.ncbi.nlm.nih.gov/gene/?term=34465	"Dmel_ BEST:LD16579, Dmel\CG17104 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011049	34465	CG17104	http://www.ncbi.nlm.nih.gov/gene/?term=34465	"Dmel_ BEST:LD16579, Dmel\CG17104 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011050	34485	CG17124	http://www.ncbi.nlm.nih.gov/gene/?term=34485	"Dmel_ Dmel\CG17124, anon-WO0118547.153 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011051	34485	CG17124	http://www.ncbi.nlm.nih.gov/gene/?term=34485	"Dmel_ Dmel\CG17124, anon-WO0118547.153 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011052	34486	CG6495	http://www.ncbi.nlm.nih.gov/gene/?term=34486	"Dmel_ BcDNA:GH10711, Dmel\CG6495, GH10711 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011053	34486	CG6495	http://www.ncbi.nlm.nih.gov/gene/?term=34486	"Dmel_ BcDNA:GH10711, Dmel\CG6495, GH10711 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011054	34503	Dnz1	http://www.ncbi.nlm.nih.gov/gene/?term=34503	"Dmel_CG6627, CG6627, DNZ1, Dmel\CG6627 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011055	34514	CG33129	http://www.ncbi.nlm.nih.gov/gene/?term=34514	"Dmel_ CG6087, CG6089, Dmel\CG33129 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011056	34514	CG33129	http://www.ncbi.nlm.nih.gov/gene/?term=34514	"Dmel_ CG6087, CG6089, Dmel\CG33129 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011057	345193	LRIT3	http://www.ncbi.nlm.nih.gov/gene/?term=345193	"CSNB1F, FIGLER4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011058	345193	LRIT3	http://www.ncbi.nlm.nih.gov/gene/?term=345193	"CSNB1F, FIGLER4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011059	34521	piwi	http://www.ncbi.nlm.nih.gov/gene/?term=34521	"Dmel_CG6122, CG6122, Dmel\CG6122, PIWI, Piwi "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011060	34521	piwi	http://www.ncbi.nlm.nih.gov/gene/?term=34521	"Dmel_CG6122, CG6122, Dmel\CG6122, PIWI, Piwi "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011061	345275	HSD17B13	http://www.ncbi.nlm.nih.gov/gene/?term=345275	"HMFN0376, NIIL497, SCDR9, SDR16C3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011062	345275	HSD17B13	http://www.ncbi.nlm.nih.gov/gene/?term=345275	"HMFN0376, NIIL497, SCDR9, SDR16C3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011063	34549	Nup160	http://www.ncbi.nlm.nih.gov/gene/?term=34549	"Dmel_CG4738, CG4738, Dmel\CG4738, Nup[mel], l(2)SH2 2055, l(2)SH2055, nup160, Nup160 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011064	34549	Nup160	http://www.ncbi.nlm.nih.gov/gene/?term=34549	"Dmel_CG4738, CG4738, Dmel\CG4738, Nup[mel], l(2)SH2 2055, l(2)SH2055, nup160, Nup160 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011065	3454	IFNAR1	http://www.ncbi.nlm.nih.gov/gene/?term=3454	"AVP, IFN-alpha-REC, IFNAR, IFNBR, IFRC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011066	3454	IFNAR1	http://www.ncbi.nlm.nih.gov/gene/?term=3454	"AVP, IFN-alpha-REC, IFNAR, IFNBR, IFRC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011067	3454	IFNAR1	http://www.ncbi.nlm.nih.gov/gene/?term=3454	"AVP, IFN-alpha-REC, IFNAR, IFNBR, IFRC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011068	3454	IFNAR1	http://www.ncbi.nlm.nih.gov/gene/?term=3454	"AVP, IFN-alpha-REC, IFNAR, IFNBR, IFRC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011069	3455	IFNAR2	http://www.ncbi.nlm.nih.gov/gene/?term=3455	"IFN-R, IFN-alpha-REC, IFNABR, IFNARB, IMD45 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011070	34565	mre11	http://www.ncbi.nlm.nih.gov/gene/?term=34565	"Dmel_CG16928, 16928, CG16928, Dmel\CG16928, MRE11, Mre11 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011071	345757	FAM174A	http://www.ncbi.nlm.nih.gov/gene/?term=345757	"HGS_RE408, TMEM157, UNQ1912 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011072	345778	MTX3	http://www.ncbi.nlm.nih.gov/gene/?term=345778		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011073	345778	MTX3	http://www.ncbi.nlm.nih.gov/gene/?term=345778		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011074	345778	MTX3	http://www.ncbi.nlm.nih.gov/gene/?term=345778		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011075	34577	CG31705	http://www.ncbi.nlm.nih.gov/gene/?term=34577	"Dmel_ BcDNA:GH07269, CG6528, Dmel\CG31705 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011076	34577	CG31705	http://www.ncbi.nlm.nih.gov/gene/?term=34577	"Dmel_ BcDNA:GH07269, CG6528, Dmel\CG31705 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011077	34592	crol	http://www.ncbi.nlm.nih.gov/gene/?term=34592	"Dmel_CG14938, CG14938, Crol, Dmel\CG14938, ORE-15, anon-EST:Liang-1.74, anon-EST:Liang-2.48, clone 1.74, clone 2.48 alpha, crol beta, crol gamma, l(2)04418, l(2)s2346, crol "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011078	3459	IFNGR1	http://www.ncbi.nlm.nih.gov/gene/?term=3459	"CD119, IFNGR, IMD27A, IMD27B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011079	3459	IFNGR1	http://www.ncbi.nlm.nih.gov/gene/?term=3459	"CD119, IFNGR, IMD27A, IMD27B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011080	3460	IFNGR2	http://www.ncbi.nlm.nih.gov/gene/?term=3460	"AF-1, IFGR2, IFNGT1, IMD28 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011081	3460	IFNGR2	http://www.ncbi.nlm.nih.gov/gene/?term=3460	"AF-1, IFGR2, IFNGT1, IMD28 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011082	3460	IFNGR2	http://www.ncbi.nlm.nih.gov/gene/?term=3460	"AF-1, IFGR2, IFNGT1, IMD28 "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmids containing either ALPP, t-ftz, or the AF1, AF2 fusion constructs and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (Ctrl), puromycin (Puro), or HHT for 30 min and then extracted with either digitonin alone, or for puromycin-treated cells, with 20 mM EDTA. The cells were then fixed, stained for mRNA using specific FISH probes (ALPP probe for AF1, ftz probe for AF2), and imaged. FIGURE 2B: quantification of the fluorescence intensities of mRNA in the ER and nucleus.  Data are collected from Figure 2. "
RLID00011083	3460	IFNGR2	http://www.ncbi.nlm.nih.gov/gene/?term=3460	"AF-1, IFGR2, IFNGT1, IMD28 "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmids containing either ALPP, t-ftz, or the AF1, AF2 fusion constructs and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (Ctrl), puromycin (Puro), or HHT for 30 min and then extracted with either digitonin alone, or for puromycin-treated cells, with 20 mM EDTA. The cells were then fixed, stained for mRNA using specific FISH probes (ALPP probe for AF1, ftz probe for AF2), and imaged. FIGURE 2B: quantification of the fluorescence intensities of mRNA in the ER and nucleus.  Data are collected from Figure 2. "
RLID00011084	3460	IFNGR2	http://www.ncbi.nlm.nih.gov/gene/?term=3460	"AF-1, IFGR2, IFNGT1, IMD28 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011085	34629	prd	http://www.ncbi.nlm.nih.gov/gene/?term=34629	"Dmel_CG6716, CG6716, Dmel\CG6716, PRD, Prd, pr "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011086	346389	MACC1	http://www.ncbi.nlm.nih.gov/gene/?term=346389	"7A5, SH3BP4L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011087	346389	MACC1	http://www.ncbi.nlm.nih.gov/gene/?term=346389	"7A5, SH3BP4L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011088	346389	MACC1	http://www.ncbi.nlm.nih.gov/gene/?term=346389	"7A5, SH3BP4L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011089	346389	MACC1	http://www.ncbi.nlm.nih.gov/gene/?term=346389	"7A5, SH3BP4L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011090	34642	CG31760	http://www.ncbi.nlm.nih.gov/gene/?term=34642	"Dmel_ BcDNA:RE52162, CG17214, CG17215, Dmel\CG31760 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011091	34642	CG31760	http://www.ncbi.nlm.nih.gov/gene/?term=34642	"Dmel_ BcDNA:RE52162, CG17214, CG17215, Dmel\CG31760 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011092	34648	aret	http://www.ncbi.nlm.nih.gov/gene/?term=34648	"Dmel_CG31762, ARET, Aret, BcDNA:GM15173, Bru, Bruno, CG31762, CG6319, Dm Bru, Dmel\CG31762, NEST:bs01g04, NEST:bs34h11/bruno1, arrest/Bruno, bru, bruno, ms(2)01284, aret "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011093	34648	aret	http://www.ncbi.nlm.nih.gov/gene/?term=34648	"Dmel_CG31762, ARET, Aret, BcDNA:GM15173, Bru, Bruno, CG31762, CG6319, Dm Bru, Dmel\CG31762, NEST:bs01g04, NEST:bs34h11/bruno1, arrest/Bruno, bru, bruno, ms(2)01284, aret "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011094	34648	aret	http://www.ncbi.nlm.nih.gov/gene/?term=34648	"Dmel_CG31762, ARET, Aret, BcDNA:GM15173, Bru, Bruno, CG31762, CG6319, Dm Bru, Dmel\CG31762, NEST:bs01g04, NEST:bs34h11/bruno1, arrest/Bruno, bru, bruno, ms(2)01284, aret "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011095	34648	aret	http://www.ncbi.nlm.nih.gov/gene/?term=34648	"Dmel_CG31762, ARET, Aret, BcDNA:GM15173, Bru, Bruno, CG31762, CG6319, Dm Bru, Dmel\CG31762, NEST:bs01g04, NEST:bs34h11/bruno1, arrest/Bruno, bru, bruno, ms(2)01284, aret "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011096	34656	CG6388	http://www.ncbi.nlm.nih.gov/gene/?term=34656	Dmel_ Dmel\CG6388	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011097	34665	bun	http://www.ncbi.nlm.nih.gov/gene/?term=34665	"Dmel_CG42281, 1550, Bun, BunA, CG31857, CG42281, CG5461, Dm_2L:60722, Dmel\CG42281, Dmel_CG31857, Dmel_CG5461, EP(2)0488, TSC-22, Tsc22, bnc, l(2)00255, l(2)02687, l(2)05479, l(2)06475, l(2)k02903, l(2)rI043, shs "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011098	34675	CG6153	http://www.ncbi.nlm.nih.gov/gene/?term=34675	"Dmel_ 6153, Dmel\CG6153 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011099	346	APOC4	http://www.ncbi.nlm.nih.gov/gene/?term=346	"APO-CIV, APOC-IV "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011100	347240	KIF24	http://www.ncbi.nlm.nih.gov/gene/?term=347240	"C9orf48, bA571F15.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011101	34728	CG5867	http://www.ncbi.nlm.nih.gov/gene/?term=34728	"Dmel_ BcDNA:GH05536, CT18390, Dmel\CG5867 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011102	34728	CG5867	http://www.ncbi.nlm.nih.gov/gene/?term=34728	"Dmel_ BcDNA:GH05536, CT18390, Dmel\CG5867 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011103	34735	Uvrag	http://www.ncbi.nlm.nih.gov/gene/?term=34735	"Dmel_CG6116, CG6116, Dmel\CG6116, UVRAG, Vps38, uvrag "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011104	34735	Uvrag	http://www.ncbi.nlm.nih.gov/gene/?term=34735	"Dmel_CG6116, CG6116, Dmel\CG6116, UVRAG, Vps38, uvrag "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011105	34735	Uvrag	http://www.ncbi.nlm.nih.gov/gene/?term=34735	"Dmel_CG6116, CG6116, Dmel\CG6116, UVRAG, Vps38, uvrag "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011106	3475	IFRD1	http://www.ncbi.nlm.nih.gov/gene/?term=3475	"PC4, TIS7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011107	3475	IFRD1	http://www.ncbi.nlm.nih.gov/gene/?term=3475	"PC4, TIS7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011108	34763	Hsp60D	http://www.ncbi.nlm.nih.gov/gene/?term=34763	"Dmel_CG16954, CG16954, Dmel\CG16954 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011109	34767	B4	http://www.ncbi.nlm.nih.gov/gene/?term=34767	"Dmel_CG9239/Susi, BG:DS07660.4, CG9239, CG9260, Dmel\CG9239, Susi, n(2)05337 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011110	347694	ECEL1P2	http://www.ncbi.nlm.nih.gov/gene/?term=347694	ECEL2	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00011111	3476	IGBP1	http://www.ncbi.nlm.nih.gov/gene/?term=3476	"ALPHA-4, IBP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011112	3476	IGBP1	http://www.ncbi.nlm.nih.gov/gene/?term=3476	"ALPHA-4, IBP1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011113	3476	IGBP1	http://www.ncbi.nlm.nih.gov/gene/?term=3476	"ALPHA-4, IBP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011114	347734	SLC35B2	http://www.ncbi.nlm.nih.gov/gene/?term=347734	"PAPST1, SLL, UGTrel4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011115	347734	SLC35B2	http://www.ncbi.nlm.nih.gov/gene/?term=347734	"PAPST1, SLL, UGTrel4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011116	347734	SLC35B2	http://www.ncbi.nlm.nih.gov/gene/?term=347734	"PAPST1, SLL, UGTrel4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011117	347735	SERINC2	http://www.ncbi.nlm.nih.gov/gene/?term=347735	"FKSG84, PRO0899, TDE2, TDE2L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011118	347735	SERINC2	http://www.ncbi.nlm.nih.gov/gene/?term=347735	"FKSG84, PRO0899, TDE2, TDE2L "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011119	347740	2900097C17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=347740	"1810005K14Rik, 4930563C06Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011120	347744	C6orf52	http://www.ncbi.nlm.nih.gov/gene/?term=347744		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011121	34778	TM9SF4	http://www.ncbi.nlm.nih.gov/gene/?term=34778	"Dmel_CG7364, BG:DS00797.1, CG16861, CG7364, Dmel\CG7364, n(2)k07245 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011122	347862	PDDC1	http://www.ncbi.nlm.nih.gov/gene/?term=347862		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011123	347862	PDDC1	http://www.ncbi.nlm.nih.gov/gene/?term=347862		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011124	347862	PDDC1	http://www.ncbi.nlm.nih.gov/gene/?term=347862		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011125	347862	PDDC1	http://www.ncbi.nlm.nih.gov/gene/?term=347862		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011126	3479	IGF1	http://www.ncbi.nlm.nih.gov/gene/?term=3479	"IGF-I, IGFI, MGF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011127	3479	IGF1	http://www.ncbi.nlm.nih.gov/gene/?term=3479	"IGF-I, IGFI, MGF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011128	3479	IGF1	http://www.ncbi.nlm.nih.gov/gene/?term=3479	"IGF-I, IGFI, MGF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011129	347	APOD	http://www.ncbi.nlm.nih.gov/gene/?term=347		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011130	3480	IGF1R	http://www.ncbi.nlm.nih.gov/gene/?term=3480	"CD221, IGFIR, IGFR, JTK13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011131	3480	IGF1R	http://www.ncbi.nlm.nih.gov/gene/?term=3480	"CD221, IGFIR, IGFR, JTK13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011132	3480	IGF1R	http://www.ncbi.nlm.nih.gov/gene/?term=3480	"CD221, IGFIR, IGFR, JTK13 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011133	3480	IGF1R	http://www.ncbi.nlm.nih.gov/gene/?term=3480	"CD221, IGFIR, IGFR, JTK13 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011134	348110	ARPIN	http://www.ncbi.nlm.nih.gov/gene/?term=348110	C15orf38	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011135	348180	CTU2	http://www.ncbi.nlm.nih.gov/gene/?term=348180	"C16orf84, NCS2, UPF0432 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011136	348180	CTU2	http://www.ncbi.nlm.nih.gov/gene/?term=348180	"C16orf84, NCS2, UPF0432 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011137	3481	IGF2	http://www.ncbi.nlm.nih.gov/gene/?term=3481	"C11orf43, GRDF, IGF-II, PP9974 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011138	348235	SKA2	http://www.ncbi.nlm.nih.gov/gene/?term=348235	FAM33A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011139	3482	IGF2R	http://www.ncbi.nlm.nih.gov/gene/?term=3482	"CD222, CIMPR, M6P-R, M6P/IGF2R, MPR 300, MPR1, MPRI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011140	3482	IGF2R	http://www.ncbi.nlm.nih.gov/gene/?term=3482	"CD222, CI-M6PR, CIMPR, M6P-R, M6P/IGF2R, MPR 300, MPR1, MPR300, MPRI "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011141	3482	IGF2R	http://www.ncbi.nlm.nih.gov/gene/?term=3482	"CD222, CI-M6PR, CIMPR, M6P-R, M6P/IGF2R, MPR 300, MPR1, MPR300, MPRI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011142	348327	ZNF530	http://www.ncbi.nlm.nih.gov/gene/?term=348327		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011143	348327	ZNF530	http://www.ncbi.nlm.nih.gov/gene/?term=348327		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011144	3485	IGFBP2	http://www.ncbi.nlm.nih.gov/gene/?term=3485	"IBP2, IGF-BP53 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011145	3485	IGFBP2	http://www.ncbi.nlm.nih.gov/gene/?term=3485	"IBP2, IGF-BP53 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011146	3485	IGFBP2	http://www.ncbi.nlm.nih.gov/gene/?term=3485	"IBP2, IGF-BP53 "	mRNA	Homo sapiens	19175411	Ribosome	T-cell|SeAx	qRT-PCR	"Using quantitative real-time RT-PCR we evaluated, whether mRNAs coding for differently located proteins are selectively enriched in one of the two analysed compartments, namely free versus membrane-associated polysomes. We selected genes coding for proteins located in the plasma membrane (GPR137B), secreted proteins (TIC2, IBP2, PAI) and cytosolic proteins (the house keeping genes GAPDH and HMBS). In fact, the distribution of the specific mRNA was as predicted ( Fig. 1): The average ratio of specific mRNA at bound ribosomes versus free ribosomes was 1 ? 4.4 for the housekeeping genes (GAPDH and HMBS) and 13.3 ? 1 for genes coding for membrane-bound or secreted proteins. Ratios for genes coding for cytosolic proteins were always below 0.6 and those for membrane or secreted genes were always above 1. The highest values were observed for PAI in MyLa (57 ? 1) and GPR137B in SeAx (34 ? 1), while the lowest ratios were detected for HMBS (1 ? 55) and GAPDH (1 ? 12) in HuT78. "
RLID00011147	348654	GEN1	http://www.ncbi.nlm.nih.gov/gene/?term=348654	Gen	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011148	34881	Su(H)	http://www.ncbi.nlm.nih.gov/gene/?term=34881	"Dmel_CG3497, BG:DS00929.10, C, CBF1, CG3497, CSL, D, Dmel\CG3497, E(H), FTZ-F2, RBJK_DROME, RBP-J kappa, RBP-J[[Kappa]], RBP-Jkappa, SU(H), SUH, Su(h), SuH, Su_H, anon-WO0257455.3, br7, dRBP-JK, dRBP-J[[Kappa]], dRBP-Jk, l(1)br7, l(2)35Bh, l(2)br7, l(2)k07904, oss, su(H) "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011149	34886	CG15270	http://www.ncbi.nlm.nih.gov/gene/?term=34886	"Dmel_ BG:DS04929.1, Dmel\CG15270 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011150	3488	IGFBP5	http://www.ncbi.nlm.nih.gov/gene/?term=3488	IBP5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011151	3488	IGFBP5	http://www.ncbi.nlm.nih.gov/gene/?term=3488	IBP5	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011152	34890	ZnT35C	http://www.ncbi.nlm.nih.gov/gene/?term=34890	"Dmel_CG3994, BG:DS07295.1, CG3994, Dmel\CG3994, cg3994, dZnT35C "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011153	348995	NUP43	http://www.ncbi.nlm.nih.gov/gene/?term=348995	"bA350J20.1, p42 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011154	348995	NUP43	http://www.ncbi.nlm.nih.gov/gene/?term=348995	"bA350J20.1, p42 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011155	348995	NUP43	http://www.ncbi.nlm.nih.gov/gene/?term=348995	"bA350J20.1, p42 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011156	348	APOE	http://www.ncbi.nlm.nih.gov/gene/?term=348	"AD2, APO-E, LDLCQ5, LPG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011157	349075	ZNF713	http://www.ncbi.nlm.nih.gov/gene/?term=349075		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011158	349075	ZNF713	http://www.ncbi.nlm.nih.gov/gene/?term=349075		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011159	3490	IGFBP7	http://www.ncbi.nlm.nih.gov/gene/?term=3490	"AGM, FSTL2, IBP-7, IGFBP-7, IGFBP-7v, IGFBPRP1, MAC25, PSF, RAMSVPS, TAF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011160	349114	LINC00265	http://www.ncbi.nlm.nih.gov/gene/?term=349114	NCRNA00265	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011161	3491	CYR61	http://www.ncbi.nlm.nih.gov/gene/?term=3491	"CCN1, GIG1, IGFBP10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011162	3491	CYR61	http://www.ncbi.nlm.nih.gov/gene/?term=3491	"CCN1, GIG1, IGFBP10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011163	34924	CycE	http://www.ncbi.nlm.nih.gov/gene/?term=34924	"Dmel_CG3938, 3938, BG:DS07108.3, CDI7, CG3938, CYCE, Cdi7, Cyc, Cyc EI, CyclE, CyeE, D-CycE, DmCycE, DmcycE, DmcyclinE, Dmel\CG3938, br37, cdi7, cycE, cyclinE, cycline, dCycE, dm-cycE, fond, l(2)05206, l(2)35Dd, l(2)br37, l(2)k02514, l(2)k02602, l(2)k05007, l35Dd, CycE "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011164	34924	CycE	http://www.ncbi.nlm.nih.gov/gene/?term=34924	"Dmel_CG3938, 3938, BG:DS07108.3, CDI7, CG3938, CYCE, Cdi7, Cyc, Cyc EI, CyclE, CyeE, D-CycE, DmCycE, DmcycE, DmcyclinE, Dmel\CG3938, br37, cdi7, cycE, cyclinE, cycline, dCycE, dm-cycE, fond, l(2)05206, l(2)35Dd, l(2)br37, l(2)k02514, l(2)k02602, l(2)k05007, l35Dd, CycE "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011165	34964	c(2)M	http://www.ncbi.nlm.nih.gov/gene/?term=34964	"Dmel_CG4249, BG:DS02740.10, C(2)M, CG4249, DS02740.10, Dmel\CG4249, MEI-910, c(2)m, mei-910 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011166	34964	c(2)M	http://www.ncbi.nlm.nih.gov/gene/?term=34964	"Dmel_CG4249, BG:DS02740.10, C(2)M, CG4249, DS02740.10, Dmel\CG4249, MEI-910, c(2)m, mei-910 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011167	34976	CaBP1	http://www.ncbi.nlm.nih.gov/gene/?term=34976	"Dmel_CG5809, AAL28897, BG:DS09218.4, CG5809, DmCaBP1, Dmel\CG5809 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011168	34985	CG5953	http://www.ncbi.nlm.nih.gov/gene/?term=34985	Dmel_ Dmel\CG5953	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011169	34993	grp	http://www.ncbi.nlm.nih.gov/gene/?term=34993	"Dmel_CG17161, 1C, CG17161, CHK1, CHK1/Grapes, Chk1, Dchk1, DmChk1, Dmel\CG17161, Grp, Grp/DChk1, Pk36A, Pk?1, chk1, dChk1(chk), grps, l(2)k15102, lemp, grp "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011170	34993	grp	http://www.ncbi.nlm.nih.gov/gene/?term=34993	"Dmel_CG17161, 1C, CG17161, CHK1, CHK1/Grapes, Chk1, Dchk1, DmChk1, Dmel\CG17161, Grp, Grp/DChk1, Pk36A, Pk?1, chk1, dChk1(chk), grps, l(2)k15102, lemp, grp "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011171	34	ACADM	http://www.ncbi.nlm.nih.gov/gene/?term=34	"ACAD1, MCAD, MCADH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011172	34	ACADM	http://www.ncbi.nlm.nih.gov/gene/?term=34	"ACAD1, MCAD, MCADH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011173	35003	LSm7	http://www.ncbi.nlm.nih.gov/gene/?term=35003	"Dmel_CG13277, BcDNA:RH73529, CG13277, Dmel\CG13277 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011174	35004	BuGZ	http://www.ncbi.nlm.nih.gov/gene/?term=35004	"Dmel_CG17912, BcDNA:LD27810, CG17912, Dm_2L:87597, Dmel\CG17912, lincRNA.S1359 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011175	35006	ppk17	http://www.ncbi.nlm.nih.gov/gene/?term=35006	"Dmel_CG13278, CG13278, Dmel\CG13278 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011176	3500	IGHG1	http://www.ncbi.nlm.nih.gov/gene/?term=3500		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011177	35037	beat-IIIc	http://www.ncbi.nlm.nih.gov/gene/?term=35037	"Dmel_CG15138, BcDNA:RE14414, Beat-IIIC, Beat-IIIc, CG15138, CG6365, Dmel\CG15138, beat IIIc "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011178	35051	BicD	http://www.ncbi.nlm.nih.gov/gene/?term=35051	"Dmel_CG6605, BIC-D, BICD, Bic-D, Bic[D], CG6605, Dmel\CG6605, almond, anon-EST:fe2A11 "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011179	35051	BicD	http://www.ncbi.nlm.nih.gov/gene/?term=35051	"Dmel_CG6605, BIC-D, BICD, Bic-D, Bic[D], CG6605, Dmel\CG6605, almond, anon-EST:fe2A11 "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011180	35051	BicD	http://www.ncbi.nlm.nih.gov/gene/?term=35051	"Dmel_CG6605, BIC-D, BICD, Bic-D, Bic[D], CG6605, Dmel\CG6605, almond, anon-EST:fe2A11 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011181	35051	BicD	http://www.ncbi.nlm.nih.gov/gene/?term=35051	"Dmel_CG6605, BIC-D, BICD, Bic-D, Bic[D], CG6605, Dmel\CG6605, almond, anon-EST:fe2A11 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011182	35052	Sgt	http://www.ncbi.nlm.nih.gov/gene/?term=35052	"Dmel_CG5094, CG5094, Dmel\CG5094, dsgt "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011183	35053	Aac11	http://www.ncbi.nlm.nih.gov/gene/?term=35053	"Dmel_CG6582, AAC-11, Api5, BcDNA.LD09852, BcDNA:LD09852, CG6582, Dmel\CG6582, l(2)k06710 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011184	35089	CG7200	http://www.ncbi.nlm.nih.gov/gene/?term=35089	Dmel_ Dmel\CG7200	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011185	35097	Fas3	http://www.ncbi.nlm.nih.gov/gene/?term=35097	"Dmel_CG5803, CG5803, Dmel\CG5803, FAS III, FAS3, FASIII, Fas, Fas III, Fas-3, Fas-III, FasIII, FasIIIface, FascIII, fas III, fas-III, fas3, fasIII, fascIII "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011186	35097	Fas3	http://www.ncbi.nlm.nih.gov/gene/?term=35097	"Dmel_CG5803, CG5803, Dmel\CG5803, FAS III, FAS3, FASIII, Fas, Fas III, Fas-3, Fas-III, FasIII, FasIIIface, FascIII, fas III, fas-III, fas3, fasIII, fascIII "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011187	35107	Pde11	http://www.ncbi.nlm.nih.gov/gene/?term=35107	"Dmel_CG34341, CG10231, CG15159, CG34341, Dmel\CG34341, Dmel_CG10231, Dmel_CG15159, PDE11 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011188	35116	MESR3	http://www.ncbi.nlm.nih.gov/gene/?term=35116	"Dmel_CG15162, CG15162, Dmel\CG15162 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011189	35121	msl-1	http://www.ncbi.nlm.nih.gov/gene/?term=35121	"Dmel_CG10385, CG10385, Dmel\CG10385, MSL, MSL-1, MSL1, MSL3, Msl 1-3, Msl-1, Msl1, i94, km(2)B, kmB, mls-1, msl, msl1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011190	35130	Grip71	http://www.ncbi.nlm.nih.gov/gene/?term=35130	"Dmel_CG10346, CG10346, Dgp71WD, Dgrip71, Dmel\CG10346wd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011191	35169	hook	http://www.ncbi.nlm.nih.gov/gene/?term=35169	"Dmel_CG10653, CG10653, Dmel\CG10653, Hook, dHk, hk "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011192	3516	RBPJ	http://www.ncbi.nlm.nih.gov/gene/?term=3516	"AOS3, CBF1, IGKJRB, IGKJRB1, KBF2, RBP-J, RBPJK, RBPSUH, SUH, csl "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011193	3516	RBPJ	http://www.ncbi.nlm.nih.gov/gene/?term=3516	"AOS3, CBF1, IGKJRB, IGKJRB1, KBF2, RBP-JK, RBPSUH, SUH, csl, RBPJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011194	35173	Acn	http://www.ncbi.nlm.nih.gov/gene/?term=35173	"Dmel_CG10473, Ba, CG10437, CG10473, Dmel\CG10473, dAcn, dacn, hkl, l(2)37Ba "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011195	351	APP	http://www.ncbi.nlm.nih.gov/gene/?term=351	"AAA, ABETA, ABPP, AD1, APPI, CTFgamma, CVAP, PN-II, PN2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011196	351	APP	http://www.ncbi.nlm.nih.gov/gene/?term=351	"AAA, ABETA, ABPP, AD1I, CTFgamma, CVAP, PN-II, PN2, APP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011197	351	APP	http://www.ncbi.nlm.nih.gov/gene/?term=351	"AAA, ABETA, ABPP, AD1I, CTFgamma, CVAP, PN-II, PN2, APP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011198	35215	Pax	http://www.ncbi.nlm.nih.gov/gene/?term=35215	"Dmel_CG31794, CG18061, CG18576, CG31794, CT40481, CT42454, DPaxillin, DPxn, DPxn37, Dmel\CG31794, Dpax, DpaxA, PDLP, dPax, pax "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011199	35246	ref(2)P	http://www.ncbi.nlm.nih.gov/gene/?term=35246	"Dmel_CG10360, CG10360, Dmel\CG10360, Ref(2)P, Ref(2)p, Ref2P, SQSTM1, p62, p63, refn, ref(2)Po2, ref(2)p, ref2p, ref(2)P "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011200	35246	ref(2)P	http://www.ncbi.nlm.nih.gov/gene/?term=35246	"Dmel_CG10360, CG10360, Dmel\CG10360, Ref(2)P, Ref(2)p, Ref2P, SQSTM1, p62, p63, refn, ref(2)Po2, ref(2)p, ref2p, ref(2)P "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011201	35260	CG10462	http://www.ncbi.nlm.nih.gov/gene/?term=35260	"Dmel_ BcDNA:SD07008, Dmel\CG10462 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011202	35282	CG10680	http://www.ncbi.nlm.nih.gov/gene/?term=35282	Dmel_ Dmel\CG10680	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011203	35288	lok	http://www.ncbi.nlm.nih.gov/gene/?term=35288	"Dmel_CG10895, 10895, 38B.4, CG10895, CHK-2, CHK2, Chk2, DmCHk2, DmChk2, Dmchk2, Dmel\CG10895, Dmnk, Dmnk-L, Dmnk-S, Dmnk/DChk2, LOKI/CHK2, MNK, chk, chk2, chk2/lok, mnk "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011204	35288	lok	http://www.ncbi.nlm.nih.gov/gene/?term=35288	"Dmel_CG10895, 10895, 38B.4, CG10895, CHK-2, CHK2, Chk2, DmCHk2, DmChk2, Dmchk2, Dmel\CG10895, Dmnk, Dmnk-L, Dmnk-S, Dmnk/DChk2, LOKI/CHK2, MNK, chk, chk2, chk2/lok, mnk "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011205	35288	lok	http://www.ncbi.nlm.nih.gov/gene/?term=35288	"Dmel_CG10895, 10895, 38B.4, CG10895, CHK-2, CHK2, Chk2, DmCHk2, DmChk2, Dmchk2, Dmel\CG10895, Dmnk, Dmnk-L, Dmnk-S, Dmnk/DChk2, LOKI/CHK2, MNK, chk, chk2, chk2/lok, mnk "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011206	35288	lok	http://www.ncbi.nlm.nih.gov/gene/?term=35288	"Dmel_CG10895, 10895, 38B.4, CG10895, CHK-2, CHK2, Chk2, DmCHk2, DmChk2, Dmchk2, Dmel\CG10895, Dmnk, Dmnk-L, Dmnk-S, Dmnk/DChk2, LOKI/CHK2, MNK, chk, chk2, chk2/lok, mnk "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011207	352945	BC005685	http://www.ncbi.nlm.nih.gov/gene/?term=352945		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011208	35311	Arpc2	http://www.ncbi.nlm.nih.gov/gene/?term=35311	"Dmel_CG10954, 38C.47, ARC-P34, ARC-p34, ARPC2, ARPC2/p34, Arc-p34, ArcP34, CG10954, Dmel\CG10954, anon-WO0118547.154, p34 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011209	353133	LCE1C	http://www.ncbi.nlm.nih.gov/gene/?term=353133	LEP3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011210	353187	Nr1d2	http://www.ncbi.nlm.nih.gov/gene/?term=353187	"RVR, Rev-erb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011211	353188	Adam32	http://www.ncbi.nlm.nih.gov/gene/?term=353188		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011212	353208	Zfp931	http://www.ncbi.nlm.nih.gov/gene/?term=353208	2810021G02Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011213	353208	Zfp931	http://www.ncbi.nlm.nih.gov/gene/?term=353208	2810021G02Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011214	353211	Prune2	http://www.ncbi.nlm.nih.gov/gene/?term=353211	"6330414G02Rik, A230083H22Rik, A330102H22Rik, Bmcc1, mKIAA0367 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011215	353235	Pcdha8	http://www.ncbi.nlm.nih.gov/gene/?term=353235		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011216	353236	Pcdhac1	http://www.ncbi.nlm.nih.gov/gene/?term=353236	CNRc1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011217	353237	Pcdhac2	http://www.ncbi.nlm.nih.gov/gene/?term=353237	CNRc2	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011218	353256	Gtf2i	http://www.ncbi.nlm.nih.gov/gene/?term=353256	Gtf2ird1	mRNA	Rattus norvegicus	25913238	Dendrite	Neuron	In situ hybridization	These findings support the idea that the G-quadruplex in the 5’UTR of Gtf2i mRNA is involved in the mechanism underlying the targeting of the Gtf2i mRNA to neuronal dendrites and/or local translation in dendrites.
RLID00011219	353258	Ltv1	http://www.ncbi.nlm.nih.gov/gene/?term=353258	2610020N02Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011220	353274	ZNF445	http://www.ncbi.nlm.nih.gov/gene/?term=353274	"ZKSCAN15, ZNF168, ZSCAN47 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011221	353274	ZNF445	http://www.ncbi.nlm.nih.gov/gene/?term=353274	"ZKSCAN15, ZNF168, ZSCAN47 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011222	353376	TICAM2	http://www.ncbi.nlm.nih.gov/gene/?term=353376	"MyD88-4, TICAM-2, TIRAP3, TIRP, TRAM "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011223	35341	cad	http://www.ncbi.nlm.nih.gov/gene/?term=35341	"Dmel_CG1759, 38E.19, CAD, CG1759, Cad, Dmel\CG1759, S67, anon-WO2004063362.83, cd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011224	35343	vari	http://www.ncbi.nlm.nih.gov/gene/?term=35343	"Dmel_CG9326, 38E.21, CG9326, Dmel\CG9326, Vari, l(2)03953, l(2)03953b, l(2)38EFa, szar "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011225	353500	BMP8A	http://www.ncbi.nlm.nih.gov/gene/?term=353500		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011226	353500	BMP8A	http://www.ncbi.nlm.nih.gov/gene/?term=353500		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011227	353500	BMP8A	http://www.ncbi.nlm.nih.gov/gene/?term=353500		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011228	353502	Hcfc1r1	http://www.ncbi.nlm.nih.gov/gene/?term=353502	HPIP	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011229	35355	CG9336	http://www.ncbi.nlm.nih.gov/gene/?term=35355	"Dmel_ BcDNA:RE71975, Dmel\CG9336 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011230	35379	CG9253	http://www.ncbi.nlm.nih.gov/gene/?term=35379	"Dmel_ DmRH24, Dmel\CG9253, anon-EST:GressD10, cg9253 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011231	3537	IGLC1	http://www.ncbi.nlm.nih.gov/gene/?term=3537	IGLC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011232	35386	CG9246	http://www.ncbi.nlm.nih.gov/gene/?term=35386	Dmel_ Dmel\CG9246	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011233	353	APRT	http://www.ncbi.nlm.nih.gov/gene/?term=353	"AMP, APRTD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011234	353	APRT	http://www.ncbi.nlm.nih.gov/gene/?term=353	"AMPD, APRT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011235	353	APRT	http://www.ncbi.nlm.nih.gov/gene/?term=353	"AMPD, APRT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011236	35400	CG8671	http://www.ncbi.nlm.nih.gov/gene/?term=35400	"Dmel_ Dmel\CG8671, anon-WO0118547.182 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011237	35407	CG8665	http://www.ncbi.nlm.nih.gov/gene/?term=35407	Dmel_ Dmel\CG8665	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011238	35418	Df31	http://www.ncbi.nlm.nih.gov/gene/?term=35418	"Dmel_CG2207, BEST:LD04967, CG2207, DF 31, DF31, Dmel\CG2207, LD04967, anon-EST:Liang-1.46, anon-EST:Posey126, anon-EST:fe1A4, anon-WO0153538.53, anon1A4, clone 1.46, l(2)k05815 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011239	35425	step	http://www.ncbi.nlm.nih.gov/gene/?term=35425	"Dmel_CG11628, CG11628, CG11633, CYH1, Dmel\CG11628, GPH, GRP1, GRP1/cytohesin 1, Grp1, Step, cytohesin/GRP1, l(2)SH0323, l(2)SH2 0323, l(2)k08110k, step "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011240	35425	step	http://www.ncbi.nlm.nih.gov/gene/?term=35425	"Dmel_CG11628, CG11628, CG11633, CYH1, Dmel\CG11628, GPH, GRP1, GRP1/cytohesin 1, Grp1, Step, cytohesin/GRP1, l(2)SH0323, l(2)SH2 0323, l(2)k08110k, step "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011241	3543	IGLL1	http://www.ncbi.nlm.nih.gov/gene/?term=3543	"14.1, AGM2, CD179b, IGL1, IGL5, IGLJ14.1, IGLL, IGO, IGVPB, VPREB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011242	35454	Tif-IA	http://www.ncbi.nlm.nih.gov/gene/?term=35454	"Dmel_CG3278, CG16938, CG3278, CG5951, Dmel\CG3278, TIF-1A, TIF-IA, TIf-IA, Tif-1A, TifIA, dTIF-IA, tif1a "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011243	35454	Tif-IA	http://www.ncbi.nlm.nih.gov/gene/?term=35454	"Dmel_CG3278, CG16938, CG3278, CG5951, Dmel\CG3278, TIF-1A, TIF-IA, TIf-IA, Tif-1A, TifIA, dTIF-IA, tif1a "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011244	35454	Tif-IA	http://www.ncbi.nlm.nih.gov/gene/?term=35454	"Dmel_CG3278, CG16938, CG3278, CG5951, Dmel\CG3278, TIF-1A, TIF-IA, TIf-IA, Tif-1A, TifIA, dTIF-IA, tif1a "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011245	35454	Tif-IA	http://www.ncbi.nlm.nih.gov/gene/?term=35454	"Dmel_CG3278, CG16938, CG3278, CG5951, Dmel\CG3278, TIF-1A, TIF-IA, TIf-IA, Tif-1A, TifIA, dTIF-IA, tif1a "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011246	3547	IGSF1	http://www.ncbi.nlm.nih.gov/gene/?term=3547	"CHTE, IGCD1, IGDC1, INHBP, PGSF2, p120 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011247	35480	Atf6	http://www.ncbi.nlm.nih.gov/gene/?term=35480	"Dmel_CG3136, ATF6, CG3136, DM15, Dmel\CG3136, atf6 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011248	35480	Atf6	http://www.ncbi.nlm.nih.gov/gene/?term=35480	"Dmel_CG3136, ATF6, CG3136, DM15, Dmel\CG3136, atf6 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011249	35483	Nipped-A	http://www.ncbi.nlm.nih.gov/gene/?term=35483	"Dmel_CG33554, 41Ah, CG10549, CG2905, CG33554, Dmel\CG33554, GroupV, Nip-A, NipA, Nipped A, Nipped[A], TRA1, TRRAP, Tra-1, Tra1, dTRRAP, dTra1, dmTRRAP, l(2)41Ah, l(2)C123, l(2)EMS34-12, tra1 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011250	35496	CG30440	http://www.ncbi.nlm.nih.gov/gene/?term=35496	"Dmel_ CG10412, CG10416, CG12183, Dmel\CG30440 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011251	35499	CG11665	http://www.ncbi.nlm.nih.gov/gene/?term=35499	Dmel_ Dmel\CG11665	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011252	354	KLK3	http://www.ncbi.nlm.nih.gov/gene/?term=354	"APS, KLK2A1, PSA, hK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011253	35501	Not3	http://www.ncbi.nlm.nih.gov/gene/?term=35501	"Dmel_CG8426, CG8426, CNOT3, Dmel\CG8426, NOT3, NOT3.5, NOT3/5, l(2)NC136, not3, not3/5 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011254	35505	scaf	http://www.ncbi.nlm.nih.gov/gene/?term=35505	"Dmel_CG11066, CG11066, CG15900, Dmel\CG11066, SPH142, scarf "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011255	35505	scaf	http://www.ncbi.nlm.nih.gov/gene/?term=35505	"Dmel_CG11066, CG11066, CG15900, Dmel\CG11066, SPH142, scarf "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011256	3550	IK	http://www.ncbi.nlm.nih.gov/gene/?term=3550	"CSA2, RED "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011257	3551	IKBKB	http://www.ncbi.nlm.nih.gov/gene/?term=3551	"IKK-beta, IKK2, IKKB, IMD15, NFKBIKB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011258	35546	Ptr	http://www.ncbi.nlm.nih.gov/gene/?term=35546	"Dmel_CG11212, CG11212, Dmel\CG11212, Dmptr_Dm, ptc-related-gene, ptr, Ptr "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011259	3554	IL1R1	http://www.ncbi.nlm.nih.gov/gene/?term=3554	"CD121A, D2S1473, IL-1R-alpha, IL1R, IL1RA, P80 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011260	3556	IL1RAP	http://www.ncbi.nlm.nih.gov/gene/?term=3556	"C3orf13, IL-1RAcP, IL1R3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011261	3557	IL1RN	http://www.ncbi.nlm.nih.gov/gene/?term=3557	"DIRA, ICIL-1RA, IL-1RN, IL-1ra, IL-1ra3, IL1F3, IL1RA, IRAP, MVCD4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011262	35584	Eb1	http://www.ncbi.nlm.nih.gov/gene/?term=35584	"Dmel_CG3265, BcDNA.LD08743, BcDNA:LD08743, CG3265, Dm EB1, DmEB1, Dmel\CG3265, EB-1, EB1, S(DmcycE[JP])2.5, anon-EST:Liang-2.33, anon-EST:Liang-2.52, clone 2.33, clone 2.52, dEB-1, dEB1, d eb1, l(2)04524, l(2)4524 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011263	35588	Epac	http://www.ncbi.nlm.nih.gov/gene/?term=35588	"Dmel_CG34392, CG15235, CG3427, CG34392, D-EPAC, D-Epac, Dm_2R:10367, Dmel\CG34392, Dmel_CG15235, Dmel_CG3427, epac "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011264	3561	IL2RG	http://www.ncbi.nlm.nih.gov/gene/?term=3561	"CD132, CIDX, IL-2RG, IMD4, P64, SCIDX, SCIDX1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011265	35654	Dhx15	http://www.ncbi.nlm.nih.gov/gene/?term=35654	"Dmel_CG11107, CG11107, DHX15, Dmel\CG11107, anon-EST:Liang-1.18, cg11107, clone 1.18 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011266	35660	Eaf	http://www.ncbi.nlm.nih.gov/gene/?term=35660	"Dmel_CG11166, CG11166, CG1706, Dmel\CG11166, EP(2)2475, LD35207, dEaf "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011267	35660	Eaf	http://www.ncbi.nlm.nih.gov/gene/?term=35660	"Dmel_CG11166, CG11166, CG1706, Dmel\CG11166, EP(2)2475, LD35207, dEaf "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011268	3566	IL4R	http://www.ncbi.nlm.nih.gov/gene/?term=3566	"CD124, IL-4RA, IL4RA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011269	35696	scra	http://www.ncbi.nlm.nih.gov/gene/?term=35696	"Dmel_CG2092, ABP8, Abp8, Ani, Anil, Anillin, CG2092, Dmel\CG2092, Scra, ani, anil, anillin, l(2)03427, l(2)43Ec, l(2)k08255 "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011270	35696	scra	http://www.ncbi.nlm.nih.gov/gene/?term=35696	"Dmel_CG2092, ABP8, Abp8, Ani, Anil, Anillin, CG2092, Dmel\CG2092, Scra, ani, anil, anillin, l(2)03427, l(2)43Ec, l(2)k08255 "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011271	35696	scra	http://www.ncbi.nlm.nih.gov/gene/?term=35696	"Dmel_CG2092, ABP8, Abp8, Ani, Anil, Anillin, CG2092, Dmel\CG2092, Scra, ani, anil, anillin, l(2)03427, l(2)43Ec, l(2)k08255 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011272	3569	IL6	http://www.ncbi.nlm.nih.gov/gene/?term=3569	"BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2, IFNB2, IL-6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011273	3569	IL6	http://www.ncbi.nlm.nih.gov/gene/?term=3569	"BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2, IFNB2, IL-6 "	mRNA	Homo sapiens	26000482	Ribosome	HeLa cell	qRT-PCR	"Knockdown of Reg1 resulted in a large increase in IL6 and PTGS2 mRNA expression in the polysome fractions (fractions 7-12) compared with control cells, whereas the mRNA in non-polysome fractions (fractions 3-6) were comparable (Figure 3 H). "
RLID00011274	3570	IL6R	http://www.ncbi.nlm.nih.gov/gene/?term=3570	"CD126, IL-6R-1, IL-6RA, IL6Q, IL6RA, IL6RQ, gp80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011275	35717	tor	http://www.ncbi.nlm.nih.gov/gene/?term=35717	"Dmel_CG1389, CG1389, Dmel\CG1389, TOR, Tor, Torso, splc "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011276	3572	IL6ST	http://www.ncbi.nlm.nih.gov/gene/?term=3572	"CD130, CDW130, GP130, IL-6RB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011277	3572	IL6ST	http://www.ncbi.nlm.nih.gov/gene/?term=3572	"CD130, CDW130, GP130, IL-6RB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011278	35731	sax	http://www.ncbi.nlm.nih.gov/gene/?term=35731	"Dmel_CG1891, Bkr43E, Brk43E, CG1891, Dmel\CG1891, SAX, STK-B, Sa, Sax "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011279	3575	IL7R	http://www.ncbi.nlm.nih.gov/gene/?term=3575	"CD127, CDW127, IL-7R-alpha, IL7RA, ILRA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011280	3575	IL7R	http://www.ncbi.nlm.nih.gov/gene/?term=3575	"CD127, CDW127, IL-7R-alphaA, ILRA, IL7R "	lncRNA	Homo sapiens	24723426	Nucleus	Monocytic cell line	Northern blot|RT-PCR|Microarray	"To do this, we measured levels of lnc-IL7R in nuclear and cytoplasmic fractions of LPS treated cells. We found that a majority of lnc-IL7R was present in nuclei (Fig. 2C).  "
RLID00011281	35781	udd	http://www.ncbi.nlm.nih.gov/gene/?term=35781	"Dmel_CG18316, CG18316, Dmel\CG18316, Udd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011282	35781	udd	http://www.ncbi.nlm.nih.gov/gene/?term=35781	"Dmel_CG18316, CG18316, Dmel\CG18316, Udd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011283	35843	rgr	http://www.ncbi.nlm.nih.gov/gene/?term=35843	"Dmel_CG8643, CG14751, CG8643, Dmel\CG8643, l(2)k02605 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011284	35864	gcl	http://www.ncbi.nlm.nih.gov/gene/?term=35864	"Dmel_CG8411, CG8411, Dmel\CG8411, GCL, Gcl-1, gcl "	mRNA	Drosophila melanogaster	15852043	Germ plasm	Oocyte	-	"MRNAs can also become localized by passively diffusing through the cytoplasm until they are trapped by a localized anchor. Several transcripts, such as nanos, gcl (germ cell-less) and Cyclin B mRNAs, become enriched in the D. melanogaster pole plasm in this way "
RLID00011285	35864	gcl	http://www.ncbi.nlm.nih.gov/gene/?term=35864	"Dmel_CG8411, CG8411, Dmel\CG8411, GCL, Gcl-1, gcl "	mRNA	Drosophila melanogaster	26242323	Germ plasm	Embryo	Fluorescence in situ hybridization	"Next we determined the distribution of the known germ plasm enriched mRNAs cycB, nos, pgc, gcl and oskar (osk) and one control mRNAccr4, which appears evenly distributed throughout the embryo4 (Fig. 2a,b,h). "
RLID00011286	35864	gcl	http://www.ncbi.nlm.nih.gov/gene/?term=35864	"Dmel_CG8411, CG8411, Dmel\CG8411, GCL, Gcl-1, gcl "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011287	35865	stmA	http://www.ncbi.nlm.nih.gov/gene/?term=35865	"Dmel_CG8739, CG8739, Dmel\CG8739, cmp44E, rbo, stambhA, stm-A "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011288	3588	IL10RB	http://www.ncbi.nlm.nih.gov/gene/?term=3588	"CDW210B, CRF2-4, CRFB4, D21S58, D21S66, IL-10R2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011289	3589	IL11	http://www.ncbi.nlm.nih.gov/gene/?term=3589	"AGIF, IL-11 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011290	3589	IL11	http://www.ncbi.nlm.nih.gov/gene/?term=3589	"AGIF, IL-11 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011291	358	AQP1	http://www.ncbi.nlm.nih.gov/gene/?term=358	"AQP-CHIP, CHIP28, CO "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011292	358	AQP1	http://www.ncbi.nlm.nih.gov/gene/?term=358	"AQP-CHIP, CHIP28, CO "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011293	358	AQP1	http://www.ncbi.nlm.nih.gov/gene/?term=358	"AQP-CHIP, CHIP28, CO "	mRNA	Homo sapiens	12923260	Endoplasmic reticulum	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011294	35909	Ance-4	http://www.ncbi.nlm.nih.gov/gene/?term=35909	"Dmel_CG8196, CG8196, Dmel\CG8196, ance-4 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011295	3590	IL11RA	http://www.ncbi.nlm.nih.gov/gene/?term=3590	CRSDA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011296	35927	Su(var)2-10	http://www.ncbi.nlm.nih.gov/gene/?term=35927	"Dmel_CG8068, CG8068, CLOT2057, DPIAS, DmPias, Dmel\CG8068, Dpias, PIAS, SU(VAR)2-10, Su(Var)2-10, Su(var)-10, Su-var(2)10, Suvar(2)10, ZIMP, ZimpA, ZimpB, dPIAS, dpias, i184, l(2)03697, pias, zimp "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011297	35929	CG18659	http://www.ncbi.nlm.nih.gov/gene/?term=35929	"Dmel_ BcDNA:GH08789, CG30347, CG30348, CG8059, Dmel\CG18659, anon-WO0118547.140, anon-WO0118547.145 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011298	35940	Rab32	http://www.ncbi.nlm.nih.gov/gene/?term=35940	"Dmel_CG8024, 24652026, 24652028, A1Z7S1, CG8024, DRABR1, DmRab32, Dmel\CG8024, DrabRP1, RAB-RP1, Rab-RP1, Rab-RP1/CG8024, Rab-r1/RP1, Rab7L1, RabRP1, anon-WO0118547.106, beck, ltd, rab32 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011299	35941	CG8026	http://www.ncbi.nlm.nih.gov/gene/?term=35941	"Dmel_ Dmel\CG8026, Dromel_CG8026_FBtr0088611_mORF, anon-WO0242455.53, anon-WO0242455.6, anon-WO0242455.7 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011300	3594	IL12RB1	http://www.ncbi.nlm.nih.gov/gene/?term=3594	"CD212, IL-12R-BETA1, IL12RB, IMD30 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011301	3594	IL12RB1	http://www.ncbi.nlm.nih.gov/gene/?term=3594	"CD212, IL-12R-BETA1, IL12RB, IMD30 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011302	35955	Drep2	http://www.ncbi.nlm.nih.gov/gene/?term=35955	"Dmel_CG1975, CG1975, DREP-2, Dmel\CG1975, Drep-2, Rep2, anon-WO0118547.162, anon-WO0118547.168, drep2, rep2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011303	35955	Drep2	http://www.ncbi.nlm.nih.gov/gene/?term=35955	"Dmel_CG1975, CG1975, DREP-2, Dmel\CG1975, Drep-2, Rep2, anon-WO0118547.162, anon-WO0118547.168, drep2, rep2 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011304	35956	Myd88	http://www.ncbi.nlm.nih.gov/gene/?term=35956	"Dmel_CG2078, CG2078, DMMYD88, DmMyD88, DmMyd88, Dmel\CG2078, EP(2)2535, Kra, LD20892, MYD88, MyD88F, dMYd88, dMyD88, dMyd88, kra, myd88 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011305	35963	Non1	http://www.ncbi.nlm.nih.gov/gene/?term=35963	"Dmel_CG8801, BcDNA:LD23830, CG30341, CG8801, Dmel\CG8801, LD23830 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011306	35963	Non1	http://www.ncbi.nlm.nih.gov/gene/?term=35963	"Dmel_CG8801, BcDNA:LD23830, CG30341, CG8801, Dmel\CG8801, LD23830 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011307	35970	Pdk	http://www.ncbi.nlm.nih.gov/gene/?term=35970	"Dmel_CG8808, BcDNA:LD09837, CG8808, DmPDK, DmPdk, Dmel\CG8808, PDK, pdk "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011308	35971	ced-6	http://www.ncbi.nlm.nih.gov/gene/?term=35971	"Dmel_CG11804, CG11804, Ced-6, Dmel\CG11804, ced6, dCed-6, d drCed-6, drced-6 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011309	3597	IL13RA1	http://www.ncbi.nlm.nih.gov/gene/?term=3597	"CD213A1, CT19, IL-13Ra, NR4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011310	3597	IL13RA1	http://www.ncbi.nlm.nih.gov/gene/?term=3597	"CD213A1, CT19, IL-13Ra, NR4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011311	359845	FAM101B	http://www.ncbi.nlm.nih.gov/gene/?term=359845	CFM1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011312	359948	IRF2BP2	http://www.ncbi.nlm.nih.gov/gene/?term=359948		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011313	359	AQP2	http://www.ncbi.nlm.nih.gov/gene/?term=359	"AQP-CD, WCH-CD "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011314	35	ACADS	http://www.ncbi.nlm.nih.gov/gene/?term=35	"ACAD3, SCAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011315	35	ACADS	http://www.ncbi.nlm.nih.gov/gene/?term=35	"ACAD3, SCAD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011316	360023	ZBTB41	http://www.ncbi.nlm.nih.gov/gene/?term=360023	"FRBZ1, ZNF924 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011317	36006	CG1698	http://www.ncbi.nlm.nih.gov/gene/?term=36006	"Dmel_ DmNAT5, Dmel\CG1698 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011318	360155	CYCSP52	http://www.ncbi.nlm.nih.gov/gene/?term=360155	"HC6, HCP2 "	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00011319	3601	IL15RA	http://www.ncbi.nlm.nih.gov/gene/?term=3601	CD215	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011320	36039	eve	http://www.ncbi.nlm.nih.gov/gene/?term=36039	"Dmel_CG2328, 10.5, 10.9, 14.10, 20.35, CG2328, Dmel\CG2328, E(eve), EVE, Eve, F, V, VI, dm-eve2, even, l(2)46CFg, l(2)46CFh, l(2)46CFj, l(2)46CFp, l(2)46Ce, l(2)46Cg, eve "	mRNA	Drosophila melanogaster	15280214	Basal	Embryo	In situ hybridization	"Whereas embryos laid by wild-type mothers have an almost exclusively apical distribution of pair-rule mRNAs such as eve, ftz, h and runt (run), those laid by egl3e/eglWU50 mothers accumulate a large proportion of these transcripts in the basal cytoplasm (Fig. 5A). "
RLID00011321	36041	Pka-R2	http://www.ncbi.nlm.nih.gov/gene/?term=36041	"Dmel_CG15862, BcDNA:GM01761, CG15862, Cos, Cos-1, Cos1, Dmel\CG15862, Epa, PKA, PKA RII, PKA-R2, PKA-RII, PKa-R2, Pka-RII, RII, RII[[DR]], cos1, pkA, pka-RII "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011322	36041	Pka-R2	http://www.ncbi.nlm.nih.gov/gene/?term=36041	"Dmel_CG15862, BcDNA:GM01761, CG15862, Cos, Cos-1, Cos1, Dmel\CG15862, Epa, PKA, PKA RII, PKA-R2, PKA-RII, PKa-R2, Pka-RII, RII, RII[[DR]], cos1, pkA, pka-RII "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011323	36042	CG12128	http://www.ncbi.nlm.nih.gov/gene/?term=36042	Dmel_ Dmel\CG12128	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011324	3604	TNFRSF9	http://www.ncbi.nlm.nih.gov/gene/?term=3604	"4-1BB, CD137, CDw137, ILA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011325	3604	TNFRSF9	http://www.ncbi.nlm.nih.gov/gene/?term=3604	"4-1BB, CD137, CDw137, ILA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011326	36064	gem	http://www.ncbi.nlm.nih.gov/gene/?term=36064	"Dmel_CG30011, BcDNA:HL07889, CG11867, CG30011, CG3459, Dmel\CG30011, anon-AE003830.1, dCP2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011327	36064	gem	http://www.ncbi.nlm.nih.gov/gene/?term=36064	"Dmel_CG30011, BcDNA:HL07889, CG11867, CG30011, CG3459, Dmel\CG30011, anon-AE003830.1, dCP2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011328	3607	FOXK2	http://www.ncbi.nlm.nih.gov/gene/?term=3607	"ILF, ILF-1, ILF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011329	3608	ILF2	http://www.ncbi.nlm.nih.gov/gene/?term=3608	"NF45, PRO3063 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011330	3608	ILF2	http://www.ncbi.nlm.nih.gov/gene/?term=3608	"NF45, PRO3063 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011331	36095	Ir47a	http://www.ncbi.nlm.nih.gov/gene/?term=36095	"Dmel_CG12900, CG12900, CG12900/CG34363, DmelIR47a, Dmel\CG12900, IR47a "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011332	3609	ILF3	http://www.ncbi.nlm.nih.gov/gene/?term=3609	"CBTF, DRBF, DRBP76, MMP4, MPHOSPH4, MPP4, NF-AT-90, NF110, NF110b, NF90, NF90a, NF90b, NFAR, NFAR-1, NFAR2, TCP110, TCP80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011333	3609	ILF3	http://www.ncbi.nlm.nih.gov/gene/?term=3609	"CBTF, DRBF, DRBP76, MMP4, MPHOSPH4, MPP4, NF-AT-90, NF110, NF110b, NF90, NF90a, NF90b, NFAR, NFAR-1, NFAR2, TCP110, TCP80 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011334	360	AQP3	http://www.ncbi.nlm.nih.gov/gene/?term=360	"AQP-3, GIL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011335	360	AQP3	http://www.ncbi.nlm.nih.gov/gene/?term=360	"AQP-3, GIL "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011336	3611	ILK	http://www.ncbi.nlm.nih.gov/gene/?term=3611	"HEL-S-28, ILK-1, ILK-2, P59, p59ILK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011337	3611	ILK	http://www.ncbi.nlm.nih.gov/gene/?term=3611	"HEL-S-28-1, ILK-2, P59, p59ILK, ILK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011338	3611	ILK	http://www.ncbi.nlm.nih.gov/gene/?term=3611	"HEL-S-28-1, ILK-2, P59, p59ILK, ILK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011339	3612	IMPA1	http://www.ncbi.nlm.nih.gov/gene/?term=3612	"IMP, IMPA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011340	3612	IMPA1	http://www.ncbi.nlm.nih.gov/gene/?term=3612	"IMP, IMPA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011341	3613	IMPA2	http://www.ncbi.nlm.nih.gov/gene/?term=3613		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011342	3613	IMPA2	http://www.ncbi.nlm.nih.gov/gene/?term=3613		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011343	36142	RpS15Ab	http://www.ncbi.nlm.nih.gov/gene/?term=36142	"Dmel_CG12324, CG12324, CT22283, Dmel\CG12324, RpS15A "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011344	3614	IMPDH1	http://www.ncbi.nlm.nih.gov/gene/?term=3614	"IMPD, IMPD1, IMPDH-I, LCA11, RP10, sWSS2608 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011345	3614	IMPDH1	http://www.ncbi.nlm.nih.gov/gene/?term=3614	"IMPD, IMPD1, IMPDH-I, LCA11, RP10, sWSS2608 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011346	36154	CG18004	http://www.ncbi.nlm.nih.gov/gene/?term=36154	Dmel_ Dmel\CG18004	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011347	3615	IMPDH2	http://www.ncbi.nlm.nih.gov/gene/?term=3615	"IMPD2, IMPDH-II "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011348	361	AQP4	http://www.ncbi.nlm.nih.gov/gene/?term=361	"MIWC, WCH4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011349	361	AQP4	http://www.ncbi.nlm.nih.gov/gene/?term=361	"MIWC, WCH4 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011350	3620	IDO1	http://www.ncbi.nlm.nih.gov/gene/?term=3620	"IDO, IDO-1, INDO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011351	362161	Rapsn	http://www.ncbi.nlm.nih.gov/gene/?term=362161	rapsyn	mRNA	Rattus norvegicus	7599960	Synapse	Muscle fibers	In situ hybridization	"N-CAM, 44K-rapsyn, and S-laminin mRNAs are concentrated at synaptic sites in muscle fibers. "
RLID00011352	3621	ING1	http://www.ncbi.nlm.nih.gov/gene/?term=3621	"p24ING1c, p33, p33ING1, p33ING1b, p47, p47ING1a "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011353	36237	CG7777	http://www.ncbi.nlm.nih.gov/gene/?term=36237	"Dmel_ Aqp7777, Dmel\CG7777 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011354	36248	Tret1-1	http://www.ncbi.nlm.nih.gov/gene/?term=36248	"Dmel_CG30035, CG30035, CG7797, CG7801, DmTret1-1, Dmel\CG30035, Tre T1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011355	36249	Tret1-2	http://www.ncbi.nlm.nih.gov/gene/?term=36249	"Dmel_CG8234, CG8234, DmTret1-2, Dmel\CG8234 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011356	36249	Tret1-2	http://www.ncbi.nlm.nih.gov/gene/?term=36249	"Dmel_CG8234, CG8234, DmTret1-2, Dmel\CG8234 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011357	3624	INHBA	http://www.ncbi.nlm.nih.gov/gene/?term=3624	"EDF, FRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011358	3625	INHBB	http://www.ncbi.nlm.nih.gov/gene/?term=3625		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011359	36260	Sobp	http://www.ncbi.nlm.nih.gov/gene/?term=36260	"Dmel_CG8991, CG8991, Dmel\CG8991, Sbp "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011360	362631	Rpl11	http://www.ncbi.nlm.nih.gov/gene/?term=362631		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00011361	362636	Usp48	http://www.ncbi.nlm.nih.gov/gene/?term=362636	"Usp31, synUSP "	mRNA	Rattus norvegicus	14535949	Dendrite	Hippocampus	In situ hybridization	"The mRNA for synUSP was localized to dendrites, as well as somas, of neuronal cells.  The dendritic localization of the synUSP mRNAs was thus confirmed in the brain section. "
RLID00011362	362636	Usp48	http://www.ncbi.nlm.nih.gov/gene/?term=362636	"Usp31, synUSP "	mRNA	Rattus norvegicus	14535949	Synapse	Hippocampus	In situ hybridization	"A novel ubiquitin-specific protease, synUSP, is localized at the post-synaptic density and post-synaptic lipid raft. "
RLID00011363	36270	ERp60	http://www.ncbi.nlm.nih.gov/gene/?term=36270	"Dmel_CG8983, CG8983, D- Dmel\CG8983, Erp60, Ov6, anon-EST:fe3D9 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011364	36270	ERp60	http://www.ncbi.nlm.nih.gov/gene/?term=36270	"Dmel_CG8983, CG8983, D- Dmel\CG8983, Erp60, Ov6, anon-EST:fe3D9 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011365	362	AQP5	http://www.ncbi.nlm.nih.gov/gene/?term=362	"AQP-5, PPKB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011366	362	AQP5	http://www.ncbi.nlm.nih.gov/gene/?term=362	"AQP-5, PPKB "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011367	3631	INPP4A	http://www.ncbi.nlm.nih.gov/gene/?term=3631	"INPP4, TVAS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011368	3633	INPP5B	http://www.ncbi.nlm.nih.gov/gene/?term=3633	5PTase	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011369	3633	INPP5B	http://www.ncbi.nlm.nih.gov/gene/?term=3633	5PTase	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011370	3633	INPP5B	http://www.ncbi.nlm.nih.gov/gene/?term=3633	5PTase	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011371	36340	CG8839	http://www.ncbi.nlm.nih.gov/gene/?term=36340	Dmel_ Dmel\CG8839	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011372	3635	INPP5D	http://www.ncbi.nlm.nih.gov/gene/?term=3635	"SHIP, SHIP-1, SHIP1, SIP-145, hp51CN, p150Ship "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011373	3636	INPPL1	http://www.ncbi.nlm.nih.gov/gene/?term=3636	"OPSMD, SHIP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011374	3636	INPPL1	http://www.ncbi.nlm.nih.gov/gene/?term=3636	"OPSMD, SHIP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011375	3636	INPPL1	http://www.ncbi.nlm.nih.gov/gene/?term=3636	"OPSMD, SHIP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011376	36383	Amph	http://www.ncbi.nlm.nih.gov/gene/?term=36383	"Dmel_CG8604, Amp, CG8604, DAMP, Damp, Dmel\CG8604, amph, dAmp, dAmph, damph "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011377	3638	INSIG1	http://www.ncbi.nlm.nih.gov/gene/?term=3638	"CL-6, CL6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011378	3638	INSIG1	http://www.ncbi.nlm.nih.gov/gene/?term=3638	"CL-6, CL6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011379	3638	INSIG1	http://www.ncbi.nlm.nih.gov/gene/?term=3638	"CL-6, CL6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011380	363	AQP6	http://www.ncbi.nlm.nih.gov/gene/?term=363	"AQP2L, KID "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011381	363	AQP6	http://www.ncbi.nlm.nih.gov/gene/?term=363	"AQP2L, KID "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011382	363	AQP6	http://www.ncbi.nlm.nih.gov/gene/?term=363	"AQP2L, KID "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011383	3640	INSL3	http://www.ncbi.nlm.nih.gov/gene/?term=3640	"RLF, RLNL, ley-I-L "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00011384	3640	INSL3	http://www.ncbi.nlm.nih.gov/gene/?term=3640	"RLF, RLNL, ley-I-L "	mRNA	Homo sapiens	22679391	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00011385	36411	sca	http://www.ncbi.nlm.nih.gov/gene/?term=36411	"Dmel_CG17579, AAA28880, AAF58455, CG17579, Dmel\CG17579, FBpp0086968, FBpp0086969, Sca, Sca1b, anon-EST:Liang-38, clone 38, mAb sca1 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011386	3642	INSM1	http://www.ncbi.nlm.nih.gov/gene/?term=3642	"IA-1, IA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011387	36436	Drl-2	http://www.ncbi.nlm.nih.gov/gene/?term=36436	"Dmel_CG3915, CG12463, CG3915, DNT-like, DRL-2, Dmel\CG3915, dnl, drl-2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011388	3643	INSR	http://www.ncbi.nlm.nih.gov/gene/?term=3643	"CD220, HHF5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011389	3643	INSR	http://www.ncbi.nlm.nih.gov/gene/?term=3643	"CD220, HHF5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011390	36460	Fsn	http://www.ncbi.nlm.nih.gov/gene/?term=36460	"Dmel_CG4643, BEST:GH20696, CG4643, DFsn, Dmel\CG4643, FBXO2, Wals, dFsn, fsn "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011391	36466	CG4679	http://www.ncbi.nlm.nih.gov/gene/?term=36466	"Dmel_ Dmel\CG4679, RE17985p "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011392	3646	EIF3E	http://www.ncbi.nlm.nih.gov/gene/?term=3646	"EIF3-P48, EIF3S6, INT6, eIF3-p46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011393	3646	EIF3E	http://www.ncbi.nlm.nih.gov/gene/?term=3646	"EIF3-P48, EIF3S6, INT6, eIF3-p46 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011394	3646	EIF3E	http://www.ncbi.nlm.nih.gov/gene/?term=3646	"EIF3-P48, EIF3S6, INT6, eIF3-p46 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011395	364	AQP7	http://www.ncbi.nlm.nih.gov/gene/?term=364	"AQP7L, AQPap, GLYCQTL "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011396	3652	IPP	http://www.ncbi.nlm.nih.gov/gene/?term=3652	KLHL27	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011397	3652	IPP	http://www.ncbi.nlm.nih.gov/gene/?term=3652	KLHL27	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011398	36542	shot	http://www.ncbi.nlm.nih.gov/gene/?term=36542	"Dmel_CG18076, 42/4, CG18076, CG18637, Dmel\CG18076, Grv, Shot, Su(Mir)1, grv, kak, kop, l(2)CA4, l(2)k03010, l(2)k04204, l(2)k05434, l(2)k05821, l(2)k10821, l(2)k15606, shortstop/kakapo "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011399	36542	shot	http://www.ncbi.nlm.nih.gov/gene/?term=36542	"Dmel_CG18076, 42/4, CG18076, CG18637, Dmel\CG18076, Grv, Shot, Su(Mir)1, grv, kak, kop, l(2)CA4, l(2)k03010, l(2)k04204, l(2)k05434, l(2)k05821, l(2)k10821, l(2)k15606, shortstop/kakapo "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011400	3654	IRAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3654	"IRAK, pelle "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011401	3654	IRAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3654	"IRAK, pelle "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011402	3655	ITGA6	http://www.ncbi.nlm.nih.gov/gene/?term=3655	"CD49fB, VLA-6, ITGA6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011403	3656	IRAK2	http://www.ncbi.nlm.nih.gov/gene/?term=3656	IRAK-2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011404	3656	IRAK2	http://www.ncbi.nlm.nih.gov/gene/?term=3656	IRAK-2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011405	36578	Opa1	http://www.ncbi.nlm.nih.gov/gene/?term=36578	"Dmel_CG8479, CG8479, Dmel\CG8479, OPA1, OPA1-like-like, dOPA1, dOpa1, l(2)s3475, opa1, opa1-like, Opa1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011406	36578	Opa1	http://www.ncbi.nlm.nih.gov/gene/?term=36578	"Dmel_CG8479, CG8479, Dmel\CG8479, OPA1, OPA1-like-like, dOPA1, dOpa1, l(2)s3475, opa1, opa1-like, Opa1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011407	36578	Opa1	http://www.ncbi.nlm.nih.gov/gene/?term=36578	"Dmel_CG8479, CG8479, Dmel\CG8479, OPA1, OPA1-like-like, dOPA1, dOpa1, l(2)s3475, opa1, opa1-like, Opa1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011408	36581	CG8503	http://www.ncbi.nlm.nih.gov/gene/?term=36581	Dmel_ Dmel\CG8503	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011409	3658	IREB2	http://www.ncbi.nlm.nih.gov/gene/?term=3658	"ACO3, IRP2, IRP2AD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011410	3658	IREB2	http://www.ncbi.nlm.nih.gov/gene/?term=3658	"ACO3, IRP2, IRP2AD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011411	3658	IREB2	http://www.ncbi.nlm.nih.gov/gene/?term=3658	"ACO3, IRP2, IRP2AD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011412	3658	IREB2	http://www.ncbi.nlm.nih.gov/gene/?term=3658	"ACO3, IRP2, IRP2AD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011413	3658	IREB2	http://www.ncbi.nlm.nih.gov/gene/?term=3658	"ACO3, IRP2, IRP2AD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011414	36592	Shroom	http://www.ncbi.nlm.nih.gov/gene/?term=36592	"Dmel_CG34379, CG13942, CG13944, CG34379, CG8603, Dmel\CG34379, Dmel_CG13942, Dmel_CG8603, Shrm, dShrm, dm "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011415	3659	IRF1	http://www.ncbi.nlm.nih.gov/gene/?term=3659	"IRF-1, MAR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011416	3659	IRF1	http://www.ncbi.nlm.nih.gov/gene/?term=3659	"IRF-1, MAR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011417	36606	phyl	http://www.ncbi.nlm.nih.gov/gene/?term=36606	"Dmel_CG10108, CG10108, D(DmcycE[JP])2.2, Dmel\CG10108, PHYL, Phyl, SR2-3, Su(Raf)2C, phy1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011418	3660	IRF2	http://www.ncbi.nlm.nih.gov/gene/?term=3660	IRF-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011419	3661	IRF3	http://www.ncbi.nlm.nih.gov/gene/?term=3661	IIAE7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011420	3661	IRF3	http://www.ncbi.nlm.nih.gov/gene/?term=3661	IIAE7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011421	3665	IRF7	http://www.ncbi.nlm.nih.gov/gene/?term=3665	"IMD39, IRF-7H, IRF7A, IRF7B, IRF7C, IRF7H "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011422	366624	Cfl2	http://www.ncbi.nlm.nih.gov/gene/?term=366624		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00011423	36668	Kank	http://www.ncbi.nlm.nih.gov/gene/?term=36668	"Dmel_CG10249, BEST:GH19041, BcDNA:GH03482, CG10249, Dmel\CG10249, kank "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011424	36668	Kank	http://www.ncbi.nlm.nih.gov/gene/?term=36668	"Dmel_CG10249, BEST:GH19041, BcDNA:GH03482, CG10249, Dmel\CG10249, kank "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011425	36668	Kank	http://www.ncbi.nlm.nih.gov/gene/?term=36668	"Dmel_CG10249, BEST:GH19041, BcDNA:GH03482, CG10249, Dmel\CG10249, kank "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011426	36676	CG10265	http://www.ncbi.nlm.nih.gov/gene/?term=36676	"Dmel_ CG30474, Dmel\CG10265 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011427	3667	IRS1	http://www.ncbi.nlm.nih.gov/gene/?term=3667	HIRS-1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011428	3667	IRS1	http://www.ncbi.nlm.nih.gov/gene/?term=3667	HIRS-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011429	36692	scb	http://www.ncbi.nlm.nih.gov/gene/?term=36692	"Dmel_CG8095, CG8095, CT21280, CT36929, Dm0620, Dmel\CG8095, E(Sev-CycE)E93, E(sev-cycE)[e93], ItgaPS3, PS3, Vol, aPS3, alpha-PS3, alphaInt3, alphaPS3, alpha[[PS3]], beta[[PS3], l(2)01288, vol "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011430	36697	Xpc	http://www.ncbi.nlm.nih.gov/gene/?term=36697	"Dmel_CG8153, CG8153, DhR4, DhXPC, DmXPC, Dmel\CG8153, Mus 210, Mus210, XPC[DM]c, mus(2)201, mus(2)201G1, mus(2)201[GI], mus201[G1], mus210, mus212, Xpc "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011431	36697	Xpc	http://www.ncbi.nlm.nih.gov/gene/?term=36697	"Dmel_CG8153, CG8153, DhR4, DhXPC, DmXPC, Dmel\CG8153, Mus 210, Mus210, XPC[DM]c, mus(2)201, mus(2)201G1, mus(2)201[GI], mus201[G1], mus210, mus212, Xpc "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011432	3669	ISG20	http://www.ncbi.nlm.nih.gov/gene/?term=3669	"CD25, HEM45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011433	3669	ISG20	http://www.ncbi.nlm.nih.gov/gene/?term=3669	"CD25, HEM45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011434	366	AQP9	http://www.ncbi.nlm.nih.gov/gene/?term=366	"AQP-9, HsT17287, SSC1, T17287 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011435	3671	ISLR	http://www.ncbi.nlm.nih.gov/gene/?term=3671	HsT17563	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011436	36743	tun	http://www.ncbi.nlm.nih.gov/gene/?term=36743	"Dmel_CG8253, BcDNA:LD38553, CG8253, Dmel\CG8253, Ntaq1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011437	3674	ITGA2B	http://www.ncbi.nlm.nih.gov/gene/?term=3674	"GT, GTA, CD41, GP2B, HPA3, CD41B, GPIIb, BDPLT2, BDPLT16, PPP1R93 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011438	3674	ITGA2B	http://www.ncbi.nlm.nih.gov/gene/?term=3674	"BDPLT16, BDPLT2, CD41, CD41B, GP2B, GPIIb, GT, GTA, HPA3, PPP1R93 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00011439	3675	ITGA3	http://www.ncbi.nlm.nih.gov/gene/?term=3675	"CD49C, FRP-2, GAP-B3, GAPB3, ILNEB, MSK18, VCA-2, VL3A, VLA3a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011440	3675	ITGA3	http://www.ncbi.nlm.nih.gov/gene/?term=3675	"CD49C, FRP-2, GAP-B3, GAPB3, ILNEB, MSK18, VCA-2, VL3A, VLA3a "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011441	36769	casp	http://www.ncbi.nlm.nih.gov/gene/?term=36769	"Dmel_CG8400, CASP, CG8400, Dmel\CG8400 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011442	36769	casp	http://www.ncbi.nlm.nih.gov/gene/?term=36769	"Dmel_CG8400, CASP, CG8400, Dmel\CG8400 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011443	36772	CG8405	http://www.ncbi.nlm.nih.gov/gene/?term=36772	Dmel_ Dmel\CG8405	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011444	36772	CG8405	http://www.ncbi.nlm.nih.gov/gene/?term=36772	Dmel_ Dmel\CG8405	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011445	36774	CG8414	http://www.ncbi.nlm.nih.gov/gene/?term=36774	Dmel_ Dmel\CG8414	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011446	36775	Rho1	http://www.ncbi.nlm.nih.gov/gene/?term=36775	"Dmel_CG8416, 19549712, 8416, AAF01186, CG8416, D- DRho, DRho1, DRhoA, Dm Rho1, DmRHO-A, Dmel\CG8416, Drho1, DrhoA, E3.10/J3.8, P48148, RHO, RHO1, Rho, Rho A, Rho GTPase, Rho kinase, RhoA, RhoN19, dRho1, dRhoA, dnRho, l(2)52Fa, l(2)k02107b, n(2)k07236, rho, rho1, rhoA "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011447	36776	Ric	http://www.ncbi.nlm.nih.gov/gene/?term=36776	"Dmel_CG8418, 17137290, CG8418, D-Ric, Dmel\CG8418, Q7JMZ0, RIC, Roc "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011448	3678	ITGA5	http://www.ncbi.nlm.nih.gov/gene/?term=3678	"FNRA, CD49e, VLA-5, VLA5A "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011449	3678	ITGA5	http://www.ncbi.nlm.nih.gov/gene/?term=3678	"CD49e, FNRA, VLA-5, VLA5A "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00011450	36797	mrj	http://www.ncbi.nlm.nih.gov/gene/?term=36797	"Dmel_CG8448, CG8448, Dmel\CG8448, MRJ, dMRJ, d "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011451	36797	mrj	http://www.ncbi.nlm.nih.gov/gene/?term=36797	"Dmel_CG8448, CG8448, Dmel\CG8448, MRJ, dMRJ, d "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011452	3679	ITGA7	http://www.ncbi.nlm.nih.gov/gene/?term=3679		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011453	367	AR	http://www.ncbi.nlm.nih.gov/gene/?term=367	"AIS, AR8, DHTR, HUMARA, HYSP1, KD, NR3C4, SBMA, SMAX1, TFM "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011454	36810	Khc	http://www.ncbi.nlm.nih.gov/gene/?term=36810	"Dmel_CG7765, CG7765, DK, DKH, DmK, DmKHC, Dmel\CG7765, Dmkin, KHC, KIF 5A, KIF5B, KIN, Kin, Kin-1, Kinesin-1, khc, kin, kinesin, kinesin-1, l(2)W12, l(2)k13219, l(2)k13314, l(2R)W12, pgs "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011455	36820	CG7747	http://www.ncbi.nlm.nih.gov/gene/?term=36820	"Dmel_ CYC4, Dmel\CG7747 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011456	3682	ITGAE	http://www.ncbi.nlm.nih.gov/gene/?term=3682	"CD103, HUMINAE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011457	3682	ITGAE	http://www.ncbi.nlm.nih.gov/gene/?term=3682	"CD103, HUMINAE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011458	3683	ITGAL	http://www.ncbi.nlm.nih.gov/gene/?term=3683	"CD11A, LFA-1, LFA1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011459	3684	ITGAM	http://www.ncbi.nlm.nih.gov/gene/?term=3684	"CD11B, CR3A, MAC-1, MAC1A, MO1A, SLEB6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011460	36858	CG8303	http://www.ncbi.nlm.nih.gov/gene/?term=36858	Dmel_ Dmel\CG8303	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011461	3685	ITGAV	http://www.ncbi.nlm.nih.gov/gene/?term=3685	"CD51, MSK8, VNRA, VTNR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011462	3685	ITGAV	http://www.ncbi.nlm.nih.gov/gene/?term=3685	"CD51, MSK8, VNRA, VTNR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011463	36868	CG5210	http://www.ncbi.nlm.nih.gov/gene/?term=36868	"Dmel_ Chit, Chit13, Cht13, DS47, DmDS47, Dmel\CG5210, chit, ds47 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011464	3687	ITGAX	http://www.ncbi.nlm.nih.gov/gene/?term=3687	"CD11C, SLEB6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011465	3687	ITGAX	http://www.ncbi.nlm.nih.gov/gene/?term=3687	"CD11C, SLEB6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011466	3688	ITGB1	http://www.ncbi.nlm.nih.gov/gene/?term=3688	"CD29, FNRB, GPIIA, MDF2, MSK12, VLA-BETA, VLAB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011467	3688	ITGB1	http://www.ncbi.nlm.nih.gov/gene/?term=3688	"CD29, FNRB, GPIIA, MDF2, MSK12, VLA-BETA, VLAB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011468	3688	ITGB1	http://www.ncbi.nlm.nih.gov/gene/?term=3688	"CD29, FNRB, GPIIA, MDF2, MSK12, VLA-BETA, VLAB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011469	3688	ITGB1	http://www.ncbi.nlm.nih.gov/gene/?term=3688	"CD29, FNRB, GPIIA, MDF2, MSK12, VLA-BETA, VLAB "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Endogenous mRNAs remain associated with the ER independently of ribosomes and translation.(A) The levels of Sec61a and bactin transcripts isolated from unbound (i.e., non-ER) cytoplasmic and ER fractions from either cycloheximide treated (¡°Control¡±) or puromycin treated EDTA extracted (  Puromycin+EDTA  ) U2OS cells were assessed by quantitative RT-PCR analysis. Each bar represents the levels of the specified transcript normalized to 28S rRNA levels, standardized to the level of mRNA in the control sample, and averaged between three independent experiments. Error bars represent the standard error of the mean. Note that 28S rRNA was used as the large ribosomal subunit is known to associate to the ER even after puromycin treatment [35] and that ribosomes are equally distributed in cytoplasmic and ER (see Figure 1F). The level of Sec61a mRNA was normalized to the ER fraction from control cells, while the b-actin mRNA was normalized to the cytoplasmic fraction from control cells. (B) The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61a, Trapa, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin b1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. "
RLID00011470	3689	ITGB2	http://www.ncbi.nlm.nih.gov/gene/?term=3689	"CD18, LAD, LCAMB, LFA-1, MAC-1, MF17, MFI7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011471	3691	ITGB4	http://www.ncbi.nlm.nih.gov/gene/?term=3691	CD104	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011472	3691	ITGB4	http://www.ncbi.nlm.nih.gov/gene/?term=3691	"CD104, GP150 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011473	36922	CG6967	http://www.ncbi.nlm.nih.gov/gene/?term=36922	"Dmel_ CT21565, Dmel\CG6967 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011474	3692	EIF6	http://www.ncbi.nlm.nih.gov/gene/?term=3692	"CAB, EIF3A, ITGB4BP, b(2)gcn, eIF-6, p27(BBP), p27BBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011475	3693	ITGB5	http://www.ncbi.nlm.nih.gov/gene/?term=3693		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011476	3693	ITGB5	http://www.ncbi.nlm.nih.gov/gene/?term=3693		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011477	3697	ITIH1	http://www.ncbi.nlm.nih.gov/gene/?term=3697	"H1P, IATIH, IGHEP1, ITI-HC1, ITIH, SHAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011478	369	ARAF	http://www.ncbi.nlm.nih.gov/gene/?term=369	"A-RAF, ARAF1, PKS2, RAFA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011479	369	ARAF	http://www.ncbi.nlm.nih.gov/gene/?term=369	"A-RAF1, PKS2, RAFA1, ARAF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011480	36	ACADSB	http://www.ncbi.nlm.nih.gov/gene/?term=36	"2-MEBCAD, ACAD7, SBCAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011481	37000	CG10936	http://www.ncbi.nlm.nih.gov/gene/?term=37000	Dmel_ Dmel\CG10936	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011482	37007	Sema-1b	http://www.ncbi.nlm.nih.gov/gene/?term=37007	"Dmel_CG6446, BcDNA:GH03186, CG6446, D-semaIII, Dmel\CG6446, Sema 1b, Sema III, Sema1b, sema-III, sema1b "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011483	3700	ITIH4	http://www.ncbi.nlm.nih.gov/gene/?term=3700	"GP120, H4P, IHRP, ITI-HC4, ITIHL1, PK-120, PK120 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011484	37029	OstDelta	http://www.ncbi.nlm.nih.gov/gene/?term=37029	"Dmel_CG6370, CG6370, Dmel\CG6370, OST "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011485	37039	olf186-M	http://www.ncbi.nlm.nih.gov/gene/?term=37039	"Dmel_CG14489, CG14489, Dmel\CG14489 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011486	3703	STT3A	http://www.ncbi.nlm.nih.gov/gene/?term=3703	"ITM1, STT3-A, TMC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011487	3703	STT3A	http://www.ncbi.nlm.nih.gov/gene/?term=3703	"ITM1, STT3-A, TMC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011488	37043	Mapmodulin	http://www.ncbi.nlm.nih.gov/gene/?term=37043	"Dmel_CG5784, CG5784, CT18148, CT42180, Dmel\CG5784, anon-EST:fe3A2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011489	37043	Mapmodulin	http://www.ncbi.nlm.nih.gov/gene/?term=37043	"Dmel_CG5784, CG5784, CT18148, CT42180, Dmel\CG5784, anon-EST:fe3A2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011490	3704	ITPA	http://www.ncbi.nlm.nih.gov/gene/?term=3704	"C20orf37, EIEE35, HLC14-06-P, My049, dJ794I6.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011491	3704	ITPA	http://www.ncbi.nlm.nih.gov/gene/?term=3704	"C20orf37, EIEE35, HLC14-06-P, My049, dJ794I6.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011492	3704	ITPA	http://www.ncbi.nlm.nih.gov/gene/?term=3704	"C20orf37, EIEE35, HLC14-06-P, My049, dJ794I6.3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011493	3705	ITPK1	http://www.ncbi.nlm.nih.gov/gene/?term=3705	ITRPK1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011494	37069	Pcl	http://www.ncbi.nlm.nih.gov/gene/?term=37069	"Dmel_CG5109, CG5109, Dmel\CG5109, PCL, l(2)s1859, pcl "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011495	37070	pAbp	http://www.ncbi.nlm.nih.gov/gene/?term=37070	"Dmel_CG5119, BcDNA:LD24412, CG16803, CG5119, Dmel\CG5119, PABP, PABP55B, PABPC1, PAbp, Pabp, anon-EST:Posey247, anon-EST:Posey249, anon-EST:fe2E5, dPABP, duo, l(2)SH1908, l(2)SH2 1908, l(2)k10109, pAB, pABP, pabp "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011496	37089	fj	http://www.ncbi.nlm.nih.gov/gene/?term=37089	"Dmel_CG10917, CG10917, Dmel\CG10917, Fj "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011497	3708	ITPR1	http://www.ncbi.nlm.nih.gov/gene/?term=3708	"ACV, CLA4, INSP3R1, IP3R, IP3R1, PPP1R94, SCA15, SCA16, SCA29 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011498	3708	ITPR1	http://www.ncbi.nlm.nih.gov/gene/?term=3708	"ACV, CLA4, INSP3R1, IP3R, IP3R1, PPP1R94, SCA15, SCA16, SCA29 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00011499	37098	CG14505	http://www.ncbi.nlm.nih.gov/gene/?term=37098	Dmel_ Dmel\CG14505	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011500	3709	ITPR2	http://www.ncbi.nlm.nih.gov/gene/?term=3709	"ANHD, CFAP48, INSP3R2, IP3R2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011501	3709	ITPR2	http://www.ncbi.nlm.nih.gov/gene/?term=3709	"ANHD, CFAP48, INSP3R2, IP3R2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011502	3709	ITPR2	http://www.ncbi.nlm.nih.gov/gene/?term=3709	"ANHD, CFAP48, INSP3R2, IP3R2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011503	3710	ITPR3	http://www.ncbi.nlm.nih.gov/gene/?term=3710	"IP3R, IP3R3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011504	3710	ITPR3	http://www.ncbi.nlm.nih.gov/gene/?term=3710	"IP3R, IP3R3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011505	3710	ITPR3	http://www.ncbi.nlm.nih.gov/gene/?term=3710	"IP3R, IP3R3 "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00011506	37119	CG30118	http://www.ncbi.nlm.nih.gov/gene/?term=37119	"Dmel_ CG16859, CG5544, Dmel\CG30118 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011507	37119	CG30118	http://www.ncbi.nlm.nih.gov/gene/?term=37119	"Dmel_ CG16859, CG5544, Dmel\CG30118 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011508	37123	Prp19	http://www.ncbi.nlm.nih.gov/gene/?term=37123	"Dmel_CG5519, BcDNA:LD02793, CG5519, Dmel\CG5519, EC2-11, GPB, Gbp, PRP19, l(2)07838, prp19 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011509	3712	IVD	http://www.ncbi.nlm.nih.gov/gene/?term=3712	ACAD2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011510	3712	IVD	http://www.ncbi.nlm.nih.gov/gene/?term=3712	ACAD2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011511	37131	Pepck	http://www.ncbi.nlm.nih.gov/gene/?term=37131	"Dmel_CG17725, 143299_at, CG10924, CG17725, Dmel\CG17725, Dromel_CG17725_FBtr0086701_pepck_mORF, PEPCK, dPEPCK, pepck "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011512	3714	JAG2	http://www.ncbi.nlm.nih.gov/gene/?term=3714	"HJ2, SER2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011513	37156	Vps51	http://www.ncbi.nlm.nih.gov/gene/?term=37156	"Dmel_CG15087, CG15087, Dmel\CG15087 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011514	37164	Jabba	http://www.ncbi.nlm.nih.gov/gene/?term=37164	"Dmel_CG42351, 141242_at, BP1008, CG1509, CG15092, CG34020, CG42351, Dmel\CG42351, Dmel_CG15092, Dmel_CG34020, anon-WO0118547.167 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011515	37164	Jabba	http://www.ncbi.nlm.nih.gov/gene/?term=37164	"Dmel_CG42351, 141242_at, BP1008, CG1509, CG15092, CG34020, CG42351, Dmel\CG42351, Dmel_CG15092, Dmel_CG34020, anon-WO0118547.167 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011516	37166	CG15093	http://www.ncbi.nlm.nih.gov/gene/?term=37166	"Dmel_ CG 15093, CT34968, Dmel\CG15093 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011517	3716	JAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3716	"JAK1A, JAK1B, JTK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011518	3716	JAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3716	"JAK1AB, JTK3, JAK1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011519	3716	JAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3716	"JAK1AB, JTK3, JAK1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011520	3718	JAK3	http://www.ncbi.nlm.nih.gov/gene/?term=3718	"JAK-3_HUMAN, JAKL, L-JAK, LJAK, JAK3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011521	3718	JAK3	http://www.ncbi.nlm.nih.gov/gene/?term=3718	"JAK-3_HUMAN, JAKL, L-JAK, LJAK, JAK3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011522	3720	JARID2	http://www.ncbi.nlm.nih.gov/gene/?term=3720	JMJ	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011523	37223	CG9416	http://www.ncbi.nlm.nih.gov/gene/?term=37223	"Dmel_CG9416-PA, Dmel\CG9416 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011524	37230	hts	http://www.ncbi.nlm.nih.gov/gene/?term=37230	"Dmel_CG43443, 1B1, ADD-87, Add, Add-hts, Adducin, CG34197, CG43443, CG9325, Dmel\CG43443, Dmel_CG34197, Dmel_CG9325, EST D, HTS, HTS-R1, HTS-RC, HTS_DROME, Hts, Hts-RC, HtsF, HtsRC, Ovhts, Ovhts-RC, add, add-like, adducin, anon-EST:Posey9RC, l(2)00634, l(2)01103, l(2)k06121, l(2)k14523, hts "	mRNA	Drosophila melanogaster	19217894	Cell cortex	Oocyte	In situ hybridization	"The htsN4 mRNA is positioned at the anterior of the oocyte, where it is largely restricted to the junctions of anterior and lateral cortex. "
RLID00011525	3725	JUN	http://www.ncbi.nlm.nih.gov/gene/?term=3725	"AP-1, AP1, c-Jun "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00011526	3725	JUN	http://www.ncbi.nlm.nih.gov/gene/?term=3725	"AP-1, AP1, c-Jun "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00011527	3726	JUNB	http://www.ncbi.nlm.nih.gov/gene/?term=3726	AP-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011528	3726	JUNB	http://www.ncbi.nlm.nih.gov/gene/?term=3726	AP-1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011529	3726	JUNB	http://www.ncbi.nlm.nih.gov/gene/?term=3726	AP-1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011530	3727	JUND	http://www.ncbi.nlm.nih.gov/gene/?term=3727	AP-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011531	3727	JUND	http://www.ncbi.nlm.nih.gov/gene/?term=3727	AP-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011532	3727	JUND	http://www.ncbi.nlm.nih.gov/gene/?term=3727	AP-1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011533	3728	JUP	http://www.ncbi.nlm.nih.gov/gene/?term=3728	"ARVD12, CTNNG, DP3, DPIII, PDGB, PKGB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011534	3728	JUP	http://www.ncbi.nlm.nih.gov/gene/?term=3728	"ARVD12, CTNNG, DP3, DPIII, PDGB, PKGB "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011535	37290	PCNA	http://www.ncbi.nlm.nih.gov/gene/?term=37290	"Dmel_CG9193, 53/13, CG9193, DmPCNA, Dmel\CG9193, MUS209, Mus209/mus209, Pcna, dPCNA, l(2)02448, l(2)56F, l(2)56Fa, l(2)s1534, mus 209, mus209, pcna, PCNA "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011536	37290	PCNA	http://www.ncbi.nlm.nih.gov/gene/?term=37290	"Dmel_CG9193, 53/13, CG9193, DmPCNA, Dmel\CG9193, MUS209, Mus209/mus209, Pcna, dPCNA, l(2)02448, l(2)56F, l(2)56Fa, l(2)s1534, mus 209, mus209, pcna, PCNA "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011537	37294	CG10444	http://www.ncbi.nlm.nih.gov/gene/?term=37294	"Dmel_ Dmel\CG10444, dSLC5A3 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011538	372	ARCN1	http://www.ncbi.nlm.nih.gov/gene/?term=372	COPD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011539	372	ARCN1	http://www.ncbi.nlm.nih.gov/gene/?term=372	COPD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011540	372	ARCN1	http://www.ncbi.nlm.nih.gov/gene/?term=372	COPD	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011541	372	ARCN1	http://www.ncbi.nlm.nih.gov/gene/?term=372	COPD	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011542	372	ARCN1	http://www.ncbi.nlm.nih.gov/gene/?term=372	COPD	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011543	37301	CG11200	http://www.ncbi.nlm.nih.gov/gene/?term=37301	"Dmel_CG11200, Dmel\CG11200 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011544	373074	dnd1	http://www.ncbi.nlm.nih.gov/gene/?term=373074	"cb736, dnd, wu:fi22d10, zgc:111864 "	mRNA	Danio rerio	16457796	Germ plasm	Embryo	Fluorescence in situ hybridization	"Fig. 1. Endogenous patterns of RNA localization of dnd, nos1, vas, and dazl RNAs during the first cell cycle. Animal views of embryos fixed at progressively older stages of development (A-D: 15 min p.f.; E-H: 30 min. p.f.; I-L: 45 min p.f.) and labeled using FISH to detect germ plasm RNAs (dnd (A, E, I); nos1 (B, F, J); vas(C,G, K); dazl (D, H, L). (A-D) Immediately after fertilization, dnd, nos1, and vas RNA aggregates can be observed as a band at the animal pole, while dazl RNA aggregates are not initially present in the animal pole. (E-H) During the initiation of furrow formation, RNA aggregates fordnd, nos1, and vas begin to be recruited as a rod at the forming furrow (arrows in E-G). At this stage, dazl RNA is not yet detectable at the furrows (H). (I-L) As the furrow matures, there is an increase in the amount of dnd, nos1, and vasRNAs recruited at the furrow, and dazlRNA becomes detectable at the furrow (arrows in I-L). Scale bar in panel (L) represents 100 μmThus, although all four RNAs are recruited to the forming furrow, RNAs for dnd, nos1, and vas are already present in the animal pole in the freshly laid egg, while dazlRNA arrives to the animal pole from the vegetal region at a later stage. Based on their different times of appearance at the animal region, we refer to the dnd, nos1, and vas RNAs as the early animal germ plasm RNAs, while dazl is also referred to as a vegetally localized germ plasm RNA. "
RLID00011545	3730	ANOS1	http://www.ncbi.nlm.nih.gov/gene/?term=3730	"ADMLX, HH1, HHA, KAL, KAL1, KALIG-1, KMS, WFDC19 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011546	373156	GSTK1	http://www.ncbi.nlm.nih.gov/gene/?term=373156	"GST, GST 13-13, GST13, GST13-13, GSTK1-1, hGSTK1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011547	373156	GSTK1	http://www.ncbi.nlm.nih.gov/gene/?term=373156	"GST, GST 13-13, GST13, GST13-13-1, hGSTK1, GSTK1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011548	3732	CD82	http://www.ncbi.nlm.nih.gov/gene/?term=3732	"4F9, C33, GR15, IA4, KAI1, R2, SAR2, ST6, TSPAN27 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011549	3732	CD82	http://www.ncbi.nlm.nih.gov/gene/?term=3732	"4F9, C33, GR15, IA4, KAI1, R2, SAR2, ST6, TSPAN27 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011550	37355	insc	http://www.ncbi.nlm.nih.gov/gene/?term=37355	"Dmel_CG11312, 25/17, CG11312, Dmel\CG11312, INSC, Ins, Insc, fam, l(2)05475, l(2)k12405, nem "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011551	3735	KARS	http://www.ncbi.nlm.nih.gov/gene/?term=3735	"CMTRIB, DFNB89, KARS1, KARS2, KRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011552	3735	KARS	http://www.ncbi.nlm.nih.gov/gene/?term=3735	"CMTRIB, DFNB891, KARS2, KRS, KARS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011553	37387	cpa	http://www.ncbi.nlm.nih.gov/gene/?term=37387	"Dmel_CG10540, CG10540, Cpa, Dmel\CG10540, miro, scrd "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011554	373	TRIM23	http://www.ncbi.nlm.nih.gov/gene/?term=373	"ARD1, ARFD1, RNF46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011555	373	TRIM23	http://www.ncbi.nlm.nih.gov/gene/?term=373	"ARD1, ARFD1, RNF46 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011556	374040	DIAPH1	http://www.ncbi.nlm.nih.gov/gene/?term=374040	DIAPH2	mRNA	Gallus gallus	23840831	Endoplasmic reticulum	Fibroblast	Fluorescence in situ hybridization	"Here, we provide evidence to demonstrate that the 5�cap-mediated immediate translation of DIAPH1 mRNA upon exiting nucleus is required for localizing the mRNA in the perinuclear ER compartment.  "
RLID00011557	374040	DIAPH1	http://www.ncbi.nlm.nih.gov/gene/?term=374040	DIAPH2	mRNA	Gallus gallus	23840831	Nucleus	Fibroblast	Fluorescence in situ hybridization	"Here, we provide evidence to demonstrate that the 5�cap-mediated immediate translation of DIAPH1 mRNA upon exiting nucleus is required for localizing the mRNA in the perinuclear ER compartment.  "
RLID00011558	374197	ACTR3	http://www.ncbi.nlm.nih.gov/gene/?term=374197		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00011559	374197	ACTR3	http://www.ncbi.nlm.nih.gov/gene/?term=374197		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00011560	37422	ASPP	http://www.ncbi.nlm.nih.gov/gene/?term=37422	"Dmel_CG18375, CG18375, Dmel\CG18375, dASPP "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011561	374286	CDRT1	http://www.ncbi.nlm.nih.gov/gene/?term=374286	"C170RF1, C17ORF1, C17ORF1A, FBXW10B, FBXW10P1, HREP, SM25H2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011562	374286	CDRT1	http://www.ncbi.nlm.nih.gov/gene/?term=374286	"C170RF1, C17ORF1, C17ORF1A, FBXW10B, FBXW10P1, HREP, SM25H2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011563	374354	NHLRC2	http://www.ncbi.nlm.nih.gov/gene/?term=374354		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011564	37437	CG30394	http://www.ncbi.nlm.nih.gov/gene/?term=37437	"Dmel_ CG10500, CG15670, Dmel\CG30394, anon-WO0172774.187, anon-WO0172774.188 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011565	374383	NCR3LG1	http://www.ncbi.nlm.nih.gov/gene/?term=374383	"B7-H6, B7H6, DKFZp686O24166 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011566	374393	FAM111B	http://www.ncbi.nlm.nih.gov/gene/?term=374393	"CANP, POIKTMP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011567	374395	TMEM179B	http://www.ncbi.nlm.nih.gov/gene/?term=374395		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011568	37447	Sdc	http://www.ncbi.nlm.nih.gov/gene/?term=37447	"Dmel_CG10497, CG10497, CT27296, Dmel\CG10497, Dsyn, Syd, Syn, dSdc, l(2)10608, sdc, syd, syn "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011569	37447	Sdc	http://www.ncbi.nlm.nih.gov/gene/?term=37447	"Dmel_CG10497, CG10497, CT27296, Dmel\CG10497, Dsyn, Syd, Syn, dSdc, l(2)10608, sdc, syd, syn "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011570	374500	THSD1P1	http://www.ncbi.nlm.nih.gov/gene/?term=374500	THSD1P	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011571	37451	MESK2	http://www.ncbi.nlm.nih.gov/gene/?term=37451	"Dmel_CG15669, BcDNA:GH12032, BcDNA:LD27504, BcDNA:RH10174, CG15668, CG15669, Dmel\CG15669, Mesk2, l(2)01467, mesk2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011572	37454	CG30283	http://www.ncbi.nlm.nih.gov/gene/?term=37454	"Dmel_ CG10450, Dmel\CG30283, SP37, SPH37 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011573	37458	CG10433	http://www.ncbi.nlm.nih.gov/gene/?term=37458	Dmel_ Dmel\CG10433	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011574	374650	GOLGA6L5P	http://www.ncbi.nlm.nih.gov/gene/?term=374650	"GOLGA6L5, GOLGA6L8 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011575	374655	ZNF710	http://www.ncbi.nlm.nih.gov/gene/?term=374655		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011576	374659	HDDC3	http://www.ncbi.nlm.nih.gov/gene/?term=374659	"(ppGpp)ase, MESH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011577	374666	WASH3P	http://www.ncbi.nlm.nih.gov/gene/?term=374666	FAM39DP	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011578	37471	NC2alpha	http://www.ncbi.nlm.nih.gov/gene/?term=37471	"Dmel_CG10318, CG10318, Dmel\CG10318, Drap1, NC2, Nc2alpha, dDrap, dDrap1, dDrap1/dNC2a, dNC2 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00011579	374868	ATP9B	http://www.ncbi.nlm.nih.gov/gene/?term=374868	"ATPASEP, ATPIIB, HUSSY-20, NEO1L, hMMR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011580	374868	ATP9B	http://www.ncbi.nlm.nih.gov/gene/?term=374868	"ATPASEP, ATPIIB, HUSSY-20, NEO1L, hMMR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011581	374872	C19orf35	http://www.ncbi.nlm.nih.gov/gene/?term=374872		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011582	374872	C19orf35	http://www.ncbi.nlm.nih.gov/gene/?term=374872		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011583	374882	TMEM205	http://www.ncbi.nlm.nih.gov/gene/?term=374882	UNQ501	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011584	374882	TMEM205	http://www.ncbi.nlm.nih.gov/gene/?term=374882	UNQ501	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011585	374920	C19orf68	http://www.ncbi.nlm.nih.gov/gene/?term=374920		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011586	374969	SVBP	http://www.ncbi.nlm.nih.gov/gene/?term=374969	CCDC23	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011587	374	AREG	http://www.ncbi.nlm.nih.gov/gene/?term=374	"AR, AREGB, CRDGF, SDGF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011588	375035	SFT2D2	http://www.ncbi.nlm.nih.gov/gene/?term=375035	"UNQ512, dJ747L4.C1.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011589	375056	MIA3	http://www.ncbi.nlm.nih.gov/gene/?term=375056	"ARNT, D320, TANGO, TANGO1, UNQ6077 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011590	375056	MIA3	http://www.ncbi.nlm.nih.gov/gene/?term=375056	"ARNT, D320, TANGO, TANGO1, UNQ6077 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011591	375061	FAM89A	http://www.ncbi.nlm.nih.gov/gene/?term=375061	C1orf153	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011592	375061	FAM89A	http://www.ncbi.nlm.nih.gov/gene/?term=375061	C1orf153	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011593	37511	Snp	http://www.ncbi.nlm.nih.gov/gene/?term=37511	"Dmel_CG44248, CG11478, CG30327, CG42257, CG44248, CG6393, Dmel\CG44248, Dmel_CG30327, Dmel_CG42257, Dmel_CG6393 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011594	37521	Vrp1	http://www.ncbi.nlm.nih.gov/gene/?term=37521	"Dmel_CG13503, CG13503, D-WIP, Dm_Vrp1, Dmel\CG13503, WIP, dWIP, sltr, solas, vrp1, wip "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011595	375248	ANKRD36	http://www.ncbi.nlm.nih.gov/gene/?term=375248	UNQ2430	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011596	375287	RBM43	http://www.ncbi.nlm.nih.gov/gene/?term=375287	C2orf38	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011597	375287	RBM43	http://www.ncbi.nlm.nih.gov/gene/?term=375287	C2orf38	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011598	375295	LINC01116	http://www.ncbi.nlm.nih.gov/gene/?term=375295		lncRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00011599	375295	LINC01116	http://www.ncbi.nlm.nih.gov/gene/?term=375295		lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00011600	375346	TMEM110	http://www.ncbi.nlm.nih.gov/gene/?term=375346	STIMATE	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011601	37534	CG11275	http://www.ncbi.nlm.nih.gov/gene/?term=37534	"Dmel_ Dmel\CG11275, i188 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011602	37534	CG11275	http://www.ncbi.nlm.nih.gov/gene/?term=37534	"Dmel_ Dmel\CG11275, i188 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011603	37535	MED16	http://www.ncbi.nlm.nih.gov/gene/?term=37535	"Dmel_CG5465, CG5465, Dmel\CG5465, Med16, Sin4/TRAP95, Trap95, dTRAP95, med16 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011604	375449	MAST4	http://www.ncbi.nlm.nih.gov/gene/?term=375449		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011605	37547	CG5819	http://www.ncbi.nlm.nih.gov/gene/?term=37547	"Dmel_ 5819, CT18212, Dmel\CG5819, tartan/capricious-like "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011606	37549	Gp150	http://www.ncbi.nlm.nih.gov/gene/?term=37549	"Dmel_CG5820, CG5820, CT18251, Dmel\CG5820, GP150, anon-EST:fe2A1, gp150, l(2)52A, p150 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011607	375513	GUSBP4	http://www.ncbi.nlm.nih.gov/gene/?term=375513	"C6orf216, GUSBL2, SMA3-L, SMAC3L "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011608	37556	CG13506	http://www.ncbi.nlm.nih.gov/gene/?term=37556	"Dmel_ 13506, CT32874, Dmel\CG13506 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011609	37557	babos	http://www.ncbi.nlm.nih.gov/gene/?term=37557	"Dmel_CG3624, CG3624, CT12183, Dmel\CG3624 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011610	375593	TRIM73	http://www.ncbi.nlm.nih.gov/gene/?term=375593	TRIM50B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011611	375690	WASH5P	http://www.ncbi.nlm.nih.gov/gene/?term=375690		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011612	375743	PTAR1	http://www.ncbi.nlm.nih.gov/gene/?term=375743		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011613	375743	PTAR1	http://www.ncbi.nlm.nih.gov/gene/?term=375743		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011614	375743	PTAR1	http://www.ncbi.nlm.nih.gov/gene/?term=375743		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011615	375748	ERCC6L2	http://www.ncbi.nlm.nih.gov/gene/?term=375748	"BMFS2, C9orf102, RAD26L, SR278 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011616	375757	SWI5	http://www.ncbi.nlm.nih.gov/gene/?term=375757	"C9orf119, SAE3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011617	37575	dnr1	http://www.ncbi.nlm.nih.gov/gene/?term=37575	"Dmel_CG12489, CG12489, DNR1, Dmel\CG12489, Dnr1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011618	375790	AGRN	http://www.ncbi.nlm.nih.gov/gene/?term=375790	"CMS8, CMSPPD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011619	375790	AGRN	http://www.ncbi.nlm.nih.gov/gene/?term=375790	"CMS8, CMSPPD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011620	375791	CYSRT1	http://www.ncbi.nlm.nih.gov/gene/?term=375791	C9orf169	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011621	3757	KCNH2	http://www.ncbi.nlm.nih.gov/gene/?term=3757	"ERG-1, ERG1, H-ERG, HERG, HERG1, Kv11.1, LQT2, SQT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011622	37588	CG3732	http://www.ncbi.nlm.nih.gov/gene/?term=37588	Dmel_ Dmel\CG3732	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011623	375	ARF1	http://www.ncbi.nlm.nih.gov/gene/?term=375		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011624	375	ARF1	http://www.ncbi.nlm.nih.gov/gene/?term=375		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011625	37601	RYBP	http://www.ncbi.nlm.nih.gov/gene/?term=37601	"Dmel_CG12190, CG12190, Dmel\CG12190, dRYBP "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011626	376132	LRRC10	http://www.ncbi.nlm.nih.gov/gene/?term=376132	"HRLRRPA, LRRC10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011627	376132	LRRC10	http://www.ncbi.nlm.nih.gov/gene/?term=376132	"HRLRRPA, LRRC10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011628	37618	CycB	http://www.ncbi.nlm.nih.gov/gene/?term=37618	"Dmel_CG3510, 2g, 3510, CG3510, CYC-B, CYCB, Cyc B, Cycb, DmcycB, Dmel\CG3510, chr2R:18312808..18312907, cyc B, cyc-B, cycB, cyclin B, cyclinB, mAbF2F4 "	mRNA	Danio rerio	11150242	Cytoplasm	Oocyte	In situ hybridization	"To examine changes in localization of cyclin B mRNA during oogenesis, we performed in situ hybridization analysis in this study. In previtellogenic oocytes,cyclin B mRNA was uniformly distributed throughout the cytoplasm. "
RLID00011629	37618	CycB	http://www.ncbi.nlm.nih.gov/gene/?term=37618	"Dmel_CG3510, 2g, 3510, CG3510, CYC-B, CYCB, Cyc B, Cycb, DmcycB, Dmel\CG3510, chr2R:18312808..18312907, cyc B, cyc-B, cycB, cyclin B, cyclinB, mAbF2F4 "	mRNA	Drosophila melanogaster	15852043	Germ plasm	Oocyte	-	"MRNAs can also become localized by passively diffusing through the cytoplasm until they are trapped by a localized anchor. Several transcripts, such as nanos, gcl (germ cell-less) and Cyclin B mRNAs, become enriched in the D. melanogaster pole plasm in this way "
RLID00011630	37618	CycB	http://www.ncbi.nlm.nih.gov/gene/?term=37618	"Dmel_CG3510, 2g, 3510, CG3510, CYC-B, CYCB, Cyc B, Cycb, DmcycB, Dmel\CG3510, chr2R:18312808..18312907, cyc B, cyc-B, cycB, cyclin B, cyclinB, mAbF2F4 "	mRNA	Drosophila melanogaster	26242323	Germ plasm	Embryo	Fluorescence in situ hybridization	"Next we determined the distribution of the known germ plasm enriched mRNAs cycB, nos, pgc, gcl and oskar (osk) and one control mRNAccr4, which appears evenly distributed throughout the embryo4 (Fig. 2a,b,h). "
RLID00011631	37618	CycB	http://www.ncbi.nlm.nih.gov/gene/?term=37618	"Dmel_CG3510, 2g, 3510, CG3510, CYC-B, CYCB, Cyc B, Cycb, DmcycB, Dmel\CG3510, chr2R:18312808..18312907, cyc B, cyc-B, cycB, cyclin B, cyclinB, mAbF2F4 "	mRNA	Drosophila melanogaster	17923096	Mitotic spindle	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011632	37618	CycB	http://www.ncbi.nlm.nih.gov/gene/?term=37618	"Dmel_CG3510, 2g, 3510, CG3510, CYC-B, CYCB, Cyc B, Cycb, DmcycB, Dmel\CG3510, chr2R:18312808..18312907, cyc B, cyc-B, cycB, cyclin B, cyclinB, mAbF2F4 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011633	37618	CycB	http://www.ncbi.nlm.nih.gov/gene/?term=37618	"Dmel_CG3510, 2g, 3510, CG3510, CYC-B, CYCB, Cyc B, Cycb, DmcycB, Dmel\CG3510, chr2R:18312808..18312907, cyc B, cyc-B, cycB, cyclin B, cyclinB, mAbF2F4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011634	376267	RAB15	http://www.ncbi.nlm.nih.gov/gene/?term=376267		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011635	3762	KCNJ5	http://www.ncbi.nlm.nih.gov/gene/?term=3762	"CIR, GIRK4, KATP1, KIR3.4, LQT13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011636	3762	KCNJ5	http://www.ncbi.nlm.nih.gov/gene/?term=3762	"CIR, GIRK4, KATP1, KIR3.4, LQT13 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011637	3762	KCNJ5	http://www.ncbi.nlm.nih.gov/gene/?term=3762	"CIR, GIRK4, KATP1, KIR3.4, LQT13 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011638	376497	SLC27A1	http://www.ncbi.nlm.nih.gov/gene/?term=376497	"ACSVL5, FATP, FATP-1, FATP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011639	3764	KCNJ8	http://www.ncbi.nlm.nih.gov/gene/?term=3764	"KIR6.1, uKATP-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011640	3766	KCNJ10	http://www.ncbi.nlm.nih.gov/gene/?term=3766	"BIRK-10, KCNJ13-PEN, KIR1.2, KIR4.1, SESAME "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011641	3766	KCNJ10	http://www.ncbi.nlm.nih.gov/gene/?term=3766	"BIRK-10, KCNJ13-PEN, KIR1.2, KIR4.1, SESAME "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011642	3767	KCNJ11	http://www.ncbi.nlm.nih.gov/gene/?term=3767	"BIR, HHF2, IKATP, KIR6.2, MODY13, PHHI, TNDM3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011643	3767	KCNJ11	http://www.ncbi.nlm.nih.gov/gene/?term=3767	"BIR, HHF2, IKATP, KIR6.2, MODY13, PHHI, TNDM3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011644	376844	SDC4P	http://www.ncbi.nlm.nih.gov/gene/?term=376844		lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00011645	376844	SDC4P	http://www.ncbi.nlm.nih.gov/gene/?term=376844		lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00011646	376940	ZC3H6	http://www.ncbi.nlm.nih.gov/gene/?term=376940	ZC3HDC6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011647	376940	ZC3H6	http://www.ncbi.nlm.nih.gov/gene/?term=376940	ZC3HDC6	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011648	376940	ZC3H6	http://www.ncbi.nlm.nih.gov/gene/?term=376940	ZC3HDC6	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011649	37708	CG3520	http://www.ncbi.nlm.nih.gov/gene/?term=37708	Dmel_ Dmel\CG3520	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011650	3771727	tRNA:P:90Ca	http://www.ncbi.nlm.nih.gov/gene/?term=3771727	"Dmel_CR31567, AE002708.trna51-ProTGG, CR31567, Dmel\CR31567, Pro, chr3R.trna57-ProTGG, tRNA:P:TGG:AE002708-e, tRNA:Pro, tRNA:pro:90Ca "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011944.html
RLID00011651	3771731	tRNA:I:49Fc	http://www.ncbi.nlm.nih.gov/gene/?term=3771731	"Dmel_CR30521, AE002787.trna38-IleAAT, CR30245, CR30521, Dmel\CR30521, chr2R.trna20-IleAAT, ile-c, tRNA:I:AAT:AE002787-d, tRNA:ile:49Fc, tRNA[Ile] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011883.html
RLID00011652	3771739	tRNA:CR30208	http://www.ncbi.nlm.nih.gov/gene/?term=3771739	"Dmel_CR30208, AE002575.trna1-TrpCCA, CR30208, Dmel\CR30208, chr2R.trna45-TrpCCA, tRNA:W:CCA:AE002575-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050208.html
RLID00011653	3771741	tRNA:CR30407	http://www.ncbi.nlm.nih.gov/gene/?term=3771741	"Dmel_CR30407, AE002575.trna11-GlyTCC, CR30205, CR30407, Dmel\CR30407, chr2R.trna55-GlyTCC, tRNA:G:58AB, tRNA:G:TCC:AE002575-b, tRNA:gly:58AB, tRNA[Gly][[GGA]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050407.html
RLID00011654	3771747	tRNA:R:12Ed	http://www.ncbi.nlm.nih.gov/gene/?term=3771747	"Dmel_CR32617, AE002593.trna7-ArgTCG, CR32617, Dmel\CR32617, chrX.trna11-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002593-e, tRNA:arg1, tRNA:arg12Ed, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011951.html
RLID00011655	3771757	snoRNA:Psi28S-3327c	http://www.ncbi.nlm.nih.gov/gene/?term=3771757	"Dmel_CR33753, CR33753, Dm-586, Dmel\CR33753, Psi28S-3327c, chr3L:13017350..13017456, psi28S-3327c, pug28S-3327, snoR586, snoRNA:586 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086601.html
RLID00011656	3771761	tRNA:R2:84Fe	http://www.ncbi.nlm.nih.gov/gene/?term=3771761	"Dmel_CR31584, AE002708.trna66-ArgACG, CR31584, Dmel\CR31584, chr3R.trna72-ArgACG, tRNA:R1, tRNA:R:ACG:AE002708-e, tRNA:arg1, tRNA:arg2:84Fe, tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011963.html
RLID00011657	3771766	tRNA:CR30249	http://www.ncbi.nlm.nih.gov/gene/?term=3771766	"Dmel_CR30249, AE002787.trna21-HisGTG, CR30249, Dmel\CR30249, chr2R.trna80-HisGTG, tRNA:H:GTG:AE002787-d, tRNA[His] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050249.html
RLID00011658	3771767	tRNA:CR30239	http://www.ncbi.nlm.nih.gov/gene/?term=3771767	"Dmel_CR30239, CR30239, Dmel\CR30239, chr2R.trna25-GluCTC, tRNA:E4:53A, tRNA:Glu, tRNA:glu4:53A "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050239.html
RLID00011659	3771768	snoRNA:Psi28S-2149	http://www.ncbi.nlm.nih.gov/gene/?term=3771768	"Dmel_CR33776, CR33776, Dm-143, Dmel\CR33776, Psi 28S-2149(SnoR143), Psi28S-2149, psi28S-2149, snoR143, snoRNA:143 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086664.html
RLID00011660	3771769	tRNA:CR30199	http://www.ncbi.nlm.nih.gov/gene/?term=3771769	"Dmel_CR30199, AE002575.trna7-AlaCGC, CR30199, Dmel\CR30199, chr2R.trna51-AlaCGC, tRNA:A:CGC:AE002575-b, tRNA[[Ala]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050199.html
RLID00011661	3771775	tRNA:K2:42Eb	http://www.ncbi.nlm.nih.gov/gene/?term=3771775	"Dmel_CR30301, AE002778.trna3-LysCTT, CR30301, Dmel\CR30301, chr2R.trna90-LysCTT, tRNA:K2, tRNA:K:CTT:AE002778-c, tRNA:lys2:42Eb, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011893.html
RLID00011662	3771776	tRNA:M3:46A	http://www.ncbi.nlm.nih.gov/gene/?term=3771776	"Dmel_CR30003, AE002787.trna31-MetCAT, CR30003, CR30262, Dmel\CR30003, chr2R.trna13-MetCAT, tRNA:M:CAT:AE002787-c, tRNA:met3:46A, tRNA:met:46A, tRNA[Met-ATG] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011921.html
RLID00011663	3771793	tRNA:N5:42Ac	http://www.ncbi.nlm.nih.gov/gene/?term=3771793	"Dmel_CR30518, AE002769.trna6-AsnGTT, CR30307, CR30518, Dmel\CR30518, asn-tRNA, chr2R.trna97-AsnGTT, tRNA:N:GTT:AE002769-b, tRNA:asn5:42Ac "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011933.html
RLID00011664	3771794	tRNA:CR30298	http://www.ncbi.nlm.nih.gov/gene/?term=3771794	"Dmel_CR30298, AE002787.trna28-ThrAGT, CR30298, Dmel\CR30298, chr2R.trna87-ThrAGT, tRNA:T3:47F, tRNA:T:AGT:AE002787-b, tRNA:thr3:47F, tRNA[Thr][[3]], tRNA[[Thr]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050298.html
RLID00011665	3771795	tRNA:E4:62Ae	http://www.ncbi.nlm.nih.gov/gene/?term=3771795	"Dmel_CR32322, AE002584.trna11-GluCTC, CR32322, Dmel\CR32322, chr3L.trna11-GluCTC, glu-trna, tRNA:E4, tRNA:E:CTC:AE002584-i, tRNA:Glu, tRNA:glu4:62Ae "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011855.html
RLID00011666	3771804	tRNA:CR30449	http://www.ncbi.nlm.nih.gov/gene/?term=3771804	"Dmel_CR30449, CR30221, CR30449, Dmel\CR30449, chr2R.trna39-GluCTC "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050449.html
RLID00011667	3771805	tRNA:I:42A	http://www.ncbi.nlm.nih.gov/gene/?term=3771805	"Dmel_CR30313, AE002769.trna15-IleAAT, CR30313, Dmel\CR30313, chr2R.trna7-IleAAT, tRNA Ile, tRNA:I:AAT:AE002769, tRNA:ile:42A, tRNA[Ile] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011880.html
RLID00011668	3771815	tRNA:V4:70BCb	http://www.ncbi.nlm.nih.gov/gene/?term=3771815	"Dmel_CR32124, AE002602.trna22-ValAAC, CR32124, Dmel\CR32124, chr3L.trna27-ValAAC, tRNA-Val-4, tRNA:V4, tRNA:V:AAC:AE002602-b, tRNA:val4:70BCb, tRNA[Val-AAC], tRNA[Val][[4]], val-tRNA-4, valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012010.html
RLID00011669	3771822	tRNA:V3b:92Ba	http://www.ncbi.nlm.nih.gov/gene/?term=3771822	"Dmel_CR31214, AE002708.trna41-ValCAC, CR31214, Dmel\CR31214, chr3R.trna47-ValCAC, tRNA:V3b, tRNA:V:CAC:AE002708-c, tRNA:val3b:92Ba, tRNA[Val][[3b]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012003.html
RLID00011670	3771843	tRNA:CR30227	http://www.ncbi.nlm.nih.gov/gene/?term=3771843	"Dmel_CR30227, AE002787.trna48-TrpCCA, CR30227, Dmel\CR30227, chr2R.trna31-TrpCCA, tRNA:W:CCA:AE002787-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050227.html
RLID00011671	3771844	tRNA:F2:89BC	http://www.ncbi.nlm.nih.gov/gene/?term=3771844	"Dmel_CR31586, AE002708.trna6-PheGAA, CR31586, Dmel\CR31586, chr3R.trna12-PheGAA, phe-tRNA-2, tRNA-Phe-2, tRNA:F:GAA:AE002708-b, tRNA:phe2:89BC "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011858.html
RLID00011672	3771847	snoRNA:Psi28S-2179	http://www.ncbi.nlm.nih.gov/gene/?term=3771847	"Dmel_CR33918, CR33918, Dm-734, Dmel\CR33918, Psi28S-2719, Psi28S-2719(SnoR734), SnoR734, psi28S-2179, snoR734, snoRNA:734 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086666.html
RLID00011673	3771850	tRNA:V3b:84Dd	http://www.ncbi.nlm.nih.gov/gene/?term=3771850	"Dmel_CR31502, AE002699.trna1-ValCAC, CR31502, Dmel\CR31502, Val-3b, chr3R.trna74-ValCAC, tRNA:V3b, tRNA:V:CAC:AE002699-a, tRNA:val3b:84Dd, tRNA[Val][[3b]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012001.html
RLID00011674	3771867	tRNA:G3:35Bc	http://www.ncbi.nlm.nih.gov/gene/?term=3771867	"Dmel_CR31982, AE002690.trna17-GlyGCC, BG:DS04641.5, CR31982, Dmel\CR31982, chr2L.trna26-GlyGCC, tRNA:G:GCC:AE002690-e, tRNA:gly3:35Bc, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011864.html
RLID00011675	3771868	tRNA:G3:57BCb	http://www.ncbi.nlm.nih.gov/gene/?term=3771868	"Dmel_CR30210, AE002575.trna3-GlyGCC, CR30210, Dmel\CR30210, chr2R.trna47-GlyGCC, tRNA:G:GCC:AE002575-a, tRNA:gly3:57BCb, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011872.html
RLID00011676	3771872	Hsp67Bb	http://www.ncbi.nlm.nih.gov/gene/?term=3771872	"Dmel_CG4456, CG32041, CG4456, Dmel\CG4456, EP(3)3247, Hsp-G2, Hspg2, anon-WO0118547.50, anon-WO0140519.138, gene 2, gene-2, gene2, gene4, hsp67B, hsp67Bb, small hsp locus 67B "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011677	3771881	tRNA:G3:22BCa	http://www.ncbi.nlm.nih.gov/gene/?term=3771881	"Dmel_CR31667, AE002638.trna7-GlyGCC, CR31667, Dmel\CR31667, chr2L.trna40-GlyGCC, phe-tRNA-2, tRNA:G:GCC:AE002638-a, tRNA:gly3:22BCa, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011859.html
RLID00011678	3771882	tRNA:G3:53E	http://www.ncbi.nlm.nih.gov/gene/?term=3771882	"Dmel_CR30236, AE002787.trna44-GlyGCC, CR30236, Dmel\CR30236, chr2R.trna27-GlyGCC, tRNA:G:GCC:AE002787-b, tRNA:gly3:53E, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011867.html
RLID00011679	3771886	snoRNA:Psi28S-3342	http://www.ncbi.nlm.nih.gov/gene/?term=3771886	"Dmel_CR33787, CR33787, Dm-644, Dmel\CR33787, Psi28S-3342(SnoR644), psi28s-3342, snoR644, snoRNA:644 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086667.html
RLID00011680	3771887	tRNA:CR30212	http://www.ncbi.nlm.nih.gov/gene/?term=3771887	"Dmel_CR30212, AE002787.trna2-ArgCCT, CR30133, CR30212, Dmel\CR30212, chr2R.trna60-ArgCCT, tRNA:R:CCT:AE002787-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050212.html
RLID00011681	3771898	tRNA:CR30220	http://www.ncbi.nlm.nih.gov/gene/?term=3771898	"Dmel_CR30220, AE002787.trna55-GluCTC, CR30220, Dmel\CR30220, FBgn:0050220, chr2R.trna38-GluCTC, tRNA:E:CTC:AE002787-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050220.html
RLID00011682	3771899	tRNA:CR32456	http://www.ncbi.nlm.nih.gov/gene/?term=3771899	"Dmel_CR32456, AE002647.trna1-LeuCAG, CR32456, Dmel\CR32456, chr3L.trna32-LeuCAG, tRNA:L2:79F, tRNA:L:CAG:AE002647, tRNA:leu2:79F, tRNA[LEU], tRNA[Leu], tRNA[Leu][[2]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0266585.html
RLID00011683	3771901	snoRNA:Psi28S-1180	http://www.ncbi.nlm.nih.gov/gene/?term=3771901	"Dmel_CR33661, CR33661, Dm-535, Dmel\CR33661, Psi 28S-1180(SnoR535), chr2R:7107301..7107415, psi28s-1180, snoR535, snoRNA:535 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086658.html
RLID00011684	3771919	tRNA:Y1:28C	http://www.ncbi.nlm.nih.gov/gene/?term=3771919	"Dmel_CR31905, CR31905, Dmel\CR31905, Tyr-tRNA, tRNA-Tyr, tRNA:Y, tRNA:tyr1:28C, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012018.html
RLID00011685	3771937	tRNA:CR30257	http://www.ncbi.nlm.nih.gov/gene/?term=3771937	"Dmel_CR30257, AE002787.trna32-ThrTGT, CR30257, Dmel\CR30257, chr2R.trna14-ThrTGT, tRNA:T3:47F, tRNA:T:TGT:AE002787-c, tRNA:thr3:47F, tRNA[Thr][[3]], tRNA[[Thr]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050257.html
RLID00011686	3771962	snoRNA:Psi28S-2622	http://www.ncbi.nlm.nih.gov/gene/?term=3771962	"Dmel_CR33656, CR33656, Dm-3, Dmel\CR33656, Psi28S-2622(SnoR3), chr3L:1472428..1472587, psi28s-2622, snoR3, snoRNA:3 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086670.html
RLID00011687	3771971	tRNA:M2:48Ba	http://www.ncbi.nlm.nih.gov/gene/?term=3771971	"Dmel_CR30255, AE002787.trna34-MetCAT, CR30255, Dmel\CR30255, chr2R.trna16-MetCAT, tRNA:M:CAT:AE002787-d, tRNA:met2:48Ba "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011915.html
RLID00011688	3771986	tRNA:R2:84Fc	http://www.ncbi.nlm.nih.gov/gene/?term=3771986	"Dmel_CR31582, AE002708.trna64-ArgACG, CR31582, Dmel\CR31582, chr3R.trna70-ArgACG, tRNA:R1, tRNA:R:ACG:AE002708-c, tRNA:arg1, tRNA:arg2:84Fc, tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011961.html
RLID00011689	3771990	tRNA:V4:89BC	http://www.ncbi.nlm.nih.gov/gene/?term=3771990	"Dmel_CR31587, AE002708.trna7-ValAAC, CR31587, Dmel\CR31587, chr3R.trna13-ValAAC, tRNA-Val-4, tRNA:V4, tRNA:V:AAC:AE002708-a, tRNA:val4:89BC, tRNA[Val-AAC], tRNA[Val][[4]], val-tRNA-4, valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012011.html
RLID00011690	3772000	tRNA:V3b:84Dc	http://www.ncbi.nlm.nih.gov/gene/?term=3772000	"Dmel_CR31500, AE002699.trna2-ValCAC, CR31500, Dmel\CR31500, Val-3b, chr3R.trna75-ValCAC, tRNA:V3b, tRNA:V:CAC:AE002699-b, tRNA:val3b:84Dc, tRNA[Val][[3b]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012000.html
RLID00011691	3772005	tRNA:CR30299	http://www.ncbi.nlm.nih.gov/gene/?term=3772005	"Dmel_CR30299, AE002787.trna27-ThrAGT, CR30299, Dmel\CR30299, chr2R.trna86-ThrAGT, tRNA:T3:47F, tRNA:T:AGT:AE002787-a, tRNA:thr3:47F, tRNA[Thr][[3]], tRNA[[Thr]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050299.html
RLID00011692	3772008	tRNA:K5:29A	http://www.ncbi.nlm.nih.gov/gene/?term=3772008	"Dmel_CR31899, AE002690.trna3-LysTTT, CR31899, Dmel\CR31899, chr2L.trna11-LysTTT, lys-tRNA-5, tRNA:K5, tRNA:K:TTT:AE002690, tRNA:lys5:29A "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011902.html
RLID00011693	3772020	tRNA:R2:42Ab	http://www.ncbi.nlm.nih.gov/gene/?term=3772020	"Dmel_CR30314, AE002769.trna16-ArgACG, CR30314, Dmel\CR30314, chr2R.trna8-ArgACG, tRNA Arg, tRNA:R1, tRNA:R:ACG:AE002769-d, tRNA:arg1, tRNA:arg2:42Ab, tRNA[Arg], tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011956.html
RLID00011694	3772021	tRNA:G3:35Bd	http://www.ncbi.nlm.nih.gov/gene/?term=3772021	"Dmel_CR31981, AE002690.trna16-GlyGCC, BG:DS04641.6, CR31981, Dmel\CR31981, chr2L.trna25-GlyGCC, tRNA:G:GCC:AE002690-d, tRNA:gly3:35Bd, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011865.html
RLID00011695	3772022	tRNA:R2:42Ad	http://www.ncbi.nlm.nih.gov/gene/?term=3772022	"Dmel_CR30304, 35DArg, AE002769.trna10-ArgACG, CR30304, Dmel\CR30304, chr2R.trna1-ArgACG, tRNA:R1, tRNA:R:ACG:AE002769-b, tRNA:arg1, tRNA:arg2:42Ad, tRNA[Arg], tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011958.html
RLID00011696	3772023	tRNA:CR30406	http://www.ncbi.nlm.nih.gov/gene/?term=3772023	"Dmel_CR30406, AE002575.trna10-GlyTCC, CR30204, CR30406, Dmel\CR30406, chr2R.trna54-GlyTCC, tRNA:G:58AB, tRNA:G:TCC:AE002575-a, tRNA:gly:58AB, tRNA[Gly][[GGA]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050406.html
RLID00011697	3772026	tRNA:L2:44EF	http://www.ncbi.nlm.nih.gov/gene/?term=3772026	"Dmel_CR30292, AE002787.trna30-LeuCAG, CR30292, Dmel\CR30292, chr2R.trna12-LeuCAG, tRNA:L:CAG:AE002787, tRNA:leu2:44EF, tRNA[LEU], tRNA[Leu], tRNA[Leu][[2]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011906.html
RLID00011698	3772033	tRNA:K5:84ABa	http://www.ncbi.nlm.nih.gov/gene/?term=3772033	"Dmel_CR31486, AE002699.trna4-LysTTT, BG:DS00276.1, CR31486, Dmel\CR31486, Lys-5, chr3R.trna77-LysTTT, lys-tRNA-5, lys5:84ABa, tRNA:K5, tRNA:K:TTT:AE002699-a, tRNA:lys5:84AB "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011904.html
RLID00011699	3772036	tRNA:CR30316	http://www.ncbi.nlm.nih.gov/gene/?term=3772036	"Dmel_CR30316, AE002769.trna17-ArgACG, CR30316, Dmel\CR30316, chr2R.trna9-ArgACG, tRNA:R:ACG:AE002769-e "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050316.html
RLID00011700	3772043	tRNA:I:49Fa	http://www.ncbi.nlm.nih.gov/gene/?term=3772043	"Dmel_CR32842, AE002787.trna18-IleAAT, CR32839, CR32842, Dmel\CR32842, chr2R.trna77-IleAAT, ile-a, tRNA:I:AAT:AE002787-a, tRNA:ile:49Fa, tRNA[Ile] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011881.html
RLID00011701	3772045	tRNA:R2:84Fd	http://www.ncbi.nlm.nih.gov/gene/?term=3772045	"Dmel_CR31585, AE002708.trna65-ArgACG, CR31585, Dmel\CR31585, chr3R.trna71-ArgACG, tRNA:R1, tRNA:R:ACG:AE002708-d, tRNA:arg1, tRNA:arg2:84Fd, tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011962.html
RLID00011702	3772055	snoRNA:Psi18S-1377a	http://www.ncbi.nlm.nih.gov/gene/?term=3772055	"Dmel_CR33750, CR33750, Dm-328, Dmel\CR33750, Psi 18S-1377a(SnoR328), Psi18S-1377a, chr3R:26033540..26033785, psi18S-1377a, snoR328, snoRNA:328 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086665.html
RLID00011703	3772062	tRNA:Y1:85Ac	http://www.ncbi.nlm.nih.gov/gene/?term=3772062	"Dmel_CR31434, 85Ac, AE002708.trna59-TyrGTA, CR31434, Dmel\CR31434, Tyr-tRNA T85c, chr3R.trna65-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002708-c, tRNA:tyr1:85Ac, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012026.html
RLID00011704	3772067	tRNA:CR30229	http://www.ncbi.nlm.nih.gov/gene/?term=3772067	"Dmel_CR30229, AE002787.trna49-LeuAAG, CR30229, Dmel\CR30229, chr2R.trna32-LeuAAG, tRNA:L:AAG:AE002787-d "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050229.html
RLID00011705	3772072	tRNA:G3:55E	http://www.ncbi.nlm.nih.gov/gene/?term=3772072	"Dmel_CR30228, AE002787.trna10-GlyGCC, CR30228, Dmel\CR30228, chr2R.trna68-GlyGCC, tRNA:G:GCC:AE002787-a, tRNA:gly3:55E, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011868.html
RLID00011706	3772079	tRNA:E4:62Ad	http://www.ncbi.nlm.nih.gov/gene/?term=3772079	"Dmel_CR32323, AE002584.trna10-GluCTC, CR32323, Dmel\CR32323, chr3L.trna10-GluCTC, tRNA:E4, tRNA:E:CTC:AE002584-h, tRNA:Glu, tRNA:glu4:62Ad "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011854.html
RLID00011707	3772089	tRNA:CR30333	http://www.ncbi.nlm.nih.gov/gene/?term=3772089	"Dmel_CR30333, AE002787.trna11-PheGAA, CR30230, CR30333, Dmel\CR30333, chr2R.trna69-PheGAA, tRNA:F:GAA:AE002787-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050333.html
RLID00011708	3772090	tRNA:M3:70Fb	http://www.ncbi.nlm.nih.gov/gene/?term=3772090	"Dmel_CR32144, AE002602.trna23-MetCAT, CR32144, Dmel\CR32144, chr3L.trna28-MetCAT, tRNA:M:CAT:AE002602-b, tRNA:met3:70Fb, tRNA[Met-ATG] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011928.html
RLID00011709	3772095	tRNA:R:12Ea	http://www.ncbi.nlm.nih.gov/gene/?term=3772095	"Dmel_CR32622, AE002593.trna4-ArgTCG, CR32622, Dmel\CR32622, chrX.trna8-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002593-b, tRNA:arg1, tRNA:arg12Ea, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011948.html
RLID00011710	3772114	tRNA:G3:22BCb	http://www.ncbi.nlm.nih.gov/gene/?term=3772114	"Dmel_CR31945, AE002638.trna11-GlyGCC, CR31945, Dmel\CR31945, chr2L.trna4-GlyGCC, tRNA:G:GCC:AE002638-b, tRNA:gly3:22BCb, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011860.html
RLID00011711	3772118	tRNA:K2:42Ad	http://www.ncbi.nlm.nih.gov/gene/?term=3772118	"Dmel_CR30515, 35SLys, AE002769.trna3-LysCTT, CR30315, CR30515, Dmel\CR30515, chr2R.trna94-LysCTT, tRNA:K2, tRNA:K:CTT:AE002769-a, tRNA:lys2:42Ad, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011890.html
RLID00011712	3772119	snoRNA:Psi28S-3436b	http://www.ncbi.nlm.nih.gov/gene/?term=3772119	"Dmel_CR33799, CR33799, Dm-75, Dmel\CR33799, Psi28S-3436b, psi28S-3436b, snoR75, snoRNA:75 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086602.html
RLID00011713	3772122	tRNA:N5:42Ab	http://www.ncbi.nlm.nih.gov/gene/?term=3772122	"Dmel_CR30511, CR30308, CR30511, Dmel\CR30511, asn-tRNA, chr2R.trna4-AsnGTT, tRNA:asn5:42Ab "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011932.html
RLID00011714	3772127	tRNA:Y1:85Ab	http://www.ncbi.nlm.nih.gov/gene/?term=3772127	"Dmel_CR31433, 85Ab, AE002708.trna58-TyrGTA, CR31433, Dmel\CR31433, Tyr-tRNA T85b, chr3R.trna64-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002708-b, tRNA:tyr1:85Ab, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012025.html
RLID00011715	3772151	tRNA:CR30250	http://www.ncbi.nlm.nih.gov/gene/?term=3772151	"Dmel_CR30250, AE002787.trna20-HisGTG, CR30250, Dmel\CR30250, chr2R.trna79-HisGTG, tRNA:H:GTG:AE002787-c, tRNA[His] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050250.html
RLID00011716	3772161	tRNA:K2:42Ec	http://www.ncbi.nlm.nih.gov/gene/?term=3772161	"Dmel_CR30302, AE002778.trna2-LysCTT, CR30302, Dmel\CR30302, chr2R.trna89-LysCTT, tRNA:K2, tRNA:K:CTT:AE002778-b, tRNA:lys2:42Ec, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011894.html
RLID00011717	3772168	tRNA:CR30215	http://www.ncbi.nlm.nih.gov/gene/?term=3772168	"Dmel_CR30215, AE002787.trna53-IleAAT, CR30215, Dmel\CR30215, chr2R.trna36-IleAAT, tRNA:I:AAT:AE002787-h "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050215.html
RLID00011718	3772177	tRNA:I:49Fd	http://www.ncbi.nlm.nih.gov/gene/?term=3772177	"Dmel_CR30246, AE002787.trna39-IleAAT, CR30246, Dmel\CR30246, chr2R.trna21-IleAAT, ile-d, tRNA:I:AAT:AE002787-e, tRNA:ile:49Fd, tRNA[Ile] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011884.html
RLID00011719	3772187	tRNA:G3:56EFa	http://www.ncbi.nlm.nih.gov/gene/?term=3772187	"Dmel_CR30214, AE002787.trna58-GlyGCC, CR30137, CR30214, Dmel\CR30214, chr2R.trna42-GlyGCC, tRNA:G:GCC:AE002787-c, tRNA:gly3:56EFa, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011869.html
RLID00011720	3772194	tRNA:CR30200	http://www.ncbi.nlm.nih.gov/gene/?term=3772194	"Dmel_CR30200, AE002575.trna8-AlaCGC, CR30200, Dmel\CR30200, chr2R.trna52-AlaCGC, tRNA:A:CGC:AE002575-c, tRNA[[Ala]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050200.html
RLID00011721	3772195	tRNA:G3:28D	http://www.ncbi.nlm.nih.gov/gene/?term=3772195	"Dmel_CR31903, AE002690.trna2-GlyGCC, CR31903, Dmel\CR31903, chr2L.trna10-GlyGCC, tRNA:G:GCC:AE002690-a, tRNA:gly3:28D, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011861.html
RLID00011722	3772201	tRNA:V3b:92Bb	http://www.ncbi.nlm.nih.gov/gene/?term=3772201	"Dmel_CR31430, AE002708.trna20-ValCAC, CR31430, Dmel\CR31430, chr3R.trna26-ValCAC, tRNA:V3b, tRNA:V3b:92Bc, tRNA:V3b:92Bd, tRNA:V:CAC:AE002708-b, tRNA:val3b:92Bb, tRNA:val3b:92Bc, tRNA:val3b:92Bd, tRNA[Val][[3b]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012004.html
RLID00011723	3772202	tRNA:G3:56EFb	http://www.ncbi.nlm.nih.gov/gene/?term=3772202	"Dmel_CR30138, AE002787.trna59-GlyGCC, CR30138, Dmel\CR30138, chr2R.trna43-GlyGCC, tRNA:G:GCC:AE002787-d, tRNA:gly3:56EFb, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011870.html
RLID00011724	3772214	tRNA:N5:42Ah	http://www.ncbi.nlm.nih.gov/gene/?term=3772214	"Dmel_CR30513, AE002769.trna8-AsnGTT, Asn-tRNA-8, Asn8, CR30305, CR30513, Dmel\CR30513, chr2R.trna99-AsnGTT, tRNA:N:GTT:AE002769-d, tRNA:asn5:42Ah, tRNA[Asn] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011938.html
RLID00011725	3772226	tRNA:CR30231	http://www.ncbi.nlm.nih.gov/gene/?term=3772226	"Dmel_CR30231, AE002787.trna47-PheGAA, CR30107, CR30231, Dmel\CR30231, chr2R.trna30-PheGAA, tRNA:F:GAA:AE002787-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050231.html
RLID00011726	3772227	snoRNA:Psi18S-841a	http://www.ncbi.nlm.nih.gov/gene/?term=3772227	"Dmel_CR33765, CR33765, Dm-66, Dmel\CR33765, Psi 18S-841a(SnoR66), Psi18S-841a, psi-18S-841a, psi18S-841a, snoR66, snoRNA:66 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086669.html
RLID00011727	3772235	snoRNA:Psi28S-2876	http://www.ncbi.nlm.nih.gov/gene/?term=3772235	"Dmel_CR33646, CR33646, Dm-825, Dmel\CR33646, Psi28S-2876, Psi28S-2876(SnoR825), psi28S-2876, snoR825, snoRNA:825 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086671.html
RLID00011728	3772238	snoRNA:Or-CD2	http://www.ncbi.nlm.nih.gov/gene/?term=3772238	"Dmel_CR33636, CR33636, Dm-461, DmOr_cd2 snoRNA, DmOr_cd2(SnoR461), Dmel\CR33636, Or-CD2, chr2R:4608869..4608988, orphan-CD2, snoR461, snoRNA:461, snoRNA:Or-cd2 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086603.html
RLID00011729	3772242	tRNA:L3:49Fa	http://www.ncbi.nlm.nih.gov/gene/?term=3772242	"Dmel_CR32841, AE002787.trna17-LeuCAA, CR32840, CR32841, Dmel\CR32841, DtL[a], chr2R.trna76-LeuCAA, leu-a, tRNA:L:CAA:AE002787-a, tRNA:leu3:49Fa, tRNA[LEU], tRNA[Leu] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011909.html
RLID00011730	3772273	tRNA:CR30241	http://www.ncbi.nlm.nih.gov/gene/?term=3772273	"Dmel_CR30241, AE002787.trna15-LeuAAG, CR30241, Dmel\CR30241, chr2R.trna74-LeuAAG, tRNA:L:AAG:AE002787-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050241.html
RLID00011731	3772279	tRNA:G3:35Ba	http://www.ncbi.nlm.nih.gov/gene/?term=3772279	"Dmel_CR31977, AE002690.trna10-GlyGCC, BG:DS04641.3, CR31977, Dmel\CR31977, chr2L.trna19-GlyGCC, tRNA:G:GCC:AE002690-b, tRNA:gly3:35Ba, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011862.html
RLID00011732	3772281	tRNA:CR30225	http://www.ncbi.nlm.nih.gov/gene/?term=3772281	"Dmel_CR30225, AE002787.trna51-ValAAC, CR30225, Dmel\CR30225, chr2R.trna34-ValAAC, tRNA:V4:56D, tRNA:V:AAC:AE002787-a, tRNA:val4:56D, tRNA[Val-AAC], tRNA[Val][[4]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050225.html
RLID00011733	3772286	tRNA:CR30240	http://www.ncbi.nlm.nih.gov/gene/?term=3772286	"Dmel_CR30240, AE002787.trna43-GluTTC, CR30240, Dmel\CR30240, chr2R.trna26-GluTTC, tRNA:E4:53A, tRNA:E:TTC:AE002787-e, tRNA:Glu, tRNA:glu4:53A "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050240.html
RLID00011734	3772296	tRNA:CR30201	http://www.ncbi.nlm.nih.gov/gene/?term=3772296	"Dmel_CR30201, AE002575.trna9-SerTGA, CR30201, Dmel\CR30201, chr2R.trna53-SerTGA, chr2R:18579596..18579746, tRNA:S:TGA:AE002575-b, tRNA[[Ser]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050201.html
RLID00011735	3772297	CR32730	http://www.ncbi.nlm.nih.gov/gene/?term=3772297	"Dmel_ BcDNA:RE54930, Dmel\CR32730, MRE32 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011736	3772298	snoRNA:Or-aca5	http://www.ncbi.nlm.nih.gov/gene/?term=3772298	"Dmel_CR33637, CR33637, Dm-227, DmOr_aca5, DmOr_aca5 snoRNA, DmOr_aca5(SnoR227), Dmel\CR33637, Or-aca5, chr2R:4607488..4607590, snoR227, snoRNA:227 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086672.html
RLID00011737	3772303	tRNA:CR30232	http://www.ncbi.nlm.nih.gov/gene/?term=3772303	"Dmel_CR30232, AE002787.trna12-AlaTGC, CR30232, Dmel\CR30232, chr2R.trna70-AlaTGC, tRNA:A:TGC:AE002787-a, tRNA[[Ala]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050232.html
RLID00011738	3772309	tRNA:CR30237	http://www.ncbi.nlm.nih.gov/gene/?term=3772309	"Dmel_CR30237, AE002787.trna14-GlnCTG, CR30237, Dmel\CR30237, chr2R.trna73-GlnCTG, tRNA:Q:CTG:AE002787 "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050237.html
RLID00011739	3772310	tRNA:R2:84Fb	http://www.ncbi.nlm.nih.gov/gene/?term=3772310	"Dmel_CR31566, AE002708.trna63-ArgACG, CR31566, Dmel\CR31566, chr3R.trna69-ArgACG, tRNA:R1, tRNA:R:ACG:AE002708-b, tRNA:arg1, tRNA:arg2:84Fb, tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011960.html
RLID00011740	3772318	tRNA:M2:83F	http://www.ncbi.nlm.nih.gov/gene/?term=3772318	"Dmel_CR31310, AE002699.trna7-MetCAT, CR31310, Dmel\CR31310, Met-2, chr3R.trna80-MetCAT, tRNA:M:CAT:AE002699, tRNA:met2:83F, tRNA[[e]][Met] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011919.html
RLID00011741	3772321	tRNA:CR30235	http://www.ncbi.nlm.nih.gov/gene/?term=3772321	"Dmel_CR30235, AE002787.trna45-LeuAAG, CR30235, Dmel\CR30235, chr2R.trna28-LeuAAG, tRNA:L:AAG:AE002787-c "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050235.html
RLID00011742	3772323	snoRNA:Psi28S-3436a	http://www.ncbi.nlm.nih.gov/gene/?term=3772323	"Dmel_CR33751, CR33751, Dm-708, Dmel\CR33751, Psi 28S-3436a(SnoR708), Psi28S-3436a, psi28S-3436a, snoR708, snoRNA:708 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086668.html
RLID00011743	3772331	tRNA:G3:35Be	http://www.ncbi.nlm.nih.gov/gene/?term=3772331	"Dmel_CR31980, AE002690.trna15-GlyGCC, BG:DS04641.7, CR31980, Dmel\CR31980, chr2L.trna24-GlyGCC, tRNA:G:GCC:AE002690-c, tRNA:gly3:35Be, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011866.html
RLID00011744	3772335	tRNA:Y1:85Aa	http://www.ncbi.nlm.nih.gov/gene/?term=3772335	"Dmel_CR31435, 85Aa, AE002708.trna57-TyrGTA, CR31435, Dmel\CR31435, Tyr-tRNA T85a, chr3R.trna63-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002708-a, tRNA:tyr1:85Aa, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012024.html
RLID00011745	3772340	tRNA:CR30234	http://www.ncbi.nlm.nih.gov/gene/?term=3772340	"Dmel_CR30234, AE002787.trna13-LeuAAG, CR30234, Dmel\CR30234, chr2R.trna71-LeuAAG, tRNA:L:AAG:AE002787-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050234.html
RLID00011746	3772347	tRNA:Y1:22Fb	http://www.ncbi.nlm.nih.gov/gene/?term=3772347	"Dmel_CR31986, AE002638.trna3-TyrGTA, CR31986, Dmel\CR31986, chr2L.trna36-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002638-a, tRNA:tyr1:22Fb, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012017.html
RLID00011747	3772356	tRNA:R:19F	http://www.ncbi.nlm.nih.gov/gene/?term=3772356	"Dmel_CR32526, AE002620.trna3-ArgTCG, CR32526, Dmel\CR32526, chrX.trna16-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002620, tRNA:arg1, tRNA:arg19F, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011954.html
RLID00011748	3772362	tRNA:H:48F	http://www.ncbi.nlm.nih.gov/gene/?term=3772362	"Dmel_CR30252, AE002787.trna35-HisGTG, CR30252, Dmel\CR30252, His-tRNA, His-tRNA-gtg-gamma, chr2R.trna17-HisGTG, tRNA:H:GTG:AE002787-e, tRNA:His, tRNA:his:48F, tRNA[His-48], tRNA[His] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011878.html
RLID00011749	3772366	tRNA:M3:70Fa	http://www.ncbi.nlm.nih.gov/gene/?term=3772366	"Dmel_CR32142, AE002602.trna2-MetCAT, CR32142, Dmel\CR32142, chr3L.trna36-MetCAT, tRNA:M:CAT:AE002602-a, tRNA:met3:70Fa, tRNA[Met-ATG] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011927.html
RLID00011750	3772368	tRNA:K2:56EF	http://www.ncbi.nlm.nih.gov/gene/?term=3772368	"Dmel_CR30520, AE002787.trna56-LysCTT, CR30520, Dmel\CR30520, chr2R.trna40-LysCTT, tRNA:K2, tRNA:K:CTT:AE002787-b, tRNA:lys2:56EF, tRNA[Lys][[2]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011897.html
RLID00011751	3772369	tRNA:R:12Eb	http://www.ncbi.nlm.nih.gov/gene/?term=3772369	"Dmel_CR32620, AE002593.trna5-ArgTCG, CR32620, Dmel\CR32620, chrX.trna9-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002593-c, tRNA:arg1, tRNA:arg12Eb, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011949.html
RLID00011752	3772373	tRNA:Y1:85Ae	http://www.ncbi.nlm.nih.gov/gene/?term=3772373	"Dmel_CR31387, 85Ae, AE002708.trna61-TyrGTA, CR31387, Dmel\CR31387, Tyr-tRNA, chr3R.trna67-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002708-e, tRNA:tyr1:85Ae, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012028.html
RLID00011753	3772376	roX1	http://www.ncbi.nlm.nih.gov/gene/?term=3772376	"Dmel_CR32777, BcDNA:GH10432, CR32777, Dmel\CR32777, EG:EG0002.2, RoX1, chrX:3706836..3706970, roX, rox1 "	lncRNA	Drosophila melanogaster	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/rox1-and-rox2/
RLID00011754	3772376	roX1	http://www.ncbi.nlm.nih.gov/gene/?term=3772376	"Dmel_CR32777, BcDNA:GH10432, CR32777, Dmel\CR32777, EG:EG0002.2, RoX1, chrX:3706836..3706970, roX, rox1 "	mRNA	Drosophila melanogaster	17923096	Nucleus	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011755	3772382	Plp	http://www.ncbi.nlm.nih.gov/gene/?term=3772382	"Dmel_CG33957, AKAP450, CG13459, CG18648, CG33957, CG6735, CP309, Cp309, D-PLP, DPLP, Dmel\CG33957, Dplp, PACT, PLP, cp309, d-plp, dPLP, dplp, l(3)s2172, pPlp, plp "	mRNA	Drosophila melanogaster	17923096	Centrosome	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00011756	3772394	tRNA:K2:42Ac	http://www.ncbi.nlm.nih.gov/gene/?term=3772394	"Dmel_CR30517, 35SLys, AE002769.trna5-LysCTT, CR30310, CR30517, Dmel\CR30517, chr2R.trna96-LysCTT, tRNA:K2, tRNA:K:CTT:AE002769-c, tRNA:lys2:42Ac, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011889.html
RLID00011757	3772395	tRNA:CR30452	http://www.ncbi.nlm.nih.gov/gene/?term=3772395	"Dmel_CR30452, AE002787.trna7-MetCAT, CR30216, CR30452, Dmel\CR30452, chr2R.trna65-MetCAT, tRNA:M3:56EF, tRNA:M:CAT:AE002787-a, tRNA:met3:56EF, tRNA[Met-ATG] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050452.html
RLID00011758	3772404	tRNA:I:49Fe	http://www.ncbi.nlm.nih.gov/gene/?term=3772404	"Dmel_CR30247, AE002787.trna40-IleAAT, CR30247, Dmel\CR30247, chr2R.trna22-IleAAT, ile-e, tRNA:I:AAT:AE002787-f, tRNA:ile:49Fe, tRNA[Ile] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011885.html
RLID00011759	3772407	tRNA:CR31023	http://www.ncbi.nlm.nih.gov/gene/?term=3772407	"Dmel_CR31023, AE002708.trna32-LeuTAG, CR31023, Dmel\CR31023, chr3R.trna38-LeuTAG, tRNA:L:TAG:AE002708-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0051023.html
RLID00011760	3772413	tRNA:K5:87BC	http://www.ncbi.nlm.nih.gov/gene/?term=3772413	"Dmel_CR31197, AE002708.trna3-LysTTT, CR31197, Dmel\CR31197, chr3R.trna9-LysTTT, tRNA:K5, tRNA:K:TTT:AE002708, tRNA:lys5:87BC "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011905.html
RLID00011761	3772415	roX2	http://www.ncbi.nlm.nih.gov/gene/?term=3772415	"Dmel_CR32665, CR32665, Dmel\CR32665, RoX2, roX, rox2 "	lncRNA	Drosophila melanogaster	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/rox1-and-rox2/
RLID00011762	3772431	tRNA:K2:42Ae	http://www.ncbi.nlm.nih.gov/gene/?term=3772431	"Dmel_CR32837, 35SLys, AE002769.trna9-LysCTT, CR32837, Dmel\CR32837, chr2R.trna100-LysCTT, tRNA:K2, tRNA:K:CTT:AE002769-d, tRNA:lys2:42Ae, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011891.html
RLID00011763	3772433	tRNA:N5:42Ae	http://www.ncbi.nlm.nih.gov/gene/?term=3772433	"Dmel_CR30519, AE002769.trna1-AsnGTT, CR30318, CR30519, Dmel\CR30519, chr2R.trna92-AsnGTT, tRNA:N:GTT:AE002769-a, tRNA:asn5:42Ae "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011935.html
RLID00011764	3772444	tRNA:K2:50C	http://www.ncbi.nlm.nih.gov/gene/?term=3772444	"Dmel_CR30507, AE002787.trna16-LysCTT, CR30242, CR30507, Dmel\CR30507, chr2R.trna75-LysCTT, tRNA:K2, tRNA:K:CTT:AE002787-a, tRNA:lys2:50C, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011896.html
RLID00011765	3772446	tRNA:H:56E	http://www.ncbi.nlm.nih.gov/gene/?term=3772446	"Dmel_CR30223, AE002787.trna9-HisGTG, CR30223, Dmel\CR30223, chr2R.trna67-HisGTG, tRNA:CR30223, tRNA:H:GTG:AE002787-a, tRNA:his:56E, tRNA[His] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050223.html
RLID00011766	3772454	tRNA:CR30251	http://www.ncbi.nlm.nih.gov/gene/?term=3772454	"Dmel_CR30251, AE002787.trna19-HisGTG, CR30251, Dmel\CR30251, chr2R.trna78-HisGTG, tRNA:H:GTG:AE002787-b, tRNA[His] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050251.html
RLID00011767	3772460	tRNA:K2:42Ed	http://www.ncbi.nlm.nih.gov/gene/?term=3772460	"Dmel_CR30303, AE002778.trna1-LysCTT, CR30303, Dmel\CR30303, chr2R.trna88-LysCTT, tRNA:K2, tRNA:K:CTT:AE002778-a, tRNA:lys2:42Ed, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011895.html
RLID00011768	3772465	tRNA:N5:42Aa	http://www.ncbi.nlm.nih.gov/gene/?term=3772465	"Dmel_CR30510, AE002769.trna13-AsnGTT, CR30309, CR30510, Dmel\CR30510, asn-tRNA, chr2R.trna5-AsnGTT, tRNA:N:GTT:AE002769-f, tRNA:asn5:42Aa "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011931.html
RLID00011769	3772466	tRNA:CR30202	http://www.ncbi.nlm.nih.gov/gene/?term=3772466	"Dmel_CR30202, AE002575.trna4-SerTGA, CR30202, Dmel\CR30202, chr2R.trna48-SerTGA, tRNA:S:TGA:AE002575-a, tRNA[[Ser]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050202.html
RLID00011770	3772473	tRNA:R2:42Aa	http://www.ncbi.nlm.nih.gov/gene/?term=3772473	"Dmel_CR30514, AE002769.trna2-ArgACG, CR30317, CR30514, DROTG121, Dmel\CR30514, chr2R.trna93-ArgACG, tRNA:R1, tRNA:R:ACG:AE002769-a, tRNA:arg1, tRNA:arg2:42Aa, tRNA[Arg], tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011955.html
RLID00011771	3772480	tRNA:CR30198	http://www.ncbi.nlm.nih.gov/gene/?term=3772480	"Dmel_CR30198, AE002575.trna6-AlaCGC, CR30198, Dmel\CR30198, chr2R.trna50-AlaCGC, tRNA:A:CGC:AE002575-a, tRNA[[Ala]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050198.html
RLID00011772	3772486	tRNA:I:49Fb	http://www.ncbi.nlm.nih.gov/gene/?term=3772486	"Dmel_CR30244, AE002787.trna37-IleAAT, CR30244, Dmel\CR30244, chr2R.trna19-IleAAT, ile-b, tRNA:I:AAT:AE002787-c, tRNA:ile:49Fb, tRNA[Ile] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011882.html
RLID00011773	3772487	tRNA:CR30155	http://www.ncbi.nlm.nih.gov/gene/?term=3772487	"Dmel_CR30155, AE002787.trna60-TrpCCA, CR30155, Dmel\CR30155, chr2R.trna44-TrpCCA, tRNA:W:CCA:AE002787-c "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050155.html
RLID00011774	3772488	tRNA:CR30238	http://www.ncbi.nlm.nih.gov/gene/?term=3772488	"Dmel_CR30238, CR30238, Dmel\CR30238, chr2R.trna72-GluTTC, tRNA:E4:53A, tRNA:Glu, tRNA:glu4:53A "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050238.html
RLID00011775	3772491	tRNA:R:83AB	http://www.ncbi.nlm.nih.gov/gene/?term=3772491	"Dmel_CR31593, AE002681.trna1-ArgTCG, CR31593, Dmel\CR31593, chr3R.trna1-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002681, tRNA:arg1, tRNA:arg83AB, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011965.html
RLID00011776	3772498	tRNA:CR30254	http://www.ncbi.nlm.nih.gov/gene/?term=3772498	"Dmel_CR30254, AE002787.trna23-ArgTCT, CR30254, Dmel\CR30254, chr2R.trna82-ArgTCT, tRNA:R:TCT:AE002787 "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050254.html
RLID00011777	37724	bw	http://www.ncbi.nlm.nih.gov/gene/?term=37724	"Dmel_CG17632, CG17632, Dmel\CG17632, Pm, Su(w[co2]), Su(w[coJ]), ptm "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011778	3772507	tRNA:K2:42Ea	http://www.ncbi.nlm.nih.gov/gene/?term=3772507	"Dmel_CR30300, AE002778.trna4-LysCTT, CR30300, Dmel\CR30300, chr2R.trna91-LysCTT, tRNA:K2, tRNA:K4, tRNA:K:CTT:AE002778-d, tRNA:lys2:42Ea, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011892.html
RLID00011779	3772508	tRNA:V3b:90BC	http://www.ncbi.nlm.nih.gov/gene/?term=3772508	"Dmel_CR31572, AE002708.trna9-ValCAC, CR31572, Dmel\CR31572, Val, chr3R.trna15-ValCAC, tRNA:V3b, tRNA:V:CAC:AE002708-a, tRNA:val3b:90BC, tRNA[Val][[3b]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012002.html
RLID00011780	3772512	tRNA:CR30326	http://www.ncbi.nlm.nih.gov/gene/?term=3772512	"Dmel_CR30326, AE002787.trna52-ValAAC, CR30226, CR30326, Dmel\CR30326, chr2R.trna35-ValAAC, tRNA:V4:56D, tRNA:V:AAC:AE002787-b, tRNA:val4:56D, tRNA[Val-AAC], tRNA[Val][[4]], valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050326.html
RLID00011781	3772515	tRNA:R:12Ee	http://www.ncbi.nlm.nih.gov/gene/?term=3772515	"Dmel_CR32624, AE002593.trna1-ArgTCG, CR32624, Dmel\CR32624, chrX.trna5-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002593-a, tRNA:arg1, tRNA:arg12Ee, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011952.html
RLID00011782	3772533	tRNA:R2:84Fa	http://www.ncbi.nlm.nih.gov/gene/?term=3772533	"Dmel_CR31581, AE002708.trna62-ArgACG, CR31581, Dmel\CR31581, chr3R.trna68-ArgACG, tRNA:R1, tRNA:R:ACG:AE002708-a, tRNA:arg1, tRNA:arg2:84Fa, tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011959.html
RLID00011783	3772544	tRNA:G3:57BCa	http://www.ncbi.nlm.nih.gov/gene/?term=3772544	"Dmel_CR30207, AE002575.trna13-GlyGCC, CR30207, Dmel\CR30207, chr2R.trna57-GlyGCC, tRNA:G:GCC:AE002575-b, tRNA:gly3:57BCa, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011871.html
RLID00011784	3772547	Hsromega	http://www.ncbi.nlm.nih.gov/gene/?term=3772547	"Dmel_CR31400, CR31400, Dmel\CR31400, HSRomega, Hsr-omega, Hsr93D-n, er3, hrsomega, hsr omega, hsr-omega, hsromega, hsrw, l(3)05241, l(3)93De, l(3)er3, n(3)05241, Hsromega "	lncRNA	Drosophila melanogaster	10984439	Nucleus	Larval|adult cell	In situ hybridization	"RNA in situ hybridization studies in various larval and adult cell types of Drosophila melanogaster showed that the noncoding hsr-omega nuclear (hsromega-n) transcripts were present in the form of many small speckles. In extreme cases, only a single large cluster of hsromega-n transcripts localizing to the hsromega locus was seen in each nucleus. "
RLID00011785	3772547	Hsromega	http://www.ncbi.nlm.nih.gov/gene/?term=3772547	"Dmel_CR31400, CR31400, Dmel\CR31400, HSRomega, Hsr-omega, Hsr93D-n, er3, hrsomega, hsr omega, hsr-omega, hsromega, hsrw, l(3)05241, l(3)93De, l(3)er3, n(3)05241, Hsromega "	lncRNA	Drosophila melanogaster	1704862	Nucleus	Schneider S3 cell 	In situ hybridization	"The hsr-omega locus produces three major transcripts,all from the same transcription start site. The largest transcript,omega-1,is>10kb. It is present only in the nucleus. The other nuclear transcript,omega-2,is a 1.9-kb RNA that appears to be produced by alternative termination near either of two polyadenylation signals some 2 kb from the TATA box. The omega-2 RNA does not accumuate to any degree in the nucleus but instead appears to be rapidly spliced and transported to the cytoplasm as omega-3, the 1.2-kb cytoplasmic RNA. "
RLID00011786	3772547	Hsromega	http://www.ncbi.nlm.nih.gov/gene/?term=3772547	"Dmel_CR31400, CR31400, Dmel\CR31400, HSRomega, Hsr-omega, Hsr93D-n, er3, hrsomega, hsr omega, hsr-omega, hsromega, hsrw, l(3)05241, l(3)93De, l(3)er3, n(3)05241, Hsromega "	lncRNA	Drosophila melanogaster	17114940	Nucleus	Fly cultures 	In situ hybridization	"The hsrw-n transcripts (arrows) in wildv type eye disc cells are distributed as several small speckles in each nucleusc (B and C), but in hsrω05241mutants they are present as 2-3 larger clustersin each nucleus. "
RLID00011787	3772554	tRNA:CR30233	http://www.ncbi.nlm.nih.gov/gene/?term=3772554	"Dmel_CR30233, AE002787.trna46-AlaTGC, CR30233, Dmel\CR30233, chr2R.trna29-AlaTGC, tRNA:A:TGC:AE002787-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011879.html
RLID00011788	3772562	tRNA:CR31071	http://www.ncbi.nlm.nih.gov/gene/?term=3772562	"Dmel_CR31071, AE002708.trna35-GlnTTG, CR31071, Dmel\CR31071, chr3R.trna41-GlnTTG, tRNA:Q:TTG:AE002708-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0051071.html
RLID00011789	3772564	tRNA:R2:42Ac	http://www.ncbi.nlm.nih.gov/gene/?term=3772564	"Dmel_CR30512, AE002769.trna12-ArgACG, Arg-tRNA, CR30306, CR30512, Dmel\CR30512, chr2R.trna3-ArgACG, tRNA:R1, tRNA:R:ACG:AE002769-c, tRNA:arg1, tRNA:arg2:42Ac, tRNA[Arg][[2]], tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011957.html
RLID00011790	3772584	tRNA:R:12Ec	http://www.ncbi.nlm.nih.gov/gene/?term=3772584	"Dmel_CR32619, AE002593.trna6-ArgTCG, CR32619, Dmel\CR32619, chrX.trna10-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002593-d, tRNA:arg1, tRNA:arg12Ec, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011950.html
RLID00011791	3772585	snoRNA:Psi18S-1347c	http://www.ncbi.nlm.nih.gov/gene/?term=3772585	"Dmel_CR33633, CR33633, Dm-203, Dmel\CR33633, Psi18S-1347c, psi18S-1347c, snoR203, snoRNA:203 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086600.html
RLID00011792	3772587	tRNA:V4:70BCa	http://www.ncbi.nlm.nih.gov/gene/?term=3772587	"Dmel_CR32122, AE002602.trna3-ValAAC, CR32122, Dmel\CR32122, chr3L.trna37-ValAAC, tRNA-Val-4, tRNA:V4, tRNA:V:AAC:AE002602-a, tRNA:val4:70BCa, tRNA[Val-AAC], tRNA[Val][[4]], val-tRNA-4, valine tRNA "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012009.html
RLID00011793	3772588	tRNA:K2:42Aa	http://www.ncbi.nlm.nih.gov/gene/?term=3772588	"Dmel_CR30312, 35SLys, AE002769.trna14-LysCTT, CR30312, Dmel\CR30312, chr2R.trna6-LysCTT, tRNA-Lys, tRNA:K2, tRNA:K:CTT:AE002769-e, tRNA:lys2:42Aa, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011887.html
RLID00011794	3772589	tRNA:CR31070	http://www.ncbi.nlm.nih.gov/gene/?term=3772589	"Dmel_CR31070, AE002708.trna34-GlnTTG, CR31070, Dmel\CR31070, chr3R.trna40-GlnTTG, tRNA:Q:TTG:AE002708-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0051070.html
RLID00011795	3772595	tRNA:CR30454	http://www.ncbi.nlm.nih.gov/gene/?term=3772595	"Dmel_CR30454, AE002787.trna3-GluCTC, CR30454, Dmel\CR30454, chr2R.trna61-GluCTC, tRNA:E:CTC:AE002787-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050454.html
RLID00011796	3772598	tRNA:Y1:85Ad	http://www.ncbi.nlm.nih.gov/gene/?term=3772598	"Dmel_CR31552, 85Ad, AE002708.trna60-TyrGTA, CR31552, Dmel\CR31552, Tyr-tRNA, chr3R.trna66-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002708-d, tRNA:tyr1:85Ad, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012027.html
RLID00011797	3772599	tRNA:R:85Ca	http://www.ncbi.nlm.nih.gov/gene/?term=3772599	"Dmel_CR31443, AE002708.trna1-ArgTCG, CR31443, Dmel\CR31443, chr3R.trna7-ArgTCG, tRNA-Arg, tRNA:R1, tRNA:R:TCG:AE002708-a, tRNA:arg1, tRNA:arg85Ca, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011966.html
RLID00011798	3772615	tRNA:CR30218	http://www.ncbi.nlm.nih.gov/gene/?term=3772615	"Dmel_CR30218, AE002787.trna54-MetCAT, CR30218, Dmel\CR30218, chr2R.trna37-MetCAT, tRNA:M3:56EF, tRNA:M:CAT:AE002787-e, tRNA:met3:56EF, tRNA[Met-ATG] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050218.html
RLID00011799	3772622	tRNA:K2:42Ab	http://www.ncbi.nlm.nih.gov/gene/?term=3772622	"Dmel_CR30516, 35SLys, AE002769.trna4-LysCTT, CR30311, CR30516, Dmel\CR30516, chr2R.trna95-LysCTT, tRNA Lys, tRNA:K2, tRNA:K:CTT:AE002769-b, tRNA:lys2:42Ab, tRNA[Lys][[2]], tRNAlys "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011888.html
RLID00011800	3772623	tRNA:M2:48Bb	http://www.ncbi.nlm.nih.gov/gene/?term=3772623	"Dmel_CR32844, AE002787.trna22-MetCAT, CR32844, Dmel\CR32844, chr2R.trna81-MetCAT, tRNA:M:CAT:AE002787-b, tRNA:met2:48Bb "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011916.html
RLID00011801	3772635	tRNA:Y1:22Fa	http://www.ncbi.nlm.nih.gov/gene/?term=3772635	"Dmel_CR31987, AE002638.trna13-TyrGTA, CR31987, Dmel\CR31987, Y22Fa, chr2L.trna6-TyrGTA, tRNA-Tyr, tRNA:Y, tRNA:Y:GTA:AE002638-b, tRNA:tyr1:22Fa, tRNA[Tyr], tRNA[Tyr][[1gamma]] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0012016.html
RLID00011802	3772636	tRNA:G3:35Bb	http://www.ncbi.nlm.nih.gov/gene/?term=3772636	"Dmel_CR31978, AE002690.trna18-GlyGCC, BG:DS04641.4, CR31978, Dmel\CR31978, chr2L.trna27-GlyGCC, tRNA:G:GCC:AE002690-f, tRNA:gly3:35Bb, tRNA[Gly-GCC] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011863.html
RLID00011803	3772643	tRNA:CR30206	http://www.ncbi.nlm.nih.gov/gene/?term=3772643	"Dmel_CR30206, AE002575.trna14-TrpCCA, CR30206, Dmel\CR30206, chr2R.trna58-TrpCCA, tRNA:W:CCA:AE002575-d "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050206.html
RLID00011804	3772654	tRNA:CR30211	http://www.ncbi.nlm.nih.gov/gene/?term=3772654	"Dmel_CR30211, AE002787.trna1-TrpCCA, CR30146, CR30211, Dmel\CR30211, chr2R.trna59-TrpCCA, tRNA:W:CCA:AE002787-a "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050211.html
RLID00011805	3772657	snoRNA:Psi18S-176	http://www.ncbi.nlm.nih.gov/gene/?term=3772657	"Dmel_CR33913, CR33913, Dm-314, Dmel\CR33913, Psi 18S-176(SnoR314), psi18s-176, snoRNA:314 "	snoRNA	Drosophila melanogaster	26467478	Nucleolus	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0086659.html
RLID00011806	3772658	CG33722	http://www.ncbi.nlm.nih.gov/gene/?term=3772658	"Dmel_ CG18238, CG31188, CG31188-ORFA, Dmel\CG33722 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011807	3772659	tRNA:L3:49Fb	http://www.ncbi.nlm.nih.gov/gene/?term=3772659	"Dmel_CR30508, AE002787.trna41-LeuCAA, CR30248, CR30508, Dmel\CR30508, DtL[b], chr2R.trna23-LeuCAA, leu-b, tRNA:L:CAA:AE002787-b, tRNA:leu3:49Fb, tRNA[LEU], tRNA[Leu] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011910.html
RLID00011808	3772684	tRNA:CR30297	http://www.ncbi.nlm.nih.gov/gene/?term=3772684	"Dmel_CR30297, AE002787.trna29-IleAAT, CR30297, Dmel\CR30297, chr2R.trna11-IleAAT, tRNA:I:AAT:AE002787-b "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050297.html
RLID00011809	3772710	tRNA:R:12Ef	http://www.ncbi.nlm.nih.gov/gene/?term=3772710	"Dmel_CR32610, AE002593.trna12-ArgTCG, ArgDm, CR32610, Dmel\CR32610, chrX.trna21-ArgTCG, tRNA:R1, tRNA:R:TCG:AE002593, tRNA:arg1, tRNA:arg12DE, tRNA:arg12Ef, tRNA[arg] "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011953.html
RLID00011810	3772714	tRNA:CR30209	http://www.ncbi.nlm.nih.gov/gene/?term=3772714	"Dmel_CR30209, AE002575.trna12-TrpCCA, CR30209, Dmel\CR30209, chr2R.trna56-TrpCCA, tRNA:W:CCA:AE002575-c "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0050209.html
RLID00011811	3772717	tRNA:P:90Cb	http://www.ncbi.nlm.nih.gov/gene/?term=3772717	"Dmel_CR31571, AE002708.trna11-ProTGG, CR31571, Dmel\CR31571, Pro, chr3R.trna17-ProTGG, tRNA:P:TGG:AE002708-a, tRNA:Pro, tRNA:pro:90Cb "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011945.html
RLID00011812	3772718	tRNA:N5:42Ad	http://www.ncbi.nlm.nih.gov/gene/?term=3772718	"Dmel_CR30319, AE002769.trna18-AsnGTT, CR30319, Dmel\CR30319, chr2R.trna10-AsnGTT, tRNA:N:GTT:AE002769-g, tRNA:asn5:42Ad "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011934.html
RLID00011813	37730	pita	http://www.ncbi.nlm.nih.gov/gene/?term=37730	"Dmel_CG3941, CG3941, Dmel\CG3941, PITA, Pita, spdk "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011814	37734	apt	http://www.ncbi.nlm.nih.gov/gene/?term=37734	"Dmel_CG5393, 3041, Apt, CG5393, Dmel\CG5393, TDF, TDF/APT, l(2)03041, l(2)06369, l(2)09049, l(2)59Ea, l(2)k11531, tdf "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011815	37742	St1	http://www.ncbi.nlm.nih.gov/gene/?term=37742	"Dmel_CG5428, CG5428, Dmel\CG5428, dmST1, st1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011816	37742	St1	http://www.ncbi.nlm.nih.gov/gene/?term=37742	"Dmel_CG5428, CG5428, Dmel\CG5428, dmST1, st1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011817	37757	egl	http://www.ncbi.nlm.nih.gov/gene/?term=37757	"Dmel_CG4051, CG4051, Dmel\CG4051, EGL, Egl, egal "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011818	37757	egl	http://www.ncbi.nlm.nih.gov/gene/?term=37757	"Dmel_CG4051, CG4051, Dmel\CG4051, EGL, Egl, egal "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011819	3775	KCNK1	http://www.ncbi.nlm.nih.gov/gene/?term=3775	"DPK, HOHO, K2P1, K2p1.1, KCNO1, TWIK-1, TWIK1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011820	37761	CG5532	http://www.ncbi.nlm.nih.gov/gene/?term=37761	Dmel_ Dmel\CG5532	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011821	377677	CA13	http://www.ncbi.nlm.nih.gov/gene/?term=377677	CAXIII	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011822	377677	CA13	http://www.ncbi.nlm.nih.gov/gene/?term=377677	CAXIII	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011823	377677	CA13	http://www.ncbi.nlm.nih.gov/gene/?term=377677	CAXIII	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011824	3777	KCNK3	http://www.ncbi.nlm.nih.gov/gene/?term=3777	"K2p3.1, OAT1, PPH4, TASK, TASK-1, TBAK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011825	37782	CG4585	http://www.ncbi.nlm.nih.gov/gene/?term=37782	"Dmel_ CK00282, Dmel\CG4585, UD2, anon-60Ab, dCCS4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011826	377841	ENTPD8	http://www.ncbi.nlm.nih.gov/gene/?term=377841	"E-NTPDase, GLSR2492, NTPDase-8, UNQ2492 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011827	3778	KCNMA1	http://www.ncbi.nlm.nih.gov/gene/?term=3778	"BKTM, KCa1.1, MaxiK, SAKCA, SLO, SLO-ALPHA, SLO1, bA205K10.1, mSLO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011828	3778	KCNMA1	http://www.ncbi.nlm.nih.gov/gene/?term=3778	"BKTM, KCa1.1, MaxiK, SAKCA, SLO, SLO-ALPHA, SLO1, bA205K10.1, mSLO1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011829	3778	KCNMA1	http://www.ncbi.nlm.nih.gov/gene/?term=3778	"BKTM, KCa1.1, MaxiK, SAKCA, SLO, SLO-ALPHA, SLO1, bA205K10.1, mSLO1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00011830	377	ARF3	http://www.ncbi.nlm.nih.gov/gene/?term=377		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011831	377	ARF3	http://www.ncbi.nlm.nih.gov/gene/?term=377		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011832	37800	kcc	http://www.ncbi.nlm.nih.gov/gene/?term=37800	"Dmel_CG5594, BEST:CK01510, CG2768, CG5594, CK01510, Dmel\CG5594, E(sda)J, KCC, Line J, l(2)60A-C, mdcds_17605 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011833	37810	thoc5	http://www.ncbi.nlm.nih.gov/gene/?term=37810	"Dmel_CG2980, CG2980, Dmel\CG2980, THOC5, garm "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011834	37810	thoc5	http://www.ncbi.nlm.nih.gov/gene/?term=37810	"Dmel_CG2980, CG2980, Dmel\CG2980, THOC5, garm "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011835	3781	KCNN2	http://www.ncbi.nlm.nih.gov/gene/?term=3781	"KCa2.2, SK2, SKCA2, SKCa 2, hSK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011836	37824	Pask	http://www.ncbi.nlm.nih.gov/gene/?term=37824	"Dmel_CG3105, CG3105, Dmel\CG3105, pask "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011837	3783	KCNN4	http://www.ncbi.nlm.nih.gov/gene/?term=3783	"DHS2, IK, IK1, IKCA1, KCA4, KCa3.1, SK4, hIKCa1, hKCa4, hSK4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011838	378460	Pram1	http://www.ncbi.nlm.nih.gov/gene/?term=378460	AY665714	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011839	378466	Gm10033	http://www.ncbi.nlm.nih.gov/gene/?term=378466	"9330175B10Rik, ENSMUSG00000057924, ENSMUSG00000071083, Gm10311 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011840	378595	znf568	http://www.ncbi.nlm.nih.gov/gene/?term=378595	"XFG 5-2, fg5-2-A "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00011841	3785	KCNQ2	http://www.ncbi.nlm.nih.gov/gene/?term=3785	"BFNC, EBN, EBN1, ENB1, HNSPC, KCNA11, KV7.2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011842	378665	sox7	http://www.ncbi.nlm.nih.gov/gene/?term=378665	"sox7-A, xSox7 "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00011843	3786	KCNQ3	http://www.ncbi.nlm.nih.gov/gene/?term=3786	"BFNC2, EBN2, KV7.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011844	378702	Serf2	http://www.ncbi.nlm.nih.gov/gene/?term=378702	"C80083, Msmac1l, m4F5rel "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011845	378706	RN7SL2	http://www.ncbi.nlm.nih.gov/gene/?term=378706	"7L1C, 7L30.1, 7SL1c, RNSRP2 "	lncRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00011846	378708	APITD1	http://www.ncbi.nlm.nih.gov/gene/?term=378708	"CENP-S, CENPS, FAAP16, MHF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011847	378805	LINC-PINT	http://www.ncbi.nlm.nih.gov/gene/?term=378805	"LincRNA-Pint, MKLN1-AS1, PINT "	lncRNA	Homo sapiens	24070194	Nucleus	Colon cancer cell	qRT-PCR	"We next investigated the mechanism by which Pint regulates gene expression. We first analyzed the subcellular localization of Pint by RT-qPCR in nuclear versus cytoplasmic fractions, and found that at least 80% of the Pint RNA was present in the cell nucleus (Figure 4A). "
RLID00011848	378805	LINC-PINT	http://www.ncbi.nlm.nih.gov/gene/?term=378805	"LincRNA-Pint, MKLN1-AS1, PINT "	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00011849	378805	LINC-PINT	http://www.ncbi.nlm.nih.gov/gene/?term=378805	"LincRNA-Pint, MKLN1-AS1, PINT "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00011850	378825	LINC00162	http://www.ncbi.nlm.nih.gov/gene/?term=378825	"C21orf113, NCRNA00162, NLC1-C, NLC1C, PRED74 "	lncRNA	Homo sapiens	26222413	Nucleus	Neuron	In situ hybridization|qRT-PCR	"In contrast to LINC00162, TRAF3IP2-AS1 transcript showed a surprisingly strong nuclear localization in DA cells (Fig. 2g and h). "
RLID00011851	37882	nord	http://www.ncbi.nlm.nih.gov/gene/?term=37882	"Dmel_CG30418, CG13574, CG30418, CG3372, Dmel\CG30418, E3272 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011852	37888	betaTub60D	http://www.ncbi.nlm.nih.gov/gene/?term=37888	"Dmel_CG3401, 143391_i_at, 3t, B3t, BETA 60D, CG3401, D.m.BETA-60D, DTB3, Dmbeta3, Dmel\CG3401, T, Tub, Tub60D, beta-Tub60D, beta-Tub6D, beta-tub, beta3, beta3 TU, beta3-Tub, beta3-tubulin, beta3TUB, beta3Tub, beta3t, beta3tub, beta60C, betaTub, betaTub3, betaTub60C, beta[[3]] tubulin, beta[[3]]-Tub, beta[[3]]-tubulin, betatub60D, p50, p50/tubulin, p53, p53/tubulin "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011853	37889	slbo	http://www.ncbi.nlm.nih.gov/gene/?term=37889	"Dmel_CG4354, C/EBP, CG4354, DC/EBP, DM8, Dm-c/EBP, DmC/EBP, Dmel\CG4354, SLBO, Slbo, fs(2)7, fs(2)8, fs(2)ry7, fs(2)ry8, slobo "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011854	37889	slbo	http://www.ncbi.nlm.nih.gov/gene/?term=37889	"Dmel_CG4354, C/EBP, CG4354, DC/EBP, DM8, Dm-c/EBP, DmC/EBP, Dmel\CG4354, SLBO, Slbo, fs(2)7, fs(2)8, fs(2)ry7, fs(2)ry8, slobo "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011855	37890	bs	http://www.ncbi.nlm.nih.gov/gene/?term=37890	"Dmel_CG3411, BS, Bs, CG3411, D-SRF, DSRF, DSrf, DSrf/bs, DmSRF, Dmel\CG3411, Group IIc, Mal, SRF, Serf, Srf, ba/DSRF, bs/Dsrf, dSRF, dsrf, l(2)03267, pruned/DSRF, px, srf, bs "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011856	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011857	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/mascRNA/
RLID00011858	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	17270048	Nucleus	Fibroblast|Lymphoblast	In situ hybridization	"NEAT2 is extraordinarily well conserved for a noncoding RNA, more so than even XIST. Bioinformatic analyses of publicly available mouse transcriptome data support our findings from human cells as they confirm that the murine homologs of these noncoding RNAs are also nuclear enriched. "
RLID00011859	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	19041754	Nucleus	HeLa cell	Northern blot	"Although the long MALAT1 transcript localizes to nuclear speckles, the small RNA is found exclusively in the cytoplasm.  "
RLID00011860	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	20797886	Nucleus	HeLa cell	In situ hybridization	The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation.
RLID00011861	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	21128942	Nucleus	Brain tissue	qRT-PCR|Microarray	Table 2: Long noncoding RNAs represented on Affymetrix U133 arrays that were reliably detected in human nucleus accumbens. An lncRNA was considered reliably detected in human NAcc if at least one probe corresponding to the transcript gave a specific signal in all control subjects. No transcripts undetected in the controls were consistently detected in drug abusers. Data are collected from Talbe 2.
RLID00011862	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	22070123	Nucleus	HeLa cell	In situ hybridization	"Here, we discuss the functions of a distinct group of vertebrate-specific lncRNAs, NEAT1/MENε/β/VINC, MALAT1/NEAT2, and Gomafu/RNCR2/MIAT, which accumulate abundantly within the nucleus as RNA components of specific nuclear bodies. "
RLID00011863	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	22078878	Nucleus	HeLa cell|Kidney|Lung fibroblast	In situ hybridizationq|RT-PCR 	"While Pc2 methylation appears to be the key determinant for relocation of growth control genes, based on a methylation/demethylation dependent switch in preference for TUG1 or NEAT2 interactions, respectively, we are tempted to speculate that other ncRNAs recognize covalent modifications of other gene-associated proteins, exerting their ncRNA scaffold functions in distinct subnuclear compartments to act as sensors for many regulated signaling pathways, and as modulators of 'reading' marks on histone tails for a variety of chromodomain-containing proteins and other histone code 'readers'. "
RLID00011864	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	23073843	Nucleus	HeLa cell	Northern blot	The MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) locus is misregulated in many human cancers and produces an abundant long nuclear-retained noncoding RNA.
RLID00011865	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011866	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	24569078	Nucleus	HeLa cell	In situ hybridization	"Treatment with tubercidin also decreased steady-state MALAT1 long ncRNA, thought to be involved in the retention of SRSF1/SF2 in nuclear speckles. "
RLID00011867	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	22855529	Nucleus	Hela cell	In situ hybridization	"Nuclear speckle-associated RNAs include uridine-rich small nuclear RNAs (UsnRNAs), 7SK RNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long ncRNA (lncRNA), and a population of uncharacterized poly(A)+ RNAs (Spector and Lamond, 2011 blue right-pointing triangle). "
RLID00011868	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/Malat1/
RLID00011869	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	25332394	Ribosome	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/Malat1/
RLID00011870	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00011871	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	22355166	Nucleus	HeLa-TO cell	Fluorescence in situ hybridization	MALAT-1 noncoding RNA is localized to nuclear speckles despite its mRNA-like characteristics.
RLID00011872	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	23152763	Nucleus	HeLa cell	RT-PCR	"MALAT1 localizes to nuclear speckles and interacts with SR splicing factors, and its depletion results in the differential distribution of pre-mRNA splicing factors. "
RLID00011873	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, mascRNA "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00011874	378	ARF4	http://www.ncbi.nlm.nih.gov/gene/?term=378	ARF2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011875	378	ARF4	http://www.ncbi.nlm.nih.gov/gene/?term=378	ARF2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011876	378	ARF4	http://www.ncbi.nlm.nih.gov/gene/?term=378	ARF2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011877	379025	PSMA3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=379025		lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00011878	379025	PSMA3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=379025		lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00011879	379025	PSMA3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=379025		lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00011880	379025	PSMA3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=379025		lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00011881	3790	KCNS3	http://www.ncbi.nlm.nih.gov/gene/?term=3790	KV9.3	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011882	379101	slc18a1	http://www.ncbi.nlm.nih.gov/gene/?term=379101		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00011883	379146	ptpn9	http://www.ncbi.nlm.nih.gov/gene/?term=379146		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00011884	379181	acsbg2	http://www.ncbi.nlm.nih.gov/gene/?term=379181		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00011885	3791	KDR	http://www.ncbi.nlm.nih.gov/gene/?term=3791	"CD309, FLK1, VEGFR, VEGFR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011886	3792	KEL	http://www.ncbi.nlm.nih.gov/gene/?term=3792	"CD238, ECE3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011887	379328	midn-b	http://www.ncbi.nlm.nih.gov/gene/?term=379328		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00011888	379352	MGC53832	http://www.ncbi.nlm.nih.gov/gene/?term=379352		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00011889	379363	frmd8	http://www.ncbi.nlm.nih.gov/gene/?term=379363		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00011890	3795	KHK	http://www.ncbi.nlm.nih.gov/gene/?term=3795		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011891	3795	KHK	http://www.ncbi.nlm.nih.gov/gene/?term=3795		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011892	3797	KIF3C	http://www.ncbi.nlm.nih.gov/gene/?term=3797		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011893	37982	CG9083	http://www.ncbi.nlm.nih.gov/gene/?term=37982	Dmel_ Dmel\CG9083	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011894	379859	odc1	http://www.ncbi.nlm.nih.gov/gene/?term=379859	"odc-a, odc2, xodc2, odc1 "	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00011895	379888	ccnb1	http://www.ncbi.nlm.nih.gov/gene/?term=379888		mRNA	Xenopus laevis	11081630	Mitotic spindle	Embryo	Whole mount In Situ Hybridization	"CPEB, Maskin, and Cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. "
RLID00011896	3798	KIF5A	http://www.ncbi.nlm.nih.gov/gene/?term=3798	"D12S1889, MY050, NKHC, SPG10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011897	37998	CG2736	http://www.ncbi.nlm.nih.gov/gene/?term=37998	"Dmel_ Dmel\CG2736, cg2736 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011898	3799	KIF5B	http://www.ncbi.nlm.nih.gov/gene/?term=3799	"HEL-S-61, KINH, KNS, KNS1, UKHC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011899	3799	KIF5B	http://www.ncbi.nlm.nih.gov/gene/?term=3799	"HEL-S-61, KINH, KNS, KNS1, UKHC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011900	3799	KIF5B	http://www.ncbi.nlm.nih.gov/gene/?term=3799	"HEL-S-61, KINH, KNS, KNS1, UKHC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011901	379	ARL4D	http://www.ncbi.nlm.nih.gov/gene/?term=379	"ARF4L, ARL6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011902	37	ACADVL	http://www.ncbi.nlm.nih.gov/gene/?term=37	"ACAD6, LCACD, VLCAD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011903	37	ACADVL	http://www.ncbi.nlm.nih.gov/gene/?term=37	"ACAD6, LCACD, VLCAD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011904	380031	znf330	http://www.ncbi.nlm.nih.gov/gene/?term=380031	noa36	mRNA	Xenopus laevis	21492502	Nucleolus	Oocyte	In situ hybridization	Here we found that XNOA 36 transcript also localises to the nucleoli and in the METRO region.
RLID00011905	380031	znf330	http://www.ncbi.nlm.nih.gov/gene/?term=380031	noa36	mRNA	Xenopus laevis	21492502	Cytoplasm	Oocyte	In situ hybridization	"Extensive analysis of serial sections of oocytes derived from nine females showed a small amount of the XNOA 36 transcript in the germinal vesicle (GV) and in the mitochondrial cloud (MC), in addition to the major cytoplasmic localisation previously described (Vaccaro et al., 2010). "
RLID00011906	380031	znf330	http://www.ncbi.nlm.nih.gov/gene/?term=380031	noa36	mRNA	Xenopus laevis	21492502	Mitochondrion	Oocyte	In situ hybridization	"Extensive analysis of serial sections of oocytes derived from nine females showed a small amount of the XNOA 36 transcript in the germinal vesicle (GV) and in the mitochondrial cloud (MC), in addition to the major cytoplasmic localisation previously described (Vaccaro et al., 2010). "
RLID00011907	38016	CG13405	http://www.ncbi.nlm.nih.gov/gene/?term=38016	"Dmel_ BcDNA:AT11049, Dmel\CG13405 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011908	38017	Pdk1	http://www.ncbi.nlm.nih.gov/gene/?term=38017	"Dmel_CG1210, 1210, CG1201, CG1210, DSTPK61, Dmel\CG1210, Dstpk61, PDK, PDK-1, PDK1, PDK1/Pk61C, PK61C, Pk61C, Pk61C/PDK1, Pk61C|PDK1, Pk61c/PDK1, dPDK, dPDK-1, dPDK1, dSTPK61, pdk1, pk61c "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011909	38017	Pdk1	http://www.ncbi.nlm.nih.gov/gene/?term=38017	"Dmel_CG1210, 1210, CG1201, CG1210, DSTPK61, Dmel\CG1210, Dstpk61, PDK, PDK-1, PDK1, PDK1/Pk61C, PK61C, Pk61C, Pk61C/PDK1, Pk61C|PDK1, Pk61c/PDK1, dPDK, dPDK-1, dPDK1, dSTPK61, pdk1, pk61c "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011910	3801	KIFC3	http://www.ncbi.nlm.nih.gov/gene/?term=3801		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011911	3801	KIFC3	http://www.ncbi.nlm.nih.gov/gene/?term=3801		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011912	38021	p130CAS	http://www.ncbi.nlm.nih.gov/gene/?term=38021	"Dmel_CG1212, CG1212, CT1293, DCas, Dcas, Dmel\CG1212, p130Cas "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011913	380601	Fastkd5	http://www.ncbi.nlm.nih.gov/gene/?term=380601	"C78212, mKIAA1792 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011914	380654	Cfap54	http://www.ncbi.nlm.nih.gov/gene/?term=380654	"4930485B16Rik, Gm872 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011915	380664	Lemd3	http://www.ncbi.nlm.nih.gov/gene/?term=380664	"AI316861, Man1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011916	380686	Cnrip1	http://www.ncbi.nlm.nih.gov/gene/?term=380686	"1500041B16Rik, 3110054C06Rik, 5330437A18Rik, AI854501, C2orf32 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011917	380730	Gm884	http://www.ncbi.nlm.nih.gov/gene/?term=380730	LRRC37	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011918	38078	MED30	http://www.ncbi.nlm.nih.gov/gene/?term=38078	"Dmel_CG17183, CG17183, Dmel\CG17183, Med11/TRAP25, Med20, Med30, Trap25, dMED20, dTRAP25, med30 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011919	38078	MED30	http://www.ncbi.nlm.nih.gov/gene/?term=38078	"Dmel_CG17183, CG17183, Dmel\CG17183, Med11/TRAP25, Med20, Med30, Trap25, dMED20, dTRAP25, med30 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011920	380845	Gm904	http://www.ncbi.nlm.nih.gov/gene/?term=380845	Gm1135	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011921	38087	CG13895	http://www.ncbi.nlm.nih.gov/gene/?term=38087	Dmel_ Dmel\CG13895	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011922	380921	Dgkh	http://www.ncbi.nlm.nih.gov/gene/?term=380921	"5930402B05Rik, D130015C16, DGK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011923	38093	CG13900	http://www.ncbi.nlm.nih.gov/gene/?term=38093	"Dmel_ Dmel\CG13900, SF3B3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011924	38093	CG13900	http://www.ncbi.nlm.nih.gov/gene/?term=38093	"Dmel_ Dmel\CG13900, SF3B3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011925	38093	CG13900	http://www.ncbi.nlm.nih.gov/gene/?term=38093	"Dmel_ Dmel\CG13900, SF3B3 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011926	381045	Ccdc58	http://www.ncbi.nlm.nih.gov/gene/?term=381045	"A930007B11Rik, AI413631 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011927	381045	Ccdc58	http://www.ncbi.nlm.nih.gov/gene/?term=381045	"A930007B11Rik, AI413631 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00011928	381062	Ermard	http://www.ncbi.nlm.nih.gov/gene/?term=381062	"2210404J11Rik, 2410011O22Rik, AI448938 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011929	381062	Ermard	http://www.ncbi.nlm.nih.gov/gene/?term=381062	"2210404J11Rik, 2410011O22Rik, AI448938 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011930	381101	Dnph1	http://www.ncbi.nlm.nih.gov/gene/?term=381101	"C76683, Rcl "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011931	381201	Ap5b1	http://www.ncbi.nlm.nih.gov/gene/?term=381201	Gm962	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011932	381201	Ap5b1	http://www.ncbi.nlm.nih.gov/gene/?term=381201	Gm962	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011933	381236	Lipo1	http://www.ncbi.nlm.nih.gov/gene/?term=381236	AI747699	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011934	381306	BC055324	http://www.ncbi.nlm.nih.gov/gene/?term=381306		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011935	381308	Mnda	http://www.ncbi.nlm.nih.gov/gene/?term=381308	"A730048F03, Ifi205b, ifi-205-B "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011936	381314	Iars2	http://www.ncbi.nlm.nih.gov/gene/?term=381314	"2010002H18Rik, C79125 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011937	381319	Batf3	http://www.ncbi.nlm.nih.gov/gene/?term=381319	"9130211I03Rik, Snft "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011938	381337	Fam178b	http://www.ncbi.nlm.nih.gov/gene/?term=381337	"1700024G10Rik, Gm990 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011939	381347	4930412O13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=381347	"ENSMUSG00000075535, Gm10853 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011940	38137	Sac1	http://www.ncbi.nlm.nih.gov/gene/?term=38137	"Dmel_CG9128, CG9128, Dmel\CG9128, dsac1, l(3)2107, sac1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011941	381405	Zfp663	http://www.ncbi.nlm.nih.gov/gene/?term=381405	Gm1008	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011942	38149	CG2469	http://www.ncbi.nlm.nih.gov/gene/?term=38149	"Dmel_ Dmel\CG2469, cg2469 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011943	38149	CG2469	http://www.ncbi.nlm.nih.gov/gene/?term=38149	"Dmel_ Dmel\CG2469, cg2469 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011944	381510	Dpy19l4	http://www.ncbi.nlm.nih.gov/gene/?term=381510	"Gm1023, Narg3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011945	381511	Pdp1	http://www.ncbi.nlm.nih.gov/gene/?term=381511	"Gm1024, Ppm2c "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011946	381591	L1td1	http://www.ncbi.nlm.nih.gov/gene/?term=381591	"AA546746, AB211064, D76865, ECAT11 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011947	381598	2610005L07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=381598	"2810038F24Rik, 6720476A01Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011948	3815	KIT	http://www.ncbi.nlm.nih.gov/gene/?term=3815	"C-Kit, CD117, PBT, SCFR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011949	38160	Ptp61F	http://www.ncbi.nlm.nih.gov/gene/?term=38160	"Dmel_CG9181, BEST:LP01280, CG9178, CG9181, CPtp62A, DCPTP62A, DPTP61F, Dmel\CG9181, PTP1B, PTP61F, Ptp-61F, R-PTP 61F, anon-WO0118547.297, anon-WO0140519.98, dPTP61F, dptp61F, ptp61F "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011950	381654	C87414	http://www.ncbi.nlm.nih.gov/gene/?term=381654		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011951	38168	rho	http://www.ncbi.nlm.nih.gov/gene/?term=38168	"Dmel_CG1004, CG1004, DMRHO, DMRHOa, DMRHOb, DRORHO, Dmel\CG1004, Dmel\rho, Dmrho, RHO, RHOb, Rho, Rho-1, Rho1, Ve, iks-1, rho1, rhom, rhomboid/veinlet, ve, rho "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011952	38168	rho	http://www.ncbi.nlm.nih.gov/gene/?term=38168	"Dmel_CG1004, CG1004, DMRHO, DMRHOa, DMRHOb, DRORHO, Dmel\CG1004, Dmel\rho, Dmrho, RHO, RHOb, Rho, Rho-1, Rho1, Ve, iks-1, rho1, rhom, rhomboid/veinlet, ve, rho "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011953	38169	stet	http://www.ncbi.nlm.nih.gov/gene/?term=38169	"Dmel_CG33166, B-Rho, Brho, CG12083, CG12504, CG33166, Dmel\CG33166, Rho-2, Rho2, brho, rho-2, rho2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011954	381759	Wee2	http://www.ncbi.nlm.nih.gov/gene/?term=381759	"Gm1065, Wee1B "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011955	381760	Ssbp1	http://www.ncbi.nlm.nih.gov/gene/?term=381760	"2810480P10Rik, G630031O20Rik, MtSSB, mtDBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011956	381778	Igkv16-104	http://www.ncbi.nlm.nih.gov/gene/?term=381778	"Gm1067, rf "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011957	3817	KLK2	http://www.ncbi.nlm.nih.gov/gene/?term=3817	"KLK2A2, hGK-1, hK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011958	381801	Tatdn2	http://www.ncbi.nlm.nih.gov/gene/?term=381801	"AI646012, mKIAA0218 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011959	381816	4922502D21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=381816	"Clec2m, Gm1074, SPATA78 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011960	381845	Rnf225	http://www.ncbi.nlm.nih.gov/gene/?term=381845	"2310014L17Rik, AV237412, C77118 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011961	38185	CG12004	http://www.ncbi.nlm.nih.gov/gene/?term=38185	"Dmel_ Dmel\CG12004, anon-EST:fe3A8 "	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011962	3818	KLKB1	http://www.ncbi.nlm.nih.gov/gene/?term=3818	"KLK3, PKK, PKKD, PPK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011963	381917	Dnah3	http://www.ncbi.nlm.nih.gov/gene/?term=381917	"BC051401, Dnahc3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011964	381979	Brsk1	http://www.ncbi.nlm.nih.gov/gene/?term=381979	"Gm1100, SAD-B, SADB "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011965	381990	Zbtb2	http://www.ncbi.nlm.nih.gov/gene/?term=381990	Gm1103	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011966	381	ARF5	http://www.ncbi.nlm.nih.gov/gene/?term=381		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011967	381	ARF5	http://www.ncbi.nlm.nih.gov/gene/?term=381		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011968	381	ARF5	http://www.ncbi.nlm.nih.gov/gene/?term=381		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011969	382030	Cnep1r1	http://www.ncbi.nlm.nih.gov/gene/?term=382030	"5033428A16Rik, NEP1-R1, Tmem188 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011970	382038	Urb2	http://www.ncbi.nlm.nih.gov/gene/?term=382038	"C77575, mKIAA0133 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011971	382073	Ccdc84	http://www.ncbi.nlm.nih.gov/gene/?term=382073	"D630044F24Rik, Gm1114 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011972	382074	Foxr1	http://www.ncbi.nlm.nih.gov/gene/?term=382074	"Foxn5, Gm1115 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011973	382090	Cep162	http://www.ncbi.nlm.nih.gov/gene/?term=382090	"4922501C03Rik, mKIAA1009 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011974	382090	Cep162	http://www.ncbi.nlm.nih.gov/gene/?term=382090	"4922501C03Rik, mKIAA1009 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011975	382117	Tcaim	http://www.ncbi.nlm.nih.gov/gene/?term=382117	"D9Ertd402e, Gm1129, TOAG-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011976	38223	Cht2	http://www.ncbi.nlm.nih.gov/gene/?term=38223	"Dmel_CG2054, CG2054, CHT2, DmCHT2, Dmel\CG2054, cht2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011977	382423	Atxn7l3b	http://www.ncbi.nlm.nih.gov/gene/?term=382423	"4921506J03Rik, 6230409E21Rik, AI315132, ENSMUSG00000074747 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011978	38246	CG12025	http://www.ncbi.nlm.nih.gov/gene/?term=38246	Dmel_ Dmel\CG12025	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011979	382620	Tmed8	http://www.ncbi.nlm.nih.gov/gene/?term=382620	"6430595O10Rik, AI447224, Gm1184, Mem1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00011980	382769	Cbx3-ps4	http://www.ncbi.nlm.nih.gov/gene/?term=382769	"EG382769, Gm5196 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011981	3827	KNG1	http://www.ncbi.nlm.nih.gov/gene/?term=3827	"BDK, BK, KNG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011982	382	ARF6	http://www.ncbi.nlm.nih.gov/gene/?term=382		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011983	382	ARF6	http://www.ncbi.nlm.nih.gov/gene/?term=382		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011984	382	ARF6	http://www.ncbi.nlm.nih.gov/gene/?term=382		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011985	38313	CG1146	http://www.ncbi.nlm.nih.gov/gene/?term=38313	Dmel_ Dmel\CG1146	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011986	3831	KLC1	http://www.ncbi.nlm.nih.gov/gene/?term=3831	"KLC, KNS2, KNS2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011987	3831	KLC1	http://www.ncbi.nlm.nih.gov/gene/?term=3831	"KLC, KNS2, KNS2A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011988	3832	KIF11	http://www.ncbi.nlm.nih.gov/gene/?term=3832	"EG5, HKSP, KNSL1, MCLMR, TRIP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011989	3832	KIF11	http://www.ncbi.nlm.nih.gov/gene/?term=3832	"EG5, HKSP, KNSL1, MCLMR, TRIP5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011990	3832	KIF11	http://www.ncbi.nlm.nih.gov/gene/?term=3832	"EG5, HKSP, KNSL1, MCLMR, TRIP5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00011991	3833	KIFC1	http://www.ncbi.nlm.nih.gov/gene/?term=3833	"HSET, KNSL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011992	3833	KIFC1	http://www.ncbi.nlm.nih.gov/gene/?term=3833	"HSET, KNSL2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011993	383548	Serpinb3b	http://www.ncbi.nlm.nih.gov/gene/?term=383548	"Scca2-rs, Scca2-rs1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00011994	3835	KIF22	http://www.ncbi.nlm.nih.gov/gene/?term=3835	"A-328A3.2, KID, KNSL4, OBP, OBP-1, OBP-2, SEMDJL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011995	3835	KIF22	http://www.ncbi.nlm.nih.gov/gene/?term=3835	"A-328A3.2, KID, KNSL4, OBP, OBP-1, OBP-2, SEMDJL2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011996	38362	scramb2	http://www.ncbi.nlm.nih.gov/gene/?term=38362	"Dmel_CG1893, CG1893, Dmel\CG1893, Scramb2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00011997	3836	KPNA1	http://www.ncbi.nlm.nih.gov/gene/?term=3836	"IPOA5, NPI-1, RCH2, SRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00011998	3836	KPNA1	http://www.ncbi.nlm.nih.gov/gene/?term=3836	"IPOA5, NPI-1, RCH2, SRP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00011999	3836	KPNA1	http://www.ncbi.nlm.nih.gov/gene/?term=3836	"IPOA5, NPI-1, RCH2, SRP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012000	38376	BtbVII	http://www.ncbi.nlm.nih.gov/gene/?term=38376	"Dmel_CG43365, BTB-VII, BTBVII, BcDNA:GH07729, CG11494, CG14956, CG43365, Dmel\CG43365, Dmel_CG11494, Dmel_CG14956 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012001	3837	KPNB1	http://www.ncbi.nlm.nih.gov/gene/?term=3837	"IMB1, IPO1, IPOB, Impnb, NTF97 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012002	3837	KPNB1	http://www.ncbi.nlm.nih.gov/gene/?term=3837	"IMB1, IPO1, IPOB, Impnb, NTF97 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012003	3837	KPNB1	http://www.ncbi.nlm.nih.gov/gene/?term=3837	"IMB1, IPO1, IPOB, Impnb, NTF97 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012004	3838	KPNA2	http://www.ncbi.nlm.nih.gov/gene/?term=3838	"IPOA1, QIP2, RCH1, SRP1alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012005	3838	KPNA2	http://www.ncbi.nlm.nih.gov/gene/?term=3838	"IPOA1, QIP2, RCH1, SRP1-alpha, SRP1alpha "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012006	3838	KPNA2	http://www.ncbi.nlm.nih.gov/gene/?term=3838	"IPOA1, QIP2, RCH1, SRP1-alpha, SRP1alpha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012007	3839	KPNA3	http://www.ncbi.nlm.nih.gov/gene/?term=3839	"IPOA4, SRP1, SRP1gamma, SRP4, hSRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012008	3839	KPNA3	http://www.ncbi.nlm.nih.gov/gene/?term=3839	"IPOA4, SRP1, SRP1gamma, SRP4, hSRP1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012009	3839	KPNA3	http://www.ncbi.nlm.nih.gov/gene/?term=3839	"IPOA4, SRP1, SRP1gamma, SRP4, hSRP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012010	38400	CG17746	http://www.ncbi.nlm.nih.gov/gene/?term=38400	"Dmel_ Cg17746, Dmel\CG17746, PP2C "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012011	384061	Fndc5	http://www.ncbi.nlm.nih.gov/gene/?term=384061	"1500001L03Rik, AI836596, C87088, PeP, Pxp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012012	38407	ZnT63C	http://www.ncbi.nlm.nih.gov/gene/?term=38407	"Dmel_CG17723, CG17723, Dmel\CG17723, ZnT1, cg17723, dZnT1, dZnT63C "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012013	3840	KPNA4	http://www.ncbi.nlm.nih.gov/gene/?term=3840	"IPOA3, QIP1, SRP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012014	384281	Gatc	http://www.ncbi.nlm.nih.gov/gene/?term=384281	2010003O18Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00012015	3842	TNPO1	http://www.ncbi.nlm.nih.gov/gene/?term=3842	"IPO2, KPNB2, MIP, MIP1, TRN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012016	3842	TNPO1	http://www.ncbi.nlm.nih.gov/gene/?term=3842	"IPO2, KPNB2, MIP, MIP1, TRN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012017	3842	TNPO1	http://www.ncbi.nlm.nih.gov/gene/?term=3842	"IPO2, KPNB2, MIP, MIP1, TRN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012018	3843	IPO5	http://www.ncbi.nlm.nih.gov/gene/?term=3843	"IMB3, KPNB3, Pse1, RANBP5, imp5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012019	38446	CG12006	http://www.ncbi.nlm.nih.gov/gene/?term=38446	Dmel_ Dmel\CG12006	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012020	38446	CG12006	http://www.ncbi.nlm.nih.gov/gene/?term=38446	Dmel_ Dmel\CG12006	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012021	38446	CG12006	http://www.ncbi.nlm.nih.gov/gene/?term=38446	Dmel_ Dmel\CG12006	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012022	38459	mge	http://www.ncbi.nlm.nih.gov/gene/?term=38459	"Dmel_CG14981, BcDNA:LP07226, CG14981, Dmel\CG14981, l(3)63Fc, l(3)SH3 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012023	3845	KRAS	http://www.ncbi.nlm.nih.gov/gene/?term=3845	"C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A, K-RAS4B, KI-RAS1, KRAS2, NS, NS3, RALD, RASK2, KRAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012024	3845	KRAS	http://www.ncbi.nlm.nih.gov/gene/?term=3845	"C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A, K-RAS4B, KI-RAS1, KRAS2, NS, NS3, RALD, RASK2, KRAS "	mRNA	Homo sapiens	16178658	Mitochondrion	HDF cell	Fluorescence in situ hybridization	"Unexpectedly, we found that both K-ras and GAPDH mRNAs colocalize with mitochondria. Extensive control studies are performed, including the use of fluorescence in-situ hybridization (FISH), negative-control beacons, and the detection of colocalization of 28S ribosomal RNA with the rough endoplasmic reticulum (ER), suggesting that the mRNA localization and colocalization patterns observed in our study are true and specific.  "
RLID00012025	38465	CG10853	http://www.ncbi.nlm.nih.gov/gene/?term=38465	"Dmel_ BcDNA:LP09837, Dmel\CG10853 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012026	384783	Irs2	http://www.ncbi.nlm.nih.gov/gene/?term=384783	Irs-2	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012027	38487	CG14995	http://www.ncbi.nlm.nih.gov/gene/?term=38487	"Dmel_ CT34848, Dmel\CG14995, NEST:bs15f01, NEST:bs17f06, anon-WO0140519.252, bs17f06.y1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012028	38490	Chd64	http://www.ncbi.nlm.nih.gov/gene/?term=38490	"Dmel_CG14996, CG-14996, CG14996, CT34849, Dmel\CG14996, anon-EST:Liang-1.80, clone 1.80 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012029	38490	Chd64	http://www.ncbi.nlm.nih.gov/gene/?term=38490	"Dmel_CG14996, CG-14996, CG14996, CT34849, Dmel\CG14996, anon-EST:Liang-1.80, clone 1.80 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012030	384	ARG2	http://www.ncbi.nlm.nih.gov/gene/?term=384		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012031	384	ARG2	http://www.ncbi.nlm.nih.gov/gene/?term=384		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012032	384	ARG2	http://www.ncbi.nlm.nih.gov/gene/?term=384		mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00012033	385138	BC061237	http://www.ncbi.nlm.nih.gov/gene/?term=385138		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012034	38513	ImpL2	http://www.ncbi.nlm.nih.gov/gene/?term=38513	"Dmel_CG15009, CG15009, CT34862, Dmel\CG15009, GH28, IMP-L2, IMPL2, Imp-12, Imp-L2, ImpL-2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012035	38513	ImpL2	http://www.ncbi.nlm.nih.gov/gene/?term=38513	"Dmel_CG15009, CG15009, CT34862, Dmel\CG15009, GH28, IMP-L2, IMPL2, Imp-12, Imp-L2, ImpL-2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012036	38513	ImpL2	http://www.ncbi.nlm.nih.gov/gene/?term=38513	"Dmel_CG15009, CG15009, CT34862, Dmel\CG15009, GH28, IMP-L2, IMPL2, Imp-12, Imp-L2, ImpL-2 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012037	38520	CG11586	http://www.ncbi.nlm.nih.gov/gene/?term=38520	Dmel_ Dmel\CG11586	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012038	385211	Gm13235	http://www.ncbi.nlm.nih.gov/gene/?term=385211	OTTMUSG00000011061	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00012039	3852	KRT5	http://www.ncbi.nlm.nih.gov/gene/?term=3852	"CK5, DDD, DDD1, EBS2, K5, KRT5A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012040	385317	4930557A04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=385317		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012041	385343	Rhox1	http://www.ncbi.nlm.nih.gov/gene/?term=385343		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012042	3853	KRT6A	http://www.ncbi.nlm.nih.gov/gene/?term=3853	"CK-6C, CK-6E, CK6A, CK6C, CK6D, K6A, K6C, K6D, KRT6C, KRT6D, PC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012043	38540	slow	http://www.ncbi.nlm.nih.gov/gene/?term=38540	"Dmel_CG7447, CG7447, CT22877, Dmel\CG7447, Slow, blr, slomo "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012044	38540	slow	http://www.ncbi.nlm.nih.gov/gene/?term=38540	"Dmel_CG7447, CG7447, CT22877, Dmel\CG7447, Slow, blr, slomo "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012045	3854	KRT6B	http://www.ncbi.nlm.nih.gov/gene/?term=3854	"CK-6B, CK6B, K6B, KRTL1, PC2, PC4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012046	3855	KRT7	http://www.ncbi.nlm.nih.gov/gene/?term=3855	"CK7, K2C7, K7, SCL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012047	385658	Nxpe3	http://www.ncbi.nlm.nih.gov/gene/?term=385658	"Fam55c, Gm1752, Gm611 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012048	3856	KRT8	http://www.ncbi.nlm.nih.gov/gene/?term=3856	"CARD2, CK-8, CK8, CYK8, K2C8, K8, KO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012049	3856	KRT8	http://www.ncbi.nlm.nih.gov/gene/?term=3856	"CARD2, CK-8, CK8, CYK8, K2C8, K8, KO "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012050	3856	KRT8	http://www.ncbi.nlm.nih.gov/gene/?term=3856	"CARD2, CK-8, CK8, CYK8, K2C8, K8, KO "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012051	3858	KRT10	http://www.ncbi.nlm.nih.gov/gene/?term=3858	"BCIE, BIE, CK10, EHK, K10, KPP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012052	38599	CHMP2B	http://www.ncbi.nlm.nih.gov/gene/?term=38599	"Dmel_CG4618, CG4618, Dmel\CG4618, cg4618 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012053	38599	CHMP2B	http://www.ncbi.nlm.nih.gov/gene/?term=38599	"Dmel_CG4618, CG4618, Dmel\CG4618, cg4618 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012054	38605	shep	http://www.ncbi.nlm.nih.gov/gene/?term=38605	"Dmel_CG32423, BcDNA:LD40028, BcDNA:RH63980, CG10647, CG10649, CG10668, CG32423, Dmel\CG32423, Shep, alan, alan-shepard, anon-EST:Posey83, anon-WO0118547.198, anon-WO0172774.41, cg10668 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012055	3860	KRT13	http://www.ncbi.nlm.nih.gov/gene/?term=3860	"CK13, K13, WSN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012056	38612	Cyt-c1	http://www.ncbi.nlm.nih.gov/gene/?term=38612	"Dmel_CG4769, CG4769, CY1, Dmel\CG4769, anon-EST:Posey141 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012057	3861	KRT14	http://www.ncbi.nlm.nih.gov/gene/?term=3861	"CK14, EBS3, EBS4, K14, NFJ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012058	38639	lin-28	http://www.ncbi.nlm.nih.gov/gene/?term=38639	"Dmel_CG17334, BcDNA:RE05342, CG17334, Dmel\CG17334, EP(3)0915, lin28 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012059	38648	scny	http://www.ncbi.nlm.nih.gov/gene/?term=38648	"Dmel_CG5505, 2331, CG5505, Dmel\CG5505, Q9VRP5, Scny, USP36, Usp36, anon-WO0118547.247, dUSP36, dUsp36, et, l(3)02331, mule "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012060	38655	CG5537	http://www.ncbi.nlm.nih.gov/gene/?term=38655	"Dmel_ Dmel\CG5537, anon-EST:Posey275, uprt "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012061	38658	CG5568	http://www.ncbi.nlm.nih.gov/gene/?term=38658	Dmel_ Dmel\CG5568	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012062	386655	Eid2	http://www.ncbi.nlm.nih.gov/gene/?term=386655	"Cri2, EID-2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00012063	38668	Vap-33B	http://www.ncbi.nlm.nih.gov/gene/?term=38668	"Dmel_CG33523, BcDNA:GH09028, CG10727, CG10977, CG32410, CG33523, Dmel\CG33523 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012064	38669	Rcc1	http://www.ncbi.nlm.nih.gov/gene/?term=38669	"Dmel_CG10480, BJ1, Bj1, CG10480, CG18640 (Bj1), Dmel\CG10480, RCC1, RanGEF, dRCC1, inxs, sdt "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012065	386701	tubb5	http://www.ncbi.nlm.nih.gov/gene/?term=386701		mRNA	Danio rerio	24089481	Axon	Embryoneuron	Whole mount in situ hybridization	"Here, we provide direct evidence of the presence of mRNAs of the tubb5, nefma, and stmnb2 genes in several types of axons in the developing zebrafish (Danio rerio) embryo, with frequent accumulation at the growth cone. We further show that axonal localization of mRNA is a specific property of a subset of genes, as mRNAs of the huc and neurod genes, abundantly expressed in neurons, were not found in axons. "
RLID00012066	38697	CG10467	http://www.ncbi.nlm.nih.gov/gene/?term=38697	Dmel_ Dmel\CG10467	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012067	387032	ZKSCAN4	http://www.ncbi.nlm.nih.gov/gene/?term=387032	"P1P373C6, ZNF307, ZNF427, ZSCAN36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012068	387066	SNHG5	http://www.ncbi.nlm.nih.gov/gene/?term=387066	"C6orf160, LINC00044, NCRNA00044, U50HG, bA33E24.2 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012069	38708	Lcp65Ac	http://www.ncbi.nlm.nih.gov/gene/?term=38708	"Dmel_CG6956, CG6956, DCP2, DMLCP65c, Dmel\CG6956, LCP65Ac, Lcp-c "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012070	387103	CENPW	http://www.ncbi.nlm.nih.gov/gene/?term=387103	"C6orf173, CENP-W, CUG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012071	387103	CENPW	http://www.ncbi.nlm.nih.gov/gene/?term=387103	"C6orf173, CENP-W, CUG2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012072	387263	C6orf120	http://www.ncbi.nlm.nih.gov/gene/?term=387263		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012073	387263	C6orf120	http://www.ncbi.nlm.nih.gov/gene/?term=387263		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012074	3872	KRT17	http://www.ncbi.nlm.nih.gov/gene/?term=3872	"39.1, CK-17, K17, PC, PC2, PCHC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012075	387338	NSUN4	http://www.ncbi.nlm.nih.gov/gene/?term=387338	SHTAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012076	387338	NSUN4	http://www.ncbi.nlm.nih.gov/gene/?term=387338	SHTAP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012077	387343	Tas2r109	http://www.ncbi.nlm.nih.gov/gene/?term=387343	"T2R09, Tas2r9, mGR09, mt2r62 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012078	387349	Tas2r121	http://www.ncbi.nlm.nih.gov/gene/?term=387349	"T2R21, Tas2r13, Tas2r21, mGR21, mT2r48 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012079	387496	RASL11A	http://www.ncbi.nlm.nih.gov/gene/?term=387496		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012080	38756	CG10077	http://www.ncbi.nlm.nih.gov/gene/?term=38756	"Dmel_ BcDNA:HL01868, BcDNA:HL07910, DmRH5, Dmel\CG10077, cg10077, p90 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012081	38756	CG10077	http://www.ncbi.nlm.nih.gov/gene/?term=38756	"Dmel_ BcDNA:HL01868, BcDNA:HL07910, DmRH5, Dmel\CG10077, cg10077, p90 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012082	387590	TPTEP1	http://www.ncbi.nlm.nih.gov/gene/?term=387590	psiTPTE22	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012083	387597	ILDR2	http://www.ncbi.nlm.nih.gov/gene/?term=387597	"C1orf32, dJ782G3.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012084	387597	ILDR2	http://www.ncbi.nlm.nih.gov/gene/?term=387597	"C1orf32, dJ782G3.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012085	3875	KRT18	http://www.ncbi.nlm.nih.gov/gene/?term=3875	"CK-18, CYK18, K18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012086	3875	KRT18	http://www.ncbi.nlm.nih.gov/gene/?term=3875	"CK-18, CYK18, K18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012087	3875	KRT18	http://www.ncbi.nlm.nih.gov/gene/?term=3875	"CK-18, CYK18, K18 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012088	387609	Zhx2	http://www.ncbi.nlm.nih.gov/gene/?term=387609	"Afr-1, Afr1, Raf, mKIAA0854 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012089	38762	Mis12	http://www.ncbi.nlm.nih.gov/gene/?term=38762	"Dmel_CG18156, BcDNA:RE19545, CG18156, Dmel\CG18156, Mis-12, dm "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012090	387640	SKIDA1	http://www.ncbi.nlm.nih.gov/gene/?term=387640	"C10orf140, DLN-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012091	387640	SKIDA1	http://www.ncbi.nlm.nih.gov/gene/?term=387640	"C10orf140, DLN-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012092	387644	LINC00202-1	http://www.ncbi.nlm.nih.gov/gene/?term=387644	"C10orf51, LINC00202, NCRNA00202, bB27G4.1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012093	387733	IFITM5	http://www.ncbi.nlm.nih.gov/gene/?term=387733	"BRIL, DSPA1, Hrmp1, OI5, fragilis4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012094	38774	Cpr65Eb	http://www.ncbi.nlm.nih.gov/gene/?term=38774	"Dmel_CG8638, BcDNA:RE28679, CG8638, DmelCpr65Eb, Dmel\CG8638 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012095	387820	LOC387820	http://www.ncbi.nlm.nih.gov/gene/?term=387820		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012096	387882	C12orf75	http://www.ncbi.nlm.nih.gov/gene/?term=387882	"AGD3, OCC-1, OCC1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012097	387893	KMT5A	http://www.ncbi.nlm.nih.gov/gene/?term=387893	"PR-Set7, SET07, SET8, SETD8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012098	387914	SHISA2	http://www.ncbi.nlm.nih.gov/gene/?term=387914	"C13orf13, PRO28631, TMEM46, WGAR9166, bA398O19.2, hShisa "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012099	387914	SHISA2	http://www.ncbi.nlm.nih.gov/gene/?term=387914	"C13orf13, PRO28631, TMEM46, WGAR9166, bA398O19.2, hShisa "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012100	387921	NHLRC3	http://www.ncbi.nlm.nih.gov/gene/?term=387921		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012101	387921	NHLRC3	http://www.ncbi.nlm.nih.gov/gene/?term=387921		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012102	387	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=387	"ARH12, ARHA, RHO12, RHOH12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012103	387	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=387	"ARH12, ARHA, RHO12, RHOH12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012104	387	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=387	"ARH12, ARHA, RHO12, RHOH12 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012105	38808	CG8602	http://www.ncbi.nlm.nih.gov/gene/?term=38808	"Dmel_ Dmel\CG8602, anon-WO0118547.349, anon-WO0118547.382 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012106	3880	KRT19	http://www.ncbi.nlm.nih.gov/gene/?term=3880	"CK19, K19, K1CS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012107	3880	KRT19	http://www.ncbi.nlm.nih.gov/gene/?term=3880	"CK19, K19, K1CS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012108	388115	C15orf52	http://www.ncbi.nlm.nih.gov/gene/?term=388115		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012109	388115	C15orf52	http://www.ncbi.nlm.nih.gov/gene/?term=388115		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012110	38814	CG14834	http://www.ncbi.nlm.nih.gov/gene/?term=38814	"Dmel_ CT34650, Dmel\CG14834 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012111	388327	C17orf100	http://www.ncbi.nlm.nih.gov/gene/?term=388327		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012112	388335	TMEM220	http://www.ncbi.nlm.nih.gov/gene/?term=388335		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012113	388335	TMEM220	http://www.ncbi.nlm.nih.gov/gene/?term=388335		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012114	38842	CG8539	http://www.ncbi.nlm.nih.gov/gene/?term=38842	Dmel_ Dmel\CG8539	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012115	38842	CG8539	http://www.ncbi.nlm.nih.gov/gene/?term=38842	Dmel_ Dmel\CG8539	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012116	38842	CG8539	http://www.ncbi.nlm.nih.gov/gene/?term=38842	Dmel_ Dmel\CG8539	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012117	38845	ltl	http://www.ncbi.nlm.nih.gov/gene/?term=38845	"Dmel_CG32372, CG14836, CG32372, CG7545, CT15760, Dmel\CG32372, F, anon-EST:CL1a11, l(3)tr, lincRNA.S4366 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012118	388512	CLEC17A	http://www.ncbi.nlm.nih.gov/gene/?term=388512		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012119	388524	RPSAP58	http://www.ncbi.nlm.nih.gov/gene/?term=388524	RPSA_30_1642	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012120	388552	BLOC1S3	http://www.ncbi.nlm.nih.gov/gene/?term=388552	"BLOS3, HPS8, RP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012121	388552	BLOC1S3	http://www.ncbi.nlm.nih.gov/gene/?term=388552	"BLOS3, HPS8, RP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012122	388552	BLOC1S3	http://www.ncbi.nlm.nih.gov/gene/?term=388552	"BLOS3, HPS8, RP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012123	388555	IGFL3	http://www.ncbi.nlm.nih.gov/gene/?term=388555	UNQ483	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012124	3885565	PIP4K	http://www.ncbi.nlm.nih.gov/gene/?term=3885565	"Dmel_CG17471, CG17471, Dmel\CG17471, PIP5K 102E, dPIP4K "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012125	3885600	tRNA:N5:42Af	http://www.ncbi.nlm.nih.gov/gene/?term=3885600	"Dmel_CR33973, AE002769.trna7-AsnGTT, Asn-tRNA-6, Asn6, CR33973, Dmel\CR33973, chr2R.trna98-AsnGTT, tRNA:N:GTT:AE002769-c, tRNA:asn5:42Af "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011936.html
RLID00012126	3885637	CG33993	http://www.ncbi.nlm.nih.gov/gene/?term=3885637	"Dmel_ CG13289, CG13290, Dmel\CG33993 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012127	388564	TMEM238	http://www.ncbi.nlm.nih.gov/gene/?term=388564		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012128	3885657	tRNA:N5:42Ag	http://www.ncbi.nlm.nih.gov/gene/?term=3885657	"Dmel_CR33972, AE002769.trna11-AsnGTT, Asn-tRNA-7, Asn7, CR33972, Dmel\CR33972, chr2R.trna2-AsnGTT, tRNA:N:GTT:AE002769-e, tRNA:asn5:42Ag "	tRNA	Drosophila melanogaster	26467478	Cytosol	-	FlyBase	Data are collected from FlyBase database: http://flybase.org/reports/FBgn0011937.html
RLID00012129	388591	RNF207	http://www.ncbi.nlm.nih.gov/gene/?term=388591	C1orf188	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012130	388591	RNF207	http://www.ncbi.nlm.nih.gov/gene/?term=388591	C1orf188	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012131	38864	CG12262	http://www.ncbi.nlm.nih.gov/gene/?term=38864	"Dmel_ ACAD, CG 12262, Dmel\CG12262, MCAD "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012132	388650	FAM69A	http://www.ncbi.nlm.nih.gov/gene/?term=388650		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012133	388677	NOTCH2NL	http://www.ncbi.nlm.nih.gov/gene/?term=388677	N2N	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012134	388677	NOTCH2NL	http://www.ncbi.nlm.nih.gov/gene/?term=388677	N2N	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012135	388743	CAPN8	http://www.ncbi.nlm.nih.gov/gene/?term=388743	nCL-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012136	388753	COA6	http://www.ncbi.nlm.nih.gov/gene/?term=388753	"C1orf31, CEMCOX4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012137	388753	COA6	http://www.ncbi.nlm.nih.gov/gene/?term=388753	"C1orf31, CEMCOX4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012138	388759	C1orf229	http://www.ncbi.nlm.nih.gov/gene/?term=388759		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012139	388759	C1orf229	http://www.ncbi.nlm.nih.gov/gene/?term=388759		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012140	388789	LINC00493	http://www.ncbi.nlm.nih.gov/gene/?term=388789		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012141	388796	SNHG17	http://www.ncbi.nlm.nih.gov/gene/?term=388796		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012142	388886	LRRC75B	http://www.ncbi.nlm.nih.gov/gene/?term=388886	"C22orf36, FAM211B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012143	38888	CG8209	http://www.ncbi.nlm.nih.gov/gene/?term=38888	"Dmel_ Dmel\CG8209, anon-WO0172774.138 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012144	38890	nmo	http://www.ncbi.nlm.nih.gov/gene/?term=38890	"Dmel_CG7892, CG7892, Dmel\CG7892, NEMO, NEMO/NLK, NLK, Nemo, Nlk, Nmo, ORE-6, adk, adk1, anon-EST:Gibbs3, anon-EST:Liang-2.43, anon-WO0118547.332, anon-WO0140519.256, anon-WO0172774.138, clone 2.43 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012145	38890	nmo	http://www.ncbi.nlm.nih.gov/gene/?term=38890	"Dmel_CG7892, CG7892, Dmel\CG7892, NEMO, NEMO/NLK, NLK, Nemo, Nlk, Nmo, ORE-6, adk, adk1, anon-EST:Gibbs3, anon-EST:Liang-2.43, anon-WO0118547.332, anon-WO0140519.256, anon-WO0172774.138, clone 2.43 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012146	38890	nmo	http://www.ncbi.nlm.nih.gov/gene/?term=38890	"Dmel_CG7892, CG7892, Dmel\CG7892, NEMO, NEMO/NLK, NLK, Nemo, Nlk, Nmo, ORE-6, adk, adk1, anon-EST:Gibbs3, anon-EST:Liang-2.43, anon-WO0118547.332, anon-WO0140519.256, anon-WO0172774.138, clone 2.43 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012147	38890	nmo	http://www.ncbi.nlm.nih.gov/gene/?term=38890	"Dmel_CG7892, CG7892, Dmel\CG7892, NEMO, NEMO/NLK, NLK, Nemo, Nlk, Nmo, ORE-6, adk, adk1, anon-EST:Gibbs3, anon-EST:Liang-2.43, anon-WO0118547.332, anon-WO0140519.256, anon-WO0172774.138, clone 2.43 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012148	388931	MFSD2B	http://www.ncbi.nlm.nih.gov/gene/?term=388931		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012149	388931	MFSD2B	http://www.ncbi.nlm.nih.gov/gene/?term=388931		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012150	388951	TSPYL6	http://www.ncbi.nlm.nih.gov/gene/?term=388951		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012151	38895	Ect4	http://www.ncbi.nlm.nih.gov/gene/?term=38895	"Dmel_CG43119, CG13680, CG13681, CG34373, CG43119, CG7905, CG7915, Dmel\CG43119, Dmel_CG13680, Dmel_CG13681, Dmel_CG34373, Dmel_CG7915/SARM, anon-WO0118547.272, dsarm, ect4, Ect4 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012152	38895	Ect4	http://www.ncbi.nlm.nih.gov/gene/?term=38895	"Dmel_CG43119, CG13680, CG13681, CG34373, CG43119, CG7905, CG7915, Dmel\CG43119, Dmel_CG13680, Dmel_CG13681, Dmel_CG34373, Dmel_CG7915/SARM, anon-WO0118547.272, dsarm, ect4, Ect4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012153	388962	BOLA3	http://www.ncbi.nlm.nih.gov/gene/?term=388962	MMDS2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012154	388969	C2orf68	http://www.ncbi.nlm.nih.gov/gene/?term=388969	HCRCN81	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012155	388969	C2orf68	http://www.ncbi.nlm.nih.gov/gene/?term=388969	HCRCN81	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012156	388	RHOB	http://www.ncbi.nlm.nih.gov/gene/?term=388	"ARH6, ARHB, MST081, MSTP081, RHOH6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012157	388	RHOB	http://www.ncbi.nlm.nih.gov/gene/?term=388	"ARH6, ARHB, MST081, MSTP081, RHOH6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012158	38900	ldbr	http://www.ncbi.nlm.nih.gov/gene/?term=38900	"Dmel_CG7942, CG7942, Dmel\CG7942, Lbdr, Ldbr "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012159	38900	ldbr	http://www.ncbi.nlm.nih.gov/gene/?term=38900	"Dmel_CG7942, CG7942, Dmel\CG7942, Lbdr, Ldbr "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012160	38905	mus301	http://www.ncbi.nlm.nih.gov/gene/?term=38905	"Dmel_CG7972, CG7972, Dmel\CG7972, Mus301, SpnC, anon-WO0118547.354, cg7972, mus(3)301, spn-C, spnC "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012161	389114	ZNF662	http://www.ncbi.nlm.nih.gov/gene/?term=389114		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012162	389114	ZNF662	http://www.ncbi.nlm.nih.gov/gene/?term=389114		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012163	389136	VGLL3	http://www.ncbi.nlm.nih.gov/gene/?term=389136	"VGL-3, VGL3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012164	389136	VGLL3	http://www.ncbi.nlm.nih.gov/gene/?term=389136	"VGL-3, VGL3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012165	3891	KRT85	http://www.ncbi.nlm.nih.gov/gene/?term=3891	"ECTD4, HB5, Hb-5, K85, KRTHB5, hHb5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012166	389203	SMIM20	http://www.ncbi.nlm.nih.gov/gene/?term=389203	C4orf52	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012167	389337	ARHGEF37	http://www.ncbi.nlm.nih.gov/gene/?term=389337		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012168	389362	PSMG4	http://www.ncbi.nlm.nih.gov/gene/?term=389362	"C6orf86, PAC4, bA506K6.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012169	389362	PSMG4	http://www.ncbi.nlm.nih.gov/gene/?term=389362	"C6orf86, PAC4, bA506K6.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012170	389400	GFRAL	http://www.ncbi.nlm.nih.gov/gene/?term=389400	"C6orf144, GRAL, UNQ9356, bA360D14.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012171	389400	GFRAL	http://www.ncbi.nlm.nih.gov/gene/?term=389400	"C6orf144, GRAL, UNQ9356, bA360D14.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012172	389432	SAMD5	http://www.ncbi.nlm.nih.gov/gene/?term=389432	dJ875H10.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012173	38944	CG7182	http://www.ncbi.nlm.nih.gov/gene/?term=38944	Dmel_ Dmel\CG7182	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012174	389524	GTF2IRD2B	http://www.ncbi.nlm.nih.gov/gene/?term=389524		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012175	389524	GTF2IRD2B	http://www.ncbi.nlm.nih.gov/gene/?term=389524		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012176	389541	LAMTOR4	http://www.ncbi.nlm.nih.gov/gene/?term=389541	C7orf59	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012177	389541	LAMTOR4	http://www.ncbi.nlm.nih.gov/gene/?term=389541	C7orf59	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012178	38958	mtrm	http://www.ncbi.nlm.nih.gov/gene/?term=38958	"Dmel_CG18543, CG18543, D52, Dmel\CG18543, anon-D52, anonD52 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012179	3895	KTN1	http://www.ncbi.nlm.nih.gov/gene/?term=3895	"CG1, KNT, MU-RMS-40.19 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012180	3895	KTN1	http://www.ncbi.nlm.nih.gov/gene/?term=3895	"CG1, KNT, MU-RMS-40.19 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012181	3895	KTN1	http://www.ncbi.nlm.nih.gov/gene/?term=3895	"CG1, KNT, MU-RMS-40.19 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012182	3895	KTN1	http://www.ncbi.nlm.nih.gov/gene/?term=3895	"CG1, KNT, MU-RMS-40.19 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012183	3895	KTN1	http://www.ncbi.nlm.nih.gov/gene/?term=3895	"CG1, KNT, MU-RMS-40.19 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012184	389610	XKR5	http://www.ncbi.nlm.nih.gov/gene/?term=389610	"HARL2754, UNQ2754, XRG5A, XRG5BM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012185	389610	XKR5	http://www.ncbi.nlm.nih.gov/gene/?term=389610	"HARL2754, UNQ2754, XRG5A, XRG5BM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012186	389641	LOC389641	http://www.ncbi.nlm.nih.gov/gene/?term=389641		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012187	389643	NUGGC	http://www.ncbi.nlm.nih.gov/gene/?term=389643	"C8orf80, HMFN0672, SLIP-GC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012188	389643	NUGGC	http://www.ncbi.nlm.nih.gov/gene/?term=389643	"C8orf80, HMFN0672, SLIP-GC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012189	389677	RBM12B	http://www.ncbi.nlm.nih.gov/gene/?term=389677	MGC:33837	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012190	389812	LCN15	http://www.ncbi.nlm.nih.gov/gene/?term=389812	"PRO6093, UNQ2541 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012191	389834	LOC389834	http://www.ncbi.nlm.nih.gov/gene/?term=389834		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012192	389834	LOC389834	http://www.ncbi.nlm.nih.gov/gene/?term=389834		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012193	389840	MAP3K15	http://www.ncbi.nlm.nih.gov/gene/?term=389840	"ASK3, bA723P2.3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012194	389840	MAP3K15	http://www.ncbi.nlm.nih.gov/gene/?term=389840	"ASK3, bA723P2.3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012195	3898	LAD1	http://www.ncbi.nlm.nih.gov/gene/?term=3898	LadA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012196	3898	LAD1	http://www.ncbi.nlm.nih.gov/gene/?term=3898	LadA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012197	389906	LOC389906	http://www.ncbi.nlm.nih.gov/gene/?term=389906		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012198	38995	h	http://www.ncbi.nlm.nih.gov/gene/?term=38995	"Dmel_CG6494, 8247, CG6494, Dmel\CG6494, H, HRY, Hairy, bHLHb39, bHLHc14, brr, dDr1ry, l(3)08247, l(3)rM384, h "	mRNA	Drosophila melanogaster	15280214	Basal	Embryo	In situ hybridization	"Whereas embryos laid by wild-type mothers have an almost exclusively apical distribution of pair-rule mRNAs such as eve, ftz, h and runt (run), those laid by egl3e/eglWU50 mothers accumulate a large proportion of these transcripts in the basal cytoplasm (Fig. 5A). "
RLID00012199	38995	h	http://www.ncbi.nlm.nih.gov/gene/?term=38995	"Dmel_CG6494, 8247, CG6494, Dmel\CG6494, H, HRY, Hairy, bHLHb39, bHLHc14, brr, dDr1ry, l(3)08247, l(3)rM384, h "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012200	3899	AFF3	http://www.ncbi.nlm.nih.gov/gene/?term=3899	"LAF4, MLLT2-like "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012201	3899	AFF3	http://www.ncbi.nlm.nih.gov/gene/?term=3899	"LAF4, MLLT2-like "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012202	3899	AFF3	http://www.ncbi.nlm.nih.gov/gene/?term=3899	"LAF4, MLLT2-like "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012203	389	RHOC	http://www.ncbi.nlm.nih.gov/gene/?term=389	"ARH9, ARHC, H9, RHOH9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012204	389	RHOC	http://www.ncbi.nlm.nih.gov/gene/?term=389	"ARH9, ARHC, H9, RHOH9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012205	389	RHOC	http://www.ncbi.nlm.nih.gov/gene/?term=389	"ARH9, ARHC, H9, RHOH9 "	mRNA	Homo sapiens	25624724	Cytoplasm	Esophageal squamous cell	In situ hybridization	"RhoC mRNA expression was mainly located within the cytoplasm of the tumor cells, appearing as blue to purple particles by in situ hybridization.  "
RLID00012206	38	ACAT1	http://www.ncbi.nlm.nih.gov/gene/?term=38	"ACAT, MAT, T2, THIL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012207	390110	ACCSL	http://www.ncbi.nlm.nih.gov/gene/?term=390110		mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00012208	39018	orb2	http://www.ncbi.nlm.nih.gov/gene/?term=39018	"Dmel_CG43782, CG43113, CG43782, CG5735, Dmel\CG43782, Dmel_CG43113, Dmel_CG5735, Dmel_CG5741, Orb2, anon-WO0140519.222, cg5735 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012209	39034	smg	http://www.ncbi.nlm.nih.gov/gene/?term=39034	"Dmel_CG5263, CG5263, D69, Dmel\CG5263, SMG, Smg, anon-D69, anonD69 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012210	3903	LAIR1	http://www.ncbi.nlm.nih.gov/gene/?term=3903	"CD305, LAIR-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012211	3903	LAIR1	http://www.ncbi.nlm.nih.gov/gene/?term=3903	"CD305, LAIR-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012212	39041	Argk	http://www.ncbi.nlm.nih.gov/gene/?term=39041	"Dmel_CG32031, AK, AK-1, ARK, ArgK, CG32031, CG4929, CG5173, Dmel\CG32031, argK, argk "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012213	39085	aay	http://www.ncbi.nlm.nih.gov/gene/?term=39085	"Dmel_CG3705, 0423/14, 24661601, CG3705, Dmel\CG3705, anon-WO0172774.117 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012214	390916	NUDT19	http://www.ncbi.nlm.nih.gov/gene/?term=390916	RP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012215	390916	NUDT19	http://www.ncbi.nlm.nih.gov/gene/?term=390916	RP2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012216	390916	NUDT19	http://www.ncbi.nlm.nih.gov/gene/?term=390916	RP2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012217	39091	Nf-YA	http://www.ncbi.nlm.nih.gov/gene/?term=39091	"Dmel_CG3891, CG3891, Dmel\CG3891, NF-YA, dNF-YA "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012218	390927	ZNF793	http://www.ncbi.nlm.nih.gov/gene/?term=390927		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012219	390927	ZNF793	http://www.ncbi.nlm.nih.gov/gene/?term=390927		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012220	3909	LAMA3	http://www.ncbi.nlm.nih.gov/gene/?term=3909	"BM600, E170, LAMNA, LOCS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012221	390	RND3	http://www.ncbi.nlm.nih.gov/gene/?term=390	"ARHE, Rho8, RhoE, memB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012222	390	RND3	http://www.ncbi.nlm.nih.gov/gene/?term=390	"ARHE, Rho8, RhoE, memB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012223	391059	FRRS1	http://www.ncbi.nlm.nih.gov/gene/?term=391059	"SDFR2, SDR2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012224	391059	FRRS1	http://www.ncbi.nlm.nih.gov/gene/?term=391059	"SDFR2, SDR2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012225	39106	path	http://www.ncbi.nlm.nih.gov/gene/?term=39106	"Dmel_CG3424, CG3424, Dmel\CG3424, Path, anon-WO0118547.271, anon-WO0118547.370, pth "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012226	39106	path	http://www.ncbi.nlm.nih.gov/gene/?term=39106	"Dmel_CG3424, CG3424, Dmel\CG3424, Path, anon-WO0118547.271, anon-WO0118547.370, pth "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012227	3910	LAMA4	http://www.ncbi.nlm.nih.gov/gene/?term=3910	"CMD1JJ, LAMA3*-1, LAMA4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012228	39111	CG42673	http://www.ncbi.nlm.nih.gov/gene/?term=39111	"Dmel_ BcDNA:RE71517, BcDNA:RE71585, CG14178, CG17357, CG3179, CG32048, CG34272, Dm_3L:44995, Dmel\CG42673, Dmel_CG32048, Dmel_CG34272 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012229	3911	LAMA5	http://www.ncbi.nlm.nih.gov/gene/?term=3911		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012230	3912	LAMB1	http://www.ncbi.nlm.nih.gov/gene/?term=3912	"CLM, LIS5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012231	3912	LAMB1	http://www.ncbi.nlm.nih.gov/gene/?term=3912	"CLM, LIS5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012232	3912	LAMB1	http://www.ncbi.nlm.nih.gov/gene/?term=3912	"CLM, LIS5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012233	391356	PTRHD1	http://www.ncbi.nlm.nih.gov/gene/?term=391356	C2orf79	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012234	391358	TRMT112P6	http://www.ncbi.nlm.nih.gov/gene/?term=391358		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012235	3913	LAMB2	http://www.ncbi.nlm.nih.gov/gene/?term=3913	"LAMS, NPHS5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012236	3913	LAMB2	http://www.ncbi.nlm.nih.gov/gene/?term=3913	"LAMS, NPHS5 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00012237	39145	CG42268	http://www.ncbi.nlm.nih.gov/gene/?term=39145	"Dmel_ CG14170, CG32044, CG32046, CG6740, Dmel\CG42268, Dmel_CG32044, Dmel_CG32046 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012238	3915	LAMC1	http://www.ncbi.nlm.nih.gov/gene/?term=3915	LAMB2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012239	39169	nudE	http://www.ncbi.nlm.nih.gov/gene/?term=39169	"Dmel_CG8104, CG8104, Dmel\CG8104, D NudE "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012240	3916	LAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=3916	"CD107a, LAMPA, LGP120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012241	3916	LAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=3916	"CD107a, LAMPA, LGP120 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012242	3916	LAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=3916	"CD107a, LAMPA, LGP120 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012243	391712	TRIM61	http://www.ncbi.nlm.nih.gov/gene/?term=391712	RNF35	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012244	391	RHOG	http://www.ncbi.nlm.nih.gov/gene/?term=391	ARHG	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012245	391	RHOG	http://www.ncbi.nlm.nih.gov/gene/?term=391	ARHG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012246	3920	LAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=3920	"CD107b, LAMP-2, LAMPB, LGP110 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012247	3920	LAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=3920	"CD107b, LAMP-2, LAMPB, LGP110 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012248	3921	RPSA	http://www.ncbi.nlm.nih.gov/gene/?term=3921	"37LRP, 67LR, ICAS, LAMBR, LAMR1, LBP, LBP/p40, LRP, LRP/LR, NEM/1CHD4, SA, lamR, p40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012249	3921	RPSA	http://www.ncbi.nlm.nih.gov/gene/?term=3921	"37LRP, 67LR, ICAS, LAMBR, LAMR1, LBP, LBP/p40, LRP, LRP/LR, NEM/1CHD4, SA, lamR, p40 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012250	3921	RPSA	http://www.ncbi.nlm.nih.gov/gene/?term=3921	"37LRP, 67LR, ICAS, LAMBR, LAMR1, LBP, LBP/p40, LRP, LRP/LR, NEM/1CHD4, SA, lamR, p40 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012251	3921	RPSA	http://www.ncbi.nlm.nih.gov/gene/?term=3921	"37LRP, 67LR, ICAS, LAMBR, LAMR1, LBP, LBP/p40, LRP, LRP/LR, NEM/1CHD4, SA, lamR, p40 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012252	3921	RPSA	http://www.ncbi.nlm.nih.gov/gene/?term=3921	"37LRP, 67LR, ICAS, LAMBR, LAMR1, LBP, LBP/p40, LRP, LRP/LR, NEM/1CHD4, SA, lamR, p40 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012253	39231	CG43693	http://www.ncbi.nlm.nih.gov/gene/?term=39231	"Dmel_ CG34239, CG6327, Dmel\CG43693, Dmel_CG34239, Dmel_CG6327 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012254	39255	NaPi-III	http://www.ncbi.nlm.nih.gov/gene/?term=39255	"Dmel_CG42575, CG42575, CG7628, CR32078, Dmel\CG42575, Dmel_CG7628, Dmel_CR32078, Dromel_CG7628_FBtr0076213_mORF, dPit "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012255	3925	STMN1	http://www.ncbi.nlm.nih.gov/gene/?term=3925	"C1orf215, LAP18, Lag, OP18, PP17, PP19, PR22, SMN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012256	3925	STMN1	http://www.ncbi.nlm.nih.gov/gene/?term=3925	"C1orf215, LAP18, Lag, OP18, PP17, PP19, PR22, SMN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012257	3925	STMN1	http://www.ncbi.nlm.nih.gov/gene/?term=3925	"C1orf215, LAP18, Lag, OP18, PP17, PP19, PR22, SMN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012258	39268	CG42671	http://www.ncbi.nlm.nih.gov/gene/?term=39268	"Dmel_ CG18490, CG34240, Dmel\CG42671, Dmel_CG18490, Dmel_CG34240 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012259	3927	LASP1	http://www.ncbi.nlm.nih.gov/gene/?term=3927	"Lasp-1, MLN50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012260	3927	LASP1	http://www.ncbi.nlm.nih.gov/gene/?term=3927	"Lasp-1, MLN50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012261	3927	LASP1	http://www.ncbi.nlm.nih.gov/gene/?term=3927	"Lasp-1, MLN50 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012262	39284	chrb	http://www.ncbi.nlm.nih.gov/gene/?term=39284	"Dmel_CG7533, BcDNA:GH09771, CG7533, Dmel\CG7533, EP(3)1035, anon-EST:Liang-2.51, char, clone 2.51 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012263	392	ARHGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=392	"CDC42GAP, RHOGAP, RHOGAP1, p50rhoGAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012264	392	ARHGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=392	"CDC42GAP, RHOGAP, RHOGAP1, p50rhoGAP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012265	392	ARHGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=392	"CDC42GAP, RHOGAP, RHOGAP1, p50rhoGAP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012266	39309	RIOK1	http://www.ncbi.nlm.nih.gov/gene/?term=39309	"Dmel_CG11660, CG11660, Dmel\CG11660, Rio1, dRIOK1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012267	3930	LBR	http://www.ncbi.nlm.nih.gov/gene/?term=3930	"DHCR14B, LMN2R, PHA, TDRD18 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012268	3930	LBR	http://www.ncbi.nlm.nih.gov/gene/?term=3930	"DHCR14B, LMN2R, PHA, TDRD18 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012269	39329	Pi3K68D	http://www.ncbi.nlm.nih.gov/gene/?term=39329	"Dmel_CG11621, 11621, BcDNA:LD15217, CG11621, Cpk, Dmel\CG11621, PI(3)K, PI3K, PI3K 68D, PI3K 68_D, PI3K-68D, PI3K-68D/E, PI3K68D, PI3K_68D, PI[[3]]K, Pi3K, cpk, dPI3K, dPIK, pi3k68d "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012270	3932	LCK	http://www.ncbi.nlm.nih.gov/gene/?term=3932	"IMD22, LSK, YT16, p56lck, pp58lck "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012271	39332	Klp68D	http://www.ncbi.nlm.nih.gov/gene/?term=39332	"Dmel_CG7293, CG7293, DmKlp68D, Dmel\CG7293, KIF 3B, KIF3B, KLP-5, KLP5, KLP68D, KLP68Ddm, KLP[[64D/68D]], Klp5, klp68d "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012272	39340	CycA	http://www.ncbi.nlm.nih.gov/gene/?term=39340	"Dmel_CG5940, 0033/02, 0040/24, 0046/23, 0104/07, 0245/34, 0521/06, 0545/13, 1329/16, 1449/05, CG5940, CLD3, CYCA, Cyc A, DmcycA, Dmel\CG5940, S(rux)3B, anon-WO0140519.128, cycA, dCycA, hari, l(3)03946, l(3)183, l(3)68Ea, l(3)j3C8, l(3)neo114, l(3)rsg11, rsg11 "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012273	3934	LCN2	http://www.ncbi.nlm.nih.gov/gene/?term=3934	"24p3, MSFI, NGAL, p25 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012274	3934	LCN2	http://www.ncbi.nlm.nih.gov/gene/?term=3934	"24p3, MSFI, NGAL, p25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012275	39368	rols	http://www.ncbi.nlm.nih.gov/gene/?term=39368	"Dmel_CG32096, ANTS, Ants, CG12277, CG17155, CG32096, CG5679, Dmel\CG32096, Rol/Ants, Rols, Rols6, Rols7, anon-WO0257455.19, ants, ants/rols, l(3)08232, l(3)68Fd, l(3)j2A6\ants, rols "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012276	39368	rols	http://www.ncbi.nlm.nih.gov/gene/?term=39368	"Dmel_CG32096, ANTS, Ants, CG12277, CG17155, CG32096, CG5679, Dmel\CG32096, Rol/Ants, Rols, Rols6, Rols7, anon-WO0257455.19, ants, ants/rols, l(3)08232, l(3)68Fd, l(3)j2A6\ants, rols "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012277	3936	LCP1	http://www.ncbi.nlm.nih.gov/gene/?term=3936	"CP64, HEL-S-37, L-PLASTIN, LC64P, LPL, PLS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012278	3936	LCP1	http://www.ncbi.nlm.nih.gov/gene/?term=3936	"CP64, HEL-S-37, L-PLASTIN, LC64P, LPL, PLS2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012279	39385	RhoGAP68F	http://www.ncbi.nlm.nih.gov/gene/?term=39385	"Dmel_CG6811, CG 6811, CG6811, Dmel\CG6811, RhoGAP "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012280	3939	LDHA	http://www.ncbi.nlm.nih.gov/gene/?term=3939	"GSD11, HEL-S-133P, LDHM, PIG19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012281	3939	LDHA	http://www.ncbi.nlm.nih.gov/gene/?term=3939	"GSD11, HEL-S-133P, LDHM, PIG19 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00012282	3939	LDHA	http://www.ncbi.nlm.nih.gov/gene/?term=3939	"GSD11, HEL-S-133P, LDHM, PIG19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012283	3939	LDHA	http://www.ncbi.nlm.nih.gov/gene/?term=3939	"GSD11, HEL-S-133P, LDHM, PIG19 "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00012284	3939	LDHA	http://www.ncbi.nlm.nih.gov/gene/?term=3939	"GSD11, HEL-S-133P, LDHM, PIG19 "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00012285	3939	LDHA	http://www.ncbi.nlm.nih.gov/gene/?term=3939	"GSD11, HEL-S-133P, LDHM, PIG19 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012286	393	ARHGAP4	http://www.ncbi.nlm.nih.gov/gene/?term=393	"C1, RGC1, RhoGAP4, SrGAP4, p115 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012287	393	ARHGAP4	http://www.ncbi.nlm.nih.gov/gene/?term=393	"C1, RGC1, RhoGAP4, SrGAP4, p115 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012288	39403	CG4300	http://www.ncbi.nlm.nih.gov/gene/?term=39403	"Dmel_ Dmel\CG4300, anon-WO0118547.387 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012289	39406	CG32105	http://www.ncbi.nlm.nih.gov/gene/?term=39406	"Dmel_ CG10432, CG17615, Dmel\CG32105 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012290	39410	Ncc69	http://www.ncbi.nlm.nih.gov/gene/?term=39410	"Dmel_CG4357, BEST:CK01027, CG43567, CG4357, CK01027, Dmel\CG4357, NCC69, NKCC, mdcds_25302 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012291	394263	MUC21	http://www.ncbi.nlm.nih.gov/gene/?term=394263	"C6orf205, KMQK697, MUC-21 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012292	394273	pgat	http://www.ncbi.nlm.nih.gov/gene/?term=394273	"pat, xpat-A "	mRNA	Xenopus laevis	9622619	Germ plasm	Oocyte	In situ hybridization	One of the novel clones isolated had an RNA expression pattern consistent with it being a component of germ plasm and it was thus named Xpat (Xenopus primordial germ cell associated transcript).
RLID00012293	394273	pgat	http://www.ncbi.nlm.nih.gov/gene/?term=394273	"pat, xpat-A "	mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00012294	394273	pgat	http://www.ncbi.nlm.nih.gov/gene/?term=394273	"pat, xpat-A "	mRNA	Xenopus laevis	12401170	Vegetal	Oocyte	In situ hybridization	"Figure 2. In Situ Hybridization of Newly Discovered Localized mRNAs In situ hybridization to Xcat-2 mRNA and Xpat mRNAs demonstrates examples of RNAs that localize via the early pathway. Note that most of the RNA is associated with the mitochondrial cloud in stage I oocytes, with little background in the rest of the cytoplasm. By stage II, these RNAs have migrated with the cloud to the vegetal cortex, and there is no detectable RNA in the remaining cytoplasm. "
RLID00012295	394292	efnb1	http://www.ncbi.nlm.nih.gov/gene/?term=394292	"LERK-2, cfnd, cfns, efl3-A, ephrinB1, eplg2, lerk2, efnb1 "	mRNA	Xenopus laevis	12401170	Vegetal	Oocyte	In situ hybridization	"Xlerk, which was identified by computational screening of Xenopus 3'UTRs for highly significant clusters of CAC-containing motifs, follows the intermediate pathway in which localization to the cloud of stage I oocytes is clearly visible but there is also a high level of signal in the remaining cytoplasm. During stage II, labeling is observed both in the cloud at the cortex and in the remaining cytoplasm.. However, by stage III, no cytoplasmic labeling is detected, and all Xlerk RNA is localized to the vegetal pole. By stage IV, this labeling pattern is broader than that of either Xcat-2 or Xpat. "
RLID00012296	394292	efnb1	http://www.ncbi.nlm.nih.gov/gene/?term=394292	"LERK-2, cfnd, cfns, efl3-A, ephrinB1, eplg2, lerk2, efnb1 "	mRNA	Xenopus laevis	12401170	Cytoplasm	Oocyte	In situ hybridization	"Xlerk, which was identified by computational screening of Xenopus 3'UTRs for highly significant clusters of CAC-containing motifs, follows the intermediate pathway in which localization to the cloud of stage I oocytes is clearly visible but there is also a high level of signal in the remaining cytoplasm. During stage II, labeling is observed both in the cloud at the cortex and in the remaining cytoplasm.. However, by stage III, no cytoplasmic labeling is detected, and all Xlerk RNA is localized to the vegetal pole. By stage IV, this labeling pattern is broader than that of either Xcat-2 or Xpat. "
RLID00012297	394326	otx1	http://www.ncbi.nlm.nih.gov/gene/?term=394326	"otx1-A, xotx1 "	mRNA	Xenopus laevis	10585568	Mitochondrion	Oocyte	In situ hybridization	"Xotx1 is a Xenopus homeobox gene related to the Drosophila gene orthodenticle (otd). We previously reported that Xotx1 transcripts are already present in unfertilized egg. Here we report that maternal Xotx1 mRNA is vegetally localized during oogenesis. In stage II oocytes Xotx1 transcripts are localized within the mitochondrial cloud, in a perinuclear position; later on, they are translocated to the vegetal cortex within the mitochondrial cloud.  "
RLID00012298	394326	otx1	http://www.ncbi.nlm.nih.gov/gene/?term=394326	"otx1-A, xotx1 "	mRNA	Xenopus laevis	10585568	Vegetal	Oocyte	In situ hybridization	"Xotx1 is a Xenopus homeobox gene related to the Drosophila gene orthodenticle (otd). We previously reported that Xotx1 transcripts are already present in unfertilized egg. Here we report that maternal Xotx1 mRNA is vegetally localized during oogenesis. In stage II oocytes Xotx1 transcripts are localized within the mitochondrial cloud, in a perinuclear position; later on, they are translocated to the vegetal cortex within the mitochondrial cloud.  "
RLID00012299	39434	nst	http://www.ncbi.nlm.nih.gov/gene/?term=39434	"Dmel_CG10627, CG10627, Dmel\CG10627 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012300	39439	ara	http://www.ncbi.nlm.nih.gov/gene/?term=39439	"Dmel_CG10571, Ara, CG10571, Dmel\CG10571, IRO-C, Iro, Iro-C, IroC, iro, iro-C "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012301	39439	ara	http://www.ncbi.nlm.nih.gov/gene/?term=39439	"Dmel_CG10571, Ara, CG10571, Dmel\CG10571, IRO-C, Iro, Iro-C, IroC, iro, iro-C "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012302	394451	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=394451	"Xcat-2, nos1, xcat2, xnos1 "	mRNA	Xenopus tropicalis	14745962	Vegetal	Oocyte	In situ hybridization	"To further address this, we examined the spatial expression of Xtcat-2 mRNA. Initially, Xtcat-2 mRNA was expressed at the vegetal pole after fertilization. The cytoplasmic islands expressing Xtcat-2 mRNA were localized at the vegetal cortical region where Xcat-2 mRNA and germ plasm were also localized (Fig. 5A,H).  "
RLID00012303	394451	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=394451	"Xcat-2, nos1, xcat2, xnos1 "	mRNA	Xenopus tropicalis	14745962	Vegetal	Oocyte	In situ hybridization	"Initially, Xtcat-2 mRNA was expressed at the vegetal pole after fertilization. The cytoplasmic islands expressing Xtcat-2 mRNA were localized at the vegetal cortical region where Xcat-2 mRNA and germ plasm were also localized (Fig. 5A,H).  "
RLID00012304	394451	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=394451	"Xcat-2, nos1, xcat2, xnos1 "	mRNA	Xenopus tropicalis	14745962	Germ plasm	Oocyte	In situ hybridization	"To further address this, we examined the spatial expression of Xtcat-2 mRNA. Initially, Xtcat-2 mRNA was expressed at the vegetal pole after fertilization. The cytoplasmic islands expressing Xtcat-2 mRNA were localized at the vegetal cortical region where Xcat-2 mRNA and germ plasm were also localized (Fig. 5A,H).  "
RLID00012305	394452	vegt	http://www.ncbi.nlm.nih.gov/gene/394452	"Apod, antipodean, brat, tVegT, xombi "	mRNA	Xenopus laevis	12142022	Vegetal	Embryo	In situ hybridization	The 1280-nt 3'UTR of VegT was found to direct localization to the vegetal cortex in oocytes after injection (Fig. 1A).FIG. 1.
RLID00012306	3945	LDHB	http://www.ncbi.nlm.nih.gov/gene/?term=3945	"HEL-S-281, LDH-B, LDH-H, LDHBD, TRG-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012307	3945	LDHB	http://www.ncbi.nlm.nih.gov/gene/?term=3945	"HEL-S-281, LDH-B, LDH-HD, TRG-5, LDHB "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00012308	3945	LDHB	http://www.ncbi.nlm.nih.gov/gene/?term=3945	"HEL-S-281, LDH-B, LDH-HD, TRG-5, LDHB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012309	3945	LDHB	http://www.ncbi.nlm.nih.gov/gene/?term=3945	"HEL-S-281, LDH-B, LDH-HD, TRG-5, LDHB "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00012310	3945	LDHB	http://www.ncbi.nlm.nih.gov/gene/?term=3945	"HEL-S-281, LDH-B, LDH-HD, TRG-5, LDHB "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00012311	3945	LDHB	http://www.ncbi.nlm.nih.gov/gene/?term=3945	"HEL-S-281, LDH-B, LDH-HD, TRG-5, LDHB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012312	394676	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=394676	"Xdazl, dazh1, dazla, spgyla, dazl "	mRNA	Xenopus tropicalis	14745962	Germ plasm	Oocyte	In situ hybridization	"In this work, we showed that Xtdazl mRNA was localized in the germ plasm and was expressed from the previtellogenic oocyte to early tadpole, in testis and ovary. "
RLID00012313	394676	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=394676	"Xdazl, dazh1, dazla, spgyla, dazl "	mRNA	Xenopus tropicalis	14745962	Germ plasm	Oocyte	In situ hybridization	Xtdazl mRNA Is Expressed Specifically in the Germ Plasm and pPGCs Until the Early Tadpole Stage.
RLID00012314	39475	MICAL-like	http://www.ncbi.nlm.nih.gov/gene/?term=39475	"Dmel_CG11259, AAK93415, CG11259, Dmel\CG11259 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012315	3948	LDHC	http://www.ncbi.nlm.nih.gov/gene/?term=3948	"CT32, LDH3, LDHX "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00012316	3948	LDHC	http://www.ncbi.nlm.nih.gov/gene/?term=3948	"CT32, LDH3, LDHX "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"However, and as depicted in Figure 4 (Cytosol), mRNAs encoding GAPDH and LDH were present in both free and membrane-bound polysomes, and mRNAs encoding Hsp90 displayed a high enrichment in the membrane-bound fraction (75%-97%). Such partitioning of mRNAs to the ER was observed in 15 independent experiments using ER derived from Jurkat and J558 cells alike, thus confirming that mRNAs encoding signal-sequence-bearing proteins and mRNAs encoding cytosolic proteins are present on the ER. "
RLID00012317	3948	LDHC	http://www.ncbi.nlm.nih.gov/gene/?term=3948	"CT32, LDH3, LDHX "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00012318	3949	LDLR	http://www.ncbi.nlm.nih.gov/gene/?term=3949	"FH, FHC, LDLCQ2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012319	3949	LDLR	http://www.ncbi.nlm.nih.gov/gene/?term=3949	"FH, FHC, LDLCQ2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012320	3949	LDLR	http://www.ncbi.nlm.nih.gov/gene/?term=3949	"FH, FHC, LDLCQ2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012321	3949	LDLR	http://www.ncbi.nlm.nih.gov/gene/?term=3949	"FH, FHC, LDLCQ2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012322	394	ARHGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=394	"GFI2, RhoGAP5, p190-B, p190BRhoGAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012323	394	ARHGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=394	"GFI2, RhoGAP5, p190-B, p190BRhoGAP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012324	394	ARHGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=394	"GFI2, RhoGAP5, p190-B, p190BRhoGAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012325	394	ARHGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=394	"GFI2, RhoGAP5, p190-B, p190BRhoGAP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012326	394	ARHGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=394	"GFI2, RhoGAP5, p190-B, p190BRhoGAP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012327	395069	COL2A1	http://www.ncbi.nlm.nih.gov/gene/?term=395069		mRNA	Gallus gallus	1795029	Endoplasmic reticulum	Corneal epithelia	In situ hybridization	"In this central region of the basal cells the probes specific for αlii) and α'l(II) hybridization showed the same pattern as the DiOCe(3) staining (Fig. 4D-F), indicating that an mRNA associated with the RER was labeled. "
RLID00012328	395069	COL2A1	http://www.ncbi.nlm.nih.gov/gene/?term=395069		mRNA	Gallus gallus	8838419	Endoplasmic reticulum	Embryo	In situ hybridization	"The distribution of type II collagen mRNA was similar to the ER staining pattern, appearing to represent a subset of total ER. This study demonstrates that ER markers have a similar distribution as type II collagen mRNA in embryonic avian corneal epithelia. The type II mRNA distribution was similar to the RER pattern observed with TEM (Fig. 1) and anti-CPH immunohistochemistry (Figs. 2 and 4). "
RLID00012329	39513	cmb	http://www.ncbi.nlm.nih.gov/gene/?term=39513	"Dmel_CG10732, CG10732, Dmel\CG10732, NEST:bs28e06 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012330	39540	ssp2	http://www.ncbi.nlm.nih.gov/gene/?term=39540	"Dmel_CG9028, CG9028, Dmel\CG9028, Ssp2 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012331	395442	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=395442		mRNA	Gallus gallus	21146522	Perinuclear	Fibroblast	Fluorescence in situ hybridization	"Figure 1A: Endogenous Arp2 mRNA (green) and Dia1 mRNA (red) are localized in the protrusions (indicated by arrows) and perinuclear region in the CEFs, respectively. Note that protrusions in this report are defined broadly to include lamellae and lamellipodia. "
RLID00012332	395442	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=395442		mRNA	Gallus gallus	21146522	Lamellipodium	Fibroblast	Fluorescence in situ hybridization	"Figure 1A: Endogenous Arp2 mRNA (green) and Dia1 mRNA (red) are localized in the protrusions (indicated by arrows) and perinuclear region in the CEFs, respectively. Note that protrusions in this report are defined broadly to include lamellae and lamellipodia. "
RLID00012333	395442	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=395442		mRNA	Gallus gallus	21266463	Endoplasmic reticulum	Fibroblast	RT-PCR	The combined results from our multiple approaches consistently demonstrate that Dia1 mRNA is localized on the ER membrane. Fig. 3. Dia1 mRNA is localized on the ER.
RLID00012334	39547	26-29-p	http://www.ncbi.nlm.nih.gov/gene/?term=39547	"Dmel_CG8947, 26/29kD-proteinase, CG8947, Dmel\CG8947, anon-SAGE:Wang-123, l(3)s3635 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012335	3954	LETM1	http://www.ncbi.nlm.nih.gov/gene/?term=3954		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012336	3954	LETM1	http://www.ncbi.nlm.nih.gov/gene/?term=3954		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012337	3954	LETM1	http://www.ncbi.nlm.nih.gov/gene/?term=3954		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012338	3954	LETM1	http://www.ncbi.nlm.nih.gov/gene/?term=3954		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012339	3955	LFNG	http://www.ncbi.nlm.nih.gov/gene/?term=3955	SCDO3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012340	3956	LGALS1	http://www.ncbi.nlm.nih.gov/gene/?term=3956	"GAL1, GBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012341	3956	LGALS1	http://www.ncbi.nlm.nih.gov/gene/?term=3956	"GAL1, GBP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012342	39572	nuf	http://www.ncbi.nlm.nih.gov/gene/?term=39572	"Dmel_CG33991, CG32140, CG33991, CG7867, CIP-D2, Cy3-23, D2, Dmel\CG33991, EP3077, FIP3, NUF, Nuf, Nuf1, Nuf2p, anon-D2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012343	39572	nuf	http://www.ncbi.nlm.nih.gov/gene/?term=39572	"Dmel_CG33991, CG32140, CG33991, CG7867, CIP-D2, Cy3-23, D2, Dmel\CG33991, EP3077, FIP3, NUF, Nuf, Nuf1, Nuf2p, anon-D2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012344	39583	bbg	http://www.ncbi.nlm.nih.gov/gene/?term=39583	"Dmel_CG42230, BBG, C96, CG42230, CG9587, CG9598, Dmel\CG42230, Dmel_CG9587, Dmel_CG9598 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012345	39583	bbg	http://www.ncbi.nlm.nih.gov/gene/?term=39583	"Dmel_CG42230, BBG, C96, CG42230, CG9587, CG9598, Dmel\CG42230, Dmel_CG9587, Dmel_CG9598 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012346	39583	bbg	http://www.ncbi.nlm.nih.gov/gene/?term=39583	"Dmel_CG42230, BBG, C96, CG42230, CG9587, CG9598, Dmel\CG42230, Dmel_CG9587, Dmel_CG9598 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012347	39583	bbg	http://www.ncbi.nlm.nih.gov/gene/?term=39583	"Dmel_CG42230, BBG, C96, CG42230, CG9587, CG9598, Dmel\CG42230, Dmel_CG9587, Dmel_CG9598 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012348	3958	LGALS3	http://www.ncbi.nlm.nih.gov/gene/?term=3958	"CBP35, GAL3, GALBP, GALIG, L31, LGALS2, MAC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012349	3958	LGALS3	http://www.ncbi.nlm.nih.gov/gene/?term=3958	"CBP35, GAL3, GALBP, GALIG, L31, LGALS2, MAC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012350	39592	shd	http://www.ncbi.nlm.nih.gov/gene/?term=39592	"Dmel_CG13478, 314a1, CG13478, CYP314A1, Cyp314a1, Dmel\CG13478, cyp314a1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012351	3959	LGALS3BP	http://www.ncbi.nlm.nih.gov/gene/?term=3959	"90K, BTBD17B, CyCAP, M2BP, MAC-2-BP, TANGO10B, gp90 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012352	3959	LGALS3BP	http://www.ncbi.nlm.nih.gov/gene/?term=3959	"90K, BTBD17B, CyCAP, M2BP, MAC-2-BP, TANGO10B, gp90 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012353	3959	LGALS3BP	http://www.ncbi.nlm.nih.gov/gene/?term=3959	"90K, BTBD17B, CyCAP, M2BP, MAC-2-BP, TANGO10B, gp90 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012354	395	ARHGAP6	http://www.ncbi.nlm.nih.gov/gene/?term=395	"RHOGAP6, RHOGAPX-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012355	3960	LGALS4	http://www.ncbi.nlm.nih.gov/gene/?term=3960	"GAL4, L36LBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012356	3960	LGALS4	http://www.ncbi.nlm.nih.gov/gene/?term=3960	"GAL4, L36LBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012357	396101	AVP	http://www.ncbi.nlm.nih.gov/gene/?term=396101		mRNA	Gallus gallus	10817905	Axon	Hypothalamus	In Situ Hybridization|RT-PCR	"AVT mRNA was detected in the median eminence and neurohypophysis representing the distal parts of the HNS, mainly consisting of axons and/or axon terminals. "
RLID00012358	396133	FN1	http://www.ncbi.nlm.nih.gov/gene/?term=396133	FN	mRNA	Gallus gallus	2103522	Cytoplasm	Embryo	In situ hybridization	"Fibronectin mRNA were essentially located in cytoplasm, associated with the rough endoplasmic reticulum (fig 5a, b, c), but a few grains were observed in the nucleus around the nucleolus (fig 5d). In some instances, the location of the label is obviously over the rough membranes of the endoplasmic reticulum (fig 5c). "
RLID00012359	396133	FN1	http://www.ncbi.nlm.nih.gov/gene/?term=396133	FN	mRNA	Gallus gallus	2103522	Endoplasmic reticulum	Embryo	In situ hybridization	"Fibronectin mRNA were essentially located in cytoplasm, associated with the rough endoplasmic reticulum (fig 5a, b, c), but a few grains were observed in the nucleus around the nucleolus (fig 5d). In some instances, the location of the label is obviously over the rough membranes of the endoplasmic reticulum (fig 5c). "
RLID00012360	396147	ACTR2	http://www.ncbi.nlm.nih.gov/gene/?term=396147		mRNA	Gallus gallus	21146522	Lamellipodium	Fibroblast	Fluorescence in situ hybridization	"Figure 1A: Endogenous Arp2 mRNA (green) and Dia1 mRNA (red) are localized in the protrusions (indicated by arrows) and perinuclear region in the CEFs, respectively. Note that protrusions in this report are defined broadly to include lamellae and lamellipodia. "
RLID00012361	396147	ACTR2	http://www.ncbi.nlm.nih.gov/gene/?term=396147		mRNA	Gallus gallus	21146522	Perinuclear	Fibroblast	Fluorescence in situ hybridization	"Figure 1A: Endogenous Arp2 mRNA (green) and Dia1 mRNA (red) are localized in the protrusions (indicated by arrows) and perinuclear region in the CEFs, respectively. Note that protrusions in this report are defined broadly to include lamellae and lamellipodia. "
RLID00012362	396147	ACTR2	http://www.ncbi.nlm.nih.gov/gene/?term=396147		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00012363	39625	mnd	http://www.ncbi.nlm.nih.gov/gene/?term=39625	"Dmel_CG3297, CG3297, Dmel\CG3297, SG29, l(3)B5, l(3)SG29, l(3)ds-5, l(3)ds5, l(3)o52, md "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012364	3963	LGALS7	http://www.ncbi.nlm.nih.gov/gene/?term=3963	"GAL7, LGALS7A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012365	3964	LGALS8	http://www.ncbi.nlm.nih.gov/gene/?term=3964	"Gal-8, PCTA-1, PCTA1, Po66-CBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012366	3964	LGALS8	http://www.ncbi.nlm.nih.gov/gene/?term=3964	"Gal-8, PCTA-1, PCTA1, Po66-CBP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012367	3964	LGALS8	http://www.ncbi.nlm.nih.gov/gene/?term=3964	"Gal-8, PCTA-1, PCTA1, Po66-CBP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012368	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	2277064	Cytoplasm	Skeletal Myoblast|Fibroblast	In situ hybridization	"In the 14% of cells with localized actin mRNA, the degree of regionalization was not as great as in cells cultured for 2 d, i.e., substantial mounts of actin mRNA were found throughout the cytoplasm (Fig. 1, c and d). "
RLID00012369	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	2738094	Lamellipodium	Skeletal Myoblast|Fibroblast	Immunocytochemistry|In situ hybridization	"Actin mRNA was found to be more predominant in lamellipodia of motile cells, confirming previous results. "
RLID00012370	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	3698103	Lamellipodium	Embryo blasts|Fibroblast	In situ hybridization	"Actin mRNA concentrations were highest at cell extremities, generally in lamellipodia, where grain densities were up to 16-fold higher than in areas near the nucleus. Vimentin mRNA, unlike actin mRNA, was distributed near the nucleus. Tubulin mRNA appeared most concentrated in the peripheral cytoplasm. These results demonstrate that cytoplasmic mRNAs are localized in specific, nonrandom cellular patterns and that localized concentrations of specific proteins may result from corresponding localization of their respective mRNAs. Hence, actin mRNA distribution may result in increased concentration of actin filaments in lamellipodia of motile cells. "
RLID00012371	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	15377515	Lamellipodium	Fibroblast	In situ hybridization	"Beta-actin mRNA signals were most abundant in active lamellipodia, which are protrusions that cells extend to adhere to surfaces. The preponderance of warmer colors in the most prominent lamellipodia indicates that β-actin mRNA was very abundant in those regions. "
RLID00012372	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00012373	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	2095368	Lamellipodium	Fibroblastic single cell	In situ hybridization	"When beta-actin probes were used, two of 11 probes were highly sensitive, and, in pooling them together, the localization of beta-actin mRNA in fibroblastic single cells was evident at the leading edge of the motile cells, the lamellipodium. beta-Actin mRNA was not detected in myotubes except at the ends where contact was made with substrate. This indicates that both beta and cardiac actin mRNA can coexist in the same myotube cytoplasm but at different locations. "
RLID00012374	396526	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=396526	"Bact, actin "	mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00012375	3965	LGALS9	http://www.ncbi.nlm.nih.gov/gene/?term=3965	"HUAT, LGALS9A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012376	396	ARHGDIA	http://www.ncbi.nlm.nih.gov/gene/?term=396	"GDIA1, HEL-S-47e, NPHS8, RHOGDI, RHOGDI-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012377	396	ARHGDIA	http://www.ncbi.nlm.nih.gov/gene/?term=396	"GDIA1, HEL-S-47e, NPHS8, RHOGDI, RHOGDI-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012378	396	ARHGDIA	http://www.ncbi.nlm.nih.gov/gene/?term=396	"GDIA1, HEL-S-47e, NPHS8, RHOGDI, RHOGDI-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012379	39720	fwe	http://www.ncbi.nlm.nih.gov/gene/?term=39720	"Dmel_CG6151, CG6151, Dmel\CG6151, anon-WO0118547.242, dFwe "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012380	39720	fwe	http://www.ncbi.nlm.nih.gov/gene/?term=39720	"Dmel_CG6151, CG6151, Dmel\CG6151, anon-WO0118547.242, dFwe "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012381	39758	CG5235	http://www.ncbi.nlm.nih.gov/gene/?term=39758	Dmel_ Dmel\CG5235	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012382	39764	Zn72D	http://www.ncbi.nlm.nih.gov/gene/?term=39764	"Dmel_CG5215, CG5215, Dmel\CG5215, ZN72D, l(3)72Dk, zn72D "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012383	3977	LIFR	http://www.ncbi.nlm.nih.gov/gene/?term=3977	"CD118, LIF-R, SJS2, STWS, SWS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012384	3977	LIFR	http://www.ncbi.nlm.nih.gov/gene/?term=3977	"CD118, LIF-R, SJS2, STWS, SWS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012385	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	7539356	Mitochondrion	Oocyte	In situ hybridization	"One of these, through which Xlsirts, Xcat2 and Xwnt11 are localized, involves transport during stages 1 and 2 of oogenesis via a region of the mitochondrial cloud that we call the message transport organizer or METRO. This pathway involved three steps, transport of RNA from the GV to the mitochondrial cloud, sorting of the RNAs to specific regions of the METRO, and translocation to and anchoring at the vegetal cortex. "
RLID00012386	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	7867501	Vegetal	Oocyte	-	"Xcat-2 is exclusively localized to the mitochondrial cloud in stage I oocytes, moves with this body into the vegetal cortex during stage II and, later, partitions into islands consistent with it being a component of the germ plasm. "
RLID00012387	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	7867501	Mitochondrion	Oocyte	-	"Xcat-2 is exclusively localized to the mitochondrial cloud in stage I oocytes, moves with this body into the vegetal cortex during stage II and, later, partitions into islands consistent with it being a component of the germ plasm. "
RLID00012388	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	7867501	Germ plasm	Embryo	-	"Xcat-2 is exclusively localized to the mitochondrial cloud in stage I oocytes, moves with this body into the vegetal cortex during stage II and, later, partitions into islands consistent with it being a component of the germ plasm. "
RLID00012389	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8223259	Cytoskeleton	Oocyte	In situ hybridization	"Furthermore, Vg1 and Xcat-2 RNA appear to co-distribute to the cortex, a region particularly concentrated in cytoskeletal elements which include intermediate laments. "
RLID00012390	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8873762	Vegetal	Oocyte	In situ hybridization	"To further analyze the mechanisms involved in RNA transport, in situ hybridization and autoradiography were used to follow the localization of endogenous Vg1 and injected Xcat-2 transcripts in stage IV oocytes. We show that Xcat-2 is competent to localize to the vegetal cortex quite independently of the mitochondrial cloud. "
RLID00012391	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8873762	Germ plasm	Oocyte	In situ hybridization	"Xcat-2 RNA, a component of the germ plasm in Xenopus, localizes with the mitochondrial cloud material to the vegetal cortex in stage II oocytes. Vg1 RNA also localizes to the vegetal cortex, but later in stage III/IV oocytes, using a microtubule dependent pathway. To further analyze the mechanisms involved in RNA transport, in situ hybridization and autoradiography were used to follow the localization of endogenous Vg1 and injected Xcat-2 transcripts in stage IV oocytes. We show that Xcat-2 is competent to localize to the vegetal cortex quite independently of the mitochondrial cloud. "
RLID00012392	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8948579	Cytoplasm	Oocyte	In situ hybridization	During translocation through the cytoplasm Xlsirt and Xcat2 RNAs were detected associated with cytoplasmic particles of different morphologies.
RLID00012393	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8948579	Mitochondrion	Oocyte	In situ hybridization	"In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud.  "
RLID00012394	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8948579	Vegetal	Oocyte	In situ hybridization	"In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud.  "
RLID00012395	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	9739112	Vegetal	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00012396	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	9739112	Mitochondrion	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00012397	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	10625548	Mitochondrion	Oocyte	In situ hybridization|Electron microscopy	"Immediately after the 16-cell nest stage, Xcat2 mRNA was detected in early meiotic oocytes localized to the mitochondrial aggregate, the precursor to the mitochondrial cloud (Fig. 1A). Xcat2 mRNA was located between the mitochondria at the periphery of the area containing the mitochondrial cement (Fig. 1A). "
RLID00012398	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	11309203	Vegetal	Oocyte	In situ hybridization	"The IVC retained mRNAs with a granular texture, and their distribution patterns resembled those of the whole oocyte. Vg1 was distributed in the entire cortex, whereas Xwnt-11 and Xcat-2 were both concentrated as a disc at the vegetal pole. "
RLID00012399	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00012400	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	12401170	Vegetal	Oocyte	In situ hybridization	"Figure 2. In Situ Hybridization of Newly Discovered Localized mRNAs In situ hybridization to Xcat-2 mRNA and Xpat mRNAs demonstrates examples of RNAs that localize via the early pathway. Note that most of the RNA is associated with the mitochondrial cloud in stage I oocytes, with little background in the rest of the cytoplasm. By stage II, these RNAs have migrated with the cloud to the vegetal cortex, and there is no detectable RNA in the remaining cytoplasm. "
RLID00012401	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	15292452	Mitochondrion	Oocyte	Immunofluorescence	"To understand the mechanism of the early pathway through which RNAs localize to the MC, we applied live confocal imaging and photobleaching analysis to oocytes microinjected with fluorescent Xcat2 and Xdazl RNA constructs. These RNAs dispersed evenly throughout the cytoplasm through diffusion and then became progressively immobilized and formed aggregates in the MC (mitochondrial cloud).  "
RLID00012402	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	19223445	Mitochondrion	Oocyte	Quantitative RNA localization assay	"Early RNAs, such as Xcat-2, Xlsirt, and Xwnt, become localized to a large subcellular structure called the Balbiani body or mitochondrial cloud. "
RLID00012403	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. "
RLID00012404	397875	nanos1	http://www.ncbi.nlm.nih.gov/gene/?term=397875	"nos1, xcat-2, xcat2, xnos1 "	mRNA	Xenopus laevis	8787767	Mitochondrion	Oocyte	In situ hybridization	Xcat-2 RNA specifically localizes to the mitochondrial cloud and moves with it to the vegetal subcortex in stage II oocytes.
RLID00012405	3978	LIG1	http://www.ncbi.nlm.nih.gov/gene/?term=3978		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012406	397986	vegt-a	http://www.ncbi.nlm.nih.gov/gene/?term=397986	"Apod, antipodean, brat, tVegT, xombi "	mRNA	Xenopus laevis	15496522	Vegetal	Oocyte	Immunofluorescence	"We show that double-stranded RNA-binding Staufen proteins are present in the oocytes of a vertebrate, Xenopus, and are localized to the vegetal cytoplasm, a region where important mRNAs including VegT and Vg1 mRNA become localized. "
RLID00012407	397986	vegt-a	http://www.ncbi.nlm.nih.gov/gene/?term=397986	"Apod, antipodean, brat, tVegT, xombi "	mRNA	Xenopus laevis	15515051	Vegetal	Oocyte	In situ hybridization	"VegT and other RNAs, involved in embryonic patterning, follow the late pathway. We have shown that the R. pipiens RNA orthologues of Xdazl and VegT are both localized to the vegetal cortex, suggesting that the two RNA localization pathways exist in R. pipiens. "
RLID00012408	397990	vegt-b	http://www.ncbi.nlm.nih.gov/gene/?term=397990	"Apod, antipodean, brat, tVegT, vegt, xombi "	mRNA	Xenopus laevis	15496522	Vegetal	Oocyte	Immunofluorescence	"We show that double-stranded RNA-binding Staufen proteins are present in the oocytes of a vertebrate, Xenopus, and are localized to the vegetal cytoplasm, a region where important mRNAs including VegT and Vg1 mRNA become localized. "
RLID00012409	397990	vegt-b	http://www.ncbi.nlm.nih.gov/gene/?term=397990	"Apod, antipodean, brat, tVegT, vegt, xombi "	mRNA	Xenopus laevis	15515051	Vegetal	Oocyte	In situ hybridization	"VegT and other RNAs, involved in embryonic patterning, follow the late pathway. We have shown that the R. pipiens RNA orthologues of Xdazl and VegT are both localized to the vegetal cortex, suggesting that the two RNA localization pathways exist in R. pipiens. "
RLID00012410	397990	vegt-b	http://www.ncbi.nlm.nih.gov/gene/?term=397990	"Apod, antipodean, brat, tVegT, vegt, xombi "	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs,Vg1 and VegT, also may localise into germ plasm. "
RLID00012411	397	ARHGDIB	http://www.ncbi.nlm.nih.gov/gene/?term=397	"D4, GDIA2, GDID4, LYGDI, Ly-GDI, RAP1GN1, RhoGDI2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012412	398019	ddx4	http://www.ncbi.nlm.nih.gov/gene/?term=398019	"vasa, vlg1 "	mRNA	Xenopus laevis	10830432	Cytoplasm	Oocyte	In situ hybridization	"By hybridization, XVLG1 ribonucleic acid (RNA) was shown to be present throughout the cytoplasm in oocytes at stages I-III, except for the mitochondrial cloud. "
RLID00012413	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	9486791	Germ plasm	Oocyte	In situ hybridization	"We have identified a localized RNA component of Xenopus germ plasm. This RNA, Xdazl (Xenopus DAZ-like), encodes a protein homologous to human DAZ (Deleted in Azoospermia), vertebrate DAZL and Drosophila Boule proteins. Human males deficient in DAZ have few or no sperm and boule mutant flies exhibit complete azoospermia and male sterility. Xdazl RNA was detected in the mitochondrial cloud and vegetal cortex of oocytes. In early embryos, the RNA was localized exclusively in the germ plasm. "
RLID00012414	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	9486791	Mitochondrion	Oocyte	In situ hybridization	"We have identified a localized RNA component of Xenopus germ plasm. This RNA, Xdazl (Xenopus DAZ-like), encodes a protein homologous to human DAZ (Deleted in Azoospermia), vertebrate DAZL and Drosophila Boule proteins. Human males deficient in DAZ have few or no sperm and boule mutant flies exhibit complete azoospermia and male sterility. Xdazl RNA was detected in the mitochondrial cloud and vegetal cortex of oocytes. In early embryos, the RNA was localized exclusively in the germ plasm. "
RLID00012415	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	9486791	Vegetal	Oocyte	In situ hybridization	"We have identified a localized RNA component of Xenopus germ plasm. This RNA, Xdazl (Xenopus DAZ-like), encodes a protein homologous to human DAZ (Deleted in Azoospermia), vertebrate DAZL and Drosophila Boule proteins. Human males deficient in DAZ have few or no sperm and boule mutant flies exhibit complete azoospermia and male sterility. Xdazl RNA was detected in the mitochondrial cloud and vegetal cortex of oocytes. In early embryos, the RNA was localized exclusively in the germ plasm. "
RLID00012416	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	10631166	Germ plasm	Embryo	In situ hybridization	Xdazl is an RNA component of Xenopus germ plasm and encodes an RNA-binding protein that can act as a functional homologue of Drosophila boule.
RLID00012417	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	11397009	Germ plasm	Oocyte	In situ hybridization	"Axdazl is homologous to Xdazl, a component of Xenopus germ plasm found in the vegetal pole of oocytes and eggs. Axdazl RNA is not localized in axolotl oocytes, and, furthermore, these oocytes do not contain the mitochondrial cloud that localizes Xdazl and other germ plasm components in Xenopus. "
RLID00012418	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00012419	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	15292452	Mitochondrion	Oocyte	Immunofluorescence	"To understand the mechanism of the early pathway through which RNAs localize to the MC, we applied live confocal imaging and photobleaching analysis to oocytes microinjected with fluorescent Xcat2 and Xdazl RNA constructs. These RNAs dispersed evenly throughout the cytoplasm through diffusion and then became progressively immobilized and formed aggregates in the MC (mitochondrial cloud).  "
RLID00012420	398041	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=398041	"Xdazl, dazh-B, dazl-a, dazl1, dazla, spgyla, dazl "	mRNA	Xenopus laevis	15515051	Vegetal	Oocyte	In situ hybridization	"VegT and other RNAs, involved in embryonic patterning, follow the late pathway. We have shown that the R. pipiens RNA orthologues of Xdazl and VegT are both localized to the vegetal cortex, suggesting that the two RNA localization pathways exist in R. pipiens. "
RLID00012421	3980	LIG3	http://www.ncbi.nlm.nih.gov/gene/?term=3980	LIG2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012422	3980	LIG3	http://www.ncbi.nlm.nih.gov/gene/?term=3980	LIG2	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00012423	3980	LIG3	http://www.ncbi.nlm.nih.gov/gene/?term=3980	LIG2	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00012424	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	10529413	Vegetal	Oocyte	In situ hybridization	"The fatvg transcript, unlike Vg1 which localizes strictly through the Late pathway, also associates with the mitochondrial cloud that is characteristic of the METRO or Early pathway. This suggests that fatvg mRNA may utilize both the METRO and Late pathways to localize to the vegetal cortex during oogenesis. "
RLID00012425	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	10529413	Mitochondrion	Oocyte	In situ hybridization	"The fatvg transcript, unlike Vg1 which localizes strictly through the Late pathway, also associates with the mitochondrial cloud that is characteristic of the METRO or Early pathway. This suggests that fatvg mRNA may utilize both the METRO and Late pathways to localize to the vegetal cortex during oogenesis. "
RLID00012426	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	11118900	Vegetal	Oocyte	In situ hybridization	"Fatvg mRNA is localized through the late pathway to the vegetal cortex. Like Vg1 mRNA fatvg is distributed throughout the entire cortex; however, unlike Vg1 there is a small fraction of the fatvg mRNA that is associated with the mitochondrial cloud. In early cleavage stage embryos, fatvg mRNA is associated with the germ plasm located at the tips of the vegetal blastomeres of the embryo. "
RLID00012427	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	11118900	Mitochondrion	Oocyte	In situ hybridization	"Fatvg mRNA is localized through the late pathway to the vegetal cortex. Like Vg1 mRNA fatvg is distributed throughout the entire cortex; however, unlike Vg1 there is a small fraction of the fatvg mRNA that is associated with the mitochondrial cloud. In early cleavage stage embryos, fatvg mRNA is associated with the germ plasm located at the tips of the vegetal blastomeres of the embryo. "
RLID00012428	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	11118900	Germ plasm	Embryo	In situ hybridization	"Fatvg mRNA is localized through the late pathway to the vegetal cortex. Like Vg1 mRNA fatvg is distributed throughout the entire cortex; however, unlike Vg1 there is a small fraction of the fatvg mRNA that is associated with the mitochondrial cloud. In early cleavage stage embryos, fatvg mRNA is associated with the germ plasm located at the tips of the vegetal blastomeres of the embryo. "
RLID00012429	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00012430	398143	plin2	http://www.ncbi.nlm.nih.gov/gene/?term=398143	"adfp, adipophilin, adrp, fatvg "	mRNA	Xenopus laevis	17939116	Germ plasm	Oocyte	In situ hybridization	"We found that centroid mRNA is localized in Xenopus oocytes by a combination of early and late pathways, a pattern of localization that is very similar to the intermediate pathway localization of fatvg mRNA, another germ-plasm-localized RNA in Xenopus oocytes. Also, centroid mRNA is present in the mitochondrial cloud and in the germ plasm at the surface of germinal granules. "
RLID00012431	398145	tacc3	http://www.ncbi.nlm.nih.gov/gene/?term=398145	"eric1, maskin, masking, xmaskin "	mRNA	Xenopus laevis	11081630	Mitotic spindle	Embryo	Whole mount In Situ Hybridization	"CPEB, Maskin, and Cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. "
RLID00012432	39816	Cpr72Ec	http://www.ncbi.nlm.nih.gov/gene/?term=39816	"Dmel_CG4784, CG4784, CT15377, Dmel\CG4784 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012433	398180	ddx25	http://www.ncbi.nlm.nih.gov/gene/?term=398180	"deadsouth, grth "	mRNA	Xenopus laevis	10906480	Vegetal	Oocyte	In situ hybridization	DEADSouth was selected in a screen for localized RNAs in Xenopus oocytes. In situ hybridization analysis shows that DEADSouth localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with germ plasm during early embryogenesis.
RLID00012434	398180	ddx25	http://www.ncbi.nlm.nih.gov/gene/?term=398180	"deadsouth, grth "	mRNA	Xenopus laevis	10906480	Mitochondrion	Oocyte	In situ hybridization	DEADSouth was selected in a screen for localized RNAs in Xenopus oocytes. In situ hybridization analysis shows that DEADSouth localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with germ plasm during early embryogenesis.
RLID00012435	398180	ddx25	http://www.ncbi.nlm.nih.gov/gene/?term=398180	"deadsouth, grth "	mRNA	Xenopus laevis	10906480	Germ plasm	Oocyte	In situ hybridization	DEADSouth was selected in a screen for localized RNAs in Xenopus oocytes. In situ hybridization analysis shows that DEADSouth localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with germ plasm during early embryogenesis.
RLID00012436	398180	ddx25	http://www.ncbi.nlm.nih.gov/gene/?term=398180	"deadsouth, grth "	mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00012437	398180	ddx25	http://www.ncbi.nlm.nih.gov/gene/?term=398180	"deadsouth, grth "	mRNA	Xenopus laevis	23429978	Germ plasm	Embryo	Fluorescence in situ hybridization	DEADSouth mRNA is a component of germ plasm in Xenopus laevis and encodes a DDX25 DEAD-box RNA helicase. 
RLID00012438	398191	chek1	http://www.ncbi.nlm.nih.gov/gene/?term=398191	chk1	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00012439	3981	LIG4	http://www.ncbi.nlm.nih.gov/gene/?term=3981	LIG4S	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012440	3981	LIG4	http://www.ncbi.nlm.nih.gov/gene/?term=3981	LIG4S	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012441	3982	LIM2	http://www.ncbi.nlm.nih.gov/gene/?term=3982	"CTRCT19, MP17, MP19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012442	39833	aos	http://www.ncbi.nlm.nih.gov/gene/?term=39833	"Dmel_CG4531, Aos, Argos, CG4531, DmAos, Dmel\CG4531, arg, gil, l(3)05845, l(3)05959, l(3)j5E11, l(3)rJ472, l(3)rJ812, l(3)rQ526, rlt, sty "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012443	3983	ABLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=3983	"ABLIM, LIMAB1, LIMATIN, abLIM-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012444	3983	ABLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=3983	"ABLIM, LIMAB1, LIMATIN, abLIM-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012445	3984	LIMK1	http://www.ncbi.nlm.nih.gov/gene/?term=3984	"LIMK, LIMK-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012446	398520	LOC398520	http://www.ncbi.nlm.nih.gov/gene/?term=398520		mRNA	Xenopus laevis	12915321	Mitochondrion	Oocyte	In situ hybridization	In situ hybridization analysis shows that Germes transcript localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with the germ plasm during early embryogenesis. Our data indicate that Germes is a novel germ plasm-specific RNA.
RLID00012447	398520	LOC398520	http://www.ncbi.nlm.nih.gov/gene/?term=398520		mRNA	Xenopus laevis	12915321	Germ plasm	Oocyte	In situ hybridization	In situ hybridization analysis shows that Germes transcript localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with the germ plasm during early embryogenesis. Our data indicate that Germes is a novel germ plasm-specific RNA.
RLID00012448	398520	LOC398520	http://www.ncbi.nlm.nih.gov/gene/?term=398520		mRNA	Xenopus laevis	12915321	Vegetal	Oocyte	In situ hybridization	In situ hybridization analysis shows that Germes transcript localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with the germ plasm during early embryogenesis. Our data indicate that Germes is a novel germ plasm-specific RNA.
RLID00012449	3985	LIMK2	http://www.ncbi.nlm.nih.gov/gene/?term=3985		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012450	398655	velo1	http://www.ncbi.nlm.nih.gov/gene/?term=398655	Xvelo1	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"Xpat is a germ plasm RNA whose protein is also present in germ plasm, in particles which we show here are distinct from those containing Hermes protein and the various germ plasm RNAs tested, including that encoding Xpat itself "
RLID00012451	398655	velo1	http://www.ncbi.nlm.nih.gov/gene/?term=398655	Xvelo1	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs,Vg1 and VegT, also may localise into germ plasm. "
RLID00012452	39871	Dbp73D	http://www.ncbi.nlm.nih.gov/gene/?term=39871	"Dmel_CG9680, CG9680, DBP73D, DmRH7, Dmel\CG9680 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012453	39871	Dbp73D	http://www.ncbi.nlm.nih.gov/gene/?term=39871	"Dmel_CG9680, CG9680, DBP73D, DmRH7, Dmel\CG9680 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012454	39877	Int6	http://www.ncbi.nlm.nih.gov/gene/?term=39877	"Dmel_CG9677, BcDNA.GM01233, BcDNA:GM01233, CG9677, DINT6, Dmel\CG9677, eIF-3p48/INT-6, eIF3-S6, eIF3-p48/INT6, eIF3e, l(3)10547, l(3)j9E8 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012455	3987	LIMS1	http://www.ncbi.nlm.nih.gov/gene/?term=3987	"PINCH, PINCH-1, PINCH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012456	398800	dgat2	http://www.ncbi.nlm.nih.gov/gene/?term=398800		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00012457	398805	exd2	http://www.ncbi.nlm.nih.gov/gene/?term=398805	"exd2-a, exdl2 "	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00012458	3988	LIPA	http://www.ncbi.nlm.nih.gov/gene/?term=3988	"CESD, LAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012459	3988	LIPA	http://www.ncbi.nlm.nih.gov/gene/?term=3988	"CESD, LAL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012460	398948	rbpms	http://www.ncbi.nlm.nih.gov/gene/?term=398948	hermes	mRNA	Xenopus laevis	14975717	Vegetal	Oocyte	In situ hybridization	"Hermes mRNA and protein are both detected at the vegetal cortex of the oocyte; however, the protein is degraded within a several hour period during oocyte maturation. "
RLID00012461	398948	rbpms	http://www.ncbi.nlm.nih.gov/gene/?term=398948	hermes	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"In addition to the Balbiani body, Hermes RNA is localised in germ plasm particles in the vegetal cortex of vitellogenic oocytes. "
RLID00012462	398948	rbpms	http://www.ncbi.nlm.nih.gov/gene/?term=398948	hermes	mRNA	Xenopus laevis	23626739	Mitochondrion	Oocyte	Microscopy	"In addition to the Balbiani body, Hermes RNA is localised in germ plasm particles in the vegetal cortex of vitellogenic oocytes. "
RLID00012463	398948	rbpms	http://www.ncbi.nlm.nih.gov/gene/?term=398948	hermes	mRNA	Xenopus laevis	23626739	Vegetal	Oocyte	Microscopy	"In addition to the Balbiani body, Hermes RNA is localised in germ plasm particles in the vegetal cortex of vitellogenic oocytes. "
RLID00012464	399008	smtn-a	http://www.ncbi.nlm.nih.gov/gene/?term=399008	smtn	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00012465	3990	LIPC	http://www.ncbi.nlm.nih.gov/gene/?term=3990	"HDLCQ12, HL, HTGL, LIPH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012466	399101	Snhg3	http://www.ncbi.nlm.nih.gov/gene/?term=399101	"Rnu17d, U17HG "	lncRNA	Mus musculus	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/snhg3/
RLID00012467	399101	Snhg3	http://www.ncbi.nlm.nih.gov/gene/?term=399101	"Rnu17d, U17HG "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012468	399106	bub3	http://www.ncbi.nlm.nih.gov/gene/?term=399106	xbub3	mRNA	Xenopus laevis	11081630	Mitotic spindle	Embryo	Whole mount In Situ Hybridization	Xbub3 and Cyclin B1 mRNAs are concentrated on the mitotic apparatus.
RLID00012469	3991	LIPE	http://www.ncbi.nlm.nih.gov/gene/?term=3991	"AOMS4, FPLD6, HSL, LHS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012470	399289	cpeb1-a	http://www.ncbi.nlm.nih.gov/gene/?term=399289	"CPEB, cpeb1 "	mRNA	Xenopus laevis	11081630	Mitotic spindle	Embryo	Whole mount In Situ Hybridization	"CPEB, Maskin, and Cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. "
RLID00012471	3992	FADS1	http://www.ncbi.nlm.nih.gov/gene/?term=3992	"D5D, FADS6, FADSD5, LLCDL1, TU12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012472	3992	FADS1	http://www.ncbi.nlm.nih.gov/gene/?term=3992	"D5D, FADS6, FADSD5, LLCDL1, TU12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012473	3992	FADS1	http://www.ncbi.nlm.nih.gov/gene/?term=3992	"D5D, FADS6, FADSD5, LLCDL1, TU12 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012474	39933	Mip	http://www.ncbi.nlm.nih.gov/gene/?term=39933	"Dmel_CG6456, ASB, AST-B, Ast-B, AstB, AstB-1, CG6456, DAP-B, DmMIP1, DmMIP2, DmMIP3, DmMIP4, DmMIP5, Dmel\CG6456, Drm-MIP, Drm-MIP-1, Drm-MIP-2, Drm-MIP-3, Drm-MIP-4, Drm-MIP-5, MIP, MIP-1, MIP-2, MIP-3, MIP-4, MIP-5, mip "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012475	39933	Mip	http://www.ncbi.nlm.nih.gov/gene/?term=39933	"Dmel_CG6456, ASB, AST-B, Ast-B, AstB, AstB-1, CG6456, DAP-B, DmMIP1, DmMIP2, DmMIP3, DmMIP4, DmMIP5, Dmel\CG6456, Drm-MIP, Drm-MIP-1, Drm-MIP-2, Drm-MIP-3, Drm-MIP-4, Drm-MIP-5, MIP, MIP-1, MIP-2, MIP-3, MIP-4, MIP-5, mip "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012476	399353	tob2	http://www.ncbi.nlm.nih.gov/gene/?term=399353	"tob4, tobl, trob2 "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00012477	39936	Cad74A	http://www.ncbi.nlm.nih.gov/gene/?term=39936	"Dmel_CG6445, CG6445, CT20086, Cad74B, DCad74B, Dmel\CG6445, cad74A "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012478	39936	Cad74A	http://www.ncbi.nlm.nih.gov/gene/?term=39936	"Dmel_CG6445, CG6445, CT20086, Cad74B, DCad74B, Dmel\CG6445, cad74A "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012479	39936	Cad74A	http://www.ncbi.nlm.nih.gov/gene/?term=39936	"Dmel_CG6445, CG6445, CT20086, Cad74B, DCad74B, Dmel\CG6445, cad74A "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012480	3993	LLGL2	http://www.ncbi.nlm.nih.gov/gene/?term=3993	"HGL, Hugl-2, LGL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012481	3993	LLGL2	http://www.ncbi.nlm.nih.gov/gene/?term=3993	"HGL, Hugl-2, LGL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012482	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	7539356	Mitochondrion	Oocyte	In situ hybridization	"One of these, through which Xlsirts, Xcat2 and Xwnt11 are localized, involves transport during stages 1 and 2 of oogenesis via a region of the mitochondrial cloud that we call the message transport organizer or METRO. This pathway involved three steps, transport of RNA from the GV to the mitochondrial cloud, sorting of the RNAs to specific regions of the METRO, and translocation to and anchoring at the vegetal cortex. "
RLID00012483	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	8948579	Mitochondrion	Oocyte	In situ hybridization	"In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud.  "
RLID00012484	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	8948579	Vegetal	Oocyte	In situ hybridization	"In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud.  "
RLID00012485	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	9739112	Vegetal	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00012486	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	9739112	Mitochondrion	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00012487	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	9739112	Germ plasm	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00012488	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	11309203	Vegetal	Oocyte	In situ hybridization	"The IVC retained mRNAs with a granular texture, and their distribution patterns resembled those of the whole oocyte. Vg1 was distributed in the entire cortex, whereas Xwnt-11 and Xcat-2 were both concentrated as a disc at the vegetal pole. "
RLID00012489	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00012490	399441	wnt11b	http://www.ncbi.nlm.nih.gov/gene/?term=399441	"WNT11, wnt-11, xwnt11 "	mRNA	Xenopus laevis	19223445	Mitochondrion	Oocyte	Quantitative RNA localization assay	"Early RNAs, such as Xcat-2, Xlsirt, and Xwnt, become localized to a large subcellular structure called the Balbiani body or mitochondrial cloud. "
RLID00012491	39958	Nedd4	http://www.ncbi.nlm.nih.gov/gene/?term=39958	"Dmel_CG42279, ACN62428.1, CG32184, CG42279, CG7555, D Dmel\CG42279, Dmel_CG32184, Dmel_CG7555, NEDD4, dNedd4, dNedd4-1, nedd4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012492	3995	FADS3	http://www.ncbi.nlm.nih.gov/gene/?term=3995	"CYB5RP, LLCDL3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012493	3995	FADS3	http://www.ncbi.nlm.nih.gov/gene/?term=3995	"CYB5RP, LLCDL3 "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00012494	399664	MEX3D	http://www.ncbi.nlm.nih.gov/gene/?term=399664	"MEX-3D, MEX3, OK/SW-cl.4, RKHD1, RNF193, TINO "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012495	399671	HEATR4	http://www.ncbi.nlm.nih.gov/gene/?term=399671		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012496	3996	LLGL1	http://www.ncbi.nlm.nih.gov/gene/?term=3996	"DLG4, HUGL, HUGL-1, HUGL1, LLGL, Lgl1, Mgl1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012497	3996	LLGL1	http://www.ncbi.nlm.nih.gov/gene/?term=3996	"DLG4, HUGL, HUGL-1, HUGL1, LLGL, Lgl1, Mgl1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012498	3996	LLGL1	http://www.ncbi.nlm.nih.gov/gene/?term=3996	"DLG4, HUGL, HUGL-1, HUGL1, LLGL, Lgl1, Mgl1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012499	3996	LLGL1	http://www.ncbi.nlm.nih.gov/gene/?term=3996	"DLG4, HUGL, HUGL-1, HUGL1, LLGL, Lgl1, Mgl1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012500	3996	LLGL1	http://www.ncbi.nlm.nih.gov/gene/?term=3996	"DLG4, HUGL, HUGL-1, HUGL1, LLGL, Lgl1, Mgl1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012501	39976	Adgf-A	http://www.ncbi.nlm.nih.gov/gene/?term=39976	"Dmel_CG5992, ADGDF-A, ADGF-A, Adgf-a, AdgfA, CG5992, Dmel\CG5992, adgf-a, adgfa "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012502	3998	LMAN1	http://www.ncbi.nlm.nih.gov/gene/?term=3998	"ERGIC-53, ERGIC53, F5F8D, FMFD1, MCFD1, MR60, gp58 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012503	3998	LMAN1	http://www.ncbi.nlm.nih.gov/gene/?term=3998	"ERGIC-53, ERGIC53, F5F8D, FMFD1, MCFD1, MR60, gp58 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012504	3998	LMAN1	http://www.ncbi.nlm.nih.gov/gene/?term=3998	"ERGIC-53, ERGIC53, F5F8D, FMFD1, MCFD1, MR60, gp58 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012505	399909	PCNX3	http://www.ncbi.nlm.nih.gov/gene/?term=399909	PCNXL3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012506	399948	COLCA1	http://www.ncbi.nlm.nih.gov/gene/?term=399948	"C11orf92, CASC12, LOH11CR1F "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012507	399948	COLCA1	http://www.ncbi.nlm.nih.gov/gene/?term=399948	"C11orf92, CASC12, LOH11CR1F "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012508	399949	C11orf88	http://www.ncbi.nlm.nih.gov/gene/?term=399949		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012509	399959	MIR100HG	http://www.ncbi.nlm.nih.gov/gene/?term=399959	"AGD1, lncRNA-N2 "	lncRNA	Homo sapiens	22193719	Cytoplasm	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00012510	39995	Tsp74F	http://www.ncbi.nlm.nih.gov/gene/?term=39995	"Dmel_CG5492, CG5492, Dm.Tsp74F, Dmel\CG5492 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012511	399979	SNX19	http://www.ncbi.nlm.nih.gov/gene/?term=399979	CHET8	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012512	399979	SNX19	http://www.ncbi.nlm.nih.gov/gene/?term=399979	CHET8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012513	399	RHOH	http://www.ncbi.nlm.nih.gov/gene/?term=399	"ARHH, TTF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012514	39	ACAT2	http://www.ncbi.nlm.nih.gov/gene/?term=39		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012515	39	ACAT2	http://www.ncbi.nlm.nih.gov/gene/?term=39		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012516	39	ACAT2	http://www.ncbi.nlm.nih.gov/gene/?term=39		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012517	400073	C12orf76	http://www.ncbi.nlm.nih.gov/gene/?term=400073		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012518	4000	LMNA	http://www.ncbi.nlm.nih.gov/gene/?term=4000	"CDCD1, CDDC, CMD1A, CMT2B1, EMD2, FPL, FPLD, FPLD2, HGPS, IDC, LDP1, LFP, LGMD1B, LMN1, LMNC, LMNL1, PRO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012519	4000	LMNA	http://www.ncbi.nlm.nih.gov/gene/?term=4000	"CDCD1, CDDC, CMD1A, CMT2B1, EMD2, FPL, FPLD, FPLD2, HGPS, IDC, LDP1, LFP, LGMD1B, LMN1, LMNC, LMNL1, PRO1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012520	4001	LMNB1	http://www.ncbi.nlm.nih.gov/gene/?term=4001	"ADLD, LMN, LMN2, LMNB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012521	40021	CG7271	http://www.ncbi.nlm.nih.gov/gene/?term=40021	Dmel_ Dmel\CG7271	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012522	400410	ST20	http://www.ncbi.nlm.nih.gov/gene/?term=400410	HCCS-1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012523	400410	ST20	http://www.ncbi.nlm.nih.gov/gene/?term=400410	HCCS-1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012524	400451	FAM174B	http://www.ncbi.nlm.nih.gov/gene/?term=400451		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012525	400506	KNOP1	http://www.ncbi.nlm.nih.gov/gene/?term=400506	"101F10.1, C16orf88, FAM191A, TSG118 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012526	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	19571010	Nucleus	HFF|HLF|HeLa cell	Fluorescence in situ hybridization	"Figure 3b: Subcellular localization analysis of lincRNAs by RNA FISH demonstrates localization of lincRNAs to the nucleus. Each panel represents the in situ hybridization of �0 fluorescently labeled DNA oligos with complementarity to the interrogated lincRNA. RNA FISH experiments were performed in male hFF for each represented lincRNA (XIST, HOTAIR, TUG-1, lincMKLN-1, lincFOXF1, and lincSFPQ), and also in female hLF for XIST (XX). White “speckles�indicate the subcellular localization of each lincRNA. The nuclear compartment is demarked by DAPI staining (purple). "
RLID00012527	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	25630241	Cytoplasm	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00012528	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00012529	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00012530	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00012531	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00012532	400550	FENDRR	http://www.ncbi.nlm.nih.gov/gene/?term=400550	"FOXF1-AS1, TCONS_00024240, lincFOXF1, onco-lncRNA-21 "	lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00012533	400569	MED11	http://www.ncbi.nlm.nih.gov/gene/?term=400569	HSPC296	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012534	4005	LMO2	http://www.ncbi.nlm.nih.gov/gene/?term=4005	"RBTN2, RBTNL1, RHOM2, TTG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012535	400619	LINC00511	http://www.ncbi.nlm.nih.gov/gene/?term=400619	"LCAL5, onco-lncRNA-12 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012536	40061	arx	http://www.ncbi.nlm.nih.gov/gene/?term=40061	"Dmel_CG3893, BcDNA:LD18018, CG3893, DmGTSF1, Dmel\CG3893, Gtsf1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012537	400713	ZNF880	http://www.ncbi.nlm.nih.gov/gene/?term=400713		mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00012538	400720	ZNF772	http://www.ncbi.nlm.nih.gov/gene/?term=400720		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012539	400720	ZNF772	http://www.ncbi.nlm.nih.gov/gene/?term=400720		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012540	400745	SH2D5	http://www.ncbi.nlm.nih.gov/gene/?term=400745		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012541	40080	CG6812	http://www.ncbi.nlm.nih.gov/gene/?term=40080	Dmel_ Dmel\CG6812	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012542	4008	LMO7	http://www.ncbi.nlm.nih.gov/gene/?term=4008	"FBX20, FBXO20, LOMP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012543	4008	LMO7	http://www.ncbi.nlm.nih.gov/gene/?term=4008	"FBX20, FBXO20, LOMP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012544	400916	CHCHD10	http://www.ncbi.nlm.nih.gov/gene/?term=400916	"C22orf16, FTDALS2, IMMD, N27C7-4, SMAJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012545	400931	MIRLET7BHG	http://www.ncbi.nlm.nih.gov/gene/?term=400931	linc-Ppara	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012546	40095	Max	http://www.ncbi.nlm.nih.gov/gene/?term=40095	"Dmel_CG9648, CG9648, Dmel\CG9648, MAX, bHLHd9, d dmax, max "	mRNA	Drosophila melanogaster	17923096	Nucleus	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012547	400960	PCBP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=400960		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012548	400961	PAIP2B	http://www.ncbi.nlm.nih.gov/gene/?term=400961		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012549	400961	PAIP2B	http://www.ncbi.nlm.nih.gov/gene/?term=400961		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012550	400961	PAIP2B	http://www.ncbi.nlm.nih.gov/gene/?term=400961		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012551	40096	CG9666	http://www.ncbi.nlm.nih.gov/gene/?term=40096	"Dmel_ Dmel\CG9666, Dromel_CG9666_FBtr0074991_mORF "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012552	400	ARL1	http://www.ncbi.nlm.nih.gov/gene/?term=400	ARFL1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012553	400	ARL1	http://www.ncbi.nlm.nih.gov/gene/?term=400	ARFL1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012554	40104	pip	http://www.ncbi.nlm.nih.gov/gene/?term=40104	"Dmel_CG9614, CG9614, Dmel\CG9614, Pipe, l(3)76BDpe-ST2, pip "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012555	401089	FOXL2NB	http://www.ncbi.nlm.nih.gov/gene/?term=401089	C3orf72	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012556	401089	FOXL2NB	http://www.ncbi.nlm.nih.gov/gene/?term=401089	C3orf72	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012557	4010	LMX1B	http://www.ncbi.nlm.nih.gov/gene/?term=4010	"LMX1.2, NPS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012558	4010	LMX1B	http://www.ncbi.nlm.nih.gov/gene/?term=4010	"LMX1.2, NPS1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012559	4010	LMX1B	http://www.ncbi.nlm.nih.gov/gene/?term=4010	"LMX1.2, NPS1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012560	401115	C4orf48	http://www.ncbi.nlm.nih.gov/gene/?term=401115	CHR4_55	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012561	401152	C4orf3	http://www.ncbi.nlm.nih.gov/gene/?term=401152		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012562	401152	C4orf3	http://www.ncbi.nlm.nih.gov/gene/?term=401152		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012563	401242	LINC01623	http://www.ncbi.nlm.nih.gov/gene/?term=401242		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012564	401251	SAPCD1	http://www.ncbi.nlm.nih.gov/gene/?term=401251	"C6orf26, NG23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012565	401262	CRIP3	http://www.ncbi.nlm.nih.gov/gene/?term=401262	"TLP, TLP-A, bA480N24.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012566	4012	LNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=4012	"CAP, IRAP, P-LAP, PLAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012567	4012	LNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=4012	"CAP, IRAP, P-LAP, PLAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012568	401397	LINC00998	http://www.ncbi.nlm.nih.gov/gene/?term=401397		lncRNA	Homo sapiens	25630241	Cytoplasm	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00012569	401466	C8orf59	http://www.ncbi.nlm.nih.gov/gene/?term=401466		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012570	40146	tey	http://www.ncbi.nlm.nih.gov/gene/?term=40146	"Dmel_CG8780, CG8780, Dmel\CG8780 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012571	401474	SAMD12	http://www.ncbi.nlm.nih.gov/gene/?term=401474		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012572	401505	TOMM5	http://www.ncbi.nlm.nih.gov/gene/?term=401505	"C9orf105, Tom5, bA613M10.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012573	401548	SNX30	http://www.ncbi.nlm.nih.gov/gene/?term=401548	ATG24A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012574	401588	ZNF674-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=401588		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012575	4015	LOX	http://www.ncbi.nlm.nih.gov/gene/?term=4015		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012576	4015	LOX	http://www.ncbi.nlm.nih.gov/gene/?term=4015		mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00012577	401612	SLC25A53	http://www.ncbi.nlm.nih.gov/gene/?term=401612	MCART6	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012578	401612	SLC25A53	http://www.ncbi.nlm.nih.gov/gene/?term=401612	MCART6	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012579	401647	GOLGA7B	http://www.ncbi.nlm.nih.gov/gene/?term=401647	"C10orf132, C10orf133, bA451M19.3, bA459F3.4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012580	40179	RhoGDI	http://www.ncbi.nlm.nih.gov/gene/?term=40179	"Dmel_CG7823, CG7823, Dmel\CG7823 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012581	40179	RhoGDI	http://www.ncbi.nlm.nih.gov/gene/?term=40179	"Dmel_CG7823, CG7823, Dmel\CG7823 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012582	402055	SRRD	http://www.ncbi.nlm.nih.gov/gene/?term=402055	"HC/HCC, SRR1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012583	40232	polo	http://www.ncbi.nlm.nih.gov/gene/?term=40232	"Dmel_CG12306, 0256/04, 1324/08, CG12306, Dmel\CG12306, PLK1, POLO, POLO/PLK1, Polo, Polo kinase, anon-WO0172774.3, l(3)01673, l(3)77Aa, l(3)S025604, l(3)S132408 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012584	402381	SOHLH1	http://www.ncbi.nlm.nih.gov/gene/?term=402381	"C9orf157, NOHLH, SPATA27, TEB2, bA100C15.3, bHLHe80 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012585	4023	LPL	http://www.ncbi.nlm.nih.gov/gene/?term=4023	"HDLCQ11, LIPD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012586	40249	RhoBTB	http://www.ncbi.nlm.nih.gov/gene/?term=40249	"Dmel_CG5701, 28574635, CG5701, Dmel\CG5701, RhoGTPase, RhoX "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012587	40249	RhoBTB	http://www.ncbi.nlm.nih.gov/gene/?term=40249	"Dmel_CG5701, 28574635, CG5701, Dmel\CG5701, RhoGTPase, RhoX "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012588	40252	CG33969	http://www.ncbi.nlm.nih.gov/gene/?term=40252	"Dmel_ CG32429, CG5571, Dmel\CG33969 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012589	40252	CG33969	http://www.ncbi.nlm.nih.gov/gene/?term=40252	"Dmel_ CG32429, CG5571, Dmel\CG33969 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012590	402665	IGLON5	http://www.ncbi.nlm.nih.gov/gene/?term=402665		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012591	4026	LPP	http://www.ncbi.nlm.nih.gov/gene/?term=4026		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012592	4026	LPP	http://www.ncbi.nlm.nih.gov/gene/?term=4026		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012593	4026	LPP	http://www.ncbi.nlm.nih.gov/gene/?term=4026		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012594	40283	Rcd2	http://www.ncbi.nlm.nih.gov/gene/?term=40283	"Dmel_CG4786, CG4786, CT15369, Dmel\CG4786 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012595	40289	CG13252	http://www.ncbi.nlm.nih.gov/gene/?term=40289	Dmel_ Dmel\CG13252	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012596	402	ARL2	http://www.ncbi.nlm.nih.gov/gene/?term=402	ARFL2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012597	402	ARL2	http://www.ncbi.nlm.nih.gov/gene/?term=402	ARFL2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012598	40314	fng	http://www.ncbi.nlm.nih.gov/gene/?term=40314	"Dmel_CG10580, CG10580, D-Fng, D-fng, Dfng, Dmel\CG10580, Fng, Frg, fg, frg, l(3)rG554 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012599	40314	fng	http://www.ncbi.nlm.nih.gov/gene/?term=40314	"Dmel_CG10580, CG10580, D-Fng, D-fng, Dfng, Dmel\CG10580, Fng, Frg, fg, frg, l(3)rG554 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012600	403187	Opa3	http://www.ncbi.nlm.nih.gov/gene/?term=403187	"D630048P19Rik, Gm1425, Gm472 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012601	40327	siz	http://www.ncbi.nlm.nih.gov/gene/?term=40327	"Dmel_CG32434, CG10577, CG12980, CG12981, CG32434, Dmel\CG32434, Loner, loner "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012602	403313	PLPP6	http://www.ncbi.nlm.nih.gov/gene/?term=403313	"PDP1, PPAPDC2, PSDP, bA6J24.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012603	4033	LRMP	http://www.ncbi.nlm.nih.gov/gene/?term=4033	JAW1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012604	403521	TPO	http://www.ncbi.nlm.nih.gov/gene/?term=403521		mRNA	Canis lupus familiaris	8269983	Nucleus	Thyroid epithelial cell	In situ hybridization	"As compared to another thyroid differentiation marker, thyroglobulin mRNA (Pohl et al., J. Cell Biol. 111, 663-672 (1990)), TPO mRNA accumulation differed by the rapidity of its control by cAMP, the pattern of its intercellular heterogeneity, and the unexpected segregation to a perinuclear region, probably the nuclear envelope that constitutes a specialized part of the endoplasmic reticulum. "
RLID00012605	403536	TPMT	http://www.ncbi.nlm.nih.gov/gene/?term=403536		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012606	4035	LRP1	http://www.ncbi.nlm.nih.gov/gene/?term=4035	"A2MR, APOER, APR, CD91, IGFBP3R, LRPA, TGFBR5, LRP1 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00012607	403647	SGK1	http://www.ncbi.nlm.nih.gov/gene/?term=403647	SGK	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012608	403680	RPL13A	http://www.ncbi.nlm.nih.gov/gene/?term=403680		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012609	403682	RPL19	http://www.ncbi.nlm.nih.gov/gene/?term=403682		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012610	40368	rgn	http://www.ncbi.nlm.nih.gov/gene/?term=40368	"Dmel_CG6014, BcDNA:GH11973, CG6014, Dmel\CG6014, l(3)00534 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012611	40368	rgn	http://www.ncbi.nlm.nih.gov/gene/?term=40368	"Dmel_CG6014, BcDNA:GH11973, CG6014, Dmel\CG6014, l(3)00534 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012612	403726	RPGR	http://www.ncbi.nlm.nih.gov/gene/?term=403726		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012613	4037	LRP3	http://www.ncbi.nlm.nih.gov/gene/?term=4037		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012614	403845	FN1	http://www.ncbi.nlm.nih.gov/gene/?term=403845	FN	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	In situ hybridization	Figure 5: Validation and expression of pseudopodial enriched mRNAs and gene products. Data are collected from Figur 5.
RLID00012615	403856	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=403856		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012616	403857	FGF2	http://www.ncbi.nlm.nih.gov/gene/?term=403857	BFGF	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012617	403871	KRAS	http://www.ncbi.nlm.nih.gov/gene/?term=403871	K-RAS	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012618	40389	VhaM9.7-b	http://www.ncbi.nlm.nih.gov/gene/?term=40389	"Dmel_CG7625, ATP6V0M9.7-2, CG7625, Dmel\CG7625, Vha M9.7-2, VhaM9.7-2, anon-WO0118547.551, vhaM9.2-2, vhaM9.7-2, vhaM9.7-b "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012619	40395	CRIF	http://www.ncbi.nlm.nih.gov/gene/?term=40395	"Dmel_CG7172, CG7172, Dmel\CG7172, anon-WO0118547.316, dCRIF "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012620	403	ARL3	http://www.ncbi.nlm.nih.gov/gene/?term=403	ARFL3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012621	404037	HAPLN4	http://www.ncbi.nlm.nih.gov/gene/?term=404037	BRAL2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012622	404093	CUEDC1	http://www.ncbi.nlm.nih.gov/gene/?term=404093		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012623	4040	LRP6	http://www.ncbi.nlm.nih.gov/gene/?term=4040	"ADCAD2, STHAG7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012624	4040	LRP6	http://www.ncbi.nlm.nih.gov/gene/?term=4040	"ADCAD2, STHAG7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012625	4041	LRP5	http://www.ncbi.nlm.nih.gov/gene/?term=4041	"BMND1, EVR1, EVR4, HBM, LR3, LRP-5, LRP7, OPPG, OPS, OPTA1, VBCH2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012626	4041	LRP5	http://www.ncbi.nlm.nih.gov/gene/?term=4041	"BMND1, EVR1, EVR4, HBM, LR3, LRP-5, LRP7, OPPG, OPS, OPTA1, VBCH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012627	404323	Olfr1040	http://www.ncbi.nlm.nih.gov/gene/?term=404323	MOR185-12	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012628	4043	LRPAP1	http://www.ncbi.nlm.nih.gov/gene/?term=4043	"A2MRAP, A2RAP, HBP44, MRAP, MYP23, RAP, alpha-2-MRAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012629	4043	LRPAP1	http://www.ncbi.nlm.nih.gov/gene/?term=4043	"A2MRAP, A2RAP, HBP44, MRAP, MYP23, RAP, alpha-2-MRAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012630	404636	FAM45A	http://www.ncbi.nlm.nih.gov/gene/?term=404636		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012631	404672	GTF2H5	http://www.ncbi.nlm.nih.gov/gene/?term=404672	"C6orf175, TFB5, TFIIH, TGF2H5, TTD, TTD-A, TTD3, TTDA, bA120J8.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012632	404672	GTF2H5	http://www.ncbi.nlm.nih.gov/gene/?term=404672	"C6orf175, TFB5, TFIIH, TGF2H5, TTD, TTD-A, TTD3, TTDA, bA120J8.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012633	4047	LSS	http://www.ncbi.nlm.nih.gov/gene/?term=4047	"CTRCT44, OSC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012634	4047	LSS	http://www.ncbi.nlm.nih.gov/gene/?term=4047	"CTRCT44, OSC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012635	40489	mael	http://www.ncbi.nlm.nih.gov/gene/?term=40489	"Dmel_CG11254, CG11254, Dmel\CG11254, MAEL, Mael, mae1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012636	4048	LTA4H	http://www.ncbi.nlm.nih.gov/gene/?term=4048		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012637	4048	LTA4H	http://www.ncbi.nlm.nih.gov/gene/?term=4048		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012638	4048	LTA4H	http://www.ncbi.nlm.nih.gov/gene/?term=4048		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012639	4048	LTA4H	http://www.ncbi.nlm.nih.gov/gene/?term=4048		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012640	40510	slif	http://www.ncbi.nlm.nih.gov/gene/?term=40510	"Dmel_CG11128, CG11128, Dmel\CG11128, SlifA, slif "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012641	4052	LTBP1	http://www.ncbi.nlm.nih.gov/gene/?term=4052		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012642	40530	abs	http://www.ncbi.nlm.nih.gov/gene/?term=40530	"Dmel_CG14637, ABS, CG14637, DmRH23, Dmel\CG14637, anon-WO0118547.315, l(3)00620, l(3)04505, l(3)06862, l(3)06863 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012643	40530	abs	http://www.ncbi.nlm.nih.gov/gene/?term=40530	"Dmel_CG14637, ABS, CG14637, DmRH23, Dmel\CG14637, anon-WO0118547.315, l(3)00620, l(3)04505, l(3)06862, l(3)06863 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012644	40535	TwdlG	http://www.ncbi.nlm.nih.gov/gene/?term=40535	"Dmel_CG14643, CG14643, Dmel\CG14643 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012645	40548	Skp2	http://www.ncbi.nlm.nih.gov/gene/?term=40548	"Dmel_CG9772, 153298_at, CG9772, Dmel\CG9772, FBXL1, SKP2, d "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012646	4054	LTBP3	http://www.ncbi.nlm.nih.gov/gene/?term=4054	"DASS, LTBP-3, LTBP2, STHAG6, pp6425 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012647	4054	LTBP3	http://www.ncbi.nlm.nih.gov/gene/?term=4054	"DASS, LTBP-3, LTBP2, STHAG6, pp6425 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012648	40554	tub	http://www.ncbi.nlm.nih.gov/gene/?term=40554	"Dmel_CG10520, CG10520, Dmel\CG10520, Tube "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012649	4055	LTBR	http://www.ncbi.nlm.nih.gov/gene/?term=4055	"CD18, D12S370, LT-BETA-R, TNF-R-III, TNFCR, TNFR-RP, TNFR2-RP, TNFR3, TNFRSF3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012650	40562	srl	http://www.ncbi.nlm.nih.gov/gene/?term=40562	"Dmel_CG9809, CG 9809, CG9809, Dmel\CG9809, PGC-1, PGC-1-alpha, Spargel, Srl, cg9809, dPCG1alpha, dPGC, dPGC-1, dPGC1 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012651	40562	srl	http://www.ncbi.nlm.nih.gov/gene/?term=40562	"Dmel_CG9809, CG 9809, CG9809, Dmel\CG9809, PGC-1, PGC-1-alpha, Spargel, Srl, cg9809, dPCG1alpha, dPGC, dPGC-1, dPGC1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012652	405754	ERVFRD-1	http://www.ncbi.nlm.nih.gov/gene/?term=405754	"ERVFRDE1, GLLL6191, HERV-FRD, HERV-W/FRD, UNQ6191, envFRD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012653	40588	Nep2	http://www.ncbi.nlm.nih.gov/gene/?term=40588	"Dmel_CG9761, BcDNA:GH07643, CG9761, DmNEP2, Dmel\CG9761, NEP2, dNEP2, nep2 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012654	40598	Hus1-like	http://www.ncbi.nlm.nih.gov/gene/?term=40598	"Dmel_CG2525, CG2525, DmHus1, Dmel\CG2525, Hus-1, Hus1, hus1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012655	405	ARNT	http://www.ncbi.nlm.nih.gov/gene/?term=405	"HIF-1-beta, HIF-1beta, HIF1-beta, HIF1B, HIF1BETA, TANGO, bHLHe2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012656	40607	Gnf1	http://www.ncbi.nlm.nih.gov/gene/?term=40607	"Dmel_CG1119, CG1119, DmRFC1, Dmel\CG1119, GTF-1, Gnf-1, Gtf1, ONF-CAACAA, RF-C 140, RFC, RFC1, RfC, RfC140, dRF-Cp140, dRFC140, gnf1, gtf1, rfc1 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012657	4061	LY6E	http://www.ncbi.nlm.nih.gov/gene/?term=4061	"RIG-E, RIGE, SCA-2, SCA2, TSA-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012658	4061	LY6E	http://www.ncbi.nlm.nih.gov/gene/?term=4061	"RIG-E, RIGE, SCA-2, SCA2, TSA-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012659	40620	cno	http://www.ncbi.nlm.nih.gov/gene/?term=40620	"Dmel_CG42312, AF-6, CG2534, CG31537, CG42312, Canoe, Cno, Dmel\CG42312, Dmel_CG2534, Dmel_CG31537, EC3-10, anon-WO0172774.47?, dlhA, lip, mis, cno "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012660	40620	cno	http://www.ncbi.nlm.nih.gov/gene/?term=40620	"Dmel_CG42312, AF-6, CG2534, CG31537, CG42312, Canoe, Cno, Dmel\CG42312, Dmel_CG2534, Dmel_CG31537, EC3-10, anon-WO0172774.47?, dlhA, lip, mis, cno "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012661	40659	Hcs	http://www.ncbi.nlm.nih.gov/gene/?term=40659	"Dmel_CG14670, CG14670, Dmel\CG14670, HCS, HSC, NEST:bs27h05 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012662	4065	LY75	http://www.ncbi.nlm.nih.gov/gene/?term=4065	"CD205, CLEC13B, DEC-205, GP200-MR6, LY-75 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012663	4065	LY75	http://www.ncbi.nlm.nih.gov/gene/?term=4065	"CD205, CLEC13B, DEC-205, GP200-MR6, LY-75 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012664	4067	LYN	http://www.ncbi.nlm.nih.gov/gene/?term=4067	"JTK8, p53Lyn, p56Lyn "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012665	4067	LYN	http://www.ncbi.nlm.nih.gov/gene/?term=4067	"JTK8, p53Lyn, p56Lyn "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012666	4067	LYN	http://www.ncbi.nlm.nih.gov/gene/?term=4067	"JTK8, p53Lyn, p56Lyn "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012667	40686	CG2911	http://www.ncbi.nlm.nih.gov/gene/?term=40686	Dmel_ Dmel\CG2911	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012668	40690	CG12171	http://www.ncbi.nlm.nih.gov/gene/?term=40690	"Dmel_ Dmel\CG12171, anon-WO0118547.83 "	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012669	4069	LYZ	http://www.ncbi.nlm.nih.gov/gene/?term=4069	"LYZF1, LZM "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012670	4069	LYZ	http://www.ncbi.nlm.nih.gov/gene/?term=4069	"LYZF1, LZM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012671	4069	LYZ	http://www.ncbi.nlm.nih.gov/gene/?term=4069	"LYZF1, LZM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012672	406	ARNTL	http://www.ncbi.nlm.nih.gov/gene/?term=406	"BMAL1, BMAL1c, JAP3, MOP3, PASD3, TIC, bHLHe5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012673	40707	CG2100	http://www.ncbi.nlm.nih.gov/gene/?term=40707	Dmel_ Dmel\CG2100	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012674	40708	CG1236	http://www.ncbi.nlm.nih.gov/gene/?term=40708	Dmel_ Dmel\CG1236	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012675	40709	Sym	http://www.ncbi.nlm.nih.gov/gene/?term=40709	"Dmel_CG2097, CG2097, Dmel\CG2097p, dSymp, Sym "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012676	4070	TACSTD2	http://www.ncbi.nlm.nih.gov/gene/?term=4070	"EGP-1, EGP1, GA733-1, GA7331, GP50, M1S1, TROP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012677	4071	TM4SF1	http://www.ncbi.nlm.nih.gov/gene/?term=4071	"H-L6, L6, M3S1, TAAL6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012678	40723	Hpr1	http://www.ncbi.nlm.nih.gov/gene/?term=40723	"Dmel_CG2031, CG2031, Dmel\CG2031, HPR1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012679	4072	EPCAM	http://www.ncbi.nlm.nih.gov/gene/?term=4072	"DIAR5, EGP-2, EGP314, EGP40, ESA, HNPCC8, KS1/4, KSA, M4S1, MIC18, MK-1, TACSTD1, TROP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012680	4072	EPCAM	http://www.ncbi.nlm.nih.gov/gene/?term=4072	"DIAR5, EGP-2, EGP314, EGP40, ESA, HNPCC8, KS1/4, KSA, M4S1, MIC18, MK-1, TACSTD1, TROP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012681	40739	Rm62	http://www.ncbi.nlm.nih.gov/gene/?term=40739	"Dmel_CG10279, 4136, CG10279, DmRH8, Dmel\CG10279, Dmp68, Lip, RM62, dmP68, l(3)01086, l(3)j3D2, l(3)j3D5, l(3)rG338, l(3)s5196, p68, rm62 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012682	4074	M6PR	http://www.ncbi.nlm.nih.gov/gene/?term=4074	"CD-M6PR, CD-MPR, MPR 46, MPR-46, MPR46, SMPR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012683	4074	M6PR	http://www.ncbi.nlm.nih.gov/gene/?term=4074	"CD-M6PR, CD-MPR, MPR 46, MPR-46, MPR46, SMPR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012684	4076	CAPRIN1	http://www.ncbi.nlm.nih.gov/gene/?term=4076	"GPIAP1, GPIP137, GRIP137, M11S1, RNG105, p137GPI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012685	4076	CAPRIN1	http://www.ncbi.nlm.nih.gov/gene/?term=4076	"GPIAP1, GPIP137, GRIP137, M11S1, RNG105, p137GPI "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012686	4076	CAPRIN1	http://www.ncbi.nlm.nih.gov/gene/?term=4076	"GPIAP1, GPIP137, GRIP137, M11S1, RNG105, p137GPI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012687	4077	NBR1	http://www.ncbi.nlm.nih.gov/gene/?term=4077	"1A1-3B, IAI3B, M17S2, MIG19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012688	4077	NBR1	http://www.ncbi.nlm.nih.gov/gene/?term=4077	"1A1-3B, IAI3B, M17S2, MIG19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012689	407800	Ecm2	http://www.ncbi.nlm.nih.gov/gene/?term=407800	"9030618O22Rik, BC065151, tenonectin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012690	407813	BC059841	http://www.ncbi.nlm.nih.gov/gene/?term=407813		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012691	407823	Baz2b	http://www.ncbi.nlm.nih.gov/gene/?term=407823	"5830435C13Rik, BC053917, D2Ertd794e "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012692	407823	Baz2b	http://www.ncbi.nlm.nih.gov/gene/?term=407823	"5830435C13Rik, BC053917, D2Ertd794e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00012693	40785	CG42724	http://www.ncbi.nlm.nih.gov/gene/?term=40785	"Dmel_ CG15187, CG31367, CG33097, Dmel\CG42724, Dmel_CG31367, Dmel_CG33097 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012694	40785	CG42724	http://www.ncbi.nlm.nih.gov/gene/?term=40785	"Dmel_ CG15187, CG31367, CG33097, Dmel\CG42724, Dmel_CG31367, Dmel_CG33097 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012695	407975	MIR17HG	http://www.ncbi.nlm.nih.gov/gene/?term=407975	"C13orf25, FGLDS2, LINC00048, MIHG1, MIRH1, MIRHG1, NCRNA00048, miR-17-92 "	lncRNA	Homo sapiens	16266980	Nucleus	Lung cancer cell	Northern blot|RT-PCR	"In addition, we were able to show predominant localization of C13orf25 transcripts within the nucleus and introduction of the expression construct of the miR-17-92 cluster, but not the putative open reading frame of C13orf25, enhancing lung cancer cell growth. "
RLID00012696	407975	MIR17HG	http://www.ncbi.nlm.nih.gov/gene/?term=407975	"C13orf25, FGLDS2, LINC00048, MIHG1, MIRH1, MIRHG1, NCRNA00048, miR-17-92 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012697	407975	MIR17HG	http://www.ncbi.nlm.nih.gov/gene/?term=407975	"C13orf25, FGLDS2, LINC00048, MIHG1, MIRH1, MIRHG1, NCRNA00048, miR-17-92 "	lncRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00012698	407	ARR3	http://www.ncbi.nlm.nih.gov/gene/?term=407	ARRX	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012699	408050	NOMO3	http://www.ncbi.nlm.nih.gov/gene/?term=408050	Nomo	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012700	408050	NOMO3	http://www.ncbi.nlm.nih.gov/gene/?term=408050	Nomo	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012701	408068	Zfp738	http://www.ncbi.nlm.nih.gov/gene/?term=408068	"3830402I07Rik, 6720487G11Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012702	40814	CG1307	http://www.ncbi.nlm.nih.gov/gene/?term=40814	"Dmel_ BG:DS00004.12, Dmel\CG1307 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012703	40815	twr	http://www.ncbi.nlm.nih.gov/gene/?term=40815	"Dmel_CG2358, AF160889, BG:DS00004.11, BcDNA:GM04682, CG2358, Dmel\CG2358, EfW5, Ov15, Spase18-21, Spase18/21, l(3)05614, l(3)84Aa "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012704	40815	twr	http://www.ncbi.nlm.nih.gov/gene/?term=40815	"Dmel_CG2358, AF160889, BG:DS00004.11, BcDNA:GM04682, CG2358, Dmel\CG2358, EfW5, Ov15, Spase18-21, Spase18/21, l(3)05614, l(3)84Aa "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012705	4082	MARCKS	http://www.ncbi.nlm.nih.gov/gene/?term=4082	"80K-L, MACS, PKCSL, PRKCSL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012706	40830	bcd	http://www.ncbi.nlm.nih.gov/gene/?term=40830	"Dmel_CG1034, BCD, BG:DS00276.7, Bcd, CG1034, Dmel\CG1034, bic, mum, prd4 "	mRNA	Drosophila melanogaster	16319114	Posterior	Oocyte	In situ hybridization	"During stages 7-9, bcd mRNA is transported to the oocyte, where it localizes as a ring in the anterior cortex. As it enters the oocyte, bcd mRNA encounters MTs necessary for its maintenance organized at the anterior cortex. In grk mutant oocytes, bcd localizes to the anterior as well as to the posterior pole. The anterior localization of bcd suggests the presence of MT minus-ends there.  "
RLID00012707	40830	bcd	http://www.ncbi.nlm.nih.gov/gene/?term=40830	"Dmel_CG1034, BCD, BG:DS00276.7, Bcd, CG1034, Dmel\CG1034, bic, mum, prd4 "	mRNA	Drosophila melanogaster	16319114	Anterior	Oocyte	In situ hybridization	"During stages 7-9, bcd mRNA is transported to the oocyte, where it localizes as a ring in the anterior cortex. "
RLID00012708	40830	bcd	http://www.ncbi.nlm.nih.gov/gene/?term=40830	"Dmel_CG1034, BCD, BG:DS00276.7, Bcd, CG1034, Dmel\CG1034, bic, mum, prd4 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012709	40831	Ama	http://www.ncbi.nlm.nih.gov/gene/?term=40831	"Dmel_CG2198, AMA, BG:DS00276.6, CG2198, CT7244, Dmel\CG2198, M109, ama "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012710	40834	ftz	http://www.ncbi.nlm.nih.gov/gene/?term=40834	"Dmel_CG2047, BG:DS07876.1, CG2047, Dm-Ftz, Dm-ftz, DmFtz, Dmel\CG2047, Dmftz, FTZ, Ftz, Ual, l(3)84Ag "	mRNA	Drosophila melanogaster	15280214	Basal	Embryo	In situ hybridization	"Whereas embryos laid by wild-type mothers have an almost exclusively apical distribution of pair-rule mRNAs such as eve, ftz, h and runt (run), those laid by egl3e/eglWU50 mothers accumulate a large proportion of these transcripts in the basal cytoplasm (Fig. 5A). "
RLID00012711	4084	MXD1	http://www.ncbi.nlm.nih.gov/gene/?term=4084	"BHLHC58, MAD, MAD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012712	4084	MXD1	http://www.ncbi.nlm.nih.gov/gene/?term=4084	"BHLHC58, MAD, MAD1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012713	40850	Alh	http://www.ncbi.nlm.nih.gov/gene/?term=40850	"Dmel_CG1070, AF10, CG1070, Dalf, Dmel\CG1070, anon-WO0118547.226, dAF10, l(3)84Be, l(3)g2, l(3)g5, l(3)j13A6, l(3)j8C8, l(3)j8c8, l(3)r13, l(3j8C8, stk "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012714	40850	Alh	http://www.ncbi.nlm.nih.gov/gene/?term=40850	"Dmel_CG1070, AF10, CG1070, Dalf, Dmel\CG1070, anon-WO0118547.226, dAF10, l(3)84Be, l(3)g2, l(3)g5, l(3)j13A6, l(3)j8C8, l(3)j8c8, l(3)r13, l(3j8C8, stk "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012715	4085	MAD2L1	http://www.ncbi.nlm.nih.gov/gene/?term=4085	"HSMAD2, MAD2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012716	4085	MAD2L1	http://www.ncbi.nlm.nih.gov/gene/?term=4085	"HSMAD2, MAD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012717	4086	SMAD1	http://www.ncbi.nlm.nih.gov/gene/?term=4086	"BSP-1, BSP1, JV4-1, JV41, MADH1, MADR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012718	4086	SMAD1	http://www.ncbi.nlm.nih.gov/gene/?term=4086	"BSP-1, BSP1, JV4-1, JV41, MADH1, MADR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012719	4087	SMAD2	http://www.ncbi.nlm.nih.gov/gene/?term=4087	"JV18, JV18-1, MADH2, MADR2, hMAD-2, hSMAD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012720	4087	SMAD2	http://www.ncbi.nlm.nih.gov/gene/?term=4087	"JV18, JV18-1, MADH2, MADR2, hMAD-2, hSMAD2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012721	4087	SMAD2	http://www.ncbi.nlm.nih.gov/gene/?term=4087	"JV18, JV18-1, MADH2, MADR2, hMAD-2, hSMAD2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012722	4087	SMAD2	http://www.ncbi.nlm.nih.gov/gene/?term=4087	"JV18, JV18-1, MADH2, MADR2, hMAD-2, hSMAD2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012723	4087	SMAD2	http://www.ncbi.nlm.nih.gov/gene/?term=4087	"JV18, JV18-1, MADH2, MADR2, hMAD-2, hSMAD2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012724	4088	SMAD3	http://www.ncbi.nlm.nih.gov/gene/?term=4088	"HSPC193, HsT17436, JV15-2, LDS1C, LDS3, MADH3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012725	4089	SMAD4	http://www.ncbi.nlm.nih.gov/gene/?term=4089	"DPC4, JIP, MADH4, MYHRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012726	4089	SMAD4	http://www.ncbi.nlm.nih.gov/gene/?term=4089	"DPC4, JIP, MADH4, MYHRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012727	4089	SMAD4	http://www.ncbi.nlm.nih.gov/gene/?term=4089	"DPC4, JIP, MADH4, MYHRS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012728	408	ARRB1	http://www.ncbi.nlm.nih.gov/gene/?term=408	"ARB1, ARR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012729	40909	alpha-Est1	http://www.ncbi.nlm.nih.gov/gene/?term=40909	"Dmel_CG1031, A, Alpha-Est1, CG1031, DmalphaE1, Dmel\CG1031, Est1, Q9VIC3_DROME, aE1, alpha est1, alphaE1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012730	4090	SMAD5	http://www.ncbi.nlm.nih.gov/gene/?term=4090	"DWFC, JV5-1, MADH5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012731	4090	SMAD5	http://www.ncbi.nlm.nih.gov/gene/?term=4090	"DWFC, JV5-1, MADH5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012732	4090	SMAD5	http://www.ncbi.nlm.nih.gov/gene/?term=4090	"DWFC, JV5-1, MADH5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012733	4091	SMAD6	http://www.ncbi.nlm.nih.gov/gene/?term=4091	"AOVD2, HsT17432, MADH6, MADH7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012734	4092	SMAD7	http://www.ncbi.nlm.nih.gov/gene/?term=4092	"CRCS3, MADH7, MADH8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012735	4092	SMAD7	http://www.ncbi.nlm.nih.gov/gene/?term=4092	"CRCS3, MADH7, MADH8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012736	40932	mRpS9	http://www.ncbi.nlm.nih.gov/gene/?term=40932	"Dmel_CG2957, CG2957, Dmel\CG2957, MRP-S9 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012737	40938	CG10445	http://www.ncbi.nlm.nih.gov/gene/?term=40938	Dmel_ Dmel\CG10445	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00012738	4093	SMAD9	http://www.ncbi.nlm.nih.gov/gene/?term=4093	"MADH6, MADH9, PPH2, SMAD8, SMAD8/9, SMAD8A, SMAD8B "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00012739	40943	CG2781	http://www.ncbi.nlm.nih.gov/gene/?term=40943	Dmel_ Dmel\CG2781	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012740	40948	CG10435	http://www.ncbi.nlm.nih.gov/gene/?term=40948	Dmel_ Dmel\CG10435	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012741	40959	CG7878	http://www.ncbi.nlm.nih.gov/gene/?term=40959	"Dmel_ DmRH26, Dmel\CG7878, cg7878 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012742	40972	RpA-70	http://www.ncbi.nlm.nih.gov/gene/?term=40972	"Dmel_CG9633, CG9633, D-RPA70, D-SSB, DRP-A, DmRPA, Dmel\CG9633, RP-A, RPA, RPA 70, RPA 70 kDa, RPA1, RPA70, RpA1, RpA70, Rpa-70, Ssb-70, dRP-A, dmrpa1, i164 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012743	40973	Mcm2	http://www.ncbi.nlm.nih.gov/gene/?term=40973	"Dmel_CG7538, CG7538, DmMCM2, DmMcm2, DmeMCM2, Dmel\CG7538, MCM2, MCM2-7, MCM2_DROME, McM2, PCR3, dMCM2, dMcm2, l(3)rL074 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012744	4097	MAFG	http://www.ncbi.nlm.nih.gov/gene/?term=4097	hMAF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012745	40980	mRpL1	http://www.ncbi.nlm.nih.gov/gene/?term=40980	"Dmel_CG7494, CG7494, Dmel\CG7494, L1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012746	40980	mRpL1	http://www.ncbi.nlm.nih.gov/gene/?term=40980	"Dmel_CG7494, CG7494, Dmel\CG7494, L1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012747	4099	MAG	http://www.ncbi.nlm.nih.gov/gene/?term=4099	"GMA, S-MAG, SIGLEC-4A, SIGLEC4A, SPG75 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012748	409	ARRB2	http://www.ncbi.nlm.nih.gov/gene/?term=409	"ARB2, ARR2, BARR2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012749	41009	CG11737	http://www.ncbi.nlm.nih.gov/gene/?term=41009	Dmel_ Dmel\CG11737	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012750	4102	MAGEA3	http://www.ncbi.nlm.nih.gov/gene/?term=4102	"CT1.3, HIP8, HYPD, MAGE3, MAGEA6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012751	4105	MAGEA6	http://www.ncbi.nlm.nih.gov/gene/?term=4105	"CT1.6, MAGE-3b, MAGE3B, MAGE6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012752	41062	pyd	http://www.ncbi.nlm.nih.gov/gene/?term=41062	"Dmel_CG43140, CG11782, CG11962, CG12409, CG31349, CG43140, CG9729, CG9731, CG9763, CT36877, DZO-1, Dmel\CG43140, Dmel_CG31349, Dmel_CG9731, Pch, Pyd, Pyd/ZO-1, Tamou, ZO-1, ZO1, dzo-1(Z01), tam, xvt, pyd "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012753	41062	pyd	http://www.ncbi.nlm.nih.gov/gene/?term=41062	"Dmel_CG43140, CG11782, CG11962, CG12409, CG31349, CG43140, CG9729, CG9731, CG9763, CT36877, DZO-1, Dmel\CG43140, Dmel_CG31349, Dmel_CG9731, Pch, Pyd, Pyd/ZO-1, Tamou, ZO-1, ZO1, dzo-1(Z01), tam, xvt, pyd "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012754	41062	pyd	http://www.ncbi.nlm.nih.gov/gene/?term=41062	"Dmel_CG43140, CG11782, CG11962, CG12409, CG31349, CG43140, CG9729, CG9731, CG9763, CT36877, DZO-1, Dmel\CG43140, Dmel_CG31349, Dmel_CG9731, Pch, Pyd, Pyd/ZO-1, Tamou, ZO-1, ZO1, dzo-1(Z01), tam, xvt, pyd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012755	41062	pyd	http://www.ncbi.nlm.nih.gov/gene/?term=41062	"Dmel_CG43140, CG11782, CG11962, CG12409, CG31349, CG43140, CG9729, CG9731, CG9763, CT36877, DZO-1, Dmel\CG43140, Dmel_CG31349, Dmel_CG9731, Pch, Pyd, Pyd/ZO-1, Tamou, ZO-1, ZO1, dzo-1(Z01), tam, xvt, pyd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012756	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	7566149	Posterior	Oocyte	In situ hybridization	"The localization of oskar (osk) RNA to the posterior pole of the developing fruit fly (Drosophila) oocyte induces the assembly of pole plasm, causing development of the abdomen and germ line. "
RLID00012757	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	11131516	Posterior	Embryo	In situ hybridization	"For its assembly, localization of gurken mRNA and its translation at the posterior pole of early oogenic stages is essential for establishing the posterior pole of the oocyte. Subsequently, oskar mRNA becomes localized to the posterior pole where its translation leads to the assembly of a functional germ plasm "
RLID00012758	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	15130488	Posterior	Oocyte	In situ hybridization	"The Staufen-dependent localization of oskar mRNA to the posterior of the Drosophila oocyte induces the formation of the pole plasm, which contains the abdominal and germline determinants "
RLID00012759	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	15939385	Posterior	Oocyte	In situ hybridization	We found anterior localized osk mRNA in 100% of the eggs from osk-bcd30 UTR heterozygous mothers while the osk transcript was also present at the posterior pole where it normally occurs.
RLID00012760	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	16319114	Posterior	Oocyte	In situ hybridization	"Oskar (osk) mRNA is transported to the posterior pole and gurken (grk) mRNA is localized to an antero-dorsal cap near the oocyte nucleus (reviewed by Riechmann and Ephrussi, 2001). The localization of these axes determining transcripts occurs in several steps and is dependent on MTs, cytoplasmic Dynein and Kinesin I.  "
RLID00012761	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	26242323	Germ plasm	Embryo	Fluorescence in situ hybridization	"Next we determined the distribution of the known germ plasm enriched mRNAs cycB, nos, pgc, gcl and oskar (osk) and one control mRNAccr4, which appears evenly distributed throughout the embryo4 (Fig. 2a,b,h). "
RLID00012762	41066	osk	http://www.ncbi.nlm.nih.gov/gene/?term=41066	"Dmel_CG10901, CG10901, Dm-osk, Dmel\CG10901, OSK, Osk, Oskar, norka "	mRNA	Drosophila melanogaster	12134163	Posterior	Oocyte	In situ hybridization	"Microtubules and the plus-end-directed microtubule motor Kinesin I are required for the selective accumulation of oskar mRNA at the posterior cortex of the Drosophila melanogaster oocyte, which is essential to posterior patterning and pole plasm assembly. "
RLID00012763	41079	Prosbeta3	http://www.ncbi.nlm.nih.gov/gene/?term=41079	"Dmel_CG11981, 11981, Beta-3, CG11981, Dmel\CG11981, Pros beta3, beta-3, beta3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012764	41087	Rel	http://www.ncbi.nlm.nih.gov/gene/?term=41087	"Dmel_CG11992, CG11992, Dmel\CG11992, NF-kappaB, NFkappaB, REL, RELI-p110, Rel/NF-kappaB, RelA, ird, ird4, l(3)neo36, rel, relish, Rel "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00012765	410	ARSA	http://www.ncbi.nlm.nih.gov/gene/?term=410	MLD	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012766	41114	CG45050	http://www.ncbi.nlm.nih.gov/gene/?term=41114	"Dmel_ BcDNA:RE70963, CG16750, CG16751, CG33187, CG33188, CG3393, CG33936, CG33937, CG43674, Dmel\CG45050, Dmel_CG33937, Dmel_CG43674, anon-85Da, anon-EST:fe1B11, anon-EST:fe2G11, drn "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012767	4111	MAGEA12	http://www.ncbi.nlm.nih.gov/gene/?term=4111	"CT1.12, MAGE12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012768	41126	alpha-Man-IIa	http://www.ncbi.nlm.nih.gov/gene/?term=41126	"Dmel_CG18802, CG18474, CG18802, CG8139, DM-GII.1, Dmel\CG18802, GMII, GmII, MAN-2, Man, Man-II, alpha-Man-II, dGMII, dGMIIb "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012769	41158	Kap-alpha3	http://www.ncbi.nlm.nih.gov/gene/?term=41158	"Dmel_CG9423, 0335/13, CG9423, Dalpha3, Dmel\CG9423, IMPalpha3, Imp alpha-3, Imp-alpha3, KAP-ALPHA3, Kap alpha3, Kap-?3, Kapalpha3, Kpna3, alphaKap3, dKap-alpha3, dimpalpha3, imp alpha3, imp-a3, imp-alpha3, impalpha3, kpn-alpha3, l(3)S033513 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012770	41158	Kap-alpha3	http://www.ncbi.nlm.nih.gov/gene/?term=41158	"Dmel_CG9423, 0335/13, CG9423, Dalpha3, Dmel\CG9423, IMPalpha3, Imp alpha-3, Imp-alpha3, KAP-ALPHA3, Kap alpha3, Kap-?3, Kapalpha3, Kpna3, alphaKap3, dKap-alpha3, dimpalpha3, imp alpha3, imp-a3, imp-alpha3, impalpha3, kpn-alpha3, l(3)S033513 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012771	4115	MAGEB4	http://www.ncbi.nlm.nih.gov/gene/?term=4115	CT3.6	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012772	4115	MAGEB4	http://www.ncbi.nlm.nih.gov/gene/?term=4115	CT3.6	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012773	4116	MAGOH	http://www.ncbi.nlm.nih.gov/gene/?term=4116	"MAGOH1A, MAGOH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012774	41171	CG9492	http://www.ncbi.nlm.nih.gov/gene/?term=41171	Dmel_ Dmel\CG9492	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012775	41178	Unc-115b	http://www.ncbi.nlm.nih.gov/gene/?term=41178	"Dmel_CG31332, CG31332, CG9489, Dmel\CG31332, anon-WO0140519.9, unc-115 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012776	41178	Unc-115b	http://www.ncbi.nlm.nih.gov/gene/?term=41178	"Dmel_CG31332, CG31332, CG9489, Dmel\CG31332, anon-WO0140519.9, unc-115 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012777	4117	MAK	http://www.ncbi.nlm.nih.gov/gene/?term=4117	RP62	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012778	4117	MAK	http://www.ncbi.nlm.nih.gov/gene/?term=4117	RP62	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012779	41180	dmt	http://www.ncbi.nlm.nih.gov/gene/?term=41180	"Dmel_CG8374, 0481/03, CG8374, Dmel\CG8374, Dmt, anon-WO0118547.317, aul, s048103 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012780	41181	hyd	http://www.ncbi.nlm.nih.gov/gene/?term=41181	"Dmel_CG9484, CG9484, Dmel\CG9484, HYD, Hyd, NP_524296.2, UBE 3A, c43, l(3)85Ea, l(3)C43, l(3)C43-3, l(3)SG33, l(3)c43, l[[3]]c43 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012781	411	ARSB	http://www.ncbi.nlm.nih.gov/gene/?term=411	"ASB, G4S, MPS6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012782	411	ARSB	http://www.ncbi.nlm.nih.gov/gene/?term=411	"ASB, G4S, MPS6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012783	41205	CG8507	http://www.ncbi.nlm.nih.gov/gene/?term=41205	Dmel_ Dmel\CG8507	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012784	41205	CG8507	http://www.ncbi.nlm.nih.gov/gene/?term=41205	Dmel_ Dmel\CG8507	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012785	41217	Glut4EF	http://www.ncbi.nlm.nih.gov/gene/?term=41217	"Dmel_CG34360, BcDNA:GH25505, BcDNA:GM06804, BcDNA:RE66512, BcDNA:RH63124, CG11676, CG12802, CG12804, CG12805, CG32469, CG33975, CG34360, CG43757, D- Dmel\CG34360, Dmel_CG12802, Dmel_CG33975, stretch "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012786	41219	Art4	http://www.ncbi.nlm.nih.gov/gene/?term=41219	"Dmel_CG5358, CARM1, CG5358, DART4, Dmel\CG5358, dArt 4 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012787	4121	MAN1A1	http://www.ncbi.nlm.nih.gov/gene/?term=4121	"HUMM3, HUMM9, MAN9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012788	4121	MAN1A1	http://www.ncbi.nlm.nih.gov/gene/?term=4121	"HUMM3, HUMM9, MAN9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012789	4122	MAN2A2	http://www.ncbi.nlm.nih.gov/gene/?term=4122	MANA2X	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012790	4122	MAN2A2	http://www.ncbi.nlm.nih.gov/gene/?term=4122	MANA2X	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012791	4123	MAN2C1	http://www.ncbi.nlm.nih.gov/gene/?term=4123	"MAN6A8, MANA, MANA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012792	4124	MAN2A1	http://www.ncbi.nlm.nih.gov/gene/?term=4124	"AMan II, GOLIM7, MANA2, MANII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012793	4124	MAN2A1	http://www.ncbi.nlm.nih.gov/gene/?term=4124	"AMan II, GOLIM7, MANA2, MANII "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012794	4124	MAN2A1	http://www.ncbi.nlm.nih.gov/gene/?term=4124	"AMan II, GOLIM7, MANA2, MANII "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00012795	41260	Bruce	http://www.ncbi.nlm.nih.gov/gene/?term=41260	"Dmel_CG6303, BRUCE, CG6303, Dmel\CG6303, bruce, dBRUCE, dBruce, dbruce, mod86 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012796	41260	Bruce	http://www.ncbi.nlm.nih.gov/gene/?term=41260	"Dmel_CG6303, BRUCE, CG6303, Dmel\CG6303, bruce, dBRUCE, dBruce, dbruce, mod86 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012797	41265	jumu	http://www.ncbi.nlm.nih.gov/gene/?term=41265	"Dmel_CG4029, 5295, CG4029, Dmel\CG4029, Dmjumu, Dom, Dwhn, E(var)631, Jumeau, Jumu, Scim31, Whn, jumeaux/Dom, l(3)06142, l(3)06439, jumu "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012798	41265	jumu	http://www.ncbi.nlm.nih.gov/gene/?term=41265	"Dmel_CG4029, 5295, CG4029, Dmel\CG4029, Dmjumu, Dom, Dwhn, E(var)631, Jumeau, Jumu, Scim31, Whn, jumeaux/Dom, l(3)06142, l(3)06439, jumu "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012799	41299	CG14693	http://www.ncbi.nlm.nih.gov/gene/?term=41299	Dmel_ Dmel\CG14693	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012800	41299	CG14693	http://www.ncbi.nlm.nih.gov/gene/?term=41299	Dmel_ Dmel\CG14693	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012801	4129	MAOB	http://www.ncbi.nlm.nih.gov/gene/?term=4129		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012802	412	STS	http://www.ncbi.nlm.nih.gov/gene/?term=412	"ARSC, ARSC1, ASC, ES, SSDD, XLI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012803	41311	Fdh	http://www.ncbi.nlm.nih.gov/gene/?term=41311	"Dmel_CG6598, ADHX, ADHX_DROME, CG6598, Dmel\CG6598, GSNOR, ODH, Odh, fdh, gfd, gfd/odh, odh "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012804	4131	MAP1B	http://www.ncbi.nlm.nih.gov/gene/?term=4131	"FUTSCH, MAP5, PPP1R102 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012805	41324	CG6629	http://www.ncbi.nlm.nih.gov/gene/?term=41324	Dmel_ Dmel\CG6629	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012806	4133	MAP2	http://www.ncbi.nlm.nih.gov/gene/?term=4133	"MAP2AB, MAP2C, MAP2 "	mRNA	Homo sapiens	1824108	Dendrite	Neuron	-	"In the case of MAP2, the mRNA that encodes the protein is also located in dendrites.  "
RLID00012807	41347	RpL3	http://www.ncbi.nlm.nih.gov/gene/?term=41347	"Dmel_CG4863, CG4863, Dmel\CG4863, L3, Rpl3, anon-EST:GressD4, chr3R:7047878..7048035, rpL3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012808	4134	MAP4	http://www.ncbi.nlm.nih.gov/gene/?term=4134		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012809	4134	MAP4	http://www.ncbi.nlm.nih.gov/gene/?term=4134		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012810	4134	MAP4	http://www.ncbi.nlm.nih.gov/gene/?term=4134		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012811	4134	MAP4	http://www.ncbi.nlm.nih.gov/gene/?term=4134		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012812	41363	pros	http://www.ncbi.nlm.nih.gov/gene/?term=41363	"Dmel_CG17228, 0244/09, 0320/10, 0441/16, 0451/09, 0563/18, 0585/13, 0664/07, 0671/02, 0763/13, 0989/01, 1135/07, 1135/09, 1167/13, 1316/02, 671/2, BcDNA:HL08040, CG17228, DMPROSPER, DROPROSA, Dmel\CG17228, PROS, PROS-1, PROS-2, Pro, Pros, Prosp, Voila, anon-WO0140519.15, l(3)10419, l(3)j12C8, l(3)j6E2, l(3)rH013, l(3)rI160, l(3)rJ806, l(3)rK137, l(3)rK204, l(3)rL433, l(3)rO534, pro, voila "	mRNA	Drosophila melanogaster	9637686	Apical	Embryo	In situ hybridization	"Miranda is required to localize prospero mRNA. prospero mRNA localizes on the apical side of neuroblasts at interphase (arrow in a) and moves to the basal cortex during mitosis (arrowhead in b). In the absence of Miranda, the RNA is evenly distributed in all neuroblasts (c,d,e).  "
RLID00012813	41363	pros	http://www.ncbi.nlm.nih.gov/gene/?term=41363	"Dmel_CG17228, 0244/09, 0320/10, 0441/16, 0451/09, 0563/18, 0585/13, 0664/07, 0671/02, 0763/13, 0989/01, 1135/07, 1135/09, 1167/13, 1316/02, 671/2, BcDNA:HL08040, CG17228, DMPROSPER, DROPROSA, Dmel\CG17228, PROS, PROS-1, PROS-2, Pro, Pros, Prosp, Voila, anon-WO0140519.15, l(3)10419, l(3)j12C8, l(3)j6E2, l(3)rH013, l(3)rI160, l(3)rJ806, l(3)rK137, l(3)rK204, l(3)rL433, l(3)rO534, pro, voila "	mRNA	Drosophila melanogaster	9637686	Basal	Embryo	In situ hybridization	"Miranda is required to localize prospero mRNA.prospero mRNA localizes on the apical side of neuroblasts at interphase (arrow in a) and moves to the basal cortex during mitosis (arrowhead in b). In the absence of Miranda, the RNA is evenly distributed in all neuroblasts (c,d,e).  "
RLID00012814	41363	pros	http://www.ncbi.nlm.nih.gov/gene/?term=41363	"Dmel_CG17228, 0244/09, 0320/10, 0441/16, 0451/09, 0563/18, 0585/13, 0664/07, 0671/02, 0763/13, 0989/01, 1135/07, 1135/09, 1167/13, 1316/02, 671/2, BcDNA:HL08040, CG17228, DMPROSPER, DROPROSA, Dmel\CG17228, PROS, PROS-1, PROS-2, Pro, Pros, Prosp, Voila, anon-WO0140519.15, l(3)10419, l(3)j12C8, l(3)j6E2, l(3)rH013, l(3)rI160, l(3)rJ806, l(3)rK137, l(3)rK204, l(3)rL433, l(3)rO534, pro, voila "	mRNA	Drosophila melanogaster	15852043	Basal	Neuroblasts	-	The localization of prospero mRNA to the basal cortex of D. melanogaster neuroblasts is also actin and myosin dependent.
RLID00012815	41391	CG6791	http://www.ncbi.nlm.nih.gov/gene/?term=41391	Dmel_ Dmel\CG6791	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012816	41397	CG14712	http://www.ncbi.nlm.nih.gov/gene/?term=41397	Dmel_ Dmel\CG14712	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012817	41397	CG14712	http://www.ncbi.nlm.nih.gov/gene/?term=41397	Dmel_ Dmel\CG14712	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012818	414070	BC026600	http://www.ncbi.nlm.nih.gov/gene/?term=414070		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012819	414093	A830082N09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=414093	Gm17567	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012820	4140	MARK3	http://www.ncbi.nlm.nih.gov/gene/?term=4140	"CTAK1, KP78, PAR1A, Par-1a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012821	4140	MARK3	http://www.ncbi.nlm.nih.gov/gene/?term=4140	"CTAK1, KP78, PAR1A, Par-1a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012822	4140	MARK3	http://www.ncbi.nlm.nih.gov/gene/?term=4140	"CTAK1, KP78, PAR1A, Par-1a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012823	4140	MARK3	http://www.ncbi.nlm.nih.gov/gene/?term=4140	"CTAK1, KP78, PAR1A, Par-1a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012824	414101	E130317F20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=414101		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012825	414109	9830163H01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=414109		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012826	414115	D330050I16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=414115		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012827	414123	Mir670hg	http://www.ncbi.nlm.nih.gov/gene/?term=414123	E530001K10Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012828	4141	MARS	http://www.ncbi.nlm.nih.gov/gene/?term=4141	"CMT2U, ILFS2, ILLD, METRS, MRS, MTRNS, SPG70 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012829	4141	MARS	http://www.ncbi.nlm.nih.gov/gene/?term=4141	"CMT2U, ILFS2, ILLD, METRS, MRS, MTRNS, SPG70 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012830	4141	MARS	http://www.ncbi.nlm.nih.gov/gene/?term=4141	"CMT2U, ILFS2, ILLD, METRS, MRS, MTRNS, SPG70 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012831	4141	MARS	http://www.ncbi.nlm.nih.gov/gene/?term=4141	"CMT2U, ILFS2, ILLD, METRS, MRS, MTRNS, SPG70 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012832	41428	ClC-a	http://www.ncbi.nlm.nih.gov/gene/?term=41428	"Dmel_CG31116, CG14726, CG31116, CG6942, CLC-2, Clc-a, DmClC-2, DmClC-a, DmClCa, Dmel\CG31116, FBgn0037951 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012833	414318	C9orf106	http://www.ncbi.nlm.nih.gov/gene/?term=414318	bA65J3.5	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00012834	414328	IDNK	http://www.ncbi.nlm.nih.gov/gene/?term=414328	"C9orf103, bA522I20.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012835	414328	IDNK	http://www.ncbi.nlm.nih.gov/gene/?term=414328	"C9orf103, bA522I20.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012836	4144	MAT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4144	"MATA2, MATII, SAMS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012837	4144	MAT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4144	"MATA2, MATII, SAMS2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012838	414519	ldlrap1-b	http://www.ncbi.nlm.nih.gov/gene/?term=414519	"arh, arh1, arh2, fhcb1, fhcb2, ldlrap1, xptb "	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00012839	414538	trim36	http://www.ncbi.nlm.nih.gov/gene/?term=414538	Haprin	mRNA	Xenopus laevis	19675128	Germ plasm	Embryo	In situ hybridization|qRT-PCR	We find that trim36 is expressed in the germ plasm and encodes a ubiquitin ligase of the Tripartite motif-containing (Trim) family.
RLID00012840	414538	trim36	http://www.ncbi.nlm.nih.gov/gene/?term=414538	Haprin	mRNA	Xenopus laevis	19675128	Vegetal	Embryo	In situ hybridization|qRT-PCR	Analysis of trim36 mRNA expression during early development further confirmed its vegetal cortex localization and also showed that trim36 is enriched in the germ plasm of oocytes and early embryos. 
RLID00012841	414538	trim36	http://www.ncbi.nlm.nih.gov/gene/?term=414538	Haprin	mRNA	Xenopus laevis	23615278	Vegetal	Oocyte|Embryo	Whole mount in situ hybridization	"Thus, Dnd1 anchors trim36 RNA to the vegetal cortex and is required for accumulation of Trim36 protein in the vegetal cortex. "
RLID00012842	414538	trim36	http://www.ncbi.nlm.nih.gov/gene/?term=414538	Haprin	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00012843	41455	mfas	http://www.ncbi.nlm.nih.gov/gene/?term=41455	"Dmel_CG3359, 87A7-9/7, BEST:GH06752, CG3359, Dmel\CG3359, Mfas, anon-87Af, anon-EST:Liang-97, anon-WO0140519.174, clone 97, gh06752 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012844	41455	mfas	http://www.ncbi.nlm.nih.gov/gene/?term=41455	"Dmel_CG3359, 87A7-9/7, BEST:GH06752, CG3359, Dmel\CG3359, Mfas, anon-87Af, anon-EST:Liang-97, anon-WO0140519.174, clone 97, gh06752 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012845	41457	Ect3	http://www.ncbi.nlm.nih.gov/gene/?term=41457	"Dmel_CG3132, 87A7-9/8, CG3132, Dmel\CG3132, anon-87Ag "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012846	414641	sesn2	http://www.ncbi.nlm.nih.gov/gene/?term=414641		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00012847	414660	MGC81075	http://www.ncbi.nlm.nih.gov/gene/?term=414660		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00012848	414660	MGC81075	http://www.ncbi.nlm.nih.gov/gene/?term=414660		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00012849	4147	MATN2	http://www.ncbi.nlm.nih.gov/gene/?term=4147		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012850	414801	Itprip	http://www.ncbi.nlm.nih.gov/gene/?term=414801	"4833424O12Rik, DANGER, mKIAA1754 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012851	41483	Su(var)3-9	http://www.ncbi.nlm.nih.gov/gene/?term=41483	"Dmel_CG43664, CG43664, CG6476, Dmel\CG43664, Dmel_CG6476, E(var)3-2, SU(VAR)3-9, SUV39, SUV39H1, Su(VAR)3-9, Su(Var)3-9, Su(var), Su(var) 3-902, Su(var)306, Su(var)310, Su(var)328, Su-var(3)9, Su-var(3)902, SuVar3-9, Suv 3-9, Suvar(3)9, Suvar3-9, Suvar39, caa56376 Suvar39 Dm, dSU(VAR)3-9, dSu(var)3-9, ptn, su(var)3-9, Su(var)3-9 "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012852	414872	Zyg11b	http://www.ncbi.nlm.nih.gov/gene/?term=414872	"1110046I03Rik, 2810482G21Rik, D4Mgi23, Gm431, mKIAA1730 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012853	414899	BLID	http://www.ncbi.nlm.nih.gov/gene/?term=414899	BRCC2	mRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	qRT-PCR	Figure S1: Polysomal gradient analysis. HT1080 cells were incubated under control (21% oxygen) or hypoxic (1% oxygen) conditions for up to 36 h as described in Figure 1. Shown are representative original RT-PCR data (30 cycles for beta-Actin and the external standard [extSt]; 35 cycles for the other genes) from pooled samples to visualize mRNA distribution following fractionation of sucrose gradients at control conditions (C) and 36 h of hypoxia (Hy). The external standard (a synthetic in vitro transcript) was diluted to appropriate concentration for qPCR and added directly after gradient fractionation and prior to RNA isolation as a technical control. The external standard served for fraction dependent normalization.
RLID00012854	414919	C8orf82	http://www.ncbi.nlm.nih.gov/gene/?term=414919		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012855	4149	MAX	http://www.ncbi.nlm.nih.gov/gene/?term=4149	bHLHd4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012856	414	ARSD	http://www.ncbi.nlm.nih.gov/gene/?term=414	ASD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012857	4150	MAZ	http://www.ncbi.nlm.nih.gov/gene/?term=4150	"PUR1, Pur-1, SAF-1, SAF-2, SAF-3, ZF87, ZNF801, Zif87 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012858	4150	MAZ	http://www.ncbi.nlm.nih.gov/gene/?term=4150	"PUR1, Pur-1, SAF-1, SAF-2, SAF-3, ZF87, ZNF801, Zif87 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012859	415115	Neurl2	http://www.ncbi.nlm.nih.gov/gene/?term=415115	"Neur2, Ozz, Ozz-E3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00012860	415116	PIM3	http://www.ncbi.nlm.nih.gov/gene/?term=415116	pim-3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012861	41511	CG10035	http://www.ncbi.nlm.nih.gov/gene/?term=41511	"Dmel_ Dmel\CG10035, anon-EST:Liang-20, clone 20 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012862	415128	CYP2E1	http://www.ncbi.nlm.nih.gov/gene/?term=415128		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00012863	4151	MB	http://www.ncbi.nlm.nih.gov/gene/?term=4151	"PVALB, myoglobgin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012864	41521	CG5167	http://www.ncbi.nlm.nih.gov/gene/?term=41521	Dmel_ Dmel\CG5167	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012865	41521	CG5167	http://www.ncbi.nlm.nih.gov/gene/?term=41521	Dmel_ Dmel\CG5167	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012866	41526	CG17202	http://www.ncbi.nlm.nih.gov/gene/?term=41526	"Dmel_ BcDNA:RH21090, Dmel\CG17202 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012867	4152	MBD1	http://www.ncbi.nlm.nih.gov/gene/?term=4152	"CXXC3, PCM1, RFT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012868	4152	MBD1	http://www.ncbi.nlm.nih.gov/gene/?term=4152	"CXXC3, PCM1, RFT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012869	4154	MBNL1	http://www.ncbi.nlm.nih.gov/gene/?term=4154	"EXP, MBNL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012870	41550	Vha55	http://www.ncbi.nlm.nih.gov/gene/?term=41550	"Dmel_CG17369, 1208/13, ATP6V1B1, CG17369, Dmel\CG17369, SzA, V-ATPase, VAT-2, l(3)87Ca, l(3)SzA, l(3)j2E9, vha55 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012871	4155	MBP	http://www.ncbi.nlm.nih.gov/gene/?term=4155		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012872	4155	MBP	http://www.ncbi.nlm.nih.gov/gene/?term=4155		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012873	41576	CG31345	http://www.ncbi.nlm.nih.gov/gene/?term=41576	"Dmel_ CG10135, CG14388, Dmel\CG31345 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012874	41576	CG31345	http://www.ncbi.nlm.nih.gov/gene/?term=41576	"Dmel_ CG10135, CG14388, Dmel\CG31345 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012875	4157	MC1R	http://www.ncbi.nlm.nih.gov/gene/?term=4157	"CMM5, MSH-R, SHEP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012876	416051	ARPC4	http://www.ncbi.nlm.nih.gov/gene/?term=416051		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00012877	416051	ARPC4	http://www.ncbi.nlm.nih.gov/gene/?term=416051		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00012878	41615	timeout	http://www.ncbi.nlm.nih.gov/gene/?term=41615	"Dmel_CG7855, CG14381, CG14382, CG7855, CG8148, Dmel\CG7855, TIM2, dtim2, tim2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012879	41627	Su(var)3-7	http://www.ncbi.nlm.nih.gov/gene/?term=41627	"Dmel_CG8599, CG8599, DmSu(var)3-7, Dmel\CG8599, SU(VAR)3-7, Su(Var)3-7, Su(var)(3)3, Su(var)(3)7, Su-var(3)7, Suvar(3)7, l(3)87El "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012880	41646	Droj2	http://www.ncbi.nlm.nih.gov/gene/?term=41646	"Dmel_CG8863, CG8863, DROJ2, Dmel\CG8863, anon-WO0118547.404 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012881	41646	Droj2	http://www.ncbi.nlm.nih.gov/gene/?term=41646	"Dmel_CG8863, CG8863, DROJ2, Dmel\CG8863, anon-WO0118547.404 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012882	416490	ARPC1B	http://www.ncbi.nlm.nih.gov/gene/?term=416490		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00012883	41650	GILT1	http://www.ncbi.nlm.nih.gov/gene/?term=41650	"Dmel_CG9796, CG9796, Dmel\CG9796, GILT "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012884	41665	CG10841	http://www.ncbi.nlm.nih.gov/gene/?term=41665	"Dmel_ Dmel\CG10841, anon-WO0140519.42 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012885	4166	CHST6	http://www.ncbi.nlm.nih.gov/gene/?term=4166	MCDC1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012886	4166	CHST6	http://www.ncbi.nlm.nih.gov/gene/?term=4166	MCDC1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012887	41670	B52	http://www.ncbi.nlm.nih.gov/gene/?term=41670	"Dmel_CG10851/SRp55, B52/dSRp55, CG10851, Dmel\CG10851, E(Dfd), E726, MabB52, RRM8, RSp55, Rbp8, SR55, SRp55, dSRp55, l(3)s2249, rrm8 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012888	41670	B52	http://www.ncbi.nlm.nih.gov/gene/?term=41670	"Dmel_CG10851/SRp55, B52/dSRp55, CG10851, Dmel\CG10851, E(Dfd), E726, MabB52, RRM8, RSp55, Rbp8, SR55, SRp55, dSRp55, l(3)s2249, rrm8 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012889	41673	Lkb1	http://www.ncbi.nlm.nih.gov/gene/?term=41673	"Dmel_CG9374, CG9374, DmLKB1, Dmel\CG9374, LKB1, LKB1/PEUTZ JEGHERS KINASE, PAR-4, PAR4, STK11, anon-EST:Posey135, dLKB1, dlkb1, lkb1, par-4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012890	416837	ARPC3	http://www.ncbi.nlm.nih.gov/gene/?term=416837		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00012891	41686	CG9312	http://www.ncbi.nlm.nih.gov/gene/?term=41686	"Dmel_ CT26517, Dmel\CG9312 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012892	4168	MCF2	http://www.ncbi.nlm.nih.gov/gene/?term=4168	"ARHGEF21, DBL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012893	41702	CG9925	http://www.ncbi.nlm.nih.gov/gene/?term=41702	Dmel_ Dmel\CG9925	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012894	4170	MCL1	http://www.ncbi.nlm.nih.gov/gene/?term=4170	"BCL2L3, EAT, MCL1-ES, MCL1L, MCL1S, Mcl-1, TM, bcl2-L-3, mcl1/EAT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012895	4170	MCL1	http://www.ncbi.nlm.nih.gov/gene/?term=4170	"BCL2L3, EAT-ES, MCL1L, MCL1S, Mcl-1, TM, bcl2-L-3, mcl1/EAT, MCL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012896	4170	MCL1	http://www.ncbi.nlm.nih.gov/gene/?term=4170	"BCL2L3, EAT-ES, MCL1L, MCL1S, Mcl-1, TM, bcl2-L-3, mcl1/EAT, MCL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012897	4170	MCL1	http://www.ncbi.nlm.nih.gov/gene/?term=4170	"BCL2L3, EAT-ES, MCL1L, MCL1S, Mcl-1, TM, bcl2-L-3, mcl1/EAT, MCL1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012898	41718	Abi	http://www.ncbi.nlm.nih.gov/gene/?term=41718	"Dmel_CG9749-1, Ablphilin, CG9749, Dmel\CG9749, abi, dAbi, Abi "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012899	4171	MCM2	http://www.ncbi.nlm.nih.gov/gene/?term=4171	"BM28, CCNL1, CDCL1, D3S3194, MITOTIN, cdc19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012900	4171	MCM2	http://www.ncbi.nlm.nih.gov/gene/?term=4171	"BM28, CCNL1, CDCL1, D3S3194, MITOTIN, cdc19 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012901	4172	MCM3	http://www.ncbi.nlm.nih.gov/gene/?term=4172	"HCC5, P1-MCM3, P1.h, RLFB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012902	4172	MCM3	http://www.ncbi.nlm.nih.gov/gene/?term=4172	"HCC5, P1-MCM3, P1.h, RLFB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012903	4172	MCM3	http://www.ncbi.nlm.nih.gov/gene/?term=4172	"HCC5, P1-MCM3, P1.h, RLFB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012904	4173	MCM4	http://www.ncbi.nlm.nih.gov/gene/?term=4173	"CDC21, CDC54, NKCD, NKGCD, P1-CDC21, hCdc21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012905	4173	MCM4	http://www.ncbi.nlm.nih.gov/gene/?term=4173	"CDC21, CDC54, NKCD, NKGCD, P1-CDC21, hCdc21 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012906	4174	MCM5	http://www.ncbi.nlm.nih.gov/gene/?term=4174	"CDC46, P1-CDC46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012907	4174	MCM5	http://www.ncbi.nlm.nih.gov/gene/?term=4174	"CDC46, P1-CDC46 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012908	41758	CG8461	http://www.ncbi.nlm.nih.gov/gene/?term=41758	Dmel_ Dmel\CG8461	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012909	4175	MCM6	http://www.ncbi.nlm.nih.gov/gene/?term=4175	"MCG40308, Mis5, P105MCM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012910	4175	MCM6	http://www.ncbi.nlm.nih.gov/gene/?term=4175	"MCG40308, Mis5, P105MCM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012911	4176	MCM7	http://www.ncbi.nlm.nih.gov/gene/?term=4176	"CDC47, MCM2, P1.1-MCM3, P1CDC47, P85MCM, PNAS146, PPP1R104 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012912	41780	BigH1	http://www.ncbi.nlm.nih.gov/gene/?term=41780	"Dmel_CG3509, CG3509, Dmel\CG3509, dBigH1 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012913	4179	CD46	http://www.ncbi.nlm.nih.gov/gene/?term=4179	"AHUS2, MCP, MIC10, TLX, TRA2.10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012914	4179	CD46	http://www.ncbi.nlm.nih.gov/gene/?term=4179	"AHUS2, MCP, MIC10, TLX, TRA2.10 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012915	4179	CD46	http://www.ncbi.nlm.nih.gov/gene/?term=4179	"AHUS2, MCP, MIC10, TLX, TRA2.10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012916	41823	GlyS	http://www.ncbi.nlm.nih.gov/gene/?term=41823	"Dmel_CG6904, CG6904, CG6940, Dmel\CG6904, GS, anon-WO0118547.108, dGS "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012917	41838	mRpS10	http://www.ncbi.nlm.nih.gov/gene/?term=41838	"Dmel_CG4247, BcDNA:GM25447, CG4247, Dmel\CG4247, MRP-S10, MrpS10 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012918	41838	mRpS10	http://www.ncbi.nlm.nih.gov/gene/?term=41838	"Dmel_CG4247, BcDNA:GM25447, CG4247, Dmel\CG4247, MRP-S10, MrpS10 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012919	41852	Tm1	http://www.ncbi.nlm.nih.gov/gene/?term=41852	"Dmel_CG4898, 1305/10, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, CG4898, Dm Tm1, Dm TmH33, Dm TmH34, DmTm1, Dmel\CG4898, PmI, TM, TM1, TMII, Tm, TmH, TmH-33, TmH-34, TmH33, TmH34, TmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, cTM, cTm, cTmII, chr3R:11122272..11122408, l(3)02299, l(3)S130510, l(3)s2958, mTmII, region 3, tm1, tmII, tropomyosin "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012920	41852	Tm1	http://www.ncbi.nlm.nih.gov/gene/?term=41852	"Dmel_CG4898, 1305/10, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, CG4898, Dm Tm1, Dm TmH33, Dm TmH34, DmTm1, Dmel\CG4898, PmI, TM, TM1, TMII, Tm, TmH, TmH-33, TmH-34, TmH33, TmH34, TmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, cTM, cTm, cTmII, chr3R:11122272..11122408, l(3)02299, l(3)S130510, l(3)s2958, mTmII, region 3, tm1, tmII, tropomyosin "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012921	41852	Tm1	http://www.ncbi.nlm.nih.gov/gene/?term=41852	"Dmel_CG4898, 1305/10, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, CG4898, Dm Tm1, Dm TmH33, Dm TmH34, DmTm1, Dmel\CG4898, PmI, TM, TM1, TMII, Tm, TmH, TmH-33, TmH-34, TmH33, TmH34, TmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, cTM, cTm, cTmII, chr3R:11122272..11122408, l(3)02299, l(3)S130510, l(3)s2958, mTmII, region 3, tm1, tmII, tropomyosin "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012922	41852	Tm1	http://www.ncbi.nlm.nih.gov/gene/?term=41852	"Dmel_CG4898, 1305/10, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, CG4898, Dm Tm1, Dm TmH33, Dm TmH34, DmTm1, Dmel\CG4898, PmI, TM, TM1, TMII, Tm, TmH, TmH-33, TmH-34, TmH33, TmH34, TmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, cTM, cTm, cTmII, chr3R:11122272..11122408, l(3)02299, l(3)S130510, l(3)s2958, mTmII, region 3, tm1, tmII, tropomyosin "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012923	41852	Tm1	http://www.ncbi.nlm.nih.gov/gene/?term=41852	"Dmel_CG4898, 1305/10, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, CG4898, Dm Tm1, Dm TmH33, Dm TmH34, DmTm1, Dmel\CG4898, PmI, TM, TM1, TMII, Tm, TmH, TmH-33, TmH-34, TmH33, TmH34, TmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, cTM, cTm, cTmII, chr3R:11122272..11122408, l(3)02299, l(3)S130510, l(3)s2958, mTmII, region 3, tm1, tmII, tropomyosin "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012924	4188	MDFI	http://www.ncbi.nlm.nih.gov/gene/?term=4188	"I-MF, I-mfa "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012925	4188	MDFI	http://www.ncbi.nlm.nih.gov/gene/?term=4188	"I-MF, I-mfa "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012926	41899	pxb	http://www.ncbi.nlm.nih.gov/gene/?term=41899	"Dmel_CG33207, BcDNA:RE16319, CG14873, CG14874, CG33207, CG33207/Pxb, Dmel\CG33207, Pxb "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012927	4189	DNAJB9	http://www.ncbi.nlm.nih.gov/gene/?term=4189	"ERdj4, MDG-1, MDG1, MST049, MSTP049 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012928	4190	MDH1	http://www.ncbi.nlm.nih.gov/gene/?term=4190	"HEL-S-32, MDH-s, MDHA, MGC:1375, MOR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012929	4190	MDH1	http://www.ncbi.nlm.nih.gov/gene/?term=4190	"HEL-S-32, MDH-s, MDHA, MGC:1375, MOR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012930	4190	MDH1	http://www.ncbi.nlm.nih.gov/gene/?term=4190	"HEL-S-32, MDH-s, MDHA, MGC:1375, MOR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012931	4191	MDH2	http://www.ncbi.nlm.nih.gov/gene/?term=4191	"M-MDH, MDH, MGC:3559, MOR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012932	4191	MDH2	http://www.ncbi.nlm.nih.gov/gene/?term=4191	"M-MDH, MDH, MGC:3559, MOR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012933	4192	MDK	http://www.ncbi.nlm.nih.gov/gene/?term=4192	"ARAP, MK, NEGF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012934	4192	MDK	http://www.ncbi.nlm.nih.gov/gene/?term=4192	"ARAP, MK, NEGF2 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00012935	4192	MDK	http://www.ncbi.nlm.nih.gov/gene/?term=4192	"ARAP, MK, NEGF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012936	4193	MDM2	http://www.ncbi.nlm.nih.gov/gene/?term=4193	"ACTFS, HDMX, hdm2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012937	4193	MDM2	http://www.ncbi.nlm.nih.gov/gene/?term=4193	"ACTFS, HDMX, hdm2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012938	4193	MDM2	http://www.ncbi.nlm.nih.gov/gene/?term=4193	"ACTFS, HDMX, hdm2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012939	4193	MDM2	http://www.ncbi.nlm.nih.gov/gene/?term=4193	"ACTFS, HDMX, hdm2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012940	4194	MDM4	http://www.ncbi.nlm.nih.gov/gene/?term=4194	"HDMX, MDMX, MRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012941	4194	MDM4	http://www.ncbi.nlm.nih.gov/gene/?term=4194	"HDMX, MDMX, MRP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012942	4194	MDM4	http://www.ncbi.nlm.nih.gov/gene/?term=4194	"HDMX, MDMX, MRP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012943	4194	MDM4	http://www.ncbi.nlm.nih.gov/gene/?term=4194	"HDMX, MDMX, MRP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012944	41967	CG6126	http://www.ncbi.nlm.nih.gov/gene/?term=41967	"Dmel_ CT19169, Dmel\CG6126 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012945	41967	CG6126	http://www.ncbi.nlm.nih.gov/gene/?term=41967	"Dmel_ CT19169, Dmel\CG6126 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012946	4199	ME1	http://www.ncbi.nlm.nih.gov/gene/?term=4199	"HUMNDME, MES "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012947	4200	ME2	http://www.ncbi.nlm.nih.gov/gene/?term=4200	ODS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012948	42015	Scp2	http://www.ncbi.nlm.nih.gov/gene/?term=42015	"Dmel_CG14904, CE, CG14904, Cex, Dcabp-A.2, Dmel\CG14904, JHDK, SCP2, cex, dSCP2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012949	4201	MEA1	http://www.ncbi.nlm.nih.gov/gene/?term=4201	"HYS, MEA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012950	4204	MECP2	http://www.ncbi.nlm.nih.gov/gene/?term=4204	"AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX, RS, RTS, RTT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012951	4204	MECP2	http://www.ncbi.nlm.nih.gov/gene/?term=4204	"AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX, RS, RTS, RTT "	mRNA	Homo sapiens	26251528	Cytoplasm	U87 cell	Immunofluorescence|Fluorescence in situ hybridization	"Providing a parsimonious explanation for these results, biochemical fractionation and in vivo localization studies revealed that MECP2 mRNA colocalized with cytoplasmic FUS(C) in insoluble aggregates, which are characteristic of ALS mutant proteins. "
RLID00012952	420519	VIM	http://www.ncbi.nlm.nih.gov/gene/?term=420519		mRNA	Gallus gallus	2738094	Lamellipodium	Skeletal Myoblast|Fibroblast	Immunocytochemistry|In situ hybridization	"Conversely only 35 % of tubulin or vimentin messages were found in lamellipodia. Two cells, analyzed for hybridization to tubulin and vimentin mRNAs showed a perinuclear localization (66% of the messages), consistent with previous work cited above. "
RLID00012953	420519	VIM	http://www.ncbi.nlm.nih.gov/gene/?term=420519		mRNA	Gallus gallus	3698103	Nucleus	Embryo blasts|Fibroblast	In situ hybridization	"Actin mRNA concentrations were highest at cell extremities, generally in lamellipodia, where grain densities were up to 16-fold higher than in areas near the nucleus. Vimentin mRNA, unlike actin mRNA, was distributed near the nucleus. Tubulin mRNA appeared most concentrated in the peripheral cytoplasm. These results demonstrate that cytoplasmic mRNAs are localized in specific, nonrandom cellular patterns and that localized concentrations of specific proteins may result from corresponding localization of their respective mRNAs. Hence, actin mRNA distribution may result in increased concentration of actin filaments in lamellipodia of motile cells. "
RLID00012954	4205	MEF2A	http://www.ncbi.nlm.nih.gov/gene/?term=4205	"ADCAD1, RSRFC4, RSRFC9, mef2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012955	42087	Brf	http://www.ncbi.nlm.nih.gov/gene/?term=42087	"Dmel_CG31256, BRF, BRF11, CG31256, CG4155, CG5419, Dmel\CG31256, TFIIIB, brf "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012956	42087	Brf	http://www.ncbi.nlm.nih.gov/gene/?term=42087	"Dmel_CG31256, BRF, BRF11, CG31256, CG4155, CG5419, Dmel\CG31256, TFIIIB, brf "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012957	4208	MEF2C	http://www.ncbi.nlm.nih.gov/gene/?term=4208	"C5DELq14.3, DEL5q14.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012958	4209	MEF2D	http://www.ncbi.nlm.nih.gov/gene/?term=4209		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012959	4210	MEFV	http://www.ncbi.nlm.nih.gov/gene/?term=4210	"FMF, MEF, TRIM20 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012960	4210	MEFV	http://www.ncbi.nlm.nih.gov/gene/?term=4210	"FMF, MEF, TRIM20 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012961	42129	CG31249	http://www.ncbi.nlm.nih.gov/gene/?term=42129	"Dmel_ CG7477, Dmel\CG31249, Q9VEG8 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012962	4212	MEIS2	http://www.ncbi.nlm.nih.gov/gene/?term=4212	"HsT18361, MRG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012963	4214	MAP3K1	http://www.ncbi.nlm.nih.gov/gene/?term=4214	"MAPKKK1, MEKK, MEKK 1, MEKK1, SRXY6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012964	4214	MAP3K1	http://www.ncbi.nlm.nih.gov/gene/?term=4214	"MAPKKK1, MEKK, MEKK 1, MEKK1, SRXY6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012965	4215	MAP3K3	http://www.ncbi.nlm.nih.gov/gene/?term=4215	"MAPKKK3, MEKK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012966	42160	htl	http://www.ncbi.nlm.nih.gov/gene/?term=42160	"Dmel_CG7223, CG7223, CT22273, CT39172, DFGF-R1, DFGF-R2, DFR-1, DFR1, DFR1/DFGF-R2, DPR3, DTRK(FR1), Dfr-1, Dfr1, DmHD-38, Dmel\CG7223, Dtk1, EMS2, FGF-R2, FGFR, FGFR2, FR1, Fr1, HD-38, HTL/FGFR1, Htl, Tk1, dtk1, i100, i150, i79, j372 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00012967	42169	PP2A-B'	http://www.ncbi.nlm.nih.gov/gene/?term=42169	"Dmel_CG7913, B', B'/PR61, B56-1, BcDNA:GM05554, CG 7913, CG7901, CG7913, Dmel\CG7913, PP2A, PP2A B', PP2A-B, PP2A[B'-1], Wrd, anon-WO0118547.420, dB56-1, dPP2A, dPP2A-B56-1, i234, pp2A-B', wrd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012968	4216	MAP3K4	http://www.ncbi.nlm.nih.gov/gene/?term=4216	"MAPKKK4, MEKK 4, MEKK4, MTK1, PRO0412 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012969	4216	MAP3K4	http://www.ncbi.nlm.nih.gov/gene/?term=4216	"MAPKKK4, MEKK 4, MEKK4, MTK1, PRO0412 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012970	4217	MAP3K5	http://www.ncbi.nlm.nih.gov/gene/?term=4217	"ASK1, MAPKKK5, MEKK5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012971	42187	CG7156	http://www.ncbi.nlm.nih.gov/gene/?term=42187	Dmel_ Dmel\CG7156	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012972	42187	CG7156	http://www.ncbi.nlm.nih.gov/gene/?term=42187	Dmel_ Dmel\CG7156	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012973	4218	RAB8A	http://www.ncbi.nlm.nih.gov/gene/?term=4218	"MEL, RAB8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012974	42196	CG8064	http://www.ncbi.nlm.nih.gov/gene/?term=42196	Dmel_ Dmel\CG8064	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012975	4221	MEN1	http://www.ncbi.nlm.nih.gov/gene/?term=4221	"MEAI, SCG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012976	4221	MEN1	http://www.ncbi.nlm.nih.gov/gene/?term=4221	"MEAI, SCG2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012977	4222	MEOX1	http://www.ncbi.nlm.nih.gov/gene/?term=4222	"KFS2, MOX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012978	42233	CG14305	http://www.ncbi.nlm.nih.gov/gene/?term=42233	Dmel_ Dmel\CG14305	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012979	42239	CstF-64	http://www.ncbi.nlm.nih.gov/gene/?term=42239	"Dmel_CG7697, CG7697, CStF 64, CstF 64, CstF64, Dmel\CG7697, dCstF64 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012980	4223	MEOX2	http://www.ncbi.nlm.nih.gov/gene/?term=4223	"GAX, MOX2 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00012981	42242	CG7702	http://www.ncbi.nlm.nih.gov/gene/?term=42242	"Dmel_ 7702, CT23351, Dmel\CG7702 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012982	42256	CG14299	http://www.ncbi.nlm.nih.gov/gene/?term=42256	Dmel_ Dmel\CG14299	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012983	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	8895662	Posterior	Oocyte	In situ hybridization	"Nos mRNA is localized to the posterior pole of the maturing oocyte during the final stages of oogenesis, af- ter the polarity of the egg chamber has broken down. "
RLID00012984	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	10415352	Posterior	Embryo	In situ hybridization	"First, the localization of nanos RNA was examined in embryos treated for 30 min with 10mg/ml of CD. Compared to control embryos (Fig. 2A), this treatment has somewhat a somewhat subtle but discernible effect on the localization of nanos RNA (Fig. 2B). In a substantial number of embryos, the RNA was still located at the posterior pole but was more diffuse and in many embryos extended further from the posterior pole. "
RLID00012985	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	15495201	Germ plasm	Oocyte|Embryo	In situ hybridization	"OSKAR (OSK) and VASA (VAS) proteins, and nanos (nos) RNA, all initially localize to the pole plasm of tud-null oocytes and embryos from tud-null mothers, while localization of germ cell-less (gcl) and polar granule component (pgc), is undetectable or severely reduced. "
RLID00012986	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	15852043	Germ plasm	Oocyte	-	"MRNAs can also become localized by passively diffusing through the cytoplasm until they are trapped by a localized anchor. Several transcripts, such as nanos, gcl (germ cell-less) and Cyclin B mRNAs, become enriched in the D. melanogaster pole plasm in this way "
RLID00012987	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	18036786	Germ plasm	Embryo	In situ hybridization	"In contrast, localization of nos to the germ plasm, but not translational regulation, is essential for nos function in the developing germ cells. "
RLID00012988	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00012989	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	25848747	Cytoplasm	Oocyte	Live imaging	Live imaging of nos mRNA showed that its localization occurs as a consequence of diffusion within the oocyte cytoplasm and entrapment at the posterior in Vas-containing RNPs known as polar granules
RLID00012990	42297	nos	http://www.ncbi.nlm.nih.gov/gene/?term=42297	"Dmel_CG5637, CG5637, DRONANOS, Dmel\CG5637, Dronanos, NANOS, NOS, Nos, l(3)07117, l(3)j3B6, l(3)j4B6, nNOS "	mRNA	Drosophila melanogaster	26242323	Germ plasm	Embryo	Fluorescence in situ hybridization	"Next we determined the distribution of the known germ plasm enriched mRNAs cycB, nos, pgc, gcl and oskar (osk) and one control mRNAccr4, which appears evenly distributed throughout the embryo4 (Fig. 2a,b,h). "
RLID00012991	42305	cry	http://www.ncbi.nlm.nih.gov/gene/?term=42305	"Dmel_CG3772, CG3772, CRY, Cry, DCry, Dm-CRY1, DmCRY, DmCRY1, Dmcry, Dmel\CG3772, anon-WO0140519.17, anon-WO0140519.19, anon-WO0140519.20, anon-WO0172774.15b, dCRY, dCry, dcry, cry "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012992	42327	Dys	http://www.ncbi.nlm.nih.gov/gene/?term=42327	"Dmel_CG34157, CG17750, CG31175, CG34157, CG7240, CG7243, CG7344, DLP, DLP1, DLP186, DLP2, DLP3, DmDLP, DmDYS, Dmel\CG34157, Dp117, Dp186, Dp205, GI3046716, IDLP, det, dmDLP, dmDp186, dmDys, dys "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012993	42327	Dys	http://www.ncbi.nlm.nih.gov/gene/?term=42327	"Dmel_CG34157, CG17750, CG31175, CG34157, CG7240, CG7243, CG7344, DLP, DLP1, DLP186, DLP2, DLP3, DmDLP, DmDYS, Dmel\CG34157, Dp117, Dp186, Dp205, GI3046716, IDLP, det, dmDLP, dmDp186, dmDys, dys "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00012994	4232	MEST	http://www.ncbi.nlm.nih.gov/gene/?term=4232	PEG1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012995	4233	MET	http://www.ncbi.nlm.nih.gov/gene/?term=4233	"AUTS9, DFNB97, HGFR, RCCP2, c-Met "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00012996	4233	MET	http://www.ncbi.nlm.nih.gov/gene/?term=4233	"AUTS9, DFNB97, HGFR, RCCP2, c-Met "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00012997	4233	MET	http://www.ncbi.nlm.nih.gov/gene/?term=4233	"AUTS9, DFNB97, HGFR, RCCP2, c-Met "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00012998	4233	MET	http://www.ncbi.nlm.nih.gov/gene/?term=4233	"AUTS9, DFNB97, HGFR, RCCP2, c-Met "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00012999	4233	MET	http://www.ncbi.nlm.nih.gov/gene/?term=4233	"AUTS9, DFNB97, HGFR, RCCP2, c-Met "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013000	4234	METTL1	http://www.ncbi.nlm.nih.gov/gene/?term=4234	"C12orf1, TRM8, TRMT8, YDL201w "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013001	4236	MFAP1	http://www.ncbi.nlm.nih.gov/gene/?term=4236		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013002	4236	MFAP1	http://www.ncbi.nlm.nih.gov/gene/?term=4236		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013003	42379	mira	http://www.ncbi.nlm.nih.gov/gene/?term=42379	"Dmel_CG12249, CG12249, Dmel\CG12249, MIR, MIRA, Mir, Mira, Miranda, mir "	mRNA	Drosophila melanogaster	9637685	Apical	Embryo	Binding assay	"We show further that Staufen, like Miranda and prospero RNA, localizes to the apical cortex then the basal cortex and that Miranda interacts with Staufen physically. "
RLID00013004	42379	mira	http://www.ncbi.nlm.nih.gov/gene/?term=42379	"Dmel_CG12249, CG12249, Dmel\CG12249, MIR, MIRA, Mir, Mira, Miranda, mir "	mRNA	Drosophila melanogaster	9637685	Basal	Embryo	Binding assay	"We show further that Staufen, like Miranda and prospero RNA, localizes to the apical cortex then the basal cortex and that Miranda interacts with Staufen physically. "
RLID00013005	42379	mira	http://www.ncbi.nlm.nih.gov/gene/?term=42379	"Dmel_CG12249, CG12249, Dmel\CG12249, MIR, MIRA, Mir, Mira, Miranda, mir "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013006	42379	mira	http://www.ncbi.nlm.nih.gov/gene/?term=42379	"Dmel_CG12249, CG12249, Dmel\CG12249, MIR, MIRA, Mir, Mira, Miranda, mir "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013007	42379	mira	http://www.ncbi.nlm.nih.gov/gene/?term=42379	"Dmel_CG12249, CG12249, Dmel\CG12249, MIR, MIRA, Mir, Mira, Miranda, mir "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013008	42385	MED25	http://www.ncbi.nlm.nih.gov/gene/?term=42385	"Dmel_CG12254, Arc92, CG12254, Dmel\CG12254, LD07688, Med25, dARC92, dDrip97, med25 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013009	4238	MFAP3	http://www.ncbi.nlm.nih.gov/gene/?term=4238		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013010	4240	MFGE8	http://www.ncbi.nlm.nih.gov/gene/?term=4240	"BA46, EDIL1, HMFG, HsT19888, MFG-E8, MFGM, OAcGD3S, SED1, SPAG10, hP47 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013011	42433	TFAM	http://www.ncbi.nlm.nih.gov/gene/?term=42433	"Dmel_CG4217, CG4217, D-mtTFA, Dmel\CG4217, MTTFA, Tfam, d-TFAM, d-mttfa, d-tfam, mtTFA, mttfa, tfam "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013012	42445	H	http://www.ncbi.nlm.nih.gov/gene/?term=42445	"Dmel_CG5460, CG5460, Dmel\CG5460 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00013013	42451	CG4000	http://www.ncbi.nlm.nih.gov/gene/?term=42451	Dmel_ Dmel\CG4000	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013014	42453	Cdk2	http://www.ncbi.nlm.nih.gov/gene/?term=42453	"Dmel_CG10498, CDC2C, CDC2c, CDK2, CDK2/CDC2c, CG10498, Cdc2c, Dcdc2c, DmCdc2, DmCdk2, Dmcdc2c, Dmel\CG10498, S(Sev-CycE)3A, cdc2c, cdk2, dCdk2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013015	4245	MGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=4245	"GLCNAC-TI, GLCT1, GLYT1, GNT-1, GNT-I, MGAT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013016	42460	Syp	http://www.ncbi.nlm.nih.gov/gene/?term=42460	"Dmel_CG17838, AI945337, CG17838, Dmel\CG17838, anon-WO0118547.613, cg17838, l(3)03806, syp "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013017	4247	MGAT2	http://www.ncbi.nlm.nih.gov/gene/?term=4247	"CDG2A, CDGS2, GLCNACTII, GNT-II, GNT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013018	4247	MGAT2	http://www.ncbi.nlm.nih.gov/gene/?term=4247	"CDG2A, CDGS2, GLCNACTII, GNT-II, GNT2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013019	4247	MGAT2	http://www.ncbi.nlm.nih.gov/gene/?term=4247	"CDG2A, CDGS2, GLCNACTII, GNT-II, GNT2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013020	4248	MGAT3	http://www.ncbi.nlm.nih.gov/gene/?term=4248	"GNT-III, GNT3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013021	4249	MGAT5	http://www.ncbi.nlm.nih.gov/gene/?term=4249	"GNT-V, GNT-VA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013022	42502	ppan	http://www.ncbi.nlm.nih.gov/gene/?term=42502	"Dmel_CG5786, CG5786, Dmel\CG5786, PPAN, Ppan, l(3)02231, l(3)j6B6 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013023	4253	CTAGE5	http://www.ncbi.nlm.nih.gov/gene/?term=4253	"MEA6, MGEA, MGEA11, MGEA6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013024	4254	KITLG	http://www.ncbi.nlm.nih.gov/gene/?term=4254	"DCUA, FPH2, FPHH, KL-1, Kitl, MGF, SCF, SF, SHEP7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013025	4254	KITLG	http://www.ncbi.nlm.nih.gov/gene/?term=4254	"DCUA, FPH2, FPHH, KL-1, Kitl, MGF, SCF, SF, SHEP7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013026	4255	MGMT	http://www.ncbi.nlm.nih.gov/gene/?term=4255		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013027	42564	tsl	http://www.ncbi.nlm.nih.gov/gene/?term=42564	"Dmel_CG6705, CG6705, Dm-tsl, Dmel\CG6705, Tsl, fs(3)00617 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013028	42564	tsl	http://www.ncbi.nlm.nih.gov/gene/?term=42564	"Dmel_CG6705, CG6705, Dm-tsl, Dmel\CG6705, Tsl, fs(3)00617 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013029	42567	CASK	http://www.ncbi.nlm.nih.gov/gene/?term=42567	"Dmel_CG6703, CAKI, CAMGUK, CG13412, CG13413, CG6703, CMG, CMG/CASK, Caki, CamGUK, CamguK, Camguk, Cask, Cmg, DLin-2, Dmel\CG6703, RE09582p, caki, camguk, cask, cmg, dCASK "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013030	42567	CASK	http://www.ncbi.nlm.nih.gov/gene/?term=42567	"Dmel_CG6703, CAKI, CAMGUK, CG13412, CG13413, CG6703, CMG, CMG/CASK, Caki, CamGUK, CamguK, Camguk, Cask, Cmg, DLin-2, Dmel\CG6703, RE09582p, caki, camguk, cask, cmg, dCASK "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013031	4257	MGST1	http://www.ncbi.nlm.nih.gov/gene/?term=4257	"GST12, MGST, MGST-I "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013032	4257	MGST1	http://www.ncbi.nlm.nih.gov/gene/?term=4257	"GST12, MGST, MGST-I "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013033	42581	CG6678	http://www.ncbi.nlm.nih.gov/gene/?term=42581	Dmel_ Dmel\CG6678	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013034	4258	MGST2	http://www.ncbi.nlm.nih.gov/gene/?term=4258	"GST2, MGST-II "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013035	4258	MGST2	http://www.ncbi.nlm.nih.gov/gene/?term=4258	"GST2, MGST-II "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013036	4258	MGST2	http://www.ncbi.nlm.nih.gov/gene/?term=4258	"GST2, MGST-II "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013037	4259	MGST3	http://www.ncbi.nlm.nih.gov/gene/?term=4259	GST-III	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013038	4259	MGST3	http://www.ncbi.nlm.nih.gov/gene/?term=4259	GST-III	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013039	4261	CIITA	http://www.ncbi.nlm.nih.gov/gene/?term=4261	"C2TAIV, MHC2TA, NLRA, CIITA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013040	4261	CIITA	http://www.ncbi.nlm.nih.gov/gene/?term=4261	"C2TAIV, MHC2TA, NLRA, CIITA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013041	42634	mats	http://www.ncbi.nlm.nih.gov/gene/?term=42634	"Dmel_CG13852, CG13852, DMob1, Dmel\CG13852, Dmob1, Mats, Mob1, anon-WO0118547.303, dmob1 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013042	42659	CG33110	http://www.ncbi.nlm.nih.gov/gene/?term=42659	"Dmel_ CG13844, CG6926, Dmel\CG33110 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013043	4267	CD99	http://www.ncbi.nlm.nih.gov/gene/?term=4267	"HBA71, MIC2, MIC2X, MIC2Y, MSK5X "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013044	4267	CD99	http://www.ncbi.nlm.nih.gov/gene/?term=4267	"HBA71, MIC2, MIC2X, MIC2Y, MSK5X "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013045	4267	CD99	http://www.ncbi.nlm.nih.gov/gene/?term=4267	"HBA71, MIC2, MIC2X, MIC2Y, MSK5X "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013046	42702	Usp12-46	http://www.ncbi.nlm.nih.gov/gene/?term=42702	"Dmel_CG7023, CG7023, Dmel\CG7023, Q9VCT9 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013047	42751	CG13827	http://www.ncbi.nlm.nih.gov/gene/?term=42751	"Dmel_ BcDNA:RE30473, Dmel\CG13827, PEX11C "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013048	42754	CG6763	http://www.ncbi.nlm.nih.gov/gene/?term=42754	Dmel_ Dmel\CG6763	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013049	42762	CG4408	http://www.ncbi.nlm.nih.gov/gene/?term=42762	"Dmel_ BEST:GH09055, Dmel\CG4408 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013050	42773	CG10175	http://www.ncbi.nlm.nih.gov/gene/?term=42773	Dmel_ Dmel\CG10175	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013051	4277	MICB	http://www.ncbi.nlm.nih.gov/gene/?term=4277	PERB11.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013052	42784	CG31145	http://www.ncbi.nlm.nih.gov/gene/?term=42784	"Dmel_ CG10187, CG13820, CG13821, Dmel\CG31145 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013053	42784	CG31145	http://www.ncbi.nlm.nih.gov/gene/?term=42784	"Dmel_ CG10187, CG13820, CG13821, Dmel\CG31145 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013054	42784	CG31145	http://www.ncbi.nlm.nih.gov/gene/?term=42784	"Dmel_ CG10187, CG13820, CG13821, Dmel\CG31145 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013055	42793	CG10254	http://www.ncbi.nlm.nih.gov/gene/?term=42793	"Dmel_ BcDNA:LD22087, Dmel\CG10254 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013056	42793	CG10254	http://www.ncbi.nlm.nih.gov/gene/?term=42793	"Dmel_ BcDNA:LD22087, Dmel\CG10254 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013057	427	ASAH1	http://www.ncbi.nlm.nih.gov/gene/?term=427	"AC, ACDase, ASAH, PHP, PHP32, SMAPME "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013058	427	ASAH1	http://www.ncbi.nlm.nih.gov/gene/?term=427	"AC, ACDase, ASAH, PHP, PHP32, SMAPME "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013059	4281	MID1	http://www.ncbi.nlm.nih.gov/gene/?term=4281	"BBBG1, FXY, GBBB1, MIDIN, OGS1, OS, OSX, RNF59, TRIM18, XPRF, ZNFXY "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013060	4281	MID1	http://www.ncbi.nlm.nih.gov/gene/?term=4281	"BBBG1, FXY, GBBB1, MIDIN, OGS1, OS, OSX, RNF59, TRIM18, XPRF, ZNFXY "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013061	4282	MIF	http://www.ncbi.nlm.nih.gov/gene/?term=4282	"GIF, GLIF, MMIF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013062	4282	MIF	http://www.ncbi.nlm.nih.gov/gene/?term=4282	"GIF, GLIF, MMIF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013063	42854	Syx1A	http://www.ncbi.nlm.nih.gov/gene/?term=42854	"Dmel_CG31136, CG10716, CG18615, CG31136, CG31136/CG33100, CG5448, CT30033, Dm Syx1, DmSyx1A, Dmel\CG31136, SYX, SYX 1A, SYX1A, Syt1A, Syx, Syx-1A, Syx1, Syx1a, SyxA, anon-EST:Gibbs4, anon-WO02059370.54, dSyx1, dsyn-1A, l(3)06737, synt, syt-1A, syx, syx-1, syx-1A, syx1, syx1A "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013064	42854	Syx1A	http://www.ncbi.nlm.nih.gov/gene/?term=42854	"Dmel_CG31136, CG10716, CG18615, CG31136, CG31136/CG33100, CG5448, CT30033, Dm Syx1, DmSyx1A, Dmel\CG31136, SYX, SYX 1A, SYX1A, Syt1A, Syx, Syx-1A, Syx1, Syx1a, SyxA, anon-EST:Gibbs4, anon-WO02059370.54, dSyx1, dsyn-1A, l(3)06737, synt, syt-1A, syx, syx-1, syx-1A, syx1, syx1A "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013065	42859	CG13607	http://www.ncbi.nlm.nih.gov/gene/?term=42859	"Dmel_ 150482_at, Dmel\CG13607 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013066	4285	MIPEP	http://www.ncbi.nlm.nih.gov/gene/?term=4285	"HMIP, MIP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013067	4286	MITF	http://www.ncbi.nlm.nih.gov/gene/?term=4286	"CMM8, MI, WS2, WS2A, bHLHe32 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013068	42879	CG17786	http://www.ncbi.nlm.nih.gov/gene/?term=42879	Dmel_ Dmel\CG17786	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013069	42879	CG17786	http://www.ncbi.nlm.nih.gov/gene/?term=42879	Dmel_ Dmel\CG17786	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013070	42879	CG17786	http://www.ncbi.nlm.nih.gov/gene/?term=42879	Dmel_ Dmel\CG17786	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013071	4287	ATXN3	http://www.ncbi.nlm.nih.gov/gene/?term=4287	"AT3, ATX3, JOS, MJD, MJD1, SCA3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013072	4287	ATXN3	http://www.ncbi.nlm.nih.gov/gene/?term=4287	"AT3, ATX3, JOS, MJD, MJD1, SCA3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013073	42880	twin	http://www.ncbi.nlm.nih.gov/gene/?term=42880	"Dmel_CG31137, BEST:GH20274, CCR4, CG17741, CG31137, CG5534, CT39331, Ccr4, Dmel\CG31137, Twin, ccr4, twn "	mRNA	Drosophila melanogaster	26242323	Germ plasm	Embryo	Fluorescence in situ hybridization	"Next we determined the distribution of the known germ plasm enriched mRNAs cycB, nos, pgc, gcl and oskar (osk) and one control mRNAccr4, which appears evenly distributed throughout the embryo4 (Fig. 2a,b,h). "
RLID00013074	42880	twin	http://www.ncbi.nlm.nih.gov/gene/?term=42880	"Dmel_CG31137, BEST:GH20274, CCR4, CG17741, CG31137, CG5534, CT39331, Ccr4, Dmel\CG31137, Twin, ccr4, twn "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013075	4288	MKI67	http://www.ncbi.nlm.nih.gov/gene/?term=4288	"KIA, MIB-, MIB-1, PPP1R105 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013076	42896	crb	http://www.ncbi.nlm.nih.gov/gene/?term=42896	"Dmel_CG6383, 0509/20, 1384/04, CG6383, CRB, CT19912, Crb, Crbs, Crumbs, DmCrb, Dmel\CG6383, crumb, far, l(3)07207, l(3)S050920, l(3)S058104, l(3)j1B5 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013077	42899	CG5728	http://www.ncbi.nlm.nih.gov/gene/?term=42899	Dmel_ Dmel\CG5728	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013078	4289	MKLN1	http://www.ncbi.nlm.nih.gov/gene/?term=4289	TWA2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013079	4289	MKLN1	http://www.ncbi.nlm.nih.gov/gene/?term=4289	TWA2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013080	429041	ARPC2	http://www.ncbi.nlm.nih.gov/gene/?term=429041		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00013081	429041	ARPC2	http://www.ncbi.nlm.nih.gov/gene/?term=429041		mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00013082	429075	ARPC5	http://www.ncbi.nlm.nih.gov/gene/?term=429075	APOBEC4	mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"The localization of the Arp2/3 complex mRNAs is dependent on both actin filaments and microtubules, because disruption of either cytoskeletal system (with cytochalasin D and colchicine, respectively) inhibited the localization of all seven subunit mRNAs. To address these questions, double detection of two types of mRNAs simultaneously in the same cells was performed by sequential FISH-TSA. As shown in Fig. 5A-C, Arp3 mRNA appears not to be precisely colocalized with β-actin mRNA, although they both concentrate together in the protrusions. In addition, the Arp2 and Arp3 mRNAs also do not colocalize, although they are both concentrated together in the protrusions (Fig. 5D-F). "
RLID00013083	429075	ARPC5	http://www.ncbi.nlm.nih.gov/gene/?term=429075	APOBEC4	mRNA	Gallus gallus	15923655	Cell leading edge	Fibroblast	Fluorescence in situ hybridization	"Figure 7: Quantification of Arp2/3-complex mRNA localization in fibroblasts. The proportion of the cells with localized mRNA was quantified by counting all the cells in randomly selected fields in the fluorescence microscope. 300-500 cells were scored for each mRNA from three independent experiments. Error bars indicate s.e.m. **, statistically significant (P<0.01) differences from control basal level of poly-A RNA. "
RLID00013084	4291	MLF1	http://www.ncbi.nlm.nih.gov/gene/?term=4291		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013085	4291	MLF1	http://www.ncbi.nlm.nih.gov/gene/?term=4291		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013086	4292	MLH1	http://www.ncbi.nlm.nih.gov/gene/?term=4292	"COCA2, FCC2, HNPCC, HNPCC2, hMLH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013087	42946	asp	http://www.ncbi.nlm.nih.gov/gene/?term=42946	"Dmel_CG6875, ASP, Asp, CG6875, Dm Asp, Dmel\CG6875, anon-96Aa, anon-WO0118547.279 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013088	4294	MAP3K10	http://www.ncbi.nlm.nih.gov/gene/?term=4294	"MEKK10, MLK2, MST "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013089	4296	MAP3K11	http://www.ncbi.nlm.nih.gov/gene/?term=4296	"MEKK11, MLK-3, MLK3, PTK1, SPRK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013090	42971	CycB3	http://www.ncbi.nlm.nih.gov/gene/?term=42971	"Dmel_CG5814, CG5814, Cyc B3, Dmel\CG5814, anon-WO0118547.414, cycB3, l(3)L6540 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013091	4297	KMT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4297	"ALL-1, CXXC7, HRX, HTRX1, MLL, MLL-AF9, MLL/GAS7, MLL1, MLL1A, TET1-MLL, TRX1, WDSTS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013092	4297	KMT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4297	"ALL-1, CXXC7, HRX, HTRX1, MLL, MLL-AF9, MLL/GAS7, MLL1, MLL1A, TET1-MLL, TRX1, WDSTS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013093	42993	Hr96	http://www.ncbi.nlm.nih.gov/gene/?term=42993	"Dmel_CG11783, CG11783, DHR96, Dhr96, Dmel\CG11783, HR96, NR1J1, dHR96 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013094	429	ASCL1	http://www.ncbi.nlm.nih.gov/gene/?term=429	"ASH1, HASH1, MASH1, bHLHa46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013095	43005	OstStt3	http://www.ncbi.nlm.nih.gov/gene/?term=43005	"Dmel_CG7748, BcDNA.GM01838, BcDNA:GM01838, CG7748, Dmel\CG7748, STT, anon-WO03054008.7, l(3)j2D9 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013096	4301	MLLT4	http://www.ncbi.nlm.nih.gov/gene/?term=4301	"AF6, MLL-AF6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013097	4301	MLLT4	http://www.ncbi.nlm.nih.gov/gene/?term=4301	"AF6, MLL-AF6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013098	4303	FOXO4	http://www.ncbi.nlm.nih.gov/gene/?term=4303	"AFX, AFX1, MLLT7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013099	43043	CG10425	http://www.ncbi.nlm.nih.gov/gene/?term=43043	Dmel_ Dmel\CG10425	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013100	43067	CHKov1	http://www.ncbi.nlm.nih.gov/gene/?term=43067	"Dmel_CG10618, BcDNA:GH03753, CG10618, Dmel\CG10618, ref(3)D "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013101	43067	CHKov1	http://www.ncbi.nlm.nih.gov/gene/?term=43067	"Dmel_CG10618, BcDNA:GH03753, CG10618, Dmel\CG10618, ref(3)D "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013102	43067	CHKov1	http://www.ncbi.nlm.nih.gov/gene/?term=43067	"Dmel_CG10618, BcDNA:GH03753, CG10618, Dmel\CG10618, ref(3)D "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013103	43067	CHKov1	http://www.ncbi.nlm.nih.gov/gene/?term=43067	"Dmel_CG10618, BcDNA:GH03753, CG10618, Dmel\CG10618, ref(3)D "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013104	43087	msi	http://www.ncbi.nlm.nih.gov/gene/?term=43087	"Dmel_CG5099, CG5099, DMSIDNA, Dmel\CG5099, MSI, Msi, SIDNA, anon-EST:Liang-2.35, clone 2.35, dMsi "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013105	43087	msi	http://www.ncbi.nlm.nih.gov/gene/?term=43087	"Dmel_CG5099, CG5099, DMSIDNA, Dmel\CG5099, MSI, Msi, SIDNA, anon-EST:Liang-2.35, clone 2.35, dMsi "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013106	4308	TRPM1	http://www.ncbi.nlm.nih.gov/gene/?term=4308	"CSNB1C, LTRPC1, MLSN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013107	43093	jigr1	http://www.ncbi.nlm.nih.gov/gene/?term=43093	"Dmel_CG17383, CG17383, Dmel\CG17383, JIGR-1, JIGR1, bs29f05.y1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013108	43096	RASSF8	http://www.ncbi.nlm.nih.gov/gene/?term=43096	"Dmel_CG5053, Boa, CG5053, Dmel\CG5053, d dmRASSF7/8 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013109	430	ASCL2	http://www.ncbi.nlm.nih.gov/gene/?term=430	"ASH2, HASH2, MASH2, bHLHa45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013110	4311	MME	http://www.ncbi.nlm.nih.gov/gene/?term=4311	"CALLA, CD10, NEP, SFE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013111	4313	MMP2	http://www.ncbi.nlm.nih.gov/gene/?term=4313	"CLG4, CLG4A, MMP-2, MMP-II, MONA, TBE-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013112	431676	krt8	http://www.ncbi.nlm.nih.gov/gene/?term=431676	"KERATIN8, XCK1, card2, ck8, cyk8, k2c8, krt2-5 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013113	43186	CG33970	http://www.ncbi.nlm.nih.gov/gene/?term=43186	"Dmel_ CG14559, CG31085, CG6162, CG6166, Dmel\CG33970 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013114	4318	MMP9	http://www.ncbi.nlm.nih.gov/gene/?term=4318	"CLG4B, GELB, MANDP2, MMP-9 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00013115	43192	CG5447	http://www.ncbi.nlm.nih.gov/gene/?term=43192	Dmel_ Dmel\CG5447	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013116	43192	CG5447	http://www.ncbi.nlm.nih.gov/gene/?term=43192	Dmel_ Dmel\CG5447	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013117	432058	pgam1	http://www.ncbi.nlm.nih.gov/gene/?term=432058		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013118	4320	MMP11	http://www.ncbi.nlm.nih.gov/gene/?term=4320	"SL-3, ST3, STMY3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013119	432219	cab39	http://www.ncbi.nlm.nih.gov/gene/?term=432219		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013120	43222	Tl	http://www.ncbi.nlm.nih.gov/gene/?term=43222	"Dmel_CG5490, CG5490, CT17414, Dmel\CG5490, EP(3)1051, EP1051, Fs(1)Tl, Fs(3)Tl, T1, TL, TOL, Toll-1, Toll1, dToll, dToll1, mat(3)9, mel(3)10, mel(3)9, tl, toll, toll-1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013121	432245	arl8b	http://www.ncbi.nlm.nih.gov/gene/?term=432245	arl10c	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013122	432264	pced1a	http://www.ncbi.nlm.nih.gov/gene/?term=432264	fam113a	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013123	43228	ball	http://www.ncbi.nlm.nih.gov/gene/?term=43228	"Dmel_CG6386, BALL, Ball, BcDNA:LD09009, CG6386, Dmel\CG6386, NHK-1, NHK1, VRK, nhk-1, trip "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013124	432369	ATP5EP2	http://www.ncbi.nlm.nih.gov/gene/?term=432369		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013125	432449	A230081H15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=432449		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013126	432450	Nkain2	http://www.ncbi.nlm.nih.gov/gene/?term=432450	"6330571D19Rik, AW455467, Tcba1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013127	432467	Hnrnph3	http://www.ncbi.nlm.nih.gov/gene/?term=432467	"AA693301, AI666703, Hnrph3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013128	432486	Gnptab	http://www.ncbi.nlm.nih.gov/gene/?term=432486	"EG432486, mKIAA1208 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013129	4324	MMP15	http://www.ncbi.nlm.nih.gov/gene/?term=4324	"MMP-15, MT2-MMP, MT2MMP, MTMMP2, SMCP-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013130	4324	MMP15	http://www.ncbi.nlm.nih.gov/gene/?term=4324	"MMP-15, MT2-MMP, MT2MMP, MTMMP2, SMCP-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013131	432500	Gm29674	http://www.ncbi.nlm.nih.gov/gene/?term=432500		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013132	432508	Cpsf6	http://www.ncbi.nlm.nih.gov/gene/?term=432508	"4733401N12Rik, AI256641, CFIM, CFIM68, HPBRII-4, HPBRII-7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013133	432518	LOC432518	http://www.ncbi.nlm.nih.gov/gene/?term=432518		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013134	432572	Specc1	http://www.ncbi.nlm.nih.gov/gene/?term=432572	"2810012G08Rik, B230396K10Rik, Cytsb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013135	4325	MMP16	http://www.ncbi.nlm.nih.gov/gene/?term=4325	"C8orf57, MMP-X2, MT-MMP2, MT-MMP3, MT3-MMP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013136	432685	LOC432685	http://www.ncbi.nlm.nih.gov/gene/?term=432685		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013137	4326	MMP17	http://www.ncbi.nlm.nih.gov/gene/?term=4326	"MMP-17, MT4-MMP, MT4MMP, MTMMP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013138	4327027	LOC4327027	http://www.ncbi.nlm.nih.gov/gene/?term=4327027	"OSNPB_010762500, GLUA-1, GLUA1, Gt2, glutelin "	mRNA	Oryza sativa	24682961	Endoplasmic reticulum	Seed	Northern blot|RT-PCR	"This particle is then exported and moves via the cytoskeleton to the cortical ER. At some point, the complex disassembles and prolamine and glutelin RNAs are targeted to either the PB- or cis-ER, respectively. "
RLID00013139	432736	Vmn1r209	http://www.ncbi.nlm.nih.gov/gene/?term=432736	"Gm11315, OTTMUSG00000000514 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013140	4327	MMP19	http://www.ncbi.nlm.nih.gov/gene/?term=4327	"CODA, MMP18, RASI-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013141	432881	Gm5466	http://www.ncbi.nlm.nih.gov/gene/?term=432881	EG432881	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013142	4328881	LOC4328881	http://www.ncbi.nlm.nih.gov/gene/?term=4328881	"OSNPB_020249600, GLUB-2, GLUB2, GluB-7, GluB7 "	mRNA	Oryza sativa	24682961	Endoplasmic reticulum	Seed	Northern blot|RT-PCR	"This particle is then exported and moves via the cytoskeleton to the cortical ER. At some point, the complex disassembles and prolamine and glutelin RNAs are targeted to either the PB- or cis-ER, respectively. "
RLID00013143	4328968	LOC4328968	http://www.ncbi.nlm.nih.gov/gene/?term=4328968	"OSNPB_020268100, GLUB-5, GluB5, glutelin "	mRNA	Oryza sativa	24682961	Endoplasmic reticulum	Seed	Northern blot|RT-PCR	"This particle is then exported and moves via the cytoskeleton to the cortical ER. At some point, the complex disassembles and prolamine and glutelin RNAs are targeted to either the PB- or cis-ER, respectively. "
RLID00013144	4328969	LOC4328969	http://www.ncbi.nlm.nih.gov/gene/?term=4328969	"OSNPB_020268300, GLUB-4, GluB4, glutelin "	mRNA	Oryza sativa	24682961	Endoplasmic reticulum	Seed	Northern blot|RT-PCR	"This particle is then exported and moves via the cytoskeleton to the cortical ER. At some point, the complex disassembles and prolamine and glutelin RNAs are targeted to either the PB- or cis-ER, respectively. "
RLID00013145	43294	Hmu	http://www.ncbi.nlm.nih.gov/gene/?term=43294	"Dmel_CG3373, CG3373, Dmel\CG3373, RRM5, Rbp5, SPH210, rrm5 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013146	432956	D030024E09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=432956		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013147	432961	LOC432961	http://www.ncbi.nlm.nih.gov/gene/?term=432961		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013148	4329	ALDH6A1	http://www.ncbi.nlm.nih.gov/gene/?term=4329	"MMSADHA, MMSDH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013149	432	ASGR1	http://www.ncbi.nlm.nih.gov/gene/?term=432	"ASGPR, ASGPR1, CLEC4H1, HL-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013150	4331	MNAT1	http://www.ncbi.nlm.nih.gov/gene/?term=4331	"CAP35, MAT1, RNF66, TFB3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013151	4331	MNAT1	http://www.ncbi.nlm.nih.gov/gene/?term=4331	"CAP35, MAT1, RNF66, TFB3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013152	433216	Gm5510	http://www.ncbi.nlm.nih.gov/gene/?term=433216	EG433216	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013153	433230	Nsa2-ps1	http://www.ncbi.nlm.nih.gov/gene/?term=433230	"EG433230, Gm19415, Gm5515 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013154	43323	Mlc1	http://www.ncbi.nlm.nih.gov/gene/?term=43323	"Dmel_CG5596, CG5596, DmMLC1, Dmel\CG5596, ELC, FBgn0002772, LC1, MLC, MLC-ALK, MLC1, Mlc-1, MlcI, Mlci, chr3R:23484557..23484663, mlc, mlc-alk, mlc1, mlcl "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013155	43323	Mlc1	http://www.ncbi.nlm.nih.gov/gene/?term=43323	"Dmel_CG5596, CG5596, DmMLC1, Dmel\CG5596, ELC, FBgn0002772, LC1, MLC, MLC-ALK, MLC1, Mlc-1, MlcI, Mlci, chr3R:23484557..23484663, mlc, mlc-alk, mlc1, mlcl "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013156	433256	Acsl5	http://www.ncbi.nlm.nih.gov/gene/?term=433256	"1700030F05Rik, ACS2, ACS5, Facl5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013157	433261	Gm5521	http://www.ncbi.nlm.nih.gov/gene/?term=433261	EG433261	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013158	4333164	LOC4333164	http://www.ncbi.nlm.nih.gov/gene/?term=4333164	"OSNPB_030427300, GLUA-3, GLUA3, Gt22, Gt3, glutelin "	mRNA	Oryza sativa	24682961	Endoplasmic reticulum	Seed	Northern blot|RT-PCR	"This particle is then exported and moves via the cytoskeleton to the cortical ER. At some point, the complex disassembles and prolamine and glutelin RNAs are targeted to either the PB- or cis-ER, respectively. "
RLID00013159	433375	Creg1	http://www.ncbi.nlm.nih.gov/gene/?term=433375	"AA755314, Creg "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013160	433394	LOC433394	http://www.ncbi.nlm.nih.gov/gene/?term=433394		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013161	433406	Gm13363	http://www.ncbi.nlm.nih.gov/gene/?term=433406	OTTMUSG00000011595	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013162	433426	Gm13490	http://www.ncbi.nlm.nih.gov/gene/?term=433426	OTTMUSG00000012405	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013163	433502	Wfdc6b	http://www.ncbi.nlm.nih.gov/gene/?term=433502	"WAP6b, Wfdc6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013164	43350	mino	http://www.ncbi.nlm.nih.gov/gene/?term=43350	"Dmel_CG5508, 152088_at, BcDNA:GH07066, CG5508, Dmel\CG5508, GPAT1 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013165	43354	Gp93	http://www.ncbi.nlm.nih.gov/gene/?term=43354	"Dmel_CG5520, CG5520, CT17486, Dmel\CG5520, GP93, Hsp90, dGRP94, gp93, p93 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013166	433586	Maml3	http://www.ncbi.nlm.nih.gov/gene/?term=433586	"AV234550, BC049812, Mam-2, mKIAA1816 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013167	433598	Gm5539	http://www.ncbi.nlm.nih.gov/gene/?term=433598	EG433598	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013168	433698	Fam205a1	http://www.ncbi.nlm.nih.gov/gene/?term=433698	"Gm12429, OTTMUSG00000006791 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013169	433702	Ncbp1	http://www.ncbi.nlm.nih.gov/gene/?term=433702	"AU014645, AW538051, CBP80 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013170	43374	Moca-cyp	http://www.ncbi.nlm.nih.gov/gene/?term=43374	"Dmel_CG1866, BEST:LD38313, CG1866, Dmel\CG1866, anon-WO0147981.13, anon-WO0147981.4, anon-WO0147981.5, moca "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013171	433759	Hdac1	http://www.ncbi.nlm.nih.gov/gene/?term=433759	"HD1-ps, MommeD5, RPD3, Hdac1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013172	433766	Trim63	http://www.ncbi.nlm.nih.gov/gene/?term=433766	"MuRF1, RF1, Rnf28 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013173	4337	MOCS1	http://www.ncbi.nlm.nih.gov/gene/?term=4337	"MIG11, MOCOD, MOCODA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013174	433844	Gm10482	http://www.ncbi.nlm.nih.gov/gene/?term=433844	"EG433844, ENSMUSG00000073226 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013175	43385	Hrb98DE	http://www.ncbi.nlm.nih.gov/gene/?term=43385	"Dmel_CG9983, CG9983, Dmel\CG9983, E7Delta6, HDP(P9), HRB98DE, HRB98DE/hrp38, Hrb1, Hrb98 de/Hrp38, Hrp38, Pen9, anon-E7Delta6, hnRNP A2/B1, hrb98 de, hrb98DE, hrp38, p9, Hrb98DE "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013176	433864	Nom1	http://www.ncbi.nlm.nih.gov/gene/?term=433864	"D5Kng1, Gm1040 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013177	4338	MOCS2	http://www.ncbi.nlm.nih.gov/gene/?term=4338	"MCBPE, MOCO1, MOCODB, MPTS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013178	4339221	LOC4339221	http://www.ncbi.nlm.nih.gov/gene/?term=4339221	"OSNPB_050499100, OJ1057_B02.5 "	mRNA	Oryza sativa	22168839	Endoplasmic reticulum	Endosperm	RT-PCR	"In situ RT-PCR analysis revealed that α-globulin RNAs are not distributed to the cisternal ER as expected for a PSV-localized protein, but instead are targeted to the protein body-ER (PB-ER) by a regulated process requiring cis-sorting sequences. "
RLID00013179	433931	Pigg	http://www.ncbi.nlm.nih.gov/gene/?term=433931	Gpi7	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013180	433941	Gm5561	http://www.ncbi.nlm.nih.gov/gene/?term=433941		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013181	43394	CG10000	http://www.ncbi.nlm.nih.gov/gene/?term=43394	"Dmel_ Dmel\CG10000, dppGalNAcT10 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013182	433955	Gm5564	http://www.ncbi.nlm.nih.gov/gene/?term=433955	EG433955	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013183	43402	WASp	http://www.ncbi.nlm.nih.gov/gene/?term=43402	"Dmel_CG1520, CG1520, D-WASP, Dm WASP, DmWASP, Dmel\CG1520, WASP, WSP, Wasp, Wsp, dWASP, wasp, wsp "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013184	4341135	LOC4341135	http://www.ncbi.nlm.nih.gov/gene/?term=4341135	"OSNPB_060507200, prolamin "	mRNA	Oryza sativa	9490759	Ribosome	Seed	RNA blot	"The increase in prolamine mRNA in the soluble fraction of the NaF gradient indicates that ribosome-free prolamine mRNA remains associated with membrane-stripped PBs. These results suggest that ribosome-free prolamine mRNA interacts with a putative RNA-binding activity near or on the PB surface. Overall, these results indicate the presence of a prolamine mRNA-binding activity that requires relatively high ionic-strength levels to release the RNA from the PBs. "
RLID00013185	43415	Doa	http://www.ncbi.nlm.nih.gov/gene/?term=43415	"Dmel_CG42320, 0844/02, CG1658, CG31049, CG33204, CG33553, CG42320, DOA, DOA/CLK2, Dmel\CG42320, Dmel_CG33204, Dmel_CG33553, Msu, doa, l(3)01705, l(3)S084402, l(3)s2784 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013186	43415	Doa	http://www.ncbi.nlm.nih.gov/gene/?term=43415	"Dmel_CG42320, 0844/02, CG1658, CG31049, CG33204, CG33553, CG42320, DOA, DOA/CLK2, Dmel\CG42320, Dmel_CG33204, Dmel_CG33553, Msu, doa, l(3)01705, l(3)S084402, l(3)s2784 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013187	43415	Doa	http://www.ncbi.nlm.nih.gov/gene/?term=43415	"Dmel_CG42320, 0844/02, CG1658, CG31049, CG33204, CG33553, CG42320, DOA, DOA/CLK2, Dmel\CG42320, Dmel_CG33204, Dmel_CG33553, Msu, doa, l(3)01705, l(3)S084402, l(3)s2784 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013188	434178	Zfp141	http://www.ncbi.nlm.nih.gov/gene/?term=434178		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013189	434200	Gm5597	http://www.ncbi.nlm.nih.gov/gene/?term=434200		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013190	434232	Iqck	http://www.ncbi.nlm.nih.gov/gene/?term=434232	A230094G09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013191	434233	Gm5601	http://www.ncbi.nlm.nih.gov/gene/?term=434233	EG434233	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013192	434234	2610020H08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=434234		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013193	43426	Cpsf100	http://www.ncbi.nlm.nih.gov/gene/?term=43426	"Dmel_CG1957, BcDNA:LD14168, CG1957, CPSF-100, CPSF100, Dmel\CG1957 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013194	43429	CG11837	http://www.ncbi.nlm.nih.gov/gene/?term=43429	"Dmel_ Dim1, Dmel\CG11837, FBgn0039627 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013195	43439	yem	http://www.ncbi.nlm.nih.gov/gene/?term=43439	"Dmel_CG14513, CG11879, CG14513, Dmel\CG14513, Yemalpha, yG4.5, yT4.5-alpha, yema, yemalpha, yem "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013196	4343	MOV10	http://www.ncbi.nlm.nih.gov/gene/?term=4343	"fSAP113, gb110 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013197	434401	Gm5616	http://www.ncbi.nlm.nih.gov/gene/?term=434401	EG434401	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013198	434404	Rps6-ps3	http://www.ncbi.nlm.nih.gov/gene/?term=434404	"EG434404, Gm5618 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013199	434423	Dppa5a	http://www.ncbi.nlm.nih.gov/gene/?term=434423	"AA536857, Dppa5, Esg1, ecat2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013200	4345	CD200	http://www.ncbi.nlm.nih.gov/gene/?term=4345	"MOX1, MOX2, MRC, OX-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013201	43466	stg	http://www.ncbi.nlm.nih.gov/gene/?term=43466	"Dmel_CG1395, 0224/06, 0245/03, 0439/22, 0730/13, 0896/05, 0967/05, 0980/06, 1083/13, 1089/08, 1143/02, 5473, CDC25, CDC25[string], CG1395, Cdc25, Cdc25[Stg], Cdc25[String], Cdc25[stg], Cdc25[string], Cdc25c, Dmel\CG1395, EP1213, S(rux)3A, STG, SY3-4, Stg, String/Cdc25, anon-EST:Liang-2.21, cdc25, cdc25[string], clone 2.21, l(3)01235, l(3)j10B9, l(3)j1D3, l(3)j1E3, l(3)j3D1, l(3)s2213, st[cdc25], str/cdc25, stg "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013202	434794	Xlr4a	http://www.ncbi.nlm.nih.gov/gene/?term=434794		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013203	43481	alph	http://www.ncbi.nlm.nih.gov/gene/?term=43481	"Dmel_CG1906, CG1906, Dmel\CG1906, PP2Cb, SK3-1, pp2c99B "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013204	43483	CG1907	http://www.ncbi.nlm.nih.gov/gene/?term=43483	"Dmel_ CG 1907, Dmel\CG1907 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013205	4348563	LOC4348563	http://www.ncbi.nlm.nih.gov/gene/?term=4348563	"OSNPB_100400200, GLUA-2, GLUA2, Gt1 "	mRNA	Oryza sativa	24682961	Endoplasmic reticulum	Seed	Northern blot|RT-PCR	"This particle is then exported and moves via the cytoskeleton to the cortical ER. At some point, the complex disassembles and prolamine and glutelin RNAs are targeted to either the PB- or cis-ER, respectively. "
RLID00013206	4350	MPG	http://www.ncbi.nlm.nih.gov/gene/?term=4350	"AAG, ADPG, APNG, CRA36.1, MDG, Mid1, PIG11, PIG16, anpg "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013207	4350	MPG	http://www.ncbi.nlm.nih.gov/gene/?term=4350	"AAG, ADPG, APNG, CRA36.1, MDG, Mid1, PIG11, PIG16, anpg "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013208	4351	MPI	http://www.ncbi.nlm.nih.gov/gene/?term=4351	"CDG1B, PMI, PMI1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013209	4351	MPI	http://www.ncbi.nlm.nih.gov/gene/?term=4351	"CDG1B, PMI, PMI1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013210	4351	MPI	http://www.ncbi.nlm.nih.gov/gene/?term=4351	"CDG1B, PMI, PMI1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013211	43523	neo	http://www.ncbi.nlm.nih.gov/gene/?term=43523	"Dmel_CG7802, CG7802, Dmel\CG7802 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013212	4352	MPL	http://www.ncbi.nlm.nih.gov/gene/?term=4352	"C-MPL, CD110V, THCYT2, TPOR, MPL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013213	4352	MPL	http://www.ncbi.nlm.nih.gov/gene/?term=4352	"C-MPL, CD110V, THCYT2, TPOR, MPL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013214	4353	MPO	http://www.ncbi.nlm.nih.gov/gene/?term=4353		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013215	4354	MPP1	http://www.ncbi.nlm.nih.gov/gene/?term=4354	"AAG12, DXS552E, EMP55, MRG1, PEMP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013216	4355	MPP2	http://www.ncbi.nlm.nih.gov/gene/?term=4355	DLG2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013217	43560	Nlp	http://www.ncbi.nlm.nih.gov/gene/?term=43560	"Dmel_CG7917, CG7917, CRP1, Crp1, Dmel\CG7917, NLP, dNLP, dNLP-S, nlp, p22 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013218	435684	Shf	http://www.ncbi.nlm.nih.gov/gene/?term=435684		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013219	43570	Sry-beta	http://www.ncbi.nlm.nih.gov/gene/?term=43570	"Dmel_CG7938, CG7938, Dmel\CG7938, Srybeta, ser, sry, sry beta, sry-b, sry-beta, sryb, srybeta "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013220	43570	Sry-beta	http://www.ncbi.nlm.nih.gov/gene/?term=43570	"Dmel_CG7938, CG7938, Dmel\CG7938, Srybeta, ser, sry, sry beta, sry-b, sry-beta, sryb, srybeta "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013221	435766	Tnni3k	http://www.ncbi.nlm.nih.gov/gene/?term=435766	"Cark, D830019J24Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013222	43588	CG1983	http://www.ncbi.nlm.nih.gov/gene/?term=43588	Dmel_ Dmel\CG1983	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013223	4358	MPV17	http://www.ncbi.nlm.nih.gov/gene/?term=4358	"MTDPS6, SYM1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013224	4358	MPV17	http://www.ncbi.nlm.nih.gov/gene/?term=4358	"MTDPS6, SYM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013225	43591	CG9747	http://www.ncbi.nlm.nih.gov/gene/?term=43591	Dmel_ Dmel\CG9747	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013226	43591	CG9747	http://www.ncbi.nlm.nih.gov/gene/?term=43591	Dmel_ Dmel\CG9747	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013227	435	ASL	http://www.ncbi.nlm.nih.gov/gene/?term=435	ASAL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013228	435	ASL	http://www.ncbi.nlm.nih.gov/gene/?term=435	ASAL	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013229	4361	MRE11A	http://www.ncbi.nlm.nih.gov/gene/?term=4361	"ATLD, HNGS1, MRE11, MRE11B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013230	43633	tmod	http://www.ncbi.nlm.nih.gov/gene/?term=43633	"Dmel_CG1539, 1309/10, CG11493, CG1539, CG15540, CT3919, CT41421, Dmel\CG1539, E42, Tmod, l(3)00848, l(3)S130910, spdo "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013231	43633	tmod	http://www.ncbi.nlm.nih.gov/gene/?term=43633	"Dmel_CG1539, 1309/10, CG11493, CG1539, CG15540, CT3919, CT41421, Dmel\CG1539, E42, Tmod, l(3)00848, l(3)S130910, spdo "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013232	4363	ABCC1	http://www.ncbi.nlm.nih.gov/gene/?term=4363	"ABC29, ABCC, GS-X, MRP, MRP1 "	mRNA	Homo sapiens	21854988	Mitochondrion	-	Next-generation sequencing	"Firstly, to validate the two-phase sequencing approach, we considered three noncoding RNAs (ncRNAs), 5S rRNA, MRP and RNase P, that have been previously shown to be present in the mitochondrial matrix (Wang et al., 2010), finding all transcripts, though lowly expressed, enriched in mitoplasts (Figure S2D). "
RLID00013233	43640	PH4alphaPV	http://www.ncbi.nlm.nih.gov/gene/?term=43640	"Dmel_CG31015, CG31015, CG9713, Dmel\CG31015 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013234	43648	Npc2g	http://www.ncbi.nlm.nih.gov/gene/?term=43648	"Dmel_CG11314, BcDNA:RE56164, CG11314, Dmel\CG11314, npc2g "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013235	43649	Npc2h	http://www.ncbi.nlm.nih.gov/gene/?term=43649	"Dmel_CG11315, BcDNA:GH26608, BcDNA:RH04252, BcDNA:RH68460, CG11315, DmML1A, Dmel\CG11315, npc2h "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013236	43650	zfh1	http://www.ncbi.nlm.nih.gov/gene/?term=43650	"Dmel_CG1322, CG1322, Dmel\CG1322, ZFH-1, ZFH1, Zfh-1, Zfh1, Zfh1a, l(3)00865, zfh-1, zfl-1, zhf1 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00013237	43654	cindr	http://www.ncbi.nlm.nih.gov/gene/?term=43654	"Dmel_CG31012, BcDNA:GH03163, CD2AP, CG11316, CG1408, CG31012, Cindr, Dmel\CG31012 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013238	43662	Sap-r	http://www.ncbi.nlm.nih.gov/gene/?term=43662	"Dmel_CG12070, Apa, BcDNA:GH08312, CG12070, DAPA, Dmel\CG12070, Ov9, P110, Sap-R, Sapr, anon-EST:ParkEST270, sap-r "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013239	43694	CG12054	http://www.ncbi.nlm.nih.gov/gene/?term=43694	Dmel_ Dmel\CG12054	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013240	43749	faf	http://www.ncbi.nlm.nih.gov/gene/?term=43749	"Dmel_CG1945, BcDNA.LD22582, BcDNA:LD22582, CG1945, Dmel\CG1945, Faf, Fat, P55824 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013241	43772	CG2316	http://www.ncbi.nlm.nih.gov/gene/?term=43772	Dmel_ Dmel\CG2316	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013242	43775	Crk	http://www.ncbi.nlm.nih.gov/gene/?term=43775	"Dmel_CG1587, CG1587, CRK, D-CRK, D-Crk, DCrk, Dcrk, Dmel\CG1587, crk, dCRK, dCrk "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013243	43777	CG31999	http://www.ncbi.nlm.nih.gov/gene/?term=43777	"Dmel_ CG10323, CG11288, CT31491, CT7856, Dmel\CG31999 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013244	43786	Zip102B	http://www.ncbi.nlm.nih.gov/gene/?term=43786	"Dmel_CG2177, CG2177, Dmel\CG2177, cg2177, dZip102B "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013245	43788	Hcf	http://www.ncbi.nlm.nih.gov/gene/?term=43788	"Dmel_CG1710, CG1710, Dmel\CG1710, HCF, HCF1, HCF_DROME1, anon-WO0172774.48, dHCF, dHcf, dHcf1, Hcf "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00013246	43792	CaMKI	http://www.ncbi.nlm.nih.gov/gene/?term=43792	"Dmel_CG1495, CG1495, Calcium/calmodulin-dependent protein kinase, CamKI, Dmel\CG1495, caMKI, camKI, dCKI "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013247	43793	bip2	http://www.ncbi.nlm.nih.gov/gene/?term=43793	"Dmel_CG2009, BIP2, Bip2, CG2009, DmTAF3, Dmel\CG2009, TAF155, TAF3, TAFII155, TAF[[II]]155, TFIID, bip-II, dBIP2, dTAFII3, dTAF[[II]]155, dmTAF3, i163, i31 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136). These 27 genes came from TABLE 1. "
RLID00013248	43797	Pur-alpha	http://www.ncbi.nlm.nih.gov/gene/?term=43797	"Dmel_CG1507, CG1507, Dmel\CG1507, PURalpha, Pur alpha, Pur-a, dPur alpha, pur-alpha "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013249	43797	Pur-alpha	http://www.ncbi.nlm.nih.gov/gene/?term=43797	"Dmel_CG1507, CG1507, Dmel\CG1507, PURalpha, Pur alpha, Pur-a, dPur alpha, pur-alpha "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013250	4379919	CG17698	http://www.ncbi.nlm.nih.gov/gene/?term=4379919	"Dmel_ CAMKIIB, CAMKIIb, CG40297, Dmel\CG17698 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013251	4379919	CG17698	http://www.ncbi.nlm.nih.gov/gene/?term=4379919	"Dmel_ CAMKIIB, CAMKIIb, CG40297, Dmel\CG17698 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013252	43804	mav	http://www.ncbi.nlm.nih.gov/gene/?term=43804	"Dmel_CG1901, CG1901, Dmel\CG1901, MAV, Mav, TGF-b "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013253	43804	mav	http://www.ncbi.nlm.nih.gov/gene/?term=43804	"Dmel_CG1901, CG1901, Dmel\CG1901, MAV, Mav, TGF-b "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013254	43811	myo	http://www.ncbi.nlm.nih.gov/gene/?term=43811	"Dmel_CG1838, BcDNA:LD02307, CG1838, Dmel\CG1838, MYO, Myo, Myoglianin, myg "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013255	43816	MED26	http://www.ncbi.nlm.nih.gov/gene/?term=43816	"Dmel_CG1793, ARC 70, Arc70, CG1793, CG1823, Dmel\CG1793, Med26, dARC70 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00013256	43816	MED26	http://www.ncbi.nlm.nih.gov/gene/?term=43816	"Dmel_CG1793, ARC 70, Arc70, CG1793, CG1823, Dmel\CG1793, Med26, dARC70 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013257	43816	MED26	http://www.ncbi.nlm.nih.gov/gene/?term=43816	"Dmel_CG1793, ARC 70, Arc70, CG1793, CG1823, Dmel\CG1793, Med26, dARC70 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013258	43819	pho	http://www.ncbi.nlm.nih.gov/gene/?term=43819	"Dmel_CG17743, CG17743, Dmel\CG17743, PHO, PHO/YY1, Pho, YY1, dYY1, l(4)102EFc, l(4)29, l(4)BU-2, l(4)OC-1, l(4)pho "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013259	43823	Arf102F	http://www.ncbi.nlm.nih.gov/gene/?term=43823	"Dmel_CG11027, ARF2, ARFII, Arf102E, Arf4, Arf5, CG11027, Dmel\CG11027, P40945, arf102F, dARFII "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013260	43830	CG11076	http://www.ncbi.nlm.nih.gov/gene/?term=43830	Dmel_ Dmel\CG11076	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013261	43830	CG11076	http://www.ncbi.nlm.nih.gov/gene/?term=43830	Dmel_ Dmel\CG11076	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013262	43839	eIF4G	http://www.ncbi.nlm.nih.gov/gene/?term=43839	"Dmel_CG10811, CG10811, Dmel\CG10811, EIF4G, Eif4G, deIF4G, eIF-4G, eIF4g, p200 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013263	43906	skd	http://www.ncbi.nlm.nih.gov/gene/?term=43906	"Dmel_CG9936, CG9936, Dmel\CG9936, LD28662, MED13, Med13, Pap, Pap/Trap, SPH203, Scad78, Skd, Skd/Med13, Skd/Pap/Bli, Srb9/AMIB/PAP/TRAP240, TRAP240, Trap240, bli, bls, dMED13, dTRAP240, dTrap240, dmMED13, l(3)L7062, l(3)rK760, pap, pap/dTRAP240, siren9 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013264	43906	skd	http://www.ncbi.nlm.nih.gov/gene/?term=43906	"Dmel_CG9936, CG9936, Dmel\CG9936, LD28662, MED13, Med13, Pap, Pap/Trap, SPH203, Scad78, Skd, Skd/Med13, Skd/Pap/Bli, Srb9/AMIB/PAP/TRAP240, TRAP240, Trap240, bli, bls, dMED13, dTRAP240, dTrap240, dmMED13, l(3)L7062, l(3)rK760, pap, pap/dTRAP240, siren9 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013265	43934	gom	http://www.ncbi.nlm.nih.gov/gene/?term=43934	"Dmel_CG6727, CG6727, Dmel\CG6727 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013266	43934	gom	http://www.ncbi.nlm.nih.gov/gene/?term=43934	"Dmel_CG6727, CG6727, Dmel\CG6727 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013267	43934	gom	http://www.ncbi.nlm.nih.gov/gene/?term=43934	"Dmel_CG6727, CG6727, Dmel\CG6727 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013268	43936	Men-b	http://www.ncbi.nlm.nih.gov/gene/?term=43936	"Dmel_CG5889, CG5889, Dmel\CG5889, MDH, Mdh, anon-EST:Posey79 "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013269	43981	DIP1	http://www.ncbi.nlm.nih.gov/gene/?term=43981	"Dmel_CG17686, CG17686, Dmel\CG17686, TO34, TO67, UbxBP1, clot 10495, clot 2020, dip1, dip1a, klt "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013270	43981	DIP1	http://www.ncbi.nlm.nih.gov/gene/?term=43981	"Dmel_CG17686, CG17686, Dmel\CG17686, TO34, TO67, UbxBP1, clot 10495, clot 2020, dip1, dip1a, klt "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013271	439921	MXRA7	http://www.ncbi.nlm.nih.gov/gene/?term=439921	"PS1TP1, TMAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013272	439921	MXRA7	http://www.ncbi.nlm.nih.gov/gene/?term=439921	"PS1TP1, TMAP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013273	439921	MXRA7	http://www.ncbi.nlm.nih.gov/gene/?term=439921	"PS1TP1, TMAP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013274	439921	MXRA7	http://www.ncbi.nlm.nih.gov/gene/?term=439921	"PS1TP1, TMAP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013275	43997	jbug	http://www.ncbi.nlm.nih.gov/gene/?term=43997	"Dmel_CG30092, AAF46896, CG11605, CG13525, CG30092, CG3550, Dmel\CG30092, Jbug "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013276	43997	jbug	http://www.ncbi.nlm.nih.gov/gene/?term=43997	"Dmel_CG30092, AAF46896, CG11605, CG13525, CG30092, CG3550, Dmel\CG30092, Jbug "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013277	43999	trbl	http://www.ncbi.nlm.nih.gov/gene/?term=43999	"Dmel_CG5408, CG5408, Dmel\CG5408, Trbl, trb "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013278	439	ASNA1	http://www.ncbi.nlm.nih.gov/gene/?term=439	"ARSA-I, ARSA1, ASNA-I, GET3, TRC40, hASNA-I "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013279	439	ASNA1	http://www.ncbi.nlm.nih.gov/gene/?term=439	"ARSA-I, ARSA1, ASNA-I, GET3, TRC40, hASNA-I "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013280	43	ACHE	http://www.ncbi.nlm.nih.gov/gene/?term=43	"ACEE, ARACHE, N-ACHE, YT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013281	440026	TMEM41B	http://www.ncbi.nlm.nih.gov/gene/?term=440026		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013282	44007	COQ7	http://www.ncbi.nlm.nih.gov/gene/?term=44007	"Dmel_CG14437, CG14437, Dclk1, Dmel\CG14437 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013283	440081	DDX12P	http://www.ncbi.nlm.nih.gov/gene/?term=440081	"CHLR2, DDX12 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013284	440087	SMCO3	http://www.ncbi.nlm.nih.gov/gene/?term=440087	C12orf69	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013285	440093	H3F3C	http://www.ncbi.nlm.nih.gov/gene/?term=440093	H3.5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013286	440138	ALG11	http://www.ncbi.nlm.nih.gov/gene/?term=440138	"CDG1P, GT8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013287	440145	MZT1	http://www.ncbi.nlm.nih.gov/gene/?term=440145	"C13orf37, MOZART1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013288	440145	MZT1	http://www.ncbi.nlm.nih.gov/gene/?term=440145	"C13orf37, MOZART1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013289	44018	cas	http://www.ncbi.nlm.nih.gov/gene/?term=44018	"Dmel_CG2102, CG2102, Cas, Dmel\CG2102, l(3)j1C2, l(3)neo33, ming "	mRNA	Drosophila melanogaster	17923096	Nucleus	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013290	44018	cas	http://www.ncbi.nlm.nih.gov/gene/?term=44018	"Dmel_CG2102, CG2102, Cas, Dmel\CG2102, l(3)j1C2, l(3)neo33, ming "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013291	44018	cas	http://www.ncbi.nlm.nih.gov/gene/?term=44018	"Dmel_CG2102, CG2102, Cas, Dmel\CG2102, l(3)j1C2, l(3)neo33, ming "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013292	44018	cas	http://www.ncbi.nlm.nih.gov/gene/?term=44018	"Dmel_CG2102, CG2102, Cas, Dmel\CG2102, l(3)j1C2, l(3)neo33, ming "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013293	440193	CCDC88C	http://www.ncbi.nlm.nih.gov/gene/?term=440193	"DAPLE, HKRP2, KIAA1509, SCA40 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013294	44021	nmd	http://www.ncbi.nlm.nih.gov/gene/?term=44021	"Dmel_CG5395, CG5395, DmCG5395, Dmel\CG5395, Msp, Msp1, Nmd, anon-EST:Liang-1.79, clone 1.79, l(2)08774, ms(2)4, ms(2)ry4 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013295	440275	EIF2AK4	http://www.ncbi.nlm.nih.gov/gene/?term=440275	"GCN2, PVOD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013296	440275	EIF2AK4	http://www.ncbi.nlm.nih.gov/gene/?term=440275	"GCN2, PVOD2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013297	440275	EIF2AK4	http://www.ncbi.nlm.nih.gov/gene/?term=440275	"GCN2, PVOD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013298	440335	SMIM22	http://www.ncbi.nlm.nih.gov/gene/?term=440335		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013299	440348	NPIPB15	http://www.ncbi.nlm.nih.gov/gene/?term=440348	"A-761H5.4, NPIPL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013300	440456	PLEKHM1P1	http://www.ncbi.nlm.nih.gov/gene/?term=440456	PLEKHM1P	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013301	440498	HSBP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=440498		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013302	44054	Ubc7	http://www.ncbi.nlm.nih.gov/gene/?term=44054	"Dmel_CG4443, CG4443, Crl, Dmel\CG4443, UBC7, Ubc47D, col, crl "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013303	44054	Ubc7	http://www.ncbi.nlm.nih.gov/gene/?term=44054	"Dmel_CG4443, CG4443, Crl, Dmel\CG4443, UBC7, Ubc47D, col, crl "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013304	440574	MINOS1	http://www.ncbi.nlm.nih.gov/gene/?term=440574	"C1orf151, MIO10, Mic10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013305	440574	MINOS1	http://www.ncbi.nlm.nih.gov/gene/?term=440574	"C1orf151, MIO10, Mic10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013306	44059	RpL30	http://www.ncbi.nlm.nih.gov/gene/?term=44059	"Dmel_CG10652, BcDNA:RE25263, BcDNA:RH09938, CG10652, Dmel\CG10652, L30, RPL30, Rp L30, Rpl30, anon-EST:fe1D4, l(2)01265, l(2)SH0229, l(2)SH2 0229, l(2)k09918, plume "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013307	440603	BCL2L15	http://www.ncbi.nlm.nih.gov/gene/?term=440603	"Bfk, C1orf178 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013308	440603	BCL2L15	http://www.ncbi.nlm.nih.gov/gene/?term=440603	"Bfk, C1orf178 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013309	440672	NUDT4P1	http://www.ncbi.nlm.nih.gov/gene/?term=440672		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013310	440689	HIST2H2BF	http://www.ncbi.nlm.nih.gov/gene/?term=440689		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013311	440712	C1orf186	http://www.ncbi.nlm.nih.gov/gene/?term=440712	RHEX	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013312	440738	MAP1LC3C	http://www.ncbi.nlm.nih.gov/gene/?term=440738	"ATG8J, LC3C "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013313	440738	MAP1LC3C	http://www.ncbi.nlm.nih.gov/gene/?term=440738	"ATG8J, LC3C "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013314	440822	PIWIL3	http://www.ncbi.nlm.nih.gov/gene/?term=440822	HIWI3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013315	440822	PIWIL3	http://www.ncbi.nlm.nih.gov/gene/?term=440822	HIWI3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013316	440823	MIAT	http://www.ncbi.nlm.nih.gov/gene/?term=440823	"C22orf35, GOMAFU, LINC00066, NCRNA00066, RNCR2, lncRNA-MIAT "	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/gomafu/
RLID00013317	440823	MIAT	http://www.ncbi.nlm.nih.gov/gene/?term=440823	"C22orf35, GOMAFU, LINC00066, NCRNA00066, RNCR2, lncRNA-MIAT "	lncRNA	Homo sapiens	21128942	Nucleus	Brain tissue	qRT-PCR|Microarray	Table 2: Long noncoding RNAs represented on Affymetrix U133 arrays that were reliably detected in human nucleus accumbens. An lncRNA was considered reliably detected in human NAcc if at least one probe corresponding to the transcript gave a specific signal in all control subjects. No transcripts undetected in the controls were consistently detected in drug abusers. Data are collected from Talbe 2.
RLID00013318	440823	MIAT	http://www.ncbi.nlm.nih.gov/gene/?term=440823	"C22orf35, GOMAFU, LINC00066, NCRNA00066, RNCR2, lncRNA-MIAT "	lncRNA	Homo sapiens	25690653	Nucleus	P493-6 cell	qRT-PCR	"To validate the isolation of nuclear and cytoplasmic fractions, the enrichment of 3 nuclear (ANRIL, MIAT, XIST) and 3 cytoplasmic (RPPH1, DANCR, tRNA-Lys) RNAs was analyzed by qRT-PCR. "
RLID00013319	440823	MIAT	http://www.ncbi.nlm.nih.gov/gene/?term=440823	"C22orf35, GOMAFU, LINC00066, NCRNA00066, RNCR2, lncRNA-MIAT "	lncRNA	Homo sapiens	22955988	Nucleus	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00013320	440957	SMIM4	http://www.ncbi.nlm.nih.gov/gene/?term=440957	C3orf78	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013321	440	ASNS	http://www.ncbi.nlm.nih.gov/gene/?term=440	"ASNSD, TS11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013322	440	ASNS	http://www.ncbi.nlm.nih.gov/gene/?term=440	"ASNSD, TS11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013323	44100	Patj	http://www.ncbi.nlm.nih.gov/gene/?term=44100	"Dmel_CG12021, BcDNA:LD22238, CG12021, D-Patj, DLT, DPATJ, DPatj, Dlt, Dmel\CG12021, Dpatj, PATJ, PaTJ, PatJ/Dlt, dPATJ, dPatj, dlt, dlt:discs lost, dpatj, patj "	mRNA	Drosophila melanogaster	17923096	Cell junction	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013324	44100	Patj	http://www.ncbi.nlm.nih.gov/gene/?term=44100	"Dmel_CG12021, BcDNA:LD22238, CG12021, D-Patj, DLT, DPATJ, DPatj, Dlt, Dmel\CG12021, Dpatj, PATJ, PaTJ, PatJ/Dlt, dPATJ, dPatj, dlt, dlt:discs lost, dpatj, patj "	mRNA	Drosophila melanogaster	17923096	Cytoskeleton	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013325	441024	MTHFD2L	http://www.ncbi.nlm.nih.gov/gene/?term=441024		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013326	441027	TMEM150C	http://www.ncbi.nlm.nih.gov/gene/?term=441027		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013327	441191	RNF216P1	http://www.ncbi.nlm.nih.gov/gene/?term=441191	"RNF216L, hCG2040556 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013328	441273	SPDYE2	http://www.ncbi.nlm.nih.gov/gene/?term=441273	SPDYB2-L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013329	44131	Mkrn1	http://www.ncbi.nlm.nih.gov/gene/?term=44131	"Dmel_CG7184, CG7184, Dmel\CG7184, MKRN1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013330	44131	Mkrn1	http://www.ncbi.nlm.nih.gov/gene/?term=44131	"Dmel_CG7184, CG7184, Dmel\CG7184, MKRN1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013331	441478	NRARP	http://www.ncbi.nlm.nih.gov/gene/?term=441478		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013332	441478	NRARP	http://www.ncbi.nlm.nih.gov/gene/?term=441478		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013333	441478	NRARP	http://www.ncbi.nlm.nih.gov/gene/?term=441478		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013334	44149	Acon	http://www.ncbi.nlm.nih.gov/gene/?term=44149	"Dmel_CG9244, ACON-1M, BEST:GH10550, CG9244, Dmel\CG9244, FBgn0010100, M-Acon, acon, hsp60, i204, i59, l(2)07054, m-Acon, m-acon, mACON, mAc, mAcon, Acon "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013335	441520	CT45A4	http://www.ncbi.nlm.nih.gov/gene/?term=441520	"CT45-4, CT45.4 "	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00013336	441531	PGAM4	http://www.ncbi.nlm.nih.gov/gene/?term=441531	"PGAM-B, PGAM1, PGAM3, dJ1000K24.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013337	441631	TSPAN11	http://www.ncbi.nlm.nih.gov/gene/?term=441631	VSSW1971	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013338	441733	PRKXP1	http://www.ncbi.nlm.nih.gov/gene/?term=441733		lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013339	441951	ZFAS1	http://www.ncbi.nlm.nih.gov/gene/?term=441951	"C20orf199, HSUP1, HSUP2, NCRNA00275, ZNFX1-AS1 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013340	441951	ZFAS1	http://www.ncbi.nlm.nih.gov/gene/?term=441951	"C20orf199, HSUP1, HSUP2, NCRNA00275, ZNFX1-AS1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013341	44227	Fatp	http://www.ncbi.nlm.nih.gov/gene/?term=44227	"Dmel_CG7400, CG7400, Dmel\CG7400, Dromel_CG7400_FBtr0080133_fatp_mORF, anon-WO0121795.74, dFATP, dFatp, fatp, l(2)k10307 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013342	44227	Fatp	http://www.ncbi.nlm.nih.gov/gene/?term=44227	"Dmel_CG7400, CG7400, Dmel\CG7400, Dromel_CG7400_FBtr0080133_fatp_mORF, anon-WO0121795.74, dFATP, dFatp, fatp, l(2)k10307 "	mRNA	Drosophila melanogaster	25838129	Apical	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013343	44227	Fatp	http://www.ncbi.nlm.nih.gov/gene/?term=44227	"Dmel_CG7400, CG7400, Dmel\CG7400, Dromel_CG7400_FBtr0080133_fatp_mORF, anon-WO0121795.74, dFATP, dFatp, fatp, l(2)k10307 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013344	44258	ps	http://www.ncbi.nlm.nih.gov/gene/?term=44258	"Dmel_CG42670, BcDNA:RE47781, CG16765, CG16776, CG16777, CG18509, CG42670, CG8144, Dmel\CG42670, Dmel_CG16765, Dmel_CG16777, EP(3)3406, NOVA1, PS, cg8144, l(3)10615 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013345	44258	ps	http://www.ncbi.nlm.nih.gov/gene/?term=44258	"Dmel_CG42670, BcDNA:RE47781, CG16765, CG16776, CG16777, CG18509, CG42670, CG8144, Dmel\CG42670, Dmel_CG16765, Dmel_CG16777, EP(3)3406, NOVA1, PS, cg8144, l(3)10615 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013346	44275	SoxN	http://www.ncbi.nlm.nih.gov/gene/?term=44275	"Dmel_CG18024, CG18024, DM64, Dmel\CG18024, SOX29F, SOXB1, Sox B1, Sry-rDM64, soxN "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013347	44275	SoxN	http://www.ncbi.nlm.nih.gov/gene/?term=44275	"Dmel_CG18024, CG18024, DM64, Dmel\CG18024, SOX29F, SOXB1, Sox B1, Sry-rDM64, soxN "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013348	442802	C330011M18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=442802		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013349	44289	flw	http://www.ncbi.nlm.nih.gov/gene/?term=44289	"Dmel_CG2096, CG15305, CG2096, DmPp1-9C, Dmel\CG2096, FLW, FLW/PP1B, PP-1, PP1, PP1 9C, PP1 b9C, PP1 beta9c, PP19C, PP1B_DROME, PP1beta, PP1beta-9C, PP1beta9C, PP1c, PP1cbeta, Pp1-9C, Pp1beta-9C, Pp1beta9C, XE55, anon-WO03040301.120, l(1)G0172 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013350	44289	flw	http://www.ncbi.nlm.nih.gov/gene/?term=44289	"Dmel_CG2096, CG15305, CG2096, DmPp1-9C, Dmel\CG2096, FLW, FLW/PP1B, PP-1, PP1, PP1 9C, PP1 b9C, PP1 beta9c, PP19C, PP1B_DROME, PP1beta, PP1beta-9C, PP1beta9C, PP1c, PP1cbeta, Pp1-9C, Pp1beta-9C, Pp1beta9C, XE55, anon-WO03040301.120, l(1)G0172 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013351	44291	Idh	http://www.ncbi.nlm.nih.gov/gene/?term=44291	"Dmel_CG7176, CG7176, CT22171, Dmel\CG7176, ICDH, IDH, IDH-NADP-NADP, cIdh, idh, isocitrate dehydrogenase, l(3)L3852, Idh "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013352	4430	MYO1B	http://www.ncbi.nlm.nih.gov/gene/?term=4430	myr1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013353	4430	MYO1B	http://www.ncbi.nlm.nih.gov/gene/?term=4430	myr1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013354	443595	tuft1	http://www.ncbi.nlm.nih.gov/gene/?term=443595		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013355	4435	CITED1	http://www.ncbi.nlm.nih.gov/gene/?term=4435	MSG1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013356	4435	CITED1	http://www.ncbi.nlm.nih.gov/gene/?term=4435	MSG1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013357	443626	mprip	http://www.ncbi.nlm.nih.gov/gene/?term=443626		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013358	4436	MSH2	http://www.ncbi.nlm.nih.gov/gene/?term=4436	"COCA1, FCC1, HNPCC, HNPCC1, LCFS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013359	443868	cnksr2	http://www.ncbi.nlm.nih.gov/gene/?term=443868		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013360	4439	MSH5	http://www.ncbi.nlm.nih.gov/gene/?term=4439	"G7, MUTSH5, NG23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013361	444146	rtn3-a	http://www.ncbi.nlm.nih.gov/gene/?term=444146	"XRTN3, asyip, hap, nspl2, nsplii, rtn31, rtn3-a "	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013362	444	ASPH	http://www.ncbi.nlm.nih.gov/gene/?term=444	"AAH, BAH, CASQ2BP1, FDLAB, HAAH, JCTN, junctin "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013363	444	ASPH	http://www.ncbi.nlm.nih.gov/gene/?term=444	"AAH, BAH, CASQ2BP1, FDLAB, HAAH, JCTN, junctin "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013364	44505	br	http://www.ncbi.nlm.nih.gov/gene/?term=44505	"Dmel_CG11491, 2B5, 2Bc, A18, BR, BR-C, BR-C Z1, BR-c, BRC, BRC-Z1, BRC-Z2, BRC-Z3, BRC-Z4, BR_C, Br, Br-C, Br-C Z2, Br-C-Z3, Br-Z4, BrC, BrC-Z1, BrZ3, CG11491, CG11509, CG11511, CG11514, Dmel\CG11491, Dmel_CG11509, EG:123F11.1, EG:17A9.1, EG:25D2.1, PP1, PP2, Z1, Z2, Z3, Z4-C, br-Z1, br-Z2, br-Z3, br-Z4, de12, ecs, l(1)2Ba, l(1)2Bab, l(1)2Bad, l(1)2Bb, l(1)2Bc, l(1)2Bd, l(1)ESHS5, l(1)G0018, l(1)G0042, l(1)G0284, l(1)G0284a, l(1)G0318, l(1)G0401, l(1)PP1, l(1)d norm-12, l(1)d.norm.1, l(1)dn1, l(1)n34, l(1)npr-1, l(1)npr1, l(1)pp-1, l(1)pp-2, l(1)pp1, l(1)pp2, l(1)ts132, l(1)ts144, l(1)ts358, l(1)ts376, npr, npr-1, npr1, nprl, nrp, nrp1, o.c.c., rbp, rdp, rds, uq, br "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013365	445329	SULT1A4	http://www.ncbi.nlm.nih.gov/gene/?term=445329	"HAST3, M-PST, ST1A3/ST1A4, ST1A4, TL-PST "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013366	44540	ct	http://www.ncbi.nlm.nih.gov/gene/?term=44540	"Dmel_CG11387, BcDNA:GH10590, CG11387, CT, CUT, Ct, Cut, Dmel\CG11387, kf, l(1)7Ba, l(1)7Bb, l(1)VE614 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013367	44540	ct	http://www.ncbi.nlm.nih.gov/gene/?term=44540	"Dmel_CG11387, BcDNA:GH10590, CG11387, CT, CUT, Ct, Cut, Dmel\CG11387, kf, l(1)7Ba, l(1)7Bb, l(1)VE614 "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013368	44540	ct	http://www.ncbi.nlm.nih.gov/gene/?term=44540	"Dmel_CG11387, BcDNA:GH10590, CG11387, CT, CUT, Ct, Cut, Dmel\CG11387, kf, l(1)7Ba, l(1)7Bb, l(1)VE614 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013369	44548	lola	http://www.ncbi.nlm.nih.gov/gene/?term=44548	"Dmel_CG12052, BEST:LD03274, BTB-IV, BcDNA:LD17006, BcDNA:RH31485, BtbIV, CG12052, CG18376, CG18378, CG18379, CG18380, CG18381, CG30012, CG30013, CG30014, Dmel\CG12052, LD03274, Lola, NEST:bs06a08, bs06a08.y1, eyeful, fus7, l(2)00642, l(2)s3697, sw59 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013370	44548	lola	http://www.ncbi.nlm.nih.gov/gene/?term=44548	"Dmel_CG12052, BEST:LD03274, BTB-IV, BcDNA:LD17006, BcDNA:RH31485, BtbIV, CG12052, CG18376, CG18378, CG18379, CG18380, CG18381, CG30012, CG30013, CG30014, Dmel\CG12052, LD03274, Lola, NEST:bs06a08, bs06a08.y1, eyeful, fus7, l(2)00642, l(2)s3697, sw59 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013371	44548	lola	http://www.ncbi.nlm.nih.gov/gene/?term=44548	"Dmel_CG12052, BEST:LD03274, BTB-IV, BcDNA:LD17006, BcDNA:RH31485, BtbIV, CG12052, CG18376, CG18378, CG18379, CG18380, CG18381, CG30012, CG30013, CG30014, Dmel\CG12052, LD03274, Lola, NEST:bs06a08, bs06a08.y1, eyeful, fus7, l(2)00642, l(2)s3697, sw59 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013372	445571	CBWD3	http://www.ncbi.nlm.nih.gov/gene/?term=445571	bA561O23.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013373	445	ASS1	http://www.ncbi.nlm.nih.gov/gene/?term=445	"ASS, CTLN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013374	445	ASS1	http://www.ncbi.nlm.nih.gov/gene/?term=445	"ASS, CTLN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013375	446296	pcsk6	http://www.ncbi.nlm.nih.gov/gene/?term=446296	"PACE4, PACE4AIIa, Xpace4, spc4 "	mRNA	Xenopus laevis	15634697	Mitochondrion	Oocyte	Whole mount In Situ Hybridization	Whole-mount in situ hybridization shows that XPACE4 is localized during early oogenesis. Inset shows XPACE4 mRNA localization in the mitochondrial cloud of stage 1 oocytes.
RLID00013376	446692	triobp	http://www.ncbi.nlm.nih.gov/gene/?term=446692	tara	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013377	446697	jak1	http://www.ncbi.nlm.nih.gov/gene/?term=446697		mRNA	Xenopus laevis	25988600	Nucleus	Spermatogonial stem cell	In situ hybridization	"When these barrel-shaped PGs were stained by in situ hybridization with JAK1-antisense probe, followed by propidium iodide staining, they were found to possess two nuclei. JAK1 mRNA were localized in a cell region wherein only one nucleus occurred (Fig. 8A� A� B� B�. "
RLID00013378	446711	nrf1	http://www.ncbi.nlm.nih.gov/gene/?term=446711	"alpha-pal, nrf-1 "	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013379	446899	fndc3a.2	http://www.ncbi.nlm.nih.gov/gene/?term=446899	"fndc3, hugo "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013380	447159	MGC85478	http://www.ncbi.nlm.nih.gov/gene/?term=447159		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013381	447246	sybu	http://www.ncbi.nlm.nih.gov/gene/?term=447246	"golsyn, ocsyn, snphl "	mRNA	Xenopus laevis	24798204	Vegetal	Oocyte	In situ hybridization	"In oocytes, syntabulin transcripts were localized to the vegetal cortex of large oocytes and the mitochondrial cloud of very young oocytes. We extended the zebrafish data by finding that during cleavage Xenopus syntabulin mRNA localized to the germ plasm and was later expressed in primordial germ cells (PGCs). "
RLID00013382	447246	sybu	http://www.ncbi.nlm.nih.gov/gene/?term=447246	"golsyn, ocsyn, snphl "	mRNA	Xenopus laevis	24798204	Germ plasm	Oocyte	In situ hybridization	"In oocytes, syntabulin transcripts were localized to the vegetal cortex of large oocytes and the mitochondrial cloud of very young oocytes. We extended the zebrafish data by finding that during cleavage Xenopus syntabulin mRNA localized to the germ plasm and was later expressed in primordial germ cells (PGCs). "
RLID00013383	447246	sybu	http://www.ncbi.nlm.nih.gov/gene/?term=447246	"golsyn, ocsyn, snphl "	mRNA	Xenopus laevis	24798204	Mitochondrion	Oocyte	In situ hybridization	"In oocytes, syntabulin transcripts were localized to the vegetal cortex of large oocytes and the mitochondrial cloud of very young oocytes. We extended the zebrafish data by finding that during cleavage Xenopus syntabulin mRNA localized to the germ plasm and was later expressed in primordial germ cells (PGCs). "
RLID00013384	447246	sybu	http://www.ncbi.nlm.nih.gov/gene/?term=447246	"golsyn, ocsyn, snphl "	mRNA	Xenopus laevis	24798204	Germ plasm	Germ cell	In situ hybridization	"In oocytes, syntabulin transcripts were localized to the vegetal cortex of large oocytes and the mitochondrial cloud of very young oocytes. We extended the zebrafish data by finding that during cleavage Xenopus syntabulin mRNA localized to the germ plasm and was later expressed in primordial germ cells (PGCs). "
RLID00013385	447365	MGC84194	http://www.ncbi.nlm.nih.gov/gene/?term=447365		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013386	447459	zfand3	http://www.ncbi.nlm.nih.gov/gene/?term=447459		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013387	44747	msk	http://www.ncbi.nlm.nih.gov/gene/?term=44747	"Dmel_CG7935, 61, CG7935, CIP-61, DIM-7, Dim-7, Dim7, DmRanBP7, Dmel\CG7935, Imp7, Imp7/8, Msk, S(ls)2, dim-7, dim7 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013388	44747	msk	http://www.ncbi.nlm.nih.gov/gene/?term=44747	"Dmel_CG7935, 61, CG7935, CIP-61, DIM-7, Dim-7, Dim7, DmRanBP7, Dmel\CG7935, Imp7, Imp7/8, Msk, S(ls)2, dim-7, dim7 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013389	447559	rbpms2	http://www.ncbi.nlm.nih.gov/gene/?term=447559	hermes	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"In addition to the Balbiani body, Hermes RNA is localised in germ plasm particles in the vegetal cortex of vitellogenic oocytes. "
RLID00013390	447559	rbpms2	http://www.ncbi.nlm.nih.gov/gene/?term=447559	hermes	mRNA	Xenopus laevis	23626739	Mitochondrion	Oocyte	Microscopy	"In addition to the Balbiani body, Hermes RNA is localised in germ plasm particles in the vegetal cortex of vitellogenic oocytes. "
RLID00013391	447559	rbpms2	http://www.ncbi.nlm.nih.gov/gene/?term=447559	hermes	mRNA	Xenopus laevis	23626739	Vegetal	Oocyte	Microscopy	"In addition to the Balbiani body, Hermes RNA is localised in germ plasm particles in the vegetal cortex of vitellogenic oocytes. "
RLID00013392	447710	MGC81667	http://www.ncbi.nlm.nih.gov/gene/?term=447710		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00013393	447760	srgap2	http://www.ncbi.nlm.nih.gov/gene/?term=447760	fnbp2	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013394	4478	MSN	http://www.ncbi.nlm.nih.gov/gene/?term=4478	HEL70	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013395	4478	MSN	http://www.ncbi.nlm.nih.gov/gene/?term=4478	HEL70	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013396	44801	bsk	http://www.ncbi.nlm.nih.gov/gene/?term=44801	"Dmel_CG5680, BSK, Bsk, CG5680, D-JNK, D-junk, DBSK/JNK, DJNK, DJNK/bsk, Dmel\CG5680, JNK, JNK/SAPK, Jnk, Junk, SAPKa, dJNK, jnk, pJNK "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013397	44811	E(bx)	http://www.ncbi.nlm.nih.gov/gene/?term=44811	"Dmel_CG32346, CG10894, CG17135, CG32346, CG32478, CG7022, Dmel\CG32346, E(BX), E(Bx), Ebx, En-bx, NURF, NURF 215, NURF-215, NURF-301, NURF215, NURF301, NuRF301, Nurf 301, Nurf-215, Nurf301, dNURF, dNURF301, e(bx), l(3)122, l(3)ry122, nurf301, p215, p301 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013398	44811	E(bx)	http://www.ncbi.nlm.nih.gov/gene/?term=44811	"Dmel_CG32346, CG10894, CG17135, CG32346, CG32478, CG7022, Dmel\CG32346, E(BX), E(Bx), Ebx, En-bx, NURF, NURF 215, NURF-215, NURF-301, NURF215, NURF301, NuRF301, Nurf 301, Nurf-215, Nurf301, dNURF, dNURF301, e(bx), l(3)122, l(3)ry122, nurf301, p215, p301 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013399	44817	for	http://www.ncbi.nlm.nih.gov/gene/?term=44817	"Dmel_CG10033, 142251_at, BcDNA:GM08338, CG10033, DG2, Dg2, Dmel\CG10033, FOR/PKG, For, PKG, Pkg2, Pkg24A, anon-WO0140519.260, anon-WO02059370.47, dg2, l(2)06860 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013400	44817	for	http://www.ncbi.nlm.nih.gov/gene/?term=44817	"Dmel_CG10033, 142251_at, BcDNA:GM08338, CG10033, DG2, Dg2, Dmel\CG10033, FOR/PKG, For, PKG, Pkg2, Pkg24A, anon-WO0140519.260, anon-WO02059370.47, dg2, l(2)06860 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013401	448274	xkrx	http://www.ncbi.nlm.nih.gov/gene/?term=448274	"xk, xrg1 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00013402	4486	MST1R	http://www.ncbi.nlm.nih.gov/gene/?term=4486	"CD136, CDw136, PTK8, RON "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013403	4486	MST1R	http://www.ncbi.nlm.nih.gov/gene/?term=4486	"CD136, CDw136, PTK8, RON "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013404	44879	rhi	http://www.ncbi.nlm.nih.gov/gene/?term=44879	"Dmel_CG10683, CG10683, Dmel\CG10683, HP1D, HP1d, RHI, Rhi, rno "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013405	4487	MSX1	http://www.ncbi.nlm.nih.gov/gene/?term=4487	"ECTD3, HOX7, HYD1, STHAG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013406	448831	FRG2	http://www.ncbi.nlm.nih.gov/gene/?term=448831	FRG2A	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013407	448831	FRG2	http://www.ncbi.nlm.nih.gov/gene/?term=448831	FRG2A	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013408	448850	Znhit3	http://www.ncbi.nlm.nih.gov/gene/?term=448850	"Myohd1, Trip3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00013409	449000	Zfp960	http://www.ncbi.nlm.nih.gov/gene/?term=449000		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00013410	4490	MT1B	http://www.ncbi.nlm.nih.gov/gene/?term=4490	"MT1, MT1Q, MTP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013411	4493	MT1E	http://www.ncbi.nlm.nih.gov/gene/?term=4493	"MT-1E, MT-IE, MT1, MTD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013412	4493	MT1E	http://www.ncbi.nlm.nih.gov/gene/?term=4493	"MT-1E, MT-IE, MT1, MTD "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00013413	4493	MT1E	http://www.ncbi.nlm.nih.gov/gene/?term=4493	"MT-1E, MT-IE, MT1, MTD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013414	4494	MT1F	http://www.ncbi.nlm.nih.gov/gene/?term=4494	MT1	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00013415	4494	MT1F	http://www.ncbi.nlm.nih.gov/gene/?term=4494	MT1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013416	4495	MT1G	http://www.ncbi.nlm.nih.gov/gene/?term=4495	"MT1, MT1K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013417	4496	MT1H	http://www.ncbi.nlm.nih.gov/gene/?term=4496	"MT-0, MT-1H, MT-IH, MT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013418	4501	MT1X	http://www.ncbi.nlm.nih.gov/gene/?term=4501	"MT-1l, MT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013419	4502	MT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4502	MT2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013420	4502	MT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4502	MT2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013421	4502	MT2A	http://www.ncbi.nlm.nih.gov/gene/?term=4502	MT2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013422	4507	MTAP	http://www.ncbi.nlm.nih.gov/gene/?term=4507	"BDMF, DMSFH, DMSMFH, HEL-249, LGMBF, MSAP, c86fus "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013423	4507	MTAP	http://www.ncbi.nlm.nih.gov/gene/?term=4507	"BDMF, DMSFH, DMSMFH, HEL-249, LGMBF, MSAP, c86fus "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013424	4507	MTAP	http://www.ncbi.nlm.nih.gov/gene/?term=4507	"BDMF, DMSFH, DMSMFH, HEL-249, LGMBF, MSAP, c86fus "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013425	4508	MT-ATP6	http://www.ncbi.nlm.nih.gov/gene/?term=4508	"ATPase6, MTATP6, ATP6 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013426	4508	MT-ATP6	http://www.ncbi.nlm.nih.gov/gene/?term=4508	"ATPase6, MTATP6, ATP6 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013427	4509	MT-ATP8	http://www.ncbi.nlm.nih.gov/gene/?term=4509	"ATPase8, MTATP8, ATP8 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013428	4509	MT-ATP8	http://www.ncbi.nlm.nih.gov/gene/?term=4509	"ATPase8, MTATP8, ATP8 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013429	4511	MT-TC	http://www.ncbi.nlm.nih.gov/gene/?term=4511	"MTTC, TRNC "	tRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00013430	4512	MT-CO1	http://www.ncbi.nlm.nih.gov/gene/?term=4512	"COI, MTCO1, COX1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013431	4512	MT-CO1	http://www.ncbi.nlm.nih.gov/gene/?term=4512	"COI, MTCO1, COX1 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013432	4513	MT-CO2	http://www.ncbi.nlm.nih.gov/gene/?term=4513	"COII, MTCO2, COX2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013433	4513	MT-CO2	http://www.ncbi.nlm.nih.gov/gene/?term=4513	"COII, MTCO2, COX2 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013434	4514	MT-CO3	http://www.ncbi.nlm.nih.gov/gene/?term=4514	"COIII, MTCO3, COX3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013435	4514	MT-CO3	http://www.ncbi.nlm.nih.gov/gene/?term=4514	"COIII, MTCO3, COX3 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013436	4519	MT-CYB	http://www.ncbi.nlm.nih.gov/gene/?term=4519	"MTCYB, CYTB "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013437	4519	MT-CYB	http://www.ncbi.nlm.nih.gov/gene/?term=4519	"MTCYB, CYTB "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013438	4520	MTF1	http://www.ncbi.nlm.nih.gov/gene/?term=4520	"MTF-1, ZRF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013439	4520	MTF1	http://www.ncbi.nlm.nih.gov/gene/?term=4520	"MTF-1, ZRF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013440	4520	MTF1	http://www.ncbi.nlm.nih.gov/gene/?term=4520	"MTF-1, ZRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013441	4521	NUDT1	http://www.ncbi.nlm.nih.gov/gene/?term=4521	MTH1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013442	4521	NUDT1	http://www.ncbi.nlm.nih.gov/gene/?term=4521	MTH1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013443	4522	MTHFD1	http://www.ncbi.nlm.nih.gov/gene/?term=4522	"MTHFC, MTHFD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013444	4522	MTHFD1	http://www.ncbi.nlm.nih.gov/gene/?term=4522	"MTHFC, MTHFD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013445	4522	MTHFD1	http://www.ncbi.nlm.nih.gov/gene/?term=4522	"MTHFC, MTHFD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013446	45247	VhaPPA1-1	http://www.ncbi.nlm.nih.gov/gene/?term=45247	"Dmel_CG7007, CG7007, Dmel\CG7007, VhaPPA1, vhaPPA1-1 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013447	45250	deltaCOP	http://www.ncbi.nlm.nih.gov/gene/?term=45250	"Dmel_CG14813, 63B12S, ARCN1, Arch, CG14813, DM63B12S, Delta COP, DeltaCop, Dmel\CG14813, EG:63B12.10, ESTS:63B12S, anon-WO03040301.246, delta-Cop, deltaCop, l(1)G0051, l(1)G0301, l(1)G0450 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013448	45278	csw	http://www.ncbi.nlm.nih.gov/gene/?term=45278	"Dmel_CG3954, 19-106, CG3954, CSW, Csw, Csw/Shp2, Dmel\CG3954, E(sev)1A, EG:BACN25G24.2, SHP-2, Shp-2, Shp2/csw, anon-WO03040301.207, anon-WO03040301.209, anon-WO03040301.219/SHP-2, l(1)2Db, l(1)2Dd, l(1)G0170, l(1)GA114, l(1)csw, csw "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013449	4528	MTIF2	http://www.ncbi.nlm.nih.gov/gene/?term=4528		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013450	4528	MTIF2	http://www.ncbi.nlm.nih.gov/gene/?term=4528		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013451	4528	MTIF2	http://www.ncbi.nlm.nih.gov/gene/?term=4528		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013452	4528	MTIF2	http://www.ncbi.nlm.nih.gov/gene/?term=4528		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013453	45307	fz	http://www.ncbi.nlm.nih.gov/gene/?term=45307	"Dmel_CG17697, CG17697, CG3646, DFZ1, DFz, DFz1, Dfz, Dfz1, Dm Fz1, Dmel\CG17697, FZ, Frz, Fz, Fz1, dFz, frz1, fz[[1]], fz "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013454	4534	MTM1	http://www.ncbi.nlm.nih.gov/gene/?term=4534	"CNM, MTMX, XLMTM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013455	4534	MTM1	http://www.ncbi.nlm.nih.gov/gene/?term=4534	"CNM, MTMX, XLMTM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013456	4535	MT-ND1	http://www.ncbi.nlm.nih.gov/gene/?term=4535	"MTND1, ND1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013457	4535	MT-ND1	http://www.ncbi.nlm.nih.gov/gene/?term=4535	"MTND1, ND1 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013458	4536	MT-ND2	http://www.ncbi.nlm.nih.gov/gene/?term=4536	"MTND2, ND2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013459	4536	MT-ND2	http://www.ncbi.nlm.nih.gov/gene/?term=4536	"MTND2, ND2 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013460	4537	MT-ND3	http://www.ncbi.nlm.nih.gov/gene/?term=4537	"MTND3, ND3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013461	4537	MT-ND3	http://www.ncbi.nlm.nih.gov/gene/?term=4537	"MTND3, ND3 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013462	4538	MT-ND4	http://www.ncbi.nlm.nih.gov/gene/?term=4538	"MTND4, ND4 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013463	4539	MT-ND4L	http://www.ncbi.nlm.nih.gov/gene/?term=4539	"MTND4L, ND4L "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013464	4539	MT-ND4L	http://www.ncbi.nlm.nih.gov/gene/?term=4539	"MTND4L, ND4L "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013465	4540	MT-ND5	http://www.ncbi.nlm.nih.gov/gene/?term=4540	"MTND5, ND5 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013466	4540	MT-ND5	http://www.ncbi.nlm.nih.gov/gene/?term=4540	"MTND5, ND5 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013467	4541	MT-ND6	http://www.ncbi.nlm.nih.gov/gene/?term=4541	"MTND6, ND6 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013468	4541	MT-ND6	http://www.ncbi.nlm.nih.gov/gene/?term=4541	"MTND6, ND6 "	mRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00013469	45467	mtd	http://www.ncbi.nlm.nih.gov/gene/?term=45467	"Dmel_CG32464, CG10196, CG10199, CG32464, Dmel\CG32464, L(3)82Fd, L82, anon-EST:Posey263, l(3)82FD, l(3)82Fd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013470	45467	mtd	http://www.ncbi.nlm.nih.gov/gene/?term=45467	"Dmel_CG32464, CG10196, CG10199, CG32464, Dmel\CG32464, L(3)82Fd, L82, anon-EST:Posey263, l(3)82FD, l(3)82Fd "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013471	4548	MTR	http://www.ncbi.nlm.nih.gov/gene/?term=4548	"HMAG, MS, cblG "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013472	4548	MTR	http://www.ncbi.nlm.nih.gov/gene/?term=4548	"HMAG, MS, cblG "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013473	4548	MTR	http://www.ncbi.nlm.nih.gov/gene/?term=4548	"HMAG, MS, cblG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013474	4550	MT-RNR2	http://www.ncbi.nlm.nih.gov/gene/?term=4550	"MTRNR2, RNR2 "	rRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00013475	45525	eIF-4E	http://www.ncbi.nlm.nih.gov/gene/?term=45525	"Dmel_CG4035, 0260/09, 0587/11, 0589/11, 0919/12, 1004/13, 2, 7238, CBP, CG4035, CT13384, CT39424, CT39426, D-eIF4E, Dmel\CG4035, EIF4E, Eif4E, Eif4e, IF4E, dEif4e, deIF-4E, deIF4E, eIF 4E1, eIF-4E2, eIF-4EII, eIF-4e, eIF4E, eIF4E-1, eIF4E-1/2, eIF4E-2, eIF4E1, eIF4EI, eIF4e, eif-4E, eif-4e, eif4e, elF4E, l(3)07238, l(3)67Af, l(3)S025007, l(3)S026009, l(3)S058711, l(3)S091912, eIF-4E "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013476	4552	MTRR	http://www.ncbi.nlm.nih.gov/gene/?term=4552	"MSR, cblE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013477	45683	milt	http://www.ncbi.nlm.nih.gov/gene/?term=45683	"Dmel_CG43227, CG13777, CG31630, CG43227, Dmel\CG43227, Dmel_CG13777, Dmel_CG31630, anon-WO0153538.19, l(2)k04704 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013478	45683	milt	http://www.ncbi.nlm.nih.gov/gene/?term=45683	"Dmel_CG43227, CG13777, CG31630, CG43227, Dmel\CG43227, Dmel_CG13777, Dmel_CG31630, anon-WO0153538.19, l(2)k04704 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013479	4569	MT-TM	http://www.ncbi.nlm.nih.gov/gene/?term=4569	"MTTM, TRNM "	tRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00013480	45706	Cyp4d14	http://www.ncbi.nlm.nih.gov/gene/?term=45706	"Dmel_CG3540, 4d14, CG3540, CYP4D14, Dmel\CG3540, EG:152A3.2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013481	4574	MT-TS1	http://www.ncbi.nlm.nih.gov/gene/?term=4574	"MTTS1, TRNS1 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00013482	4575	MT-TS2	http://www.ncbi.nlm.nih.gov/gene/?term=4575	"MTTS2, TRNS2 "	tRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00013483	45775	mei-P26	http://www.ncbi.nlm.nih.gov/gene/?term=45775	"Dmel_CG12218, AF145661, BcDNA:GH10646, CG12218, Dmel\CG12218, MEI-P26, Mei-P26, mei-p26 "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00013484	4577	MT-TV	http://www.ncbi.nlm.nih.gov/gene/?term=4577	"MTTV, TRNV "	tRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00013485	45780	Prosalpha1	http://www.ncbi.nlm.nih.gov/gene/?term=45780	"Dmel_CG18495, 18495, Alpha-1, CG18495, Dmel\CG18495, PSA6_DROME, Prosalpha6, alpha-1, alpha1, l(2)SH2 2342, l(2)SH2342, prosalpha1, prosalpha6 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013486	4580	MTX1	http://www.ncbi.nlm.nih.gov/gene/?term=4580	"MTX, MTXN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013487	4580	MTX1	http://www.ncbi.nlm.nih.gov/gene/?term=4580	"MTX, MTXN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013488	45827	bic	http://www.ncbi.nlm.nih.gov/gene/?term=45827	"Dmel_CG3644, 107/12, 5A, BcDNA.GM05329, BcDNA:GM05329, Bic, Btf, CG3644, Dmel\CG3644, E(2)Bic, E(Bic), l(2)49Da, l(2)k10712, l(2)vr22, vr22 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013489	45827	bic	http://www.ncbi.nlm.nih.gov/gene/?term=45827	"Dmel_CG3644, 107/12, 5A, BcDNA.GM05329, BcDNA:GM05329, Bic, Btf, CG3644, Dmel\CG3644, E(2)Bic, E(Bic), l(2)49Da, l(2)k10712, l(2)vr22, vr22 "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013490	4582	MUC1	http://www.ncbi.nlm.nih.gov/gene/?term=4582	"ADMCKD, ADMCKD1, CA 15-3, CD227, EMA, H23AG, KL-6, MAM6, MCD, MCKD, MCKD1, MUC-1, MUC-1/SEC, MUC-1/X, MUC1/ZD, PEM, PEMT, PUM "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013491	4583	MUC2	http://www.ncbi.nlm.nih.gov/gene/?term=4583	"MLP, MUC-2, SMUC "	mRNA	Homo sapiens	11724906	Endoplasmic reticulum	Colorectal tissues	In situ hybridization|Electron microscopy	"Furthermore, electron microscopic in situ hybridization revealed that gold particles representing MUC2 mRNA are primarily localized over the RER. "
RLID00013492	45840	cpo	http://www.ncbi.nlm.nih.gov/gene/?term=45840	"Dmel_CG43738, 1824, 3603, 5339, 6015, BcDNA:AT31405, CG12349, CG18434, CG18435, CG31243, CG42457, CG43738, CPO, Cpo, Dmel\CG43738, Dmel_CG31243, Dmel_CG42457, E(sda)N, Line N, ORE-17, cg18435, l(3)01432, l(3)6015, l(3)j4A1, l(3)j4D4, l(3)j7E2, l(3)j9B3, l(3)rJ553, l(3)s2336 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013493	4588	MUC6	http://www.ncbi.nlm.nih.gov/gene/?term=4588	MUC-6	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013494	4591	TRIM37	http://www.ncbi.nlm.nih.gov/gene/?term=4591	"MUL, POB1, TEF3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013495	45931	spir	http://www.ncbi.nlm.nih.gov/gene/?term=45931	"Dmel_CG10076, 38C.34, 38C.37, CG10076, CG18621, Dmel\CG10076, NP2788, Spir, Spire, l(2)08327, p150-Spir, p150Spir "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013496	4594	MUT	http://www.ncbi.nlm.nih.gov/gene/?term=4594	MCM	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013497	4595	MUTYH	http://www.ncbi.nlm.nih.gov/gene/?term=4595	MYH	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013498	45960	aly	http://www.ncbi.nlm.nih.gov/gene/?term=45960	"Dmel_CG2075, 143450_at, Aly, CG2075, Dmel\CG2075, ms(3)2, ms(3)ry2 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013499	45969	gwl	http://www.ncbi.nlm.nih.gov/gene/?term=45969	"Dmel_CG7719, 1J, CG7719, CG7719-related, CT23435, Dmel\CG7719, EP0515, Gwl, Pk91C, Pk?2, anon-WO2004063362.73, scant "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013500	45973	fs(1)N	http://www.ncbi.nlm.nih.gov/gene/?term=45973	"Dmel_CG11411, 371, 8D8.1, CG11411, Dmel\CG11411, EG:8D8.1, Fs(1)N, Nas, fs(1)A371, fs(1)K1540, fs(1)M6as, fs(1)Nasrat, fs(1)[nas], nas, fs(1)N "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013501	45973	fs(1)N	http://www.ncbi.nlm.nih.gov/gene/?term=45973	"Dmel_CG11411, 371, 8D8.1, CG11411, Dmel\CG11411, EG:8D8.1, Fs(1)N, Nas, fs(1)A371, fs(1)K1540, fs(1)M6as, fs(1)Nasrat, fs(1)[nas], nas, fs(1)N "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013502	45973	fs(1)N	http://www.ncbi.nlm.nih.gov/gene/?term=45973	"Dmel_CG11411, 371, 8D8.1, CG11411, Dmel\CG11411, EG:8D8.1, Fs(1)N, Nas, fs(1)A371, fs(1)K1540, fs(1)M6as, fs(1)Nasrat, fs(1)[nas], nas, fs(1)N "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013503	4597	MVD	http://www.ncbi.nlm.nih.gov/gene/?term=4597	"FP17780, MDDase, MPD, POROK7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013504	4597	MVD	http://www.ncbi.nlm.nih.gov/gene/?term=4597	"FP17780, MDDase, MPD, POROK7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013505	4598	MVK	http://www.ncbi.nlm.nih.gov/gene/?term=4598	"LRBP, MK, MVLK, POROK3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013506	4598	MVK	http://www.ncbi.nlm.nih.gov/gene/?term=4598	"LRBP, MK, MVLK, POROK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013507	4601	MXI1	http://www.ncbi.nlm.nih.gov/gene/?term=4601	"MAD2, MXD2, MXI, bHLHc11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013508	4602	MYB	http://www.ncbi.nlm.nih.gov/gene/?term=4602	"Cmyb, c-myb, c-myb_CDS, efg "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013509	4602	MYB	http://www.ncbi.nlm.nih.gov/gene/?term=4602	"Cmyb, c-myb, c-myb_CDS, efg "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013510	4605	MYBL2	http://www.ncbi.nlm.nih.gov/gene/?term=4605	"B-MYB, BMYB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013511	46078	vlc	http://www.ncbi.nlm.nih.gov/gene/?term=46078	"Dmel_CG8390, CG8390, Dmel\CG8390, X, anon-41Fa, anon-WO0118547.98, l(2)07022 "	mRNA	Drosophila melanogaster	25838129	Cell cortex	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013512	4609	MYC	http://www.ncbi.nlm.nih.gov/gene/?term=4609	"MRTLC, bHLHe39, c-Myc, MYC "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013513	4609	MYC	http://www.ncbi.nlm.nih.gov/gene/?term=4609	"MRTLC, bHLHe39, c-Myc, MYC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013514	4609	MYC	http://www.ncbi.nlm.nih.gov/gene/?term=4609	"MRTLC, bHLHe39, c-Myc, MYC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013515	4609	MYC	http://www.ncbi.nlm.nih.gov/gene/?term=4609	"MRTL, MYCC, bHLHe39, c-Myc "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013516	4610	MYCL	http://www.ncbi.nlm.nih.gov/gene/?term=4610	"L-Myc, LMYC1, bHLHe38, MYCL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013517	4610	MYCL	http://www.ncbi.nlm.nih.gov/gene/?term=4610	"L-Myc, LMYC, MYCL1, bHLHe38 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013518	4613	MYCN	http://www.ncbi.nlm.nih.gov/gene/?term=4613	"MODED, N-myc, NMYC, ODED, bHLHe37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013519	4615	MYD88	http://www.ncbi.nlm.nih.gov/gene/?term=4615	MYD88D	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013520	4615	MYD88	http://www.ncbi.nlm.nih.gov/gene/?term=4615	MYD88D	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013521	4619	MYH1	http://www.ncbi.nlm.nih.gov/gene/?term=4619	"HEL71, MYHSA1, MYHa, MyHC-2X/D, MyHC-2x "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013522	4627	MYH9	http://www.ncbi.nlm.nih.gov/gene/?term=4627	"BDPLT6, DFNA17, EPSTS, FTNS, MHA, NMHC-II-A, NMMHC-IIA, NMMHCA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013523	4627	MYH9	http://www.ncbi.nlm.nih.gov/gene/?term=4627	"BDPLT6, DFNA17, EPSTS, FTNS, MHA, NMHC-II-A, NMMHC-IIA, NMMHCA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013524	4627	MYH9	http://www.ncbi.nlm.nih.gov/gene/?term=4627	"BDPLT6, DFNA17, EPSTS, FTNS, MHA, NMHC-II-A, NMMHC-IIA, NMMHCA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013525	4628	MYH10	http://www.ncbi.nlm.nih.gov/gene/?term=4628	"NMMHC-IIB, NMMHCB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013526	4628	MYH10	http://www.ncbi.nlm.nih.gov/gene/?term=4628	"NMMHC-IIB, NMMHCB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013527	4629	MYH11	http://www.ncbi.nlm.nih.gov/gene/?term=4629	"AAT4, FAA4, SMHC, SMMHC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013528	462	SERPINC1	http://www.ncbi.nlm.nih.gov/gene/?term=462	"AT3, AT3D, ATIII, THPH7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013529	4632	MYL1	http://www.ncbi.nlm.nih.gov/gene/?term=4632	"MLC1F, MLC3F "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013530	4635	MYL4	http://www.ncbi.nlm.nih.gov/gene/?term=4635	"ALC1, AMLC, GT1, PRO1957 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013531	4637	MYL6	http://www.ncbi.nlm.nih.gov/gene/?term=4637	"ESMLC, LC17, LC17-GI, LC17-NM, LC17A, LC17B, MLC-3, MLC1SM, MLC3NM, MLC3SM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013532	4637	MYL6	http://www.ncbi.nlm.nih.gov/gene/?term=4637	"ESMLC, LC17, LC17-GI, LC17-NM, LC17A, LC17B, MLC-3, MLC1SM, MLC3NM, MLC3SM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013533	4638	MYLK	http://www.ncbi.nlm.nih.gov/gene/?term=4638	"AAT7, KRP, MLCK, MLCK1, MLCK108, MLCK210, MSTP083, MYLK1, smMLCK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013534	4641	MYO1C	http://www.ncbi.nlm.nih.gov/gene/?term=4641	"MMI-beta, MMIb, NMI, myr2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013535	4641	MYO1C	http://www.ncbi.nlm.nih.gov/gene/?term=4641	"MMI-beta, MMIb, NMI, myr2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013536	4643	MYO1E	http://www.ncbi.nlm.nih.gov/gene/?term=4643	"FSGS6, HuncM-IC, MYO1C "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013537	4645	MYO5B	http://www.ncbi.nlm.nih.gov/gene/?term=4645		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013538	4645	MYO5B	http://www.ncbi.nlm.nih.gov/gene/?term=4645		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013539	4646	MYO6	http://www.ncbi.nlm.nih.gov/gene/?term=4646	"DFNA22, DFNB37 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013540	4646	MYO6	http://www.ncbi.nlm.nih.gov/gene/?term=4646	"DFNA22, DFNB37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013541	4647	MYO7A	http://www.ncbi.nlm.nih.gov/gene/?term=4647	"DFNA11, DFNB2, MYOVIIA, MYU7A, NSRD2, USH1B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013542	4649	MYO9A	http://www.ncbi.nlm.nih.gov/gene/?term=4649		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013543	4650	MYO9B	http://www.ncbi.nlm.nih.gov/gene/?term=4650	"CELIAC4, MYR5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013544	4650	MYO9B	http://www.ncbi.nlm.nih.gov/gene/?term=4650	"CELIAC4, MYR5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013545	4651	MYO10	http://www.ncbi.nlm.nih.gov/gene/?term=4651		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013546	4651	MYO10	http://www.ncbi.nlm.nih.gov/gene/?term=4651		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013547	4651	MYO10	http://www.ncbi.nlm.nih.gov/gene/?term=4651		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013548	4651	MYO10	http://www.ncbi.nlm.nih.gov/gene/?term=4651		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013549	4659	PPP1R12A	http://www.ncbi.nlm.nih.gov/gene/?term=4659	"M130, MBS, MYPT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013550	4659	PPP1R12A	http://www.ncbi.nlm.nih.gov/gene/?term=4659	"M130, MBS, MYPT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013551	4659	PPP1R12A	http://www.ncbi.nlm.nih.gov/gene/?term=4659	"M130, MBS, MYPT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013552	4660	PPP1R12B	http://www.ncbi.nlm.nih.gov/gene/?term=4660	"MYPT2, PP1bp55 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013553	4660	PPP1R12B	http://www.ncbi.nlm.nih.gov/gene/?term=4660	"MYPT2, PP1bp55 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013554	4660	PPP1R12B	http://www.ncbi.nlm.nih.gov/gene/?term=4660	"MYPT2, PP1bp55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013555	4664	NAB1	http://www.ncbi.nlm.nih.gov/gene/?term=4664		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013556	4665	NAB2	http://www.ncbi.nlm.nih.gov/gene/?term=4665	MADER	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013557	4666	NACA	http://www.ncbi.nlm.nih.gov/gene/?term=4666	"HSD48, NAC-alpha1, skNAC, NACA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013558	4666	NACA	http://www.ncbi.nlm.nih.gov/gene/?term=4666	"HSD48, NAC-alpha1, skNAC, NACA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013559	4666	NACA	http://www.ncbi.nlm.nih.gov/gene/?term=4666	"HSD48, NAC-alpha, NACA1, skNAC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013560	4668	NAGA	http://www.ncbi.nlm.nih.gov/gene/?term=4668	"D22S674, GALB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013561	4668	NAGA	http://www.ncbi.nlm.nih.gov/gene/?term=4668	"D22S674, GALB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013562	4668	NAGA	http://www.ncbi.nlm.nih.gov/gene/?term=4668	"D22S674, GALB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013563	4669	NAGLU	http://www.ncbi.nlm.nih.gov/gene/?term=4669	"CMT2V, MPS-IIIB, MPS3B, NAG, UFHSD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013564	466	ATF1	http://www.ncbi.nlm.nih.gov/gene/?term=466	"EWS-ATF1, FUS/ATF-1, TREB36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013565	4670	HNRNPM	http://www.ncbi.nlm.nih.gov/gene/?term=4670	"CEAR4, HNRPM, HNRPM4, HTGR1, NAGR1, hnRNP M, HNRNPM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013566	4670	HNRNPM	http://www.ncbi.nlm.nih.gov/gene/?term=4670	"CEAR, HNRNPM4, HNRPM, HNRPM4, HTGR1, NAGR1, hnRNP M "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013567	46719	dlt	http://www.ncbi.nlm.nih.gov/gene/?term=46719	"Dmel_CG32315, CG1977, CG32315, DLT, Dlt, Dmel\CG32315, Van, dre1, l(3)04276, l(3)62Ba, l(3)dre1 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013568	46719	dlt	http://www.ncbi.nlm.nih.gov/gene/?term=46719	"Dmel_CG32315, CG1977, CG32315, DLT, Dlt, Dmel\CG32315, Van, dre1, l(3)04276, l(3)62Ba, l(3)dre1 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013569	4673	NAP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=4673	"NAP1, NAP1L, NRP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013570	4673	NAP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=4673	"NAP1, NAP1L, NRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013571	4674	NAP1L2	http://www.ncbi.nlm.nih.gov/gene/?term=4674	BPX	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013572	4676	NAP1L4	http://www.ncbi.nlm.nih.gov/gene/?term=4676	"NAP1L4b, NAP2, NAP2L, hNAP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013573	4676	NAP1L4	http://www.ncbi.nlm.nih.gov/gene/?term=4676	"NAP1L4b, NAP2, NAP2L, hNAP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013574	4676	NAP1L4	http://www.ncbi.nlm.nih.gov/gene/?term=4676	"NAP1L4b, NAP2, NAP2L, hNAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013575	4677	NARS	http://www.ncbi.nlm.nih.gov/gene/?term=4677	"ASNRS1, NARS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013576	4678	NASP	http://www.ncbi.nlm.nih.gov/gene/?term=4678	"FLB7527, HMDRA1, PRO1999 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013577	4678	NASP	http://www.ncbi.nlm.nih.gov/gene/?term=4678	"FLB7527, HMDRA1, PRO1999 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013578	4678	NASP	http://www.ncbi.nlm.nih.gov/gene/?term=4678	"FLB7527, HMDRA1, PRO1999 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013579	467	ATF3	http://www.ncbi.nlm.nih.gov/gene/?term=467		mRNA	Homo sapiens	16109718	Cytoplasm	HepG2 cell	qRT-PCR	"In vivo HuR and AUF1 binding to the ATF3 mRNA in the cytoplasm. For the data shown in B and C, the immunoprecipitated RNA was analyzed by qPCR to quantify the relative amount of HuR or AUF1 protein bound to the ATF3 mRNA during incubation in complete MEM and MEM lacking histidine (MEM-His). "
RLID00013580	467	ATF3	http://www.ncbi.nlm.nih.gov/gene/?term=467		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013581	4680	CEACAM6	http://www.ncbi.nlm.nih.gov/gene/?term=4680	"CD66c, CEAL, NCA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013582	4681	NBL1	http://www.ncbi.nlm.nih.gov/gene/?term=4681	"D1S1733E, DAN, DAND1, NB, NO3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013583	4681	NBL1	http://www.ncbi.nlm.nih.gov/gene/?term=4681	"D1S1733E, DAN, DAND1, NB, NO3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013584	4682	NUBP1	http://www.ncbi.nlm.nih.gov/gene/?term=4682	"NBP, NBP1, NBP35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013585	4682	NUBP1	http://www.ncbi.nlm.nih.gov/gene/?term=4682	"NBP, NBP1, NBP35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013586	4683	NBN	http://www.ncbi.nlm.nih.gov/gene/?term=4683	"AT-V1, AT-V2, ATV, NBS, NBS1, P95 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013587	4683	NBN	http://www.ncbi.nlm.nih.gov/gene/?term=4683	"AT-V1, AT-V2, ATV, NBS, NBS1, P95 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013588	4684	NCAM1	http://www.ncbi.nlm.nih.gov/gene/?term=4684	"CD56, MSK39, NCAM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013589	4685	NCAM2	http://www.ncbi.nlm.nih.gov/gene/?term=4685	NCAM21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013590	4686	NCBP1	http://www.ncbi.nlm.nih.gov/gene/?term=4686	"CBP80, NCBP, Sto1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013591	4686	NCBP1	http://www.ncbi.nlm.nih.gov/gene/?term=4686	"CBP80, NCBP, Sto1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013592	468	ATF4	http://www.ncbi.nlm.nih.gov/gene/?term=468	"CREB-2, CREB2, TAXREB67, TXREB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013593	468	ATF4	http://www.ncbi.nlm.nih.gov/gene/?term=468	"CREB-2, CREB2, TAXREB67, TXREB "	mRNA	Homo sapiens	26239904	Endoplasmic reticulum	Kidney	RT-PCR	"Although the underlying mechanisms were not known, this increased association might be attributed to the diffused localization of the 32-447aa mutant, thereby allowing the mutant to associate not only with ATF4 mRNAs on the ER but also with the mRNAs in cytoplasm. (D-F) The abundance of ATF4 or β-actin mRNA in the subpolysome or polysome pool. "
RLID00013594	468	ATF4	http://www.ncbi.nlm.nih.gov/gene/?term=468	"CREB-2, CREB2, TAXREB67, TXREB "	mRNA	Homo sapiens	26239904	Cytoplasm	Kidney	RT-PCR	"Although the underlying mechanisms were not known, this increased association might be attributed to the diffused localization of the 32-447aa mutant, thereby allowing the mutant to associate not only with ATF4 mRNAs on the ER but also with the mRNAs in cytoplasm. (D-F) The abundance of ATF4 or β-actin mRNA in the subpolysome or polysome pool. "
RLID00013595	468	ATF4	http://www.ncbi.nlm.nih.gov/gene/?term=468	"CREB-2, CREB2, TAXREB67, TXREB "	mRNA	Homo sapiens	26239904	Ribosome	Kidney	RT-PCR	"Although the underlying mechanisms were not known, this increased association might be attributed to the diffused localization of the 32-447aa mutant, thereby allowing the mutant to associate not only with ATF4 mRNAs on the ER but also with the mRNAs in cytoplasm. (D-F) The abundance of ATF4 or β-actin mRNA in the subpolysome or polysome pool. "
RLID00013596	468	ATF4	http://www.ncbi.nlm.nih.gov/gene/?term=468	"CREB-2, CREB2, TAXREB67, TXREB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013597	468	ATF4	http://www.ncbi.nlm.nih.gov/gene/?term=468	"CREB-2, CREB2, TAXREB67, TXREB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013598	4690	NCK1	http://www.ncbi.nlm.nih.gov/gene/?term=4690	"NCK, NCKalpha, nck-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013599	4690	NCK1	http://www.ncbi.nlm.nih.gov/gene/?term=4690	"NCK, NCKalpha, nck-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013600	4690	NCK1	http://www.ncbi.nlm.nih.gov/gene/?term=4690	"NCK, NCKalpha, nck-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013601	4691	NCL	http://www.ncbi.nlm.nih.gov/gene/?term=4691	C23	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013602	4691	NCL	http://www.ncbi.nlm.nih.gov/gene/?term=4691	C23	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013603	4692	NDN	http://www.ncbi.nlm.nih.gov/gene/?term=4692	"HsT16328, PWCR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013604	4693	NDP	http://www.ncbi.nlm.nih.gov/gene/?term=4693	"EVR2, FEVR, ND "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013605	4694	NDUFA1	http://www.ncbi.nlm.nih.gov/gene/?term=4694	"CI-MWFE, MWFE, ZNF183 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013606	4694	NDUFA1	http://www.ncbi.nlm.nih.gov/gene/?term=4694	"CI-MWFE, MWFE, ZNF183 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013607	4695	NDUFA2	http://www.ncbi.nlm.nih.gov/gene/?term=4695	"B8, CD14, CIB8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013608	4696	NDUFA3	http://www.ncbi.nlm.nih.gov/gene/?term=4696	"B9, CI-B9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013609	4696	NDUFA3	http://www.ncbi.nlm.nih.gov/gene/?term=4696	"B9, CI-B9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013610	4697	NDUFA4	http://www.ncbi.nlm.nih.gov/gene/?term=4697	"CI-9k, CI-MLRQ, MLRQ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013611	4697	NDUFA4	http://www.ncbi.nlm.nih.gov/gene/?term=4697	"CI-9k, CI-MLRQ, MLRQ "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013612	4698	NDUFA5	http://www.ncbi.nlm.nih.gov/gene/?term=4698	"B13, CI-13KD-B, CI-13kB, NUFM, UQOR13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013613	4698	NDUFA5	http://www.ncbi.nlm.nih.gov/gene/?term=4698	"B13, CI-13KD-B, CI-13kB, NUFM, UQOR13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013614	4700	NDUFA6	http://www.ncbi.nlm.nih.gov/gene/?term=4700	"B14, CI-B14, LYRM6, NADHB14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013615	4701	NDUFA7	http://www.ncbi.nlm.nih.gov/gene/?term=4701	B14.5a	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013616	4702	NDUFA8	http://www.ncbi.nlm.nih.gov/gene/?term=4702	"CI-19KD, CI-PGIV, PGIV "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013617	4703	NEB	http://www.ncbi.nlm.nih.gov/gene/?term=4703	"NEB177D, NEM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013618	4704	NDUFA9	http://www.ncbi.nlm.nih.gov/gene/?term=4704	"CC6, CI-39k, CI39k, NDUFS2L, SDR22E1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013619	4704	NDUFA9	http://www.ncbi.nlm.nih.gov/gene/?term=4704	"CC6, CI-39k, CI39k, NDUFS2L, SDR22E1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013620	4705	NDUFA10	http://www.ncbi.nlm.nih.gov/gene/?term=4705	"CI-42KD, CI-42k "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013621	4705	NDUFA10	http://www.ncbi.nlm.nih.gov/gene/?term=4705	"CI-42KD, CI-42k "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013622	4706	NDUFAB1	http://www.ncbi.nlm.nih.gov/gene/?term=4706	"ACP, FASN2A, SDAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013623	4706	NDUFAB1	http://www.ncbi.nlm.nih.gov/gene/?term=4706	"ACP, FASN2A, SDAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013624	4707	NDUFB1	http://www.ncbi.nlm.nih.gov/gene/?term=4707	"CI-MNLL, CI-SGDH, MNLL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013625	4707	NDUFB1	http://www.ncbi.nlm.nih.gov/gene/?term=4707	"CI-MNLL, CI-SGDH, MNLL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013626	4708	NDUFB2	http://www.ncbi.nlm.nih.gov/gene/?term=4708	"AGGG, CI-AGGG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013627	4708	NDUFB2	http://www.ncbi.nlm.nih.gov/gene/?term=4708	"AGGG, CI-AGGG "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013628	4708	NDUFB2	http://www.ncbi.nlm.nih.gov/gene/?term=4708	"AGGG, CI-AGGG "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013629	4708	NDUFB2	http://www.ncbi.nlm.nih.gov/gene/?term=4708	"AGGG, CI-AGGG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013630	4709	NDUFB3	http://www.ncbi.nlm.nih.gov/gene/?term=4709	"B12, CI-B12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013631	4710	NDUFB4	http://www.ncbi.nlm.nih.gov/gene/?term=4710	"B15, CI-B15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013632	4711	NDUFB5	http://www.ncbi.nlm.nih.gov/gene/?term=4711	"CISGDH, SGDH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013633	4711	NDUFB5	http://www.ncbi.nlm.nih.gov/gene/?term=4711	"CISGDH, SGDH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013634	4712	NDUFB6	http://www.ncbi.nlm.nih.gov/gene/?term=4712	"B17, CI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013635	4713	NDUFB7	http://www.ncbi.nlm.nih.gov/gene/?term=4713	"B18, CI-B18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013636	4713	NDUFB7	http://www.ncbi.nlm.nih.gov/gene/?term=4713	"B18, CI-B18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013637	4714	NDUFB8	http://www.ncbi.nlm.nih.gov/gene/?term=4714	"ASHI, CI-ASHI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013638	4715	NDUFB9	http://www.ncbi.nlm.nih.gov/gene/?term=4715	"B22, CI-B22, LYRM3, UQOR22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013639	4716	NDUFB10	http://www.ncbi.nlm.nih.gov/gene/?term=4716	PDSW	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013640	4716	NDUFB10	http://www.ncbi.nlm.nih.gov/gene/?term=4716	PDSW	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013641	4717	NDUFC1	http://www.ncbi.nlm.nih.gov/gene/?term=4717	KFYI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013642	4717	NDUFC1	http://www.ncbi.nlm.nih.gov/gene/?term=4717	KFYI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013643	4718	NDUFC2	http://www.ncbi.nlm.nih.gov/gene/?term=4718	"B14.5b, CI-B14.5b, HLC-1, NADHDH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013644	4718	NDUFC2	http://www.ncbi.nlm.nih.gov/gene/?term=4718	"B14.5b, CI-B14.5b, HLC-1, NADHDH2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013645	4718	NDUFC2	http://www.ncbi.nlm.nih.gov/gene/?term=4718	"B14.5b, CI-B14.5b, HLC-1, NADHDH2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013646	4719	NDUFS1	http://www.ncbi.nlm.nih.gov/gene/?term=4719	"CI-75Kd, CI-75k, PRO1304 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013647	4719	NDUFS1	http://www.ncbi.nlm.nih.gov/gene/?term=4719	"CI-75Kd, CI-75k, PRO1304 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013648	4720	NDUFS2	http://www.ncbi.nlm.nih.gov/gene/?term=4720	CI-49	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013649	47220	Fur1	http://www.ncbi.nlm.nih.gov/gene/?term=47220	"Dmel_CG10772, CG10772, Dfur1, Dfurin1, Dmel\CG10772, Furin, Furl, Klip1, dFur1, dFurin 1, dKLIP-1, fur-1, fur1, fur[1], furin, l(3)rL205 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013650	47220	Fur1	http://www.ncbi.nlm.nih.gov/gene/?term=47220	"Dmel_CG10772, CG10772, Dfur1, Dfurin1, Dmel\CG10772, Furin, Furl, Klip1, dFur1, dFurin 1, dKLIP-1, fur-1, fur1, fur[1], furin, l(3)rL205 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013651	4722	NDUFS3	http://www.ncbi.nlm.nih.gov/gene/?term=4722	CI-30	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013652	4723	NDUFV1	http://www.ncbi.nlm.nih.gov/gene/?term=4723	"CI-51K, CI51KD, UQOR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013653	4724	NDUFS4	http://www.ncbi.nlm.nih.gov/gene/?term=4724	"AQDQ, CI-18, CI-18 kDa, CI-AQDQ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013654	4725	NDUFS5	http://www.ncbi.nlm.nih.gov/gene/?term=4725	"CI-15k, CI15K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013655	4725	NDUFS5	http://www.ncbi.nlm.nih.gov/gene/?term=4725	"CI-15k, CI15K "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013656	4726	NDUFS6	http://www.ncbi.nlm.nih.gov/gene/?term=4726	"CI-13kA, CI-13kD-A, CI13KDA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013657	4728	NDUFS8	http://www.ncbi.nlm.nih.gov/gene/?term=4728	"CI-23k, CI23KD, TYKY "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013658	4728	NDUFS8	http://www.ncbi.nlm.nih.gov/gene/?term=4728	"CI-23k, CI23KD, TYKY "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013659	4729	NDUFV2	http://www.ncbi.nlm.nih.gov/gene/?term=4729	CI-24k	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013660	472	ATM	http://www.ncbi.nlm.nih.gov/gene/?term=472	"AT1, ATA, ATC, ATD, ATDC, ATE, TEL1, TELO1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013661	472	ATM	http://www.ncbi.nlm.nih.gov/gene/?term=472	"AT1, ATA, ATC, ATD, ATDC, ATE, TEL1, TELO1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013662	472	ATM	http://www.ncbi.nlm.nih.gov/gene/?term=472	"AT1, ATA, ATC, ATD, ATDC, ATE, TEL1, TELO1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013663	4731	NDUFV3	http://www.ncbi.nlm.nih.gov/gene/?term=4731	"CI-10k, CI-9KD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013664	4731	NDUFV3	http://www.ncbi.nlm.nih.gov/gene/?term=4731	"CI-10k, CI-9KD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013665	4731	NDUFV3	http://www.ncbi.nlm.nih.gov/gene/?term=4731	"CI-10k, CI-9KD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013666	4733	DRG1	http://www.ncbi.nlm.nih.gov/gene/?term=4733	NEDD3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013667	4733	DRG1	http://www.ncbi.nlm.nih.gov/gene/?term=4733	NEDD3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013668	4733	DRG1	http://www.ncbi.nlm.nih.gov/gene/?term=4733	NEDD3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013669	4734	NEDD4	http://www.ncbi.nlm.nih.gov/gene/?term=4734	"NEDD4-1, RPF1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013670	4734	NEDD4	http://www.ncbi.nlm.nih.gov/gene/?term=4734	"NEDD4-1, RPF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013671	4734	NEDD4	http://www.ncbi.nlm.nih.gov/gene/?term=4734	"NEDD4-1, RPF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013672	4735	SEPT2	http://www.ncbi.nlm.nih.gov/gene/?term=4735	"DIFF6, NEDD-5, NEDD5, Pnutl3, hNedd5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013673	4736	RPL10A	http://www.ncbi.nlm.nih.gov/gene/?term=4736	"CSA19, Csa-19, L10A, NEDD6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013674	4738	NEDD8	http://www.ncbi.nlm.nih.gov/gene/?term=4738	NEDD-8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013675	4738	NEDD8	http://www.ncbi.nlm.nih.gov/gene/?term=4738	NEDD-8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013676	47399	Reph	http://www.ncbi.nlm.nih.gov/gene/?term=47399	"Dmel_CG3920, CG3920, Dmel\CG3920, l(2)k16918, reph "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013677	473	RERE	http://www.ncbi.nlm.nih.gov/gene/?term=473	"ARG, ARP, ATN1L, DNB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013678	474526	PWP1	http://www.ncbi.nlm.nih.gov/gene/?term=474526		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013679	474536	TXNRD1	http://www.ncbi.nlm.nih.gov/gene/?term=474536		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013680	474568	ANKRD39	http://www.ncbi.nlm.nih.gov/gene/?term=474568		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013681	474595	ACYP2	http://www.ncbi.nlm.nih.gov/gene/?term=474595		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013682	474624	GFPT1	http://www.ncbi.nlm.nih.gov/gene/?term=474624		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013683	474625	AAK1	http://www.ncbi.nlm.nih.gov/gene/?term=474625		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013684	474635	COMMD10	http://www.ncbi.nlm.nih.gov/gene/?term=474635		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013685	474844	CSNK2B	http://www.ncbi.nlm.nih.gov/gene/?term=474844		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013686	474884	RPL10A	http://www.ncbi.nlm.nih.gov/gene/?term=474884		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013687	474891	PPIL1	http://www.ncbi.nlm.nih.gov/gene/?term=474891		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013688	474977	SH3BGRL2	http://www.ncbi.nlm.nih.gov/gene/?term=474977		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013689	475041	PDCD2	http://www.ncbi.nlm.nih.gov/gene/?term=475041		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013690	475043	HRSP12	http://www.ncbi.nlm.nih.gov/gene/?term=475043		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013691	475057	ODF1	http://www.ncbi.nlm.nih.gov/gene/?term=475057		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013692	4750	NEK1	http://www.ncbi.nlm.nih.gov/gene/?term=4750	"NY-REN-55, SRPS2, SRPS2A, SRTD6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013693	475148	MSI2	http://www.ncbi.nlm.nih.gov/gene/?term=475148		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013694	475158	CENPC	http://www.ncbi.nlm.nih.gov/gene/?term=475158	CENPC1	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013695	4751	NEK2	http://www.ncbi.nlm.nih.gov/gene/?term=4751	"HsPK21A, NLK1, PPP1R111, RP67, NEK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013696	4751	NEK2	http://www.ncbi.nlm.nih.gov/gene/?term=4751	"HsPK21A, NLK1, PPP1R111, RP67, NEK2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013697	4751	NEK2	http://www.ncbi.nlm.nih.gov/gene/?term=4751	"HsPK21, NEK2A, NLK1, PPP1R111, RP67 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013698	475231	BET1	http://www.ncbi.nlm.nih.gov/gene/?term=475231		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013699	475261	SNX10	http://www.ncbi.nlm.nih.gov/gene/?term=475261		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013700	475289	ZNF277	http://www.ncbi.nlm.nih.gov/gene/?term=475289	ZNF277P	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013701	4752	NEK3	http://www.ncbi.nlm.nih.gov/gene/?term=4752	HSPK36	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013702	475333	MRPS15	http://www.ncbi.nlm.nih.gov/gene/?term=475333		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013703	475346	VPS35	http://www.ncbi.nlm.nih.gov/gene/?term=475346		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013704	475358	RNF11	http://www.ncbi.nlm.nih.gov/gene/?term=475358		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013705	475385	DMAP1	http://www.ncbi.nlm.nih.gov/gene/?term=475385		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013706	475403	TOX4	http://www.ncbi.nlm.nih.gov/gene/?term=475403		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013707	475450	NFYB	http://www.ncbi.nlm.nih.gov/gene/?term=475450		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013708	475453	ANAPC10	http://www.ncbi.nlm.nih.gov/gene/?term=475453		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013709	475455	OTUD4	http://www.ncbi.nlm.nih.gov/gene/?term=475455		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013710	475467	ARFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=475467		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013711	475524	SSBP1	http://www.ncbi.nlm.nih.gov/gene/?term=475524		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013712	475566	FNTA	http://www.ncbi.nlm.nih.gov/gene/?term=475566		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013713	475590	EIF4EBP1	http://www.ncbi.nlm.nih.gov/gene/?term=475590		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013714	475675	SMC6	http://www.ncbi.nlm.nih.gov/gene/?term=475675		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013715	4756	NEO1	http://www.ncbi.nlm.nih.gov/gene/?term=4756	"IGDCC2, NGN, NTN1R2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013716	4756	NEO1	http://www.ncbi.nlm.nih.gov/gene/?term=4756	"IGDCC2, NGN, NTN1R2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013717	475733	MORN2	http://www.ncbi.nlm.nih.gov/gene/?term=475733		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013718	475746	MRPS5	http://www.ncbi.nlm.nih.gov/gene/?term=475746		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013719	475816	SEC22B	http://www.ncbi.nlm.nih.gov/gene/?term=475816		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013720	4758	NEU1	http://www.ncbi.nlm.nih.gov/gene/?term=4758	"NANH, NEU, SIAL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013721	4758	NEU1	http://www.ncbi.nlm.nih.gov/gene/?term=4758	"NANH, NEU, SIAL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013722	475	ATOX1	http://www.ncbi.nlm.nih.gov/gene/?term=475	"ATX1, HAH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013723	475	ATOX1	http://www.ncbi.nlm.nih.gov/gene/?term=475	"ATX1, HAH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013724	476015	SF3B2	http://www.ncbi.nlm.nih.gov/gene/?term=476015		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013725	476070	MAD2L1	http://www.ncbi.nlm.nih.gov/gene/?term=476070		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013726	47611	Gpo-1	http://www.ncbi.nlm.nih.gov/gene/?term=47611	"Dmel_CG8256, 1(2) K05713, CG 8256, CG18786, CG8256, Dmel\CG8256, GPO, GPO-1, Gpo, alpha-GPO, alphaGPO, anon-WO0118547.114, l(2)k05713 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013727	476156	TXNL4A	http://www.ncbi.nlm.nih.gov/gene/?term=476156		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013728	476206	RPS12	http://www.ncbi.nlm.nih.gov/gene/?term=476206		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013729	476258	SOD2	http://www.ncbi.nlm.nih.gov/gene/?term=476258		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013730	476311	GKAP1	http://www.ncbi.nlm.nih.gov/gene/?term=476311		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013731	476366	RPS5	http://www.ncbi.nlm.nih.gov/gene/?term=476366		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013732	4763	NF1	http://www.ncbi.nlm.nih.gov/gene/?term=4763	"NFNS, VRNF, WSS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013733	4763	NF1	http://www.ncbi.nlm.nih.gov/gene/?term=4763	"NFNS, VRNF, WSS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013734	476476	POLR2I	http://www.ncbi.nlm.nih.gov/gene/?term=476476		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013735	476567	THOC7	http://www.ncbi.nlm.nih.gov/gene/?term=476567		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013736	476601	RPL29	http://www.ncbi.nlm.nih.gov/gene/?term=476601		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013737	476603	PCBP4	http://www.ncbi.nlm.nih.gov/gene/?term=476603		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013738	476766	CEP57	http://www.ncbi.nlm.nih.gov/gene/?term=476766		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013739	476804	RPS3	http://www.ncbi.nlm.nih.gov/gene/?term=476804		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013740	476895	CCDC34	http://www.ncbi.nlm.nih.gov/gene/?term=476895		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013741	476924	TPT1	http://www.ncbi.nlm.nih.gov/gene/?term=476924		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013742	476935	WBP4	http://www.ncbi.nlm.nih.gov/gene/?term=476935		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013743	476946	COMMD6	http://www.ncbi.nlm.nih.gov/gene/?term=476946		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013744	476968	RAP2A	http://www.ncbi.nlm.nih.gov/gene/?term=476968		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013745	476974	CLYBL	http://www.ncbi.nlm.nih.gov/gene/?term=476974		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013746	476	ATP1A1	http://www.ncbi.nlm.nih.gov/gene/?term=476		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013747	476	ATP1A1	http://www.ncbi.nlm.nih.gov/gene/?term=476		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013748	477031	RPL14	http://www.ncbi.nlm.nih.gov/gene/?term=477031		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013749	477042	FTL	http://www.ncbi.nlm.nih.gov/gene/?term=477042		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013750	477046	RPL15	http://www.ncbi.nlm.nih.gov/gene/?term=477046		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013751	477082	MRAS	http://www.ncbi.nlm.nih.gov/gene/?term=477082		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	In situ hybridization	Figure 5: Validation and expression of pseudopodial enriched mRNAs and gene products. Data are collected from Figur 5.
RLID00013752	477082	MRAS	http://www.ncbi.nlm.nih.gov/gene/?term=477082		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013753	477099	TFDP2	http://www.ncbi.nlm.nih.gov/gene/?term=477099		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013754	477143	POLR3F	http://www.ncbi.nlm.nih.gov/gene/?term=477143		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013755	477146	CSRP2BP	http://www.ncbi.nlm.nih.gov/gene/?term=477146		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013756	477147	DSTN	http://www.ncbi.nlm.nih.gov/gene/?term=477147		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013757	477160	PLCB4	http://www.ncbi.nlm.nih.gov/gene/?term=477160		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013758	4771	NF2	http://www.ncbi.nlm.nih.gov/gene/?term=4771	"ACN, BANF, SCH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013759	4771	NF2	http://www.ncbi.nlm.nih.gov/gene/?term=4771	"ACN, BANF, SCH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013760	4771	NF2	http://www.ncbi.nlm.nih.gov/gene/?term=4771	"ACN, BANF, SCH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013761	4771	NF2	http://www.ncbi.nlm.nih.gov/gene/?term=4771	"ACN, BANF, SCH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013762	477259	DDX27	http://www.ncbi.nlm.nih.gov/gene/?term=477259		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013763	477297	UFM1	http://www.ncbi.nlm.nih.gov/gene/?term=477297		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013764	4772	NFATC1	http://www.ncbi.nlm.nih.gov/gene/?term=4772	"NF-ATC, NF-ATc1.2, NFAT2, NFATc "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013765	477308	RFC3	http://www.ncbi.nlm.nih.gov/gene/?term=477308		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013766	477329	GTF3A	http://www.ncbi.nlm.nih.gov/gene/?term=477329		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013767	477488	PTPN11	http://www.ncbi.nlm.nih.gov/gene/?term=477488	SHP-2	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	In situ hybridization	Figure 5: Validation and expression of pseudopodial enriched mRNAs and gene products. Data are collected from Figur 5.
RLID00013768	477488	PTPN11	http://www.ncbi.nlm.nih.gov/gene/?term=477488	SHP-2	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013769	4774	NFIA	http://www.ncbi.nlm.nih.gov/gene/?term=4774	"CTF, NF-I/A, NF1-A, NFI-A, NFI-L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013770	4774	NFIA	http://www.ncbi.nlm.nih.gov/gene/?term=4774	"CTF, NF-I/A, NF1-A, NFI-A, NFI-L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013771	4775	NFATC3	http://www.ncbi.nlm.nih.gov/gene/?term=4775	"NFAT4, NFATX "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013772	4775	NFATC3	http://www.ncbi.nlm.nih.gov/gene/?term=4775	"NFAT4, NFATX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013773	4775	NFATC3	http://www.ncbi.nlm.nih.gov/gene/?term=4775	"NFAT4, NFATX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013774	477640	ZCRB1	http://www.ncbi.nlm.nih.gov/gene/?term=477640		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013775	47765	c(3)G	http://www.ncbi.nlm.nih.gov/gene/?term=47765	"Dmel_CG17604, C(3)G, C3G, CG17604, Dmel\CG17604, c(3)g, c3G, cx "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013776	47765	c(3)G	http://www.ncbi.nlm.nih.gov/gene/?term=47765	"Dmel_CG17604, C(3)G, C3G, CG17604, Dmel\CG17604, c(3)g, c3G, cx "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013777	477660	MRPS35	http://www.ncbi.nlm.nih.gov/gene/?term=477660		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013778	477664	MED21	http://www.ncbi.nlm.nih.gov/gene/?term=477664	SURB7	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013779	477813	GSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=477813		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013780	47781	fs(1)K10	http://www.ncbi.nlm.nih.gov/gene/?term=47781	"Dmel_CG3218, CG3218, Dmel\CG3218, EG:30B8.5, K-10, K10, f(s)K10, fs(1)M9, fs(1)k10, k10 "	mRNA	Drosophila melanogaster	17923096	Apical	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013781	47781	fs(1)K10	http://www.ncbi.nlm.nih.gov/gene/?term=47781	"Dmel_CG3218, CG3218, Dmel\CG3218, EG:30B8.5, K-10, K10, f(s)K10, fs(1)M9, fs(1)k10, k10 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013782	47781	fs(1)K10	http://www.ncbi.nlm.nih.gov/gene/?term=47781	"Dmel_CG3218, CG3218, Dmel\CG3218, EG:30B8.5, K-10, K10, f(s)K10, fs(1)M9, fs(1)k10, k10 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013783	477876	RB1CC1	http://www.ncbi.nlm.nih.gov/gene/?term=477876		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013784	477879	TCEA1	http://www.ncbi.nlm.nih.gov/gene/?term=477879		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013785	477884	RAB28	http://www.ncbi.nlm.nih.gov/gene/?term=477884		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013786	4778	NFE2	http://www.ncbi.nlm.nih.gov/gene/?term=4778	"NF-E2, p45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013787	477912	RPL7	http://www.ncbi.nlm.nih.gov/gene/?term=477912		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013788	477913	STAU2	http://www.ncbi.nlm.nih.gov/gene/?term=477913		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013789	477919	MRPS28	http://www.ncbi.nlm.nih.gov/gene/?term=477919		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013790	477939	TMEM55A	http://www.ncbi.nlm.nih.gov/gene/?term=477939		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013791	477990	STAM	http://www.ncbi.nlm.nih.gov/gene/?term=477990		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013792	477995	SUV39H2	http://www.ncbi.nlm.nih.gov/gene/?term=477995		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013793	4779	NFE2L1	http://www.ncbi.nlm.nih.gov/gene/?term=4779	"LCR-F1, NRF1, TCF11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013794	4779	NFE2L1	http://www.ncbi.nlm.nih.gov/gene/?term=4779	"LCR-F1, NRF1, TCF11 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00013795	4779	NFE2L1	http://www.ncbi.nlm.nih.gov/gene/?term=4779	"LCR-F1, NRF1, TCF11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013796	4779	NFE2L1	http://www.ncbi.nlm.nih.gov/gene/?term=4779	"NRF1, TCF11, LCR-F1 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00013797	478023	ZMYND11	http://www.ncbi.nlm.nih.gov/gene/?term=478023		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013798	478053	PPP2R2B	http://www.ncbi.nlm.nih.gov/gene/?term=478053		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013799	478076	CWC27	http://www.ncbi.nlm.nih.gov/gene/?term=478076	SDCCAG10	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013800	478091	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=478091		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013801	478097	ANKRA2	http://www.ncbi.nlm.nih.gov/gene/?term=478097		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013802	4780	NFE2L2	http://www.ncbi.nlm.nih.gov/gene/?term=4780	"HEBP1, NRF2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013803	4780	NFE2L2	http://www.ncbi.nlm.nih.gov/gene/?term=4780	"HEBP1, NRF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013804	4780	NFE2L2	http://www.ncbi.nlm.nih.gov/gene/?term=4780	"HEBP1, NRF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013805	478149	RBBP4	http://www.ncbi.nlm.nih.gov/gene/?term=478149		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013806	478188	TCEB3	http://www.ncbi.nlm.nih.gov/gene/?term=478188		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013807	478190	TCEA3	http://www.ncbi.nlm.nih.gov/gene/?term=478190		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013808	4781	NFIB	http://www.ncbi.nlm.nih.gov/gene/?term=4781	"CTF, HMGIC/NFIB, NF-I/B, NF1-B, NFI-B, NFI-RED2, NFIB3, NFIB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013809	478295	COPS2	http://www.ncbi.nlm.nih.gov/gene/?term=478295		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013810	4782	NFIC	http://www.ncbi.nlm.nih.gov/gene/?term=4782	"CTF, CTF5, NF-I, NFI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013811	4782	NFIC	http://www.ncbi.nlm.nih.gov/gene/?term=4782	"CTF, CTF5, NF-I, NFI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013812	478312	MYO5A	http://www.ncbi.nlm.nih.gov/gene/?term=478312		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013813	478398	USP16	http://www.ncbi.nlm.nih.gov/gene/?term=478398		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013814	4783	NFIL3	http://www.ncbi.nlm.nih.gov/gene/?term=4783	"E4BP4, IL3BP1, NF-IL3A, NFIL3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013815	478452	ENOPH1	http://www.ncbi.nlm.nih.gov/gene/?term=478452		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013816	4784	NFIX	http://www.ncbi.nlm.nih.gov/gene/?term=4784	"MRSHSS, NF1A, SOTOS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013817	4784	NFIX	http://www.ncbi.nlm.nih.gov/gene/?term=4784	"MRSHSS, NF1A, SOTOS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013818	478637	ACTL6A	http://www.ncbi.nlm.nih.gov/gene/?term=478637		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013819	478639	NDUFB5	http://www.ncbi.nlm.nih.gov/gene/?term=478639		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013820	478670	LPP	http://www.ncbi.nlm.nih.gov/gene/?term=478670		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013821	478717	EEF1E1	http://www.ncbi.nlm.nih.gov/gene/?term=478717		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013822	478725	TBC1D7	http://www.ncbi.nlm.nih.gov/gene/?term=478725		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013823	478726	SIRT5	http://www.ncbi.nlm.nih.gov/gene/?term=478726		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013824	478770	GRB14	http://www.ncbi.nlm.nih.gov/gene/?term=478770		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013825	478779	STK39	http://www.ncbi.nlm.nih.gov/gene/?term=478779		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013826	478788	METTL5	http://www.ncbi.nlm.nih.gov/gene/?term=478788		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013827	478855	HSPE1	http://www.ncbi.nlm.nih.gov/gene/?term=478855	"MOB4, MOBKL3, PREI3 "	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013828	478897	LANCL1	http://www.ncbi.nlm.nih.gov/gene/?term=478897		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013829	478	ATP1A3	http://www.ncbi.nlm.nih.gov/gene/?term=478	"AHC2, CAPOS, DYT12, RDP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013830	479057	BTBD1	http://www.ncbi.nlm.nih.gov/gene/?term=479057		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013831	479059	HDGFRP3	http://www.ncbi.nlm.nih.gov/gene/?term=479059		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013832	479066	IDH3A	http://www.ncbi.nlm.nih.gov/gene/?term=479066		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013833	4790	NFKB1	http://www.ncbi.nlm.nih.gov/gene/?term=4790	"CVID12, EBP-1, KBF1, NF-kB1, NF-kappa-B, NF-kappaB, NFKB-p105, NFKB-p50, NFkappaB, p105, p50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013834	4790	NFKB1	http://www.ncbi.nlm.nih.gov/gene/?term=4790	"CVID12, EBP-1, KBF1, NF-kB1, NF-kappa-B, NF-kappaB, NFKB-p105, NFKB-p50, NFkappaB, p105, p50 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013835	4790	NFKB1	http://www.ncbi.nlm.nih.gov/gene/?term=4790	"CVID12, EBP-1, KBF1, NF-kB1, NF-kappa-B, NF-kappaB, NFKB-p105, NFKB-p50, NFkappaB, p105, p50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013836	479238	PPA1	http://www.ncbi.nlm.nih.gov/gene/?term=479238		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013837	4792	NFKBIA	http://www.ncbi.nlm.nih.gov/gene/?term=4792	"IKBA, MAD-3, NFKBI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013838	4792	NFKBIA	http://www.ncbi.nlm.nih.gov/gene/?term=4792	"IKBA, MAD-3, NFKBI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013839	4792	NFKBIA	http://www.ncbi.nlm.nih.gov/gene/?term=4792	"IKBA, MAD-3, NFKBI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013840	479331	CSNK1A1	http://www.ncbi.nlm.nih.gov/gene/?term=479331		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013841	4793	NFKBIB	http://www.ncbi.nlm.nih.gov/gene/?term=4793	"IKBB, TRIP9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013842	4793	NFKBIB	http://www.ncbi.nlm.nih.gov/gene/?term=4793	"IKBB, TRIP9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013843	479532	TMEM11	http://www.ncbi.nlm.nih.gov/gene/?term=479532		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013844	479605	KIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=479605		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013845	479636	DYNLRB2	http://www.ncbi.nlm.nih.gov/gene/?term=479636		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013846	479693	DYNC1LI2	http://www.ncbi.nlm.nih.gov/gene/?term=479693		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013847	4796	TONSL	http://www.ncbi.nlm.nih.gov/gene/?term=4796	"IKBR, NFKBIL2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013848	4796	TONSL	http://www.ncbi.nlm.nih.gov/gene/?term=4796	"IKBR, NFKBIL2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013849	4796	TONSL	http://www.ncbi.nlm.nih.gov/gene/?term=4796	"IKBR, NFKBIL2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013850	479745	ARPC1A	http://www.ncbi.nlm.nih.gov/gene/?term=479745		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	In situ hybridization	Figure 5: Validation and expression of pseudopodial enriched mRNAs and gene products. Data are collected from Figur 5.
RLID00013851	479745	ARPC1A	http://www.ncbi.nlm.nih.gov/gene/?term=479745		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013852	479776	BCKDK	http://www.ncbi.nlm.nih.gov/gene/?term=479776		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013853	4798	NFRKB	http://www.ncbi.nlm.nih.gov/gene/?term=4798	INO80G	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013854	4798	NFRKB	http://www.ncbi.nlm.nih.gov/gene/?term=4798	INO80G	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013855	4799	NFX1	http://www.ncbi.nlm.nih.gov/gene/?term=4799	"NFX2, TEG-42, Tex42 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013856	4799	NFX1	http://www.ncbi.nlm.nih.gov/gene/?term=4799	"NFX2, TEG-42, Tex42 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013857	479	ATP12A	http://www.ncbi.nlm.nih.gov/gene/?term=479	"#945, ATP1AL1, HK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013858	479	ATP12A	http://www.ncbi.nlm.nih.gov/gene/?term=479	"#945, ATP1AL1, HK "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013859	47	ACLY	http://www.ncbi.nlm.nih.gov/gene/?term=47	"ACL, ATPCL, CLATP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013860	47	ACLY	http://www.ncbi.nlm.nih.gov/gene/?term=47	"ACL, ATPCL, CLATP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013861	47	ACLY	http://www.ncbi.nlm.nih.gov/gene/?term=47	"ACL, ATPCL, CLATP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013862	4800	NFYA	http://www.ncbi.nlm.nih.gov/gene/?term=4800	"CBF-A, CBF-B, HAP2, NF-YA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013863	480146	HDHD2	http://www.ncbi.nlm.nih.gov/gene/?term=480146		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013864	480147	PIAS2	http://www.ncbi.nlm.nih.gov/gene/?term=480147		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013865	480149	ATP5A1	http://www.ncbi.nlm.nih.gov/gene/?term=480149		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013866	480165	RNF138	http://www.ncbi.nlm.nih.gov/gene/?term=480165		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013867	4801	NFYB	http://www.ncbi.nlm.nih.gov/gene/?term=4801	"CBF-A, CBF-B, HAP3, NF-YB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013868	480221	LOC480221	http://www.ncbi.nlm.nih.gov/gene/?term=480221	"RPL17, RPL17L "	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013869	480242	PRMT5	http://www.ncbi.nlm.nih.gov/gene/?term=480242		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013870	4802	NFYC	http://www.ncbi.nlm.nih.gov/gene/?term=4802	"CBF-C, CBFC, H1TF2A, HAP5, HSM, NF-YC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013871	480326	DDHD1	http://www.ncbi.nlm.nih.gov/gene/?term=480326		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013872	480513	BECN1	http://www.ncbi.nlm.nih.gov/gene/?term=480513		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013873	480519	DNAJC7	http://www.ncbi.nlm.nih.gov/gene/?term=480519		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013874	4807	NHLH1	http://www.ncbi.nlm.nih.gov/gene/?term=4807	"HEN1, NSCL, NSCL1, bHLHa35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013875	480830	SLC25A6	http://www.ncbi.nlm.nih.gov/gene/?term=480830		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013876	480897	CDK16	http://www.ncbi.nlm.nih.gov/gene/?term=480897	PCTK1	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013877	480986	TIMM8A	http://www.ncbi.nlm.nih.gov/gene/?term=480986		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013878	4809	SNU13	http://www.ncbi.nlm.nih.gov/gene/?term=4809	"15.5K, FA-1, FA1, NHP2L1, NHPX, OTK27, SNRNP15-5, SPAG12, SSFA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013879	4809	SNU13	http://www.ncbi.nlm.nih.gov/gene/?term=4809	"15.5K, FA-1, FA1, NHP2L1, NHPX, OTK27, SNRNP15-5, SPAG12, SSFA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013880	481038	MCTS1	http://www.ncbi.nlm.nih.gov/gene/?term=481038		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013881	481049	ZNF280C	http://www.ncbi.nlm.nih.gov/gene/?term=481049	SUHW3	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013882	481063	RBMX	http://www.ncbi.nlm.nih.gov/gene/?term=481063		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013883	481070	FMR1	http://www.ncbi.nlm.nih.gov/gene/?term=481070		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013884	4811	NID1	http://www.ncbi.nlm.nih.gov/gene/?term=4811	NID	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013885	4811	NID1	http://www.ncbi.nlm.nih.gov/gene/?term=4811	NID	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013886	4814	NINJ1	http://www.ncbi.nlm.nih.gov/gene/?term=4814	"NIN1, NINJURIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013887	4814	NINJ1	http://www.ncbi.nlm.nih.gov/gene/?term=4814	"NIN1, NINJURIN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013888	481617	DCAF10	http://www.ncbi.nlm.nih.gov/gene/?term=481617	WDR32	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013889	4818	NKG7	http://www.ncbi.nlm.nih.gov/gene/?term=4818	"GIG1, GMP-17, p15-TIA-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013890	481	ATP1B1	http://www.ncbi.nlm.nih.gov/gene/?term=481	ATP1B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013891	481	ATP1B1	http://www.ncbi.nlm.nih.gov/gene/?term=481	ATP1B	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00013892	481	ATP1B1	http://www.ncbi.nlm.nih.gov/gene/?term=481	ATP1B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013893	4820	NKTR	http://www.ncbi.nlm.nih.gov/gene/?term=4820	p104	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013894	4828	NMB	http://www.ncbi.nlm.nih.gov/gene/?term=4828		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013895	482916	ING2	http://www.ncbi.nlm.nih.gov/gene/?term=482916	INGX	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013896	482992	UBXN2A	http://www.ncbi.nlm.nih.gov/gene/?term=482992	UBXD4	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013897	482	ATP1B2	http://www.ncbi.nlm.nih.gov/gene/?term=482	AMOG	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013898	482	ATP1B2	http://www.ncbi.nlm.nih.gov/gene/?term=482	AMOG	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013899	482	ATP1B2	http://www.ncbi.nlm.nih.gov/gene/?term=482	AMOG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013900	4830	NME1	http://www.ncbi.nlm.nih.gov/gene/?term=4830	"AWD, GAAD, NB, NBS, NDKA, NDPK-A, NDPKA, NM23, NM23-H1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013901	4830	NME1	http://www.ncbi.nlm.nih.gov/gene/?term=4830	"AWD, GAAD, NB, NBS, NDKA, NDPK-A, NDPKA, NM23, NM23-H1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013902	4830	NME1	http://www.ncbi.nlm.nih.gov/gene/?term=4830	"AWD, GAAD, NB, NBS, NDKA, NDPK-A, NDPKA, NM23, NM23-H1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013903	48317	ttk	http://www.ncbi.nlm.nih.gov/gene/?term=48317	"Dmel_CG1856, 0037/17, 0250/25, 0438/31, 0702/07, 1049/07, 1119/04, 1184/16, 1209/05, 1209/10, 1260/10, 1281/04, 1325/15, 1372/08, 1396/14, 1418/06, 3540, 5125, 5311, CG11558, CG1856, Dmel\CG1856, E(yan)100D, FTZ-F2, TTK, TTK69, TTK88, TTKA, Ttk, Ttk69, Ttk88, anon-EST:Liang-2.9, clone 2.9, ftz-f2, ftzf2/ttk, l(3)02667, l(3)j2A1, l(3)j7B8, osn, oss, ovs, tramtrak/FTZ-F2, ttk69, ttkp69, twk, ttk "	mRNA	Drosophila melanogaster	18956321	Germ plasm	Embryo	In situ hybridization	"Our in situ hybridization analysis revealed that 27 of the 68 transcripts were enriched in the germ plasm. Among the 27 transcripts, six were found to be required for germline-specific gene expression of vasa and/or nanos by knockdown experiments using RNA interference (RNAi). The identified transcripts encode a transcriptional activator (ovo), components of the transcriptional initiation complexes (Trf2, bip2 and Tif-IA), and the Ccr4-Not complex (CG31716 and l(2)NC136).  "
RLID00013904	48317	ttk	http://www.ncbi.nlm.nih.gov/gene/?term=48317	"Dmel_CG1856, 0037/17, 0250/25, 0438/31, 0702/07, 1049/07, 1119/04, 1184/16, 1209/05, 1209/10, 1260/10, 1281/04, 1325/15, 1372/08, 1396/14, 1418/06, 3540, 5125, 5311, CG11558, CG1856, Dmel\CG1856, E(yan)100D, FTZ-F2, TTK, TTK69, TTK88, TTKA, Ttk, Ttk69, Ttk88, anon-EST:Liang-2.9, clone 2.9, ftz-f2, ftzf2/ttk, l(3)02667, l(3)j2A1, l(3)j7B8, osn, oss, ovs, tramtrak/FTZ-F2, ttk69, ttkp69, twk, ttk "	mRNA	Drosophila melanogaster	17923096	Posterior	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00013905	48317	ttk	http://www.ncbi.nlm.nih.gov/gene/?term=48317	"Dmel_CG1856, 0037/17, 0250/25, 0438/31, 0702/07, 1049/07, 1119/04, 1184/16, 1209/05, 1209/10, 1260/10, 1281/04, 1325/15, 1372/08, 1396/14, 1418/06, 3540, 5125, 5311, CG11558, CG1856, Dmel\CG1856, E(yan)100D, FTZ-F2, TTK, TTK69, TTK88, TTKA, Ttk, Ttk69, Ttk88, anon-EST:Liang-2.9, clone 2.9, ftz-f2, ftzf2/ttk, l(3)02667, l(3)j2A1, l(3)j7B8, osn, oss, ovs, tramtrak/FTZ-F2, ttk69, ttkp69, twk, ttk "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013906	483282	COG1	http://www.ncbi.nlm.nih.gov/gene/?term=483282		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013907	4832	NME3	http://www.ncbi.nlm.nih.gov/gene/?term=4832	"DR-nm23, NDPK-C, NDPKC, NM23-H3, NM23H3, c371H6.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013908	4832	NME3	http://www.ncbi.nlm.nih.gov/gene/?term=4832	"DR-nm23, NDPK-C, NDPKC, NM23-H3, NM23H3, c371H6.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013909	483338	SEC14L1	http://www.ncbi.nlm.nih.gov/gene/?term=483338		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013910	4833	NME4	http://www.ncbi.nlm.nih.gov/gene/?term=4833	"NDPK-D, NM23H4, nm23-H4 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013911	4833	NME4	http://www.ncbi.nlm.nih.gov/gene/?term=4833	"NDPK-D, NM23H4, nm23-H4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013912	483424	TRIM44	http://www.ncbi.nlm.nih.gov/gene/?term=483424		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013913	4835	NQO2	http://www.ncbi.nlm.nih.gov/gene/?term=4835	"DHQV, DIA6, NMOR2, QR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013914	4835	NQO2	http://www.ncbi.nlm.nih.gov/gene/?term=4835	"DHQV, DIA6, NMOR2, QR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013915	4835	NQO2	http://www.ncbi.nlm.nih.gov/gene/?term=4835	"DHQV, DIA6, NMOR2, QR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013916	4836	NMT1	http://www.ncbi.nlm.nih.gov/gene/?term=4836	NMT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013917	4836	NMT1	http://www.ncbi.nlm.nih.gov/gene/?term=4836	NMT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013918	4836	NMT1	http://www.ncbi.nlm.nih.gov/gene/?term=4836	NMT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013919	4837	NNMT	http://www.ncbi.nlm.nih.gov/gene/?term=4837		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013920	4839	NOP2	http://www.ncbi.nlm.nih.gov/gene/?term=4839	"NOL1, NOP120, NSUN1, p120 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013921	4839	NOP2	http://www.ncbi.nlm.nih.gov/gene/?term=4839	"NOL1, NOP120, NSUN1, p120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013922	483	ATP1B3	http://www.ncbi.nlm.nih.gov/gene/?term=483	"ATPB-3, CD298 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013923	483	ATP1B3	http://www.ncbi.nlm.nih.gov/gene/?term=483	"ATPB-3, CD298 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013924	483	ATP1B3	http://www.ncbi.nlm.nih.gov/gene/483	"CD298, ATPB-3 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00013925	484176	CBWD2	http://www.ncbi.nlm.nih.gov/gene/?term=484176	CBWD1	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013926	4841	NONO	http://www.ncbi.nlm.nih.gov/gene/?term=4841	"MRXS34, NMT55, NRB54, P54, P54NRB, PPP1R114 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013927	4841	NONO	http://www.ncbi.nlm.nih.gov/gene/?term=4841	"MRXS34, NMT55, NRB54, P54, P54NRB, PPP1R114 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013928	4841	NONO	http://www.ncbi.nlm.nih.gov/gene/?term=4841	"MRXS34, NMT55, NRB54, P54, P54NRB, PPP1R114 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013929	4841	NONO	http://www.ncbi.nlm.nih.gov/gene/?term=4841	"NMT55, NRB54, P54, P54NRB, PPP1R114 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013930	48440	Kebab	http://www.ncbi.nlm.nih.gov/gene/?term=48440	"Dmel_CG31672, BEST:LD15963, CG31672, CG4248, Dmel\CG31672, keb, kebab, n(2)k09932 "	mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013931	48440	Kebab	http://www.ncbi.nlm.nih.gov/gene/?term=48440	"Dmel_CG31672, BEST:LD15963, CG31672, CG4248, Dmel\CG31672, keb, kebab, n(2)k09932 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013932	48445	Acph-1	http://www.ncbi.nlm.nih.gov/gene/?term=48445	"Dmel_CG7899, ACP, ACPH, APH, Acph, CG7899, Dmel\CG7899 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013933	484820	ELL	http://www.ncbi.nlm.nih.gov/gene/?term=484820		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013934	4848	CNOT2	http://www.ncbi.nlm.nih.gov/gene/?term=4848	"CDC36, HSPC131, NOT2, NOT2H "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013935	4848	CNOT2	http://www.ncbi.nlm.nih.gov/gene/?term=4848	"CDC36, HSPC131, NOT2, NOT2H "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013936	4848	CNOT2	http://www.ncbi.nlm.nih.gov/gene/?term=4848	"CDC36, HSPC131, NOT2, NOT2H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013937	4849	CNOT3	http://www.ncbi.nlm.nih.gov/gene/?term=4849	"LENG2, NOT3, NOT3H "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013938	4849	CNOT3	http://www.ncbi.nlm.nih.gov/gene/?term=4849	"LENG2, NOT3, NOT3H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013939	4850	CNOT4	http://www.ncbi.nlm.nih.gov/gene/?term=4850	"CLONE243, NOT4, NOT4H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013940	4853	NOTCH2	http://www.ncbi.nlm.nih.gov/gene/?term=4853	"AGS2, HJCYS, hN2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013941	4853	NOTCH2	http://www.ncbi.nlm.nih.gov/gene/?term=4853	"AGS2, HJCYS, hN2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013942	4854	NOTCH3	http://www.ncbi.nlm.nih.gov/gene/?term=4854	"CADASIL, CADASIL1, CASIL, IMF2, LMNS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013943	48552	Sam-S	http://www.ncbi.nlm.nih.gov/gene/?term=48552	"Dmel_CG2674, CG2674, Dmel\CG2674, M(2)21A-B, M(2)21AB, METK, SamS, Su(z)5, m(2)21ab "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013944	4855	NOTCH4	http://www.ncbi.nlm.nih.gov/gene/?term=4855	INT3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013945	485684	ARMC8	http://www.ncbi.nlm.nih.gov/gene/?term=485684		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013946	48572	Hsp60B	http://www.ncbi.nlm.nih.gov/gene/?term=48572	"Dmel_CG2830, 152031_at, CG2830, Dmel\CG2830, Hsp60b, anon-WO0140519.61, hsp60B, ms(2)06619, ms(2)21D "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013947	485756	BFSP1	http://www.ncbi.nlm.nih.gov/gene/?term=485756		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013948	485837	SNTA1	http://www.ncbi.nlm.nih.gov/gene/?term=485837		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	In situ hybridization	Figure 5: Validation and expression of pseudopodial enriched mRNAs and gene products. Data are collected from Figur 5.
RLID00013949	485837	SNTA1	http://www.ncbi.nlm.nih.gov/gene/?term=485837		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013950	485856	MYL9	http://www.ncbi.nlm.nih.gov/gene/?term=485856		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013951	4860	PNP	http://www.ncbi.nlm.nih.gov/gene/?term=4860	"NP, PRO1837, PUNP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013952	4860	PNP	http://www.ncbi.nlm.nih.gov/gene/?term=4860	"NP, PRO1837, PUNP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013953	486354	PES1	http://www.ncbi.nlm.nih.gov/gene/?term=486354		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013954	4863	NPAT	http://www.ncbi.nlm.nih.gov/gene/?term=4863	"E14, E14/NPAT, p220 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013955	4863	NPAT	http://www.ncbi.nlm.nih.gov/gene/?term=4863	"E14, E14/NPAT, p220 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013956	4864	NPC1	http://www.ncbi.nlm.nih.gov/gene/?term=4864	NPC	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013957	4864	NPC1	http://www.ncbi.nlm.nih.gov/gene/?term=4864	NPC	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013958	4869	NPM1	http://www.ncbi.nlm.nih.gov/gene/?term=4869	"B23, NPM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013959	4869	NPM1	http://www.ncbi.nlm.nih.gov/gene/?term=4869	"B23, NPM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013960	4869	NPM1	http://www.ncbi.nlm.nih.gov/gene/?term=4869	"B23, NPM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013961	4869	NPM1	http://www.ncbi.nlm.nih.gov/gene/?term=4869	"B23, NPM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013962	4869	NPM1	http://www.ncbi.nlm.nih.gov/gene/?term=4869	"B23, NPM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013963	487147	NET1	http://www.ncbi.nlm.nih.gov/gene/?term=487147		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013964	487218	ACTBL2	http://www.ncbi.nlm.nih.gov/gene/?term=487218		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	In situ hybridization	Figure 5: Validation and expression of pseudopodial enriched mRNAs and gene products. Data are collected from Figur 5.
RLID00013965	487233	SREK1	http://www.ncbi.nlm.nih.gov/gene/?term=487233	SFRS12	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013966	488025	TNK2	http://www.ncbi.nlm.nih.gov/gene/?term=488025		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013967	488164	EIF5A2	http://www.ncbi.nlm.nih.gov/gene/?term=488164		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013968	4881	NPR1	http://www.ncbi.nlm.nih.gov/gene/?term=4881	"ANPRA, ANPa, GUC2A, GUCY2A, NPRA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013969	488475	TRAK2	http://www.ncbi.nlm.nih.gov/gene/?term=488475		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013970	488	ATP2A2	http://www.ncbi.nlm.nih.gov/gene/?term=488	"ATP2B, DAR, DD, SERCA2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013971	488	ATP2A2	http://www.ncbi.nlm.nih.gov/gene/?term=488	"ATP2B, DAR, DD, SERCA2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013972	4891	SLC11A2	http://www.ncbi.nlm.nih.gov/gene/?term=4891	"AHMIO1, DCT1, DMT1, NRAMP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013973	4891	SLC11A2	http://www.ncbi.nlm.nih.gov/gene/?term=4891	"DCT1, DMT1, NRAMP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013974	4892	NRAP	http://www.ncbi.nlm.nih.gov/gene/?term=4892	N-RAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013975	489533	EPN2	http://www.ncbi.nlm.nih.gov/gene/?term=489533		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013976	48973	Src64B	http://www.ncbi.nlm.nih.gov/gene/?term=48973	"Dmel_CG7524, C-src1, CG7524, D-Src64B, D-src, DSRC64, DSrc, DSrc64, DSrc64B, Dm SRC1, DmHD-358, Dmel\CG7524, Dsrc, Dsrc64, Dsrc64B, HD-358, MRE5, SRC 64B, SRC64B, Src, Src1, Src64, Src64b, c-src, dSrc, dsrc, src, src1, src64, src64B, src64b "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013977	4897	NRCAM	http://www.ncbi.nlm.nih.gov/gene/?term=4897		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013978	4898	NRDC	http://www.ncbi.nlm.nih.gov/gene/?term=4898	"NRD1, hNRD1, hNRD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013979	48	ACO1	http://www.ncbi.nlm.nih.gov/gene/?term=48	"ACONS, HEL60, IREB1, IREBP, IREBP1, IRP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013980	48	ACO1	http://www.ncbi.nlm.nih.gov/gene/?term=48	"ACONS, HEL60, IREB1, IREBP, IREBP1, IRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013981	490068	FAHD1	http://www.ncbi.nlm.nih.gov/gene/?term=490068		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013982	4900	NRGN	http://www.ncbi.nlm.nih.gov/gene/?term=4900	"RC3, hng "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013983	4902	NRTN	http://www.ncbi.nlm.nih.gov/gene/?term=4902	NTN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013984	4902	NRTN	http://www.ncbi.nlm.nih.gov/gene/?term=4902	NTN	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013985	4902	NRTN	http://www.ncbi.nlm.nih.gov/gene/?term=4902	NTN	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00013986	4904	YBX1	http://www.ncbi.nlm.nih.gov/gene/?term=4904	"BP-8, CBF-A, CSDA2, CSDB, DBPB, EFI-A, MDR-NF1, NSEP-1, NSEP1, YB-1, YB1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013987	4905	NSF	http://www.ncbi.nlm.nih.gov/gene/?term=4905	SKD2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013988	4905	NSF	http://www.ncbi.nlm.nih.gov/gene/?term=4905	SKD2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013989	49070	Mbs	http://www.ncbi.nlm.nih.gov/gene/?term=49070	"Dmel_CG32156, 0573/06, 0953/04, CG32156, CG5600, CG5891, DMBS, DMYPT, DMbs, Dmel\CG32156, MBS, Mypt, l(3)03802, l(3)72Dd, l(3)S005331b, l(3)S057306, l(3)S057306b, l(3)S095304, l(3)j3B4, l(3)j7A1, mbs "	mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013990	49070	Mbs	http://www.ncbi.nlm.nih.gov/gene/?term=49070	"Dmel_CG32156, 0573/06, 0953/04, CG32156, CG5600, CG5891, DMBS, DMYPT, DMbs, Dmel\CG32156, MBS, Mypt, l(3)03802, l(3)72Dd, l(3)S005331b, l(3)S057306, l(3)S057306b, l(3)S095304, l(3)j3B4, l(3)j7A1, mbs "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00013991	490967	STAT3	http://www.ncbi.nlm.nih.gov/gene/?term=490967		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013992	4909	NTF4	http://www.ncbi.nlm.nih.gov/gene/?term=4909	"GLC10, GLC1O, NT-4, NT-4/5, NT-5, NT4, NT5, NTF5 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00013993	4909	NTF4	http://www.ncbi.nlm.nih.gov/gene/?term=4909	"NT4, NT5, NT-4, NT-5, NTF5, GLC10, GLC1O, NT-4/5 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00013994	490	ATP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=490	"PMCA1, PMCA1kb "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013995	490	ATP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=490	"PMCA1, PMCA1kb "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00013996	490	ATP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=490	"PMCA1, PMCA1kb "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00013997	491185	GOSR1	http://www.ncbi.nlm.nih.gov/gene/?term=491185		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00013998	4913	NTHL1	http://www.ncbi.nlm.nih.gov/gene/?term=4913	"FAP3, NTH1, OCTS3, hNTH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00013999	491539	CIB2	http://www.ncbi.nlm.nih.gov/gene/?term=491539		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00014000	4915	NTRK2	http://www.ncbi.nlm.nih.gov/gene/?term=4915	"GP145-TrkB, TRKB, trk-B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014001	491853	RP2	http://www.ncbi.nlm.nih.gov/gene/?term=491853		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00014002	492030	BEX4	http://www.ncbi.nlm.nih.gov/gene/?term=492030	BEXL1	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00014003	4920	ROR2	http://www.ncbi.nlm.nih.gov/gene/?term=4920	"BDB, BDB1, NTRKR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014004	49228	mod(mdg4)	http://www.ncbi.nlm.nih.gov/gene/?term=49228	"Dmel_CG32491, BcDNA:GH07769, BcDNA:SD03001, CG15500, CG15501, CG15802, CG18151, CG32491, CG7836, CG7859, CG8076, Dmel\CG32491, Doom, E(var)129, E(var)3-93D, E(var)93D, E-(var)3-93D, E-var(3)1, E-var(3)3, MOD(MDG4), MOD(MDG4)56.3, MOD2.2, Mod(mdg 4), Mod(mdg 4)67.2, Mod(mdg)4, Mod(mdg4), Mod(mdg4)-67.2, Mod(mdg4)2.2, Mod(mdg4)67.2, Mod2.2, Mod67.2, Mod[mdg4], bpd, doom, l(3)03852, l(3)L3101, l(3)j2B7, mdg4, mnm, mnn, mod, mod (mdg4), mod(gypsy), mod(mdg-4), mod(mdg4-67.2, mod(mdg4)67.2, mod2.2, modMDG4, mod[mdg4], pf-2, mod(mdg4) "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00014005	4922	NTS	http://www.ncbi.nlm.nih.gov/gene/?term=4922	"NMN-125, NN, NT, NT/N1, NTS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014006	4924	NUCB1	http://www.ncbi.nlm.nih.gov/gene/?term=4924	"CALNUC, NUC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014007	4924	NUCB1	http://www.ncbi.nlm.nih.gov/gene/?term=4924	"CALNUC, NUC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014008	4924	NUCB1	http://www.ncbi.nlm.nih.gov/gene/?term=4924	"NUC, CALNUC "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00014009	4925	NUCB2	http://www.ncbi.nlm.nih.gov/gene/?term=4925	"HEL-S-109, NEFA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014010	4925	NUCB2	http://www.ncbi.nlm.nih.gov/gene/?term=4925	"HEL-S-109, NEFA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014011	4925	NUCB2	http://www.ncbi.nlm.nih.gov/gene/?term=4925	"HEL-S-109, NEFA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014012	4925	NUCB2	http://www.ncbi.nlm.nih.gov/gene/?term=4925	"NEFA, HEL-S-109 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00014013	4926	NUMA1	http://www.ncbi.nlm.nih.gov/gene/?term=4926	"NMP-22, NUMA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014014	4926	NUMA1	http://www.ncbi.nlm.nih.gov/gene/?term=4926	"NMP-22, NUMA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014015	4927	NUP88	http://www.ncbi.nlm.nih.gov/gene/?term=4927		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014016	4927	NUP88	http://www.ncbi.nlm.nih.gov/gene/?term=4927		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014017	4928	NUP98	http://www.ncbi.nlm.nih.gov/gene/?term=4928	"ADIR2, NUP196, NUP96 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014018	4928	NUP98	http://www.ncbi.nlm.nih.gov/gene/?term=4928	"ADIR2, NUP196, NUP96 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014019	4931	NVL	http://www.ncbi.nlm.nih.gov/gene/?term=4931	NVL2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014020	493753	COA5	http://www.ncbi.nlm.nih.gov/gene/?term=493753	"6330578E17Rik, C2orf64, CEMCOX3, Pet191 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014021	493856	CISD2	http://www.ncbi.nlm.nih.gov/gene/?term=493856	"ERIS, Miner1, NAF-1, WFS2, ZCD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014022	493856	CISD2	http://www.ncbi.nlm.nih.gov/gene/?term=493856	"ERIS, Miner1, NAF-1, WFS2, ZCD2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014023	493869	GPX8	http://www.ncbi.nlm.nih.gov/gene/?term=493869	"EPLA847, GPx-8, GSHPx-8, UNQ847 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014024	4938	OAS1	http://www.ncbi.nlm.nih.gov/gene/?term=4938	"E18/E16, IFI-4, OIAS, OIASI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014025	493	ATP2B4	http://www.ncbi.nlm.nih.gov/gene/?term=493	"ATP2B2, MXRA1, PMCA4, PMCA4b, PMCA4x "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014026	4940	OAS3	http://www.ncbi.nlm.nih.gov/gene/?term=4940	"p100, p100OAS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014027	494115	RBMXL1	http://www.ncbi.nlm.nih.gov/gene/?term=494115	RBM1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014028	494143	CHAC2	http://www.ncbi.nlm.nih.gov/gene/?term=494143		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014029	4942	OAT	http://www.ncbi.nlm.nih.gov/gene/?term=4942	"GACR, HOGAASE, OKT, OAT "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014030	4942	OAT	http://www.ncbi.nlm.nih.gov/gene/?term=4942	"GACR, HOGAASE, OKT, OAT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014031	4942	OAT	http://www.ncbi.nlm.nih.gov/gene/?term=4942	"GACR, HOGA, OATASE, OKT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014032	494448	Cbx6	http://www.ncbi.nlm.nih.gov/gene/?term=494448		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014033	494468	Armcx5	http://www.ncbi.nlm.nih.gov/gene/?term=494468	AW556585	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014034	4946	OAZ1	http://www.ncbi.nlm.nih.gov/gene/?term=4946	"AZI, OAZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014035	4946	OAZ1	http://www.ncbi.nlm.nih.gov/gene/?term=4946	"AZI, OAZ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014036	4947	OAZ2	http://www.ncbi.nlm.nih.gov/gene/?term=4947	AZ2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014037	4947	OAZ2	http://www.ncbi.nlm.nih.gov/gene/?term=4947	AZ2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014038	4948	OCA2	http://www.ncbi.nlm.nih.gov/gene/?term=4948	"BEY, BEY1, BEY2, BOCA, D15S12, EYCL, EYCL2, EYCL3, HCL3, P, PED, SHEP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014039	495071	LOC495071	http://www.ncbi.nlm.nih.gov/gene/?term=495071		mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00014040	495252	lima1	http://www.ncbi.nlm.nih.gov/gene/?term=495252		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00014041	4952	OCRL	http://www.ncbi.nlm.nih.gov/gene/?term=4952	"INPP5F, LOCR, NPHL2, OCRL-1, OCRL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014042	4953	ODC1	http://www.ncbi.nlm.nih.gov/gene/?term=4953	ODC	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014043	4953	ODC1	http://www.ncbi.nlm.nih.gov/gene/?term=4953	ODC	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014044	4953	ODC1	http://www.ncbi.nlm.nih.gov/gene/?term=4953	ODC	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014045	4953	ODC1	http://www.ncbi.nlm.nih.gov/gene/?term=4953	ODC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014046	495440	atp2a3	http://www.ncbi.nlm.nih.gov/gene/?term=495440	serca3	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00014047	4957	ODF2	http://www.ncbi.nlm.nih.gov/gene/?term=4957	"CT134, ODF2/1, ODF2/2, ODF84 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014048	495823	ccni-b	http://www.ncbi.nlm.nih.gov/gene/?term=495823	"cyc1, cyi "	mRNA	Xenopus laevis	20503379	Vegetal	Oocyte	RT-PCR	Figure1: Confirmation of vegetal cortex enrichment of selected genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of novel cortex-enriched transcript expression in whole oocyte (Oo) and vegetal cortex (VgCx) samples. The-RT lane is an oocyte sample processed in the absence of reverse transcriptase. ornithine decarboxylase (odc) is shown as a loading control. Data are collected from Figure 1.
RLID00014049	4967	OGDH	http://www.ncbi.nlm.nih.gov/gene/?term=4967	"AKGDH, E1k, OGDC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014050	4967	OGDH	http://www.ncbi.nlm.nih.gov/gene/?term=4967	"AKGDH, E1k, OGDC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014051	4968	OGG1	http://www.ncbi.nlm.nih.gov/gene/?term=4968	"HMMH, HOGG1, MUTM, OGH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014052	4974	OMG	http://www.ncbi.nlm.nih.gov/gene/?term=4974	OMGP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014053	497652	Acd	http://www.ncbi.nlm.nih.gov/gene/?term=497652		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014054	497661	C18orf32	http://www.ncbi.nlm.nih.gov/gene/?term=497661		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014055	4976	OPA1	http://www.ncbi.nlm.nih.gov/gene/?term=4976	"BERHS, MGM1, MTDPS14, NPG, NTG, largeG "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014056	4976	OPA1	http://www.ncbi.nlm.nih.gov/gene/?term=4976	"MGM1, NPG, NTG, largeG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014057	4978	OPCML	http://www.ncbi.nlm.nih.gov/gene/?term=4978	"IGLON1, OBCAM, OPCM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014058	49856	WRAP73	http://www.ncbi.nlm.nih.gov/gene/?term=49856	WDR8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014059	49856	WRAP73	http://www.ncbi.nlm.nih.gov/gene/?term=49856	WDR8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014060	49895	CG17018	http://www.ncbi.nlm.nih.gov/gene/?term=49895	"Dmel_ BcDNA:RE40762, CG17410, Dmel\CG17018 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00014061	498	ATP5A1	http://www.ncbi.nlm.nih.gov/gene/?term=498	"ATP5A, ATP5AL2, ATPM, COXPD22, HEL-S-123m, MC5DN4, MOM2, OMR, ORM, hATP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014062	49953	GCS2alpha	http://www.ncbi.nlm.nih.gov/gene/?term=49953	"Dmel_CG14476, BcDNA:GH04962, CG14476, Dmel\CG14476, clot#312 "	mRNA	Drosophila melanogaster	25838129	Basal	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00014063	4998	ORC1	http://www.ncbi.nlm.nih.gov/gene/?term=4998	"HSORC1L, PARC1, ORC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014064	4998	ORC1	http://www.ncbi.nlm.nih.gov/gene/?term=4998	"HSORC1L, PARC1, ORC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014065	4998	ORC1	http://www.ncbi.nlm.nih.gov/gene/?term=4998	"HSORC1L, PARC1, ORC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014066	4998	ORC1	http://www.ncbi.nlm.nih.gov/gene/?term=4998	"HSORC1, ORC1L, PARC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014067	4999	ORC2	http://www.ncbi.nlm.nih.gov/gene/?term=4999	ORC2L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014068	5000	ORC4	http://www.ncbi.nlm.nih.gov/gene/?term=5000	"ORC4LP, ORC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014069	5001	ORC5	http://www.ncbi.nlm.nih.gov/gene/?term=5001	"ORC5LP, ORC5T, PPP1R117, ORC5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014070	5002	SLC22A18	http://www.ncbi.nlm.nih.gov/gene/?term=5002	"BWR1A, BWSCR1A, HET, IMPT1, ITM, ORCTL2, SLC22A1L, TSSC5, p45-BWR1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014071	5002	SLC22A18	http://www.ncbi.nlm.nih.gov/gene/?term=5002	"BWR1A, BWSCR1A, HET, IMPT1, ITM, ORCTL2, SLC22A1L, TSSC5, p45-BWR1A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014072	5007	OSBP	http://www.ncbi.nlm.nih.gov/gene/?term=5007	OSBP1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014073	5007	OSBP	http://www.ncbi.nlm.nih.gov/gene/?term=5007	OSBP1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014074	5007	OSBP	http://www.ncbi.nlm.nih.gov/gene/?term=5007	OSBP1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014075	5010	CLDN11	http://www.ncbi.nlm.nih.gov/gene/?term=5010	"OSP, OTM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014076	5013355	GSPATT00030812001	http://www.ncbi.nlm.nih.gov/gene/?term=5013355	GSPATT00030812001	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014077	5018	OXA1L	http://www.ncbi.nlm.nih.gov/gene/?term=5018	OXA1	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014078	5018	OXA1L	http://www.ncbi.nlm.nih.gov/gene/?term=5018	OXA1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014079	5019	OXCT1	http://www.ncbi.nlm.nih.gov/gene/?term=5019	"OXCT, SCOT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014080	50250	CG14767	http://www.ncbi.nlm.nih.gov/gene/?term=50250	"Dmel_ CG8575, Dmel\CG14767, dmCG14767 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00014081	5025	P2RX4	http://www.ncbi.nlm.nih.gov/gene/?term=5025	"P2X4, P2X4R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014082	5026	P2RX5	http://www.ncbi.nlm.nih.gov/gene/?term=5026	"LRH-1, P2X5, P2X5R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014083	5027	P2RX7	http://www.ncbi.nlm.nih.gov/gene/?term=5027	P2X7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014084	5028	P2RY1	http://www.ncbi.nlm.nih.gov/gene/?term=5028	P2Y1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014085	50296	dpr6	http://www.ncbi.nlm.nih.gov/gene/?term=50296	"Dmel_CG14162, BcDNA:LD13525, CG14162, Dmel\CG14162, Dpr-6, Dpr6 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00014086	50296	dpr6	http://www.ncbi.nlm.nih.gov/gene/?term=50296	"Dmel_CG14162, BcDNA:LD13525, CG14162, Dmel\CG14162, Dpr-6, Dpr6 "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00014087	5033	P4HA1	http://www.ncbi.nlm.nih.gov/gene/?term=5033	P4HA	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00014088	5033	P4HA1	http://www.ncbi.nlm.nih.gov/gene/?term=5033	P4HA	mRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	qRT-PCR	Figure S1: Polysomal gradient analysis. HT1080 cells were incubated under control (21% oxygen) or hypoxic (1% oxygen) conditions for up to 36 h as described in Figure 1. Shown are representative original RT-PCR data (30 cycles for beta-Actin and the external standard [extSt]; 35 cycles for the other genes) from pooled samples to visualize mRNA distribution following fractionation of sucrose gradients at control conditions (C) and 36 h of hypoxia (Hy). The external standard (a synthetic in vitro transcript) was diluted to appropriate concentration for qPCR and added directly after gradient fractionation and prior to RNA isolation as a technical control. The external standard served for fraction dependent normalization.
RLID00014089	5033	P4HA1	http://www.ncbi.nlm.nih.gov/gene/?term=5033	P4HA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014090	5034	P4HB	http://www.ncbi.nlm.nih.gov/gene/?term=5034	"CLCRP1, DSI, ERBA2L, GIT, P4Hbeta, PDI, PDIA1, PHDB, PO4DB, PO4HB, PROHB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014091	5034	P4HB	http://www.ncbi.nlm.nih.gov/gene/?term=5034	"CLCRP1, DSI, ERBA2L, GIT, P4Hbeta, PDI, PDIA1, PHDB, PO4DB, PO4HB, PROHB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014092	5034	P4HB	http://www.ncbi.nlm.nih.gov/gene/?term=5034	"CLCRP1, DSI, ERBA2L, GIT, P4Hbeta, PDI, PDIA1, PHDB, PO4DB, PO4HB, PROHB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014093	5034	P4HB	http://www.ncbi.nlm.nih.gov/gene/?term=5034	"CLCRP1, DSI, ERBA2L, GIT, P4Hbeta, PDI, PDIA1, PHDB, PO4DB, PO4HB, PROHB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014094	5034	P4HB	http://www.ncbi.nlm.nih.gov/gene/?term=5034	"CLCRP1, DSI, ERBA2L, GIT, P4Hbeta, PDI, PDIA1, PHDB, PO4DB, PO4HB, PROHB "	mRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	qRT-PCR	Figure S1: Polysomal gradient analysis. HT1080 cells were incubated under control (21% oxygen) or hypoxic (1% oxygen) conditions for up to 36 h as described in Figure 1. Shown are representative original RT-PCR data (30 cycles for beta-Actin and the external standard [extSt]; 35 cycles for the other genes) from pooled samples to visualize mRNA distribution following fractionation of sucrose gradients at control conditions (C) and 36 h of hypoxia (Hy). The external standard (a synthetic in vitro transcript) was diluted to appropriate concentration for qPCR and added directly after gradient fractionation and prior to RNA isolation as a technical control. The external standard served for fraction dependent normalization.
RLID00014095	5034	P4HB	http://www.ncbi.nlm.nih.gov/gene/?term=5034	"CLCRP1, DSI, ERBA2L, GIT, P4Hbeta, PDI, PDIA1, PHDB, PO4DB, PO4HB, PROHB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014096	503550	Klri1	http://www.ncbi.nlm.nih.gov/gene/?term=503550		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014097	503582	ARGFX	http://www.ncbi.nlm.nih.gov/gene/?term=503582		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014098	503582	ARGFX	http://www.ncbi.nlm.nih.gov/gene/?term=503582		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014099	503693	LOH12CR2	http://www.ncbi.nlm.nih.gov/gene/?term=503693	LOH2CR12	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00014100	5036	PA2G4	http://www.ncbi.nlm.nih.gov/gene/?term=5036	"EBP1, HG4-1, p38-2G4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014101	5036	PA2G4	http://www.ncbi.nlm.nih.gov/gene/?term=5036	"EBP1, HG4-1, p38-2G4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014102	5036	PA2G4	http://www.ncbi.nlm.nih.gov/gene/?term=5036	"EBP1, HG4-1, p38-2G4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014103	5037	PEBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5037	"HCNP, HCNPpp, HEL-210, HEL-S-34, HEL-S-96, PBP, PEBP, PEBP-1, RKIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014104	5037	PEBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5037	"HCNP, HCNPpp, HEL-210, HEL-S-34, HEL-S-96, PBP, PEBP, PEBP-1, RKIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014105	5037	PEBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5037	"HCNP, HCNPpp, HEL-210, HEL-S-34, HEL-S-96, PBP, PEBP, PEBP-1, RKIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014106	503835	DUXA	http://www.ncbi.nlm.nih.gov/gene/?term=503835		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014107	503835	DUXA	http://www.ncbi.nlm.nih.gov/gene/?term=503835		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014108	5042	PABPC3	http://www.ncbi.nlm.nih.gov/gene/?term=5042	"PABP3, PABPL3, tPABP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014109	5042	PABPC3	http://www.ncbi.nlm.nih.gov/gene/?term=5042	"PABP3, PABPL3, tPABP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014110	5045	FURIN	http://www.ncbi.nlm.nih.gov/gene/?term=5045	"FUR, PACE, PCSK3, SPC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014111	5045	FURIN	http://www.ncbi.nlm.nih.gov/gene/?term=5045	"FUR, PACE, PCSK3, SPC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014112	5046	PCSK6	http://www.ncbi.nlm.nih.gov/gene/?term=5046	"PACE4, SPC4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014113	50484	RRM2B	http://www.ncbi.nlm.nih.gov/gene/?term=50484	"MTDPS8A, MTDPS8B, P53R2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014114	50484	RRM2B	http://www.ncbi.nlm.nih.gov/gene/?term=50484	"MTDPS8A, MTDPS8B, P53R2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014115	50487	PLA2G3	http://www.ncbi.nlm.nih.gov/gene/?term=50487	"GIII-SPLA2, SPLA2III, sPLA2-III "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014116	50488	MINK1	http://www.ncbi.nlm.nih.gov/gene/?term=50488	"B55, MAP4K6, MINK, YSK2, ZC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014117	50488	MINK1	http://www.ncbi.nlm.nih.gov/gene/?term=50488	"B55, MAP4K6, MINK, YSK2, ZC3, hMINK, hMINKbeta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014118	5048	PAFAH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=5048	"LIS1, LIS2, MDCR, MDS, PAFAH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014119	5048	PAFAH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=5048	"LIS1, LIS2, MDCR, MDS, PAFAH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014120	5048	PAFAH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=5048	"LIS1, LIS2, MDCR, MDS, PAFAH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014121	50492	Thop1	http://www.ncbi.nlm.nih.gov/gene/?term=50492	"AI131655, AI327041, EP24.15 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014122	50493	Txnrd1	http://www.ncbi.nlm.nih.gov/gene/?term=50493	"TR, TR1, TrxR1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014123	50496	E2f6	http://www.ncbi.nlm.nih.gov/gene/?term=50496	"AI462434, E2F6b, EMA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014124	50497	Hspa14	http://www.ncbi.nlm.nih.gov/gene/?term=50497	"70kDa, HSP70L1, Hsp70-4, NST-1, hsr.1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014125	5049	PAFAH1B2	http://www.ncbi.nlm.nih.gov/gene/?term=5049	HEL-S-303	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014126	5049	PAFAH1B2	http://www.ncbi.nlm.nih.gov/gene/?term=5049	HEL-S-303	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014127	5049	PAFAH1B2	http://www.ncbi.nlm.nih.gov/gene/?term=5049	HEL-S-303	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014128	50507	NOX4	http://www.ncbi.nlm.nih.gov/gene/?term=50507	"KOX, KOX-1, RENOX "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00014129	5050	PAFAH1B3	http://www.ncbi.nlm.nih.gov/gene/?term=5050	PAFAHG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014130	5050	PAFAH1B3	http://www.ncbi.nlm.nih.gov/gene/?term=5050	PAFAHG	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014131	50518	a	http://www.ncbi.nlm.nih.gov/gene/?term=50518	"A<y>, ASIP, ASP, As "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014132	5051	PAFAH2	http://www.ncbi.nlm.nih.gov/gene/?term=5051	HSD-PLA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014133	50523	Lats2	http://www.ncbi.nlm.nih.gov/gene/?term=50523	"4932411G09Rik, AV277261, AW228608 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014134	50525	Spag6	http://www.ncbi.nlm.nih.gov/gene/?term=50525	PF16	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014135	50527	Ero1l	http://www.ncbi.nlm.nih.gov/gene/?term=50527	"ERO1-L, Ero1a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014136	5052	PRDX1	http://www.ncbi.nlm.nih.gov/gene/?term=5052	"MSP23, NKEF-A, NKEFA, PAG, PAGA, PAGB, PRX1, PRXI, TDPX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014137	5052	PRDX1	http://www.ncbi.nlm.nih.gov/gene/?term=5052	"MSP23, NKEF-A, NKEFA, PAG, PAGA, PAGB, PRX1, PRXI, TDPX2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014138	5052	PRDX1	http://www.ncbi.nlm.nih.gov/gene/?term=5052	"MSP23, NKEF-A, NKEFA, PAG, PAGA, PAGB, PRX1, PRXI, TDPX2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014139	5054	SERPINE1	http://www.ncbi.nlm.nih.gov/gene/?term=5054	"PAI, PAI-1, PAI1, PLANH1 "	mRNA	Homo sapiens	19175411	Ribosome	T-cell|SeAx	qRT-PCR	"Using quantitative real-time RT-PCR we evaluated, whether mRNAs coding for differently located proteins are selectively enriched in one of the two analysed compartments, namely free versus membrane-associated polysomes. We selected genes coding for proteins located in the plasma membrane (GPR137B), secreted proteins (TIC2, IBP2, PAI) and cytosolic proteins (the house keeping genes GAPDH and HMBS). In fact, the distribution of the specific mRNA was as predicted ( Fig. 1): The average ratio of specific mRNA at bound ribosomes versus free ribosomes was 1 ? 4.4 for the housekeeping genes (GAPDH and HMBS) and 13.3 ? 1 for genes coding for membrane-bound or secreted proteins. Ratios for genes coding for cytosolic proteins were always below 0.6 and those for membrane or secreted genes were always above 1. The highest values were observed for PAI in MyLa (57 ? 1) and GPR137B in SeAx (34 ? 1), while the lowest ratios were detected for HMBS (1 ? 55) and GAPDH (1 ? 12) in HuT78. "
RLID00014140	5058	PAK1	http://www.ncbi.nlm.nih.gov/gene/?term=5058	PAKalpha	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014141	5058	PAK1	http://www.ncbi.nlm.nih.gov/gene/?term=5058	PAKalpha	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014142	50592	Gria1	http://www.ncbi.nlm.nih.gov/gene/?term=50592	"GluA1, gluR-A "	mRNA	Rattus norvegicus	19073915	Dendrite	Hippocampus	In situ hybridization	"We found that RARa protein co-immunoprecipitated with GluR1 mRNA as well as mRNAs encoding GluR2 and eukaryotic elongation factor 2 (eEF2), all of which have been shown to be dendritically localized by in situ hybridization "
RLID00014143	50592	Gria1	http://www.ncbi.nlm.nih.gov/gene/?term=50592	"GluA1, gluR-A "	mRNA	Rattus norvegicus	23166306	Dendrite	Cortical cultures	In situ hybridization	The hybridization signals of GluA1 and GluA2 mRNAs were present in both the cell soma and dendrites of cultured cortical cells immunolabeled with a specific marker for Microtubule-Associated Protein-2 a (MAP2a).
RLID00014144	50592	Gria1	http://www.ncbi.nlm.nih.gov/gene/?term=50592	"GluA1, gluR-A "	mRNA	Rattus norvegicus	23296627	Dendrite	Pyramidal cell	Fluorescence in situ hybridization	"GluA1-4 subunit mRNAs were highly localized to the apical dendrites of pyramidal cells, whereas in interneurons they were present in multiple dendrites. In contrast, in the dentate gyrus, GluA1-4 subunit mRNAs were virtually restricted to the somata and were absent from the dendrites of granule cells. "
RLID00014145	50592	Gria1	http://www.ncbi.nlm.nih.gov/gene/?term=50592	"GluA1, gluR-A "	mRNA	Rattus norvegicus	16899729	Dendrite	Hippocampus	Northern blot	"Using quantitative high-resolution in situ hybridization, we show that mRNAs encoding the AMPA-type glutamate receptor subunits (GluRs) 1 and 2 are localized to dendrites of hippocampal neurons and are regulated by paradigms that alter synaptic efficacy.  "
RLID00014146	50592	Gria1	http://www.ncbi.nlm.nih.gov/gene/?term=50592	"GluA1, gluR-A "	mRNA	Rattus norvegicus	23166306	Cell body	Cortical cultures	In situ hybridization	"In vivo, GluA1 and GluA2 mRNAs showed a strong signal in the cell bodies across hippocampal and cortical regions, together with the presence of a clear signal in the proximal dendrites. "
RLID00014147	50614	GALNT9	http://www.ncbi.nlm.nih.gov/gene/?term=50614	"GALNAC-T9, GALNACT9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014148	50618	ITSN2	http://www.ncbi.nlm.nih.gov/gene/?term=50618	"PRO2015, SH3D1B, SH3P18, SWA, SWAP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014149	50618	ITSN2	http://www.ncbi.nlm.nih.gov/gene/?term=50618	"PRO2015, SH3D1B, SH3P18, SWA, SWAP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014150	50618	ITSN2	http://www.ncbi.nlm.nih.gov/gene/?term=50618	"PRO2015, SH3D1B, SH3P18, SWA, SWAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014151	50619	DEF6	http://www.ncbi.nlm.nih.gov/gene/?term=50619	"IBP, SLAT, SWAP70L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014152	50619	DEF6	http://www.ncbi.nlm.nih.gov/gene/?term=50619	"IBP, SLAT, SWAP70L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014153	50626	CYHR1	http://www.ncbi.nlm.nih.gov/gene/?term=50626	CHRP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014154	50628	GEMIN4	http://www.ncbi.nlm.nih.gov/gene/?term=50628	"HC56, HCAP1, HHRF-1, p97 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014155	50628	GEMIN4	http://www.ncbi.nlm.nih.gov/gene/?term=50628	"HC56, HCAP1, HHRF-1, p97 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014156	50628	GEMIN4	http://www.ncbi.nlm.nih.gov/gene/?term=50628	"HC56, HCAP1, HHRF-1, p97 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014157	5062	PAK2	http://www.ncbi.nlm.nih.gov/gene/?term=5062	"PAK65, PAKgamma "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014158	5062	PAK2	http://www.ncbi.nlm.nih.gov/gene/?term=5062	"PAK65, PAKgamma "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014159	5062	PAK2	http://www.ncbi.nlm.nih.gov/gene/?term=5062	"PAK65, PAKgamma "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014160	50640	PNPLA8	http://www.ncbi.nlm.nih.gov/gene/?term=50640	"IPLA2-2, IPLA2G, MMLA, PNPLA-gamma, iPLA2gamma "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014161	50640	PNPLA8	http://www.ncbi.nlm.nih.gov/gene/?term=50640	"IPLA2-2, IPLA2G, MMLA, PNPLA-gamma, iPLA2gamma "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014162	5064	PALM	http://www.ncbi.nlm.nih.gov/gene/?term=5064		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014163	50650	ARHGEF3	http://www.ncbi.nlm.nih.gov/gene/?term=50650	"GEF3, STA3, XPLN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014164	5066	PAM	http://www.ncbi.nlm.nih.gov/gene/?term=5066	"PAL, PHM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014165	5066	PAM	http://www.ncbi.nlm.nih.gov/gene/?term=5066	"PAL, PHM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014166	5066	PAM	http://www.ncbi.nlm.nih.gov/gene/?term=5066	"PAL, PHM "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00014167	50686	Gsk3a	http://www.ncbi.nlm.nih.gov/gene/?term=50686		mRNA	Rattus norvegicus	24898526	Axon	Spinal motoneuron 	In situ hybridization|qRT-PCR	"In cultured cortical neurons which do not store glycogen but nevertheless express glycogen synthase, the GS mRNA is also subject to axonal and dendritic localization. In spinal motoneurons and trigeminal neurons in situ, however, the mRNAs could only be demonstrated in the neuronal somata but not in the nerves. "
RLID00014168	50686	Gsk3a	http://www.ncbi.nlm.nih.gov/gene/?term=50686		mRNA	Rattus norvegicus	24898526	Dendrite	Spinal motoneuron 	In situ hybridization|qRT-PCR	"In cultured cortical neurons which do not store glycogen but nevertheless express glycogen synthase, the GS mRNA is also subject to axonal and dendritic localization. In spinal motoneurons and trigeminal neurons in situ, however, the mRNAs could only be demonstrated in the neuronal somata but not in the nerves. "
RLID00014169	5069	PAPPA	http://www.ncbi.nlm.nih.gov/gene/?term=5069	"ASBABP2, DIPLA1, IGFBP-4ase, PAPA, PAPP-A, PAPPA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014170	506	ATP5B	http://www.ncbi.nlm.nih.gov/gene/?term=506	"ATPMB, ATPSB, HEL-S-271 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014171	506	ATP5B	http://www.ncbi.nlm.nih.gov/gene/?term=506	"ATPMB, ATPSB, HEL-S-271 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014172	50717	DCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=50717	"GAN2, H326, WDR42A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014173	50717	DCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=50717	"GAN2, H326, WDR42A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014174	50720	Sacs	http://www.ncbi.nlm.nih.gov/gene/?term=50720	"A230052M14, DNAJC29, E130115J16Rik, mKIAA0730 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014175	50721	Sirt6	http://www.ncbi.nlm.nih.gov/gene/?term=50721	"2810449N18Rik, AI043036, Sir2l6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014176	5073	PARN	http://www.ncbi.nlm.nih.gov/gene/?term=5073	"DAN, DKCB6, PFBMFT4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014177	5074	PAWR	http://www.ncbi.nlm.nih.gov/gene/?term=5074	"PAR4, Par-4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014178	50753	Fbxo8	http://www.ncbi.nlm.nih.gov/gene/?term=50753	Fbx8	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014179	50754	Fbxw7	http://www.ncbi.nlm.nih.gov/gene/?term=50754	"1110001A17Rik, AGO, Cdc4, Fbw7, Fbwd6, Fbx30, Fbxo30, Fbxw6, SEL-10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014180	50766	Crim1	http://www.ncbi.nlm.nih.gov/gene/?term=50766	AU015004	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014181	50767	Pnpla6	http://www.ncbi.nlm.nih.gov/gene/?term=50767	"AI661849, MSws, Nte "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014182	5076	PAX2	http://www.ncbi.nlm.nih.gov/gene/?term=5076	"FSGS7, PAPRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014183	50771	Atp9b	http://www.ncbi.nlm.nih.gov/gene/?term=50771	"AA934181, Atpc2b, IIb, MMR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014184	50772	Mapk6	http://www.ncbi.nlm.nih.gov/gene/?term=50772	"2610021I23Rik, D130053K17Rik, Erk3, Mapk43, Prkm4, Prkm6, Mapk6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014185	50781	Dkk3	http://www.ncbi.nlm.nih.gov/gene/?term=50781	"AW061014, C87148 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014186	50788	Fbxl8	http://www.ncbi.nlm.nih.gov/gene/?term=50788	FBL8	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014187	50790	Acsl4	http://www.ncbi.nlm.nih.gov/gene/?term=50790	"9430020A05Rik, ACS4, AU018108, Facl4, Lacs4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014188	50793	Orc3	http://www.ncbi.nlm.nih.gov/gene/?term=50793	Orc3l	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014189	50796	Dmrt1	http://www.ncbi.nlm.nih.gov/gene/?term=50796		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014190	50797	Copb2	http://www.ncbi.nlm.nih.gov/gene/?term=50797	AI256832	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014191	50804	MYEF2	http://www.ncbi.nlm.nih.gov/gene/?term=50804	"HsT18564, MEF-2, MST156, MSTP156, myEF-2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014192	50804	MYEF2	http://www.ncbi.nlm.nih.gov/gene/?term=50804	"HsT18564, MEF-2, MST156, MSTP156, myEF-2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014193	50807	ASAP1	http://www.ncbi.nlm.nih.gov/gene/?term=50807	"AMAP1, CENTB4, DDEF1, PAG2, PAP, ZG14P "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014194	50807	ASAP1	http://www.ncbi.nlm.nih.gov/gene/?term=50807	"AMAP1, CENTB4, DDEF1, PAG2, PAP, ZG14P "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014195	50807	ASAP1	http://www.ncbi.nlm.nih.gov/gene/?term=50807	"AMAP1, CENTB4, DDEF1, PAG2, PAP, ZG14P "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014196	50807	ASAP1	http://www.ncbi.nlm.nih.gov/gene/?term=50807	"AMAP1, CENTB4, DDEF1, PAG2, PAP, ZG14P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014197	50808	AK3	http://www.ncbi.nlm.nih.gov/gene/?term=50808	"AK3L1, AK6, AKL3L, AKL3L1, FIX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014198	50808	AK3	http://www.ncbi.nlm.nih.gov/gene/?term=50808	"AK3L1, AK6, AKL3L, AKL3L1, FIX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014199	50809	HP1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=50809	"HP1-BP74, HP1BP74 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014200	50809	HP1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=50809	"HP1-BP74, HP1BP74 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014201	5080	PAX6	http://www.ncbi.nlm.nih.gov/gene/?term=5080	"AN, AN2, D11S812E, FVH1, MGDA, WAGR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014202	50810	HDGFRP3	http://www.ncbi.nlm.nih.gov/gene/?term=50810	"CGI-142, HDGF-2, HDGF2, HRP-3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014203	50813	COPS7A	http://www.ncbi.nlm.nih.gov/gene/?term=50813	"CSN7, CSN7A, SGN7a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014204	50814	NSDHL	http://www.ncbi.nlm.nih.gov/gene/?term=50814	"H105E3, SDR31E1, XAP104 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014205	50814	NSDHL	http://www.ncbi.nlm.nih.gov/gene/?term=50814	"H105E3, SDR31E1, XAP104 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014206	5082	PDCL	http://www.ncbi.nlm.nih.gov/gene/?term=5082	PhLP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014207	5082	PDCL	http://www.ncbi.nlm.nih.gov/gene/?term=5082	PhLP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014208	50848	F11R	http://www.ncbi.nlm.nih.gov/gene/?term=50848	"CD321, JAM, JAM1, JAMA, JCAM, KAT, PAM-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014209	50848	F11R	http://www.ncbi.nlm.nih.gov/gene/?term=50848	"CD321, JAM, JAM1, JAMA, JCAM, KAT, PAM-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014210	50848	F11R	http://www.ncbi.nlm.nih.gov/gene/?term=50848	"CD321, JAM, JAM1, JAMA, JCAM, KAT, PAM-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014211	50848	F11R	http://www.ncbi.nlm.nih.gov/gene/?term=50848	"CD321, JAM, JAM1, JAMA, JCAM, KAT, PAM-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014212	50850	Spast	http://www.ncbi.nlm.nih.gov/gene/?term=50850	"Spg4, mKIAA1083 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014213	50854	C6orf48	http://www.ncbi.nlm.nih.gov/gene/?term=50854	"D6S57, G8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014214	50854	C6orf48	http://www.ncbi.nlm.nih.gov/gene/?term=50854	"D6S57, G8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014215	50854	C6orf48	http://www.ncbi.nlm.nih.gov/gene/?term=50854	"D6S57, G8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014216	50855	PARD6A	http://www.ncbi.nlm.nih.gov/gene/?term=50855	"PAR-6A, PAR6, PAR6C, PAR6alpha, TAX40, TIP-40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014217	50855	PARD6A	http://www.ncbi.nlm.nih.gov/gene/?term=50855	"PAR-6A, PAR6, PAR6C, PAR6alpha, TAX40, TIP-40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014218	50862	RNF141	http://www.ncbi.nlm.nih.gov/gene/?term=50862	"ZFP26, ZNF230 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014219	50862	RNF141	http://www.ncbi.nlm.nih.gov/gene/?term=50862	"ZFP26, ZNF230 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014220	50863	NTM	http://www.ncbi.nlm.nih.gov/gene/?term=50863	"HNT, IGLON2, NTRI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014221	50865	HEBP1	http://www.ncbi.nlm.nih.gov/gene/?term=50865	"HBP, HEBP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014222	50865	HEBP1	http://www.ncbi.nlm.nih.gov/gene/?term=50865	"HBP, HEBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014223	50868	Keap1	http://www.ncbi.nlm.nih.gov/gene/?term=50868	"INRF2, mKIAA0132 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014224	50873	Park2	http://www.ncbi.nlm.nih.gov/gene/?term=50873	PRKN	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014225	50874	Tmod4	http://www.ncbi.nlm.nih.gov/gene/?term=50874	"MTMOD, Sk-Tmod "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014226	50875	Tmod3	http://www.ncbi.nlm.nih.gov/gene/?term=50875	"U-Tmod, UTMOD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014227	50875	Tmod3	http://www.ncbi.nlm.nih.gov/gene/?term=50875	"U-Tmod, UTMOD "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014228	50876	Tmod2	http://www.ncbi.nlm.nih.gov/gene/?term=50876	"N-Tmod, NTMOD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014229	5087	PBX1	http://www.ncbi.nlm.nih.gov/gene/?term=5087		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014230	50884	Nckap1	http://www.ncbi.nlm.nih.gov/gene/?term=50884	"C79304, H19, Hem-2, Hem2, Nap1, mKIAA0587, mh19, p125Nap1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014231	50887	Hmgn5	http://www.ncbi.nlm.nih.gov/gene/?term=50887	"GARP45, NBP-45, Nsbp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014232	50887	Hmgn5	http://www.ncbi.nlm.nih.gov/gene/?term=50887	"GARP45, NBP-45, Nsbp1 "	mRNA	Mus musculus	25825524	Growth cone	N1E-115 cell	Fluorescence in situ hybridization	"Fluorescent in situ hybridization (FISH) with riboprobes antisense to Hmgn5 mRNA showed that Hmgn5 mRNA localizes to bright punctate structures in the growth cones of N1E-115 cells, similarly to other known localized mRNAs (4, 9). "
RLID00014233	5089	PBX2	http://www.ncbi.nlm.nih.gov/gene/?term=5089	"G17, HOX12MHC, PBX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014234	5089	PBX2	http://www.ncbi.nlm.nih.gov/gene/?term=5089	"G17, HOX12, PBX2MHC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014235	50908	C1s1	http://www.ncbi.nlm.nih.gov/gene/?term=50908	"AA959438, AI255193, AI327365, C1s, C1sa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014236	50911	Exosc9	http://www.ncbi.nlm.nih.gov/gene/?term=50911	"PM/Scl-75, Pmscl1, RRP45, p5, p6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014237	5091	PC	http://www.ncbi.nlm.nih.gov/gene/?term=5091	PCB	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014238	50926	Hnrnpdl	http://www.ncbi.nlm.nih.gov/gene/?term=50926	"AA407431, AA959857, D5Ertd650e, D5Wsu145e1, Hnrpdl, JKTBP, hnRNP DL, hnRNP-DL, Hnrnpdl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014239	50928	Klrg1	http://www.ncbi.nlm.nih.gov/gene/?term=50928	"2F1-Ag, MAFA, MAFA-L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014240	5092	PCBD1	http://www.ncbi.nlm.nih.gov/gene/?term=5092	"DCOH, PCBD, PCD, PHS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014241	5092	PCBD1	http://www.ncbi.nlm.nih.gov/gene/?term=5092	"DCOH, PCBD, PCD, PHS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014242	5092	PCBD1	http://www.ncbi.nlm.nih.gov/gene/?term=5092	"DCOH, PCBD, PCD, PHS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014243	50933	Uchl3	http://www.ncbi.nlm.nih.gov/gene/?term=50933		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014244	50937	CDON	http://www.ncbi.nlm.nih.gov/gene/?term=50937	"CDO1, HPE11, ORCAM, CDON "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014245	50937	CDON	http://www.ncbi.nlm.nih.gov/gene/?term=50937	"CDO1, HPE11, ORCAM, CDON "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014246	5093	PCBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5093	"HEL-S-85, HNRPE1, HNRPX, hnRNP-E1, hnRNP-X "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014247	5093	PCBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5093	"HEL-S-85, HNRPE1, HNRPX, hnRNP-E1, hnRNP-X "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014248	5093	PCBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5093	"HEL-S-85, HNRPE1, HNRPX, hnRNP-E1, hnRNP-X "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014249	50940	PDE11A	http://www.ncbi.nlm.nih.gov/gene/?term=50940	PPNAD2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014250	50940	PDE11A	http://www.ncbi.nlm.nih.gov/gene/?term=50940	PPNAD2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014251	50940	PDE11A	http://www.ncbi.nlm.nih.gov/gene/?term=50940	PPNAD2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014252	5094	PCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=5094	"HNRNPE2, HNRPE2, hnRNP-E2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014253	5094	PCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=5094	"HNRNPE2, HNRPE2, hnRNP-E2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014254	5094	PCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=5094	"HNRNPE2, HNRPE2, hnRNP-E2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014255	5095	PCCA	http://www.ncbi.nlm.nih.gov/gene/?term=5095		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014256	5096	PCCB	http://www.ncbi.nlm.nih.gov/gene/?term=5096		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014257	5096	PCCB	http://www.ncbi.nlm.nih.gov/gene/?term=5096		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014258	5097	PCDH1	http://www.ncbi.nlm.nih.gov/gene/?term=5097	"PC42, PCDH42 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014259	5097	PCDH1	http://www.ncbi.nlm.nih.gov/gene/?term=5097	"PC42, PCDH42 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014260	5098	PCDHGC3	http://www.ncbi.nlm.nih.gov/gene/?term=5098	"PC43, PCDH-GAMMA-C3, PCDH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014261	50995	Uba2	http://www.ncbi.nlm.nih.gov/gene/?term=50995	"AA986091, Arx, Sae2, UBA1, Ubl1a2, Uble1b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014262	50997	Mpp2	http://www.ncbi.nlm.nih.gov/gene/?term=50997	"D11Bwg0652e, Dlg2, Dlgh2, Pals4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014263	50999	TMED5	http://www.ncbi.nlm.nih.gov/gene/?term=50999	"CGI-100, p24g2, p28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014264	50999	TMED5	http://www.ncbi.nlm.nih.gov/gene/?term=50999	"CGI-100, p24g2, p28 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014265	50999	TMED5	http://www.ncbi.nlm.nih.gov/gene/?term=50999	"CGI-100, p24g2, p28 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014266	5099	PCDH7	http://www.ncbi.nlm.nih.gov/gene/?term=5099	"BH-Pcdh, BHPCDH, PPP1R120 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014267	509	ATP5C1	http://www.ncbi.nlm.nih.gov/gene/?term=509	"ATP5C, ATP5CL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014268	509	ATP5C1	http://www.ncbi.nlm.nih.gov/gene/?term=509	"ATP5C, ATP5CL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014269	51000	SLC35B3	http://www.ncbi.nlm.nih.gov/gene/?term=51000	"C6orf196, CGI-19, PAPST2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014270	51002	TPRKB	http://www.ncbi.nlm.nih.gov/gene/?term=51002	CGI-121	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014271	51002	TPRKB	http://www.ncbi.nlm.nih.gov/gene/?term=51002	CGI-121	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014272	51002	TPRKB	http://www.ncbi.nlm.nih.gov/gene/?term=51002	CGI-121	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014273	51003	MED31	http://www.ncbi.nlm.nih.gov/gene/?term=51003	"3110004H13Rik, CGI-125, Soh1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014274	51004	COQ6	http://www.ncbi.nlm.nih.gov/gene/?term=51004	"CGI-10, CGI10, COQ10D6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014275	51004	COQ6	http://www.ncbi.nlm.nih.gov/gene/?term=51004	"CGI-10, CGI10, COQ10D6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014276	51005	AMDHD2	http://www.ncbi.nlm.nih.gov/gene/?term=51005	CGI-14	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014277	5100	PCDH8	http://www.ncbi.nlm.nih.gov/gene/?term=5100	"ARCADLIN, PAPC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014278	51010	EXOSC3	http://www.ncbi.nlm.nih.gov/gene/?term=51010	"CGI-102, PCH1B, RRP40, Rrp40p, bA3J10.7, hRrp-40, p10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014279	51010	EXOSC3	http://www.ncbi.nlm.nih.gov/gene/?term=51010	"CGI-102, PCH1B, RRP40, Rrp40p, bA3J10.7, hRrp-40, p10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014280	51010	EXOSC3	http://www.ncbi.nlm.nih.gov/gene/?term=51010	"CGI-102, PCH1B, RRP40, Rrp40p, bA3J10.7, hRrp-40, p10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014281	51011	FAHD2A	http://www.ncbi.nlm.nih.gov/gene/?term=51011	CGI-105	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014282	51013	EXOSC1	http://www.ncbi.nlm.nih.gov/gene/?term=51013	"CGI-108, CSL4, Csl4p, SKI4, Ski4p, p13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014283	51014	TMED7	http://www.ncbi.nlm.nih.gov/gene/?term=51014	"CGI-109, p24g3, p24gamma3, p27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014284	51014	TMED7	http://www.ncbi.nlm.nih.gov/gene/?term=51014	"CGI-109, p24g3, p24gamma3, p27 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014285	51014	TMED7	http://www.ncbi.nlm.nih.gov/gene/?term=51014	"CGI-109, p24g3, p24gamma3, p27 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014286	51015	ISOC1	http://www.ncbi.nlm.nih.gov/gene/?term=51015	CGI-111	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014287	51015	ISOC1	http://www.ncbi.nlm.nih.gov/gene/?term=51015	CGI-111	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014288	51016	EMC9	http://www.ncbi.nlm.nih.gov/gene/?term=51016	"C14orf122, CGI-112, FAM158A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014289	51016	EMC9	http://www.ncbi.nlm.nih.gov/gene/?term=51016	"C14orf122, CGI-112, FAM158A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014290	51018	RRP15	http://www.ncbi.nlm.nih.gov/gene/?term=51018	"CGI-115, KIAA0507 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014291	51018	RRP15	http://www.ncbi.nlm.nih.gov/gene/?term=51018	"CGI-115, KIAA0507 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014292	51018	RRP15	http://www.ncbi.nlm.nih.gov/gene/?term=51018	"CGI-115, KIAA0507 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014293	51018	RRP15	http://www.ncbi.nlm.nih.gov/gene/?term=51018	"CGI-115, KIAA0507 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014294	51019	CCDC53	http://www.ncbi.nlm.nih.gov/gene/?term=51019	CGI-116	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014295	5101	PCDH9	http://www.ncbi.nlm.nih.gov/gene/?term=5101		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014296	51020	HDDC2	http://www.ncbi.nlm.nih.gov/gene/?term=51020	"C6orf74, CGI-130, NS5ATP2, dJ167O5.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014297	51021	MRPS16	http://www.ncbi.nlm.nih.gov/gene/?term=51021	"CGI-132, COXPD2, MRP-S16, RPMS16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014298	51021	MRPS16	http://www.ncbi.nlm.nih.gov/gene/?term=51021	"CGI-132, COXPD2, MRP-S16, RPMS16 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014299	51021	MRPS16	http://www.ncbi.nlm.nih.gov/gene/?term=51021	"CGI-132, COXPD2, MRP-S16, RPMS16 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014300	51022	GLRX2	http://www.ncbi.nlm.nih.gov/gene/?term=51022	"CGI-133, GRX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014301	51023	MRPS18C	http://www.ncbi.nlm.nih.gov/gene/?term=51023	"CGI-134, MRP-S18-1, MRP-S18-c, MRPS18-1, S18mt-c, mrps18-c "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014302	51023	MRPS18C	http://www.ncbi.nlm.nih.gov/gene/?term=51023	"CGI-134, MRP-S18-1, MRP-S18-c, MRPS18-1, S18mt-c, mrps18-c "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014303	51024	FIS1	http://www.ncbi.nlm.nih.gov/gene/?term=51024	"CGI-135, TTC11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014304	51024	FIS1	http://www.ncbi.nlm.nih.gov/gene/?term=51024	"CGI-135, TTC11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014305	51025	PAM16	http://www.ncbi.nlm.nih.gov/gene/?term=51025	"CGI-136, MAGMAS, SMDMDM, TIM16, TIMM16 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014306	51026	GOLT1B	http://www.ncbi.nlm.nih.gov/gene/?term=51026	"CGI-141, GCT2, GOT1, GOT1B, YMR292W "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014307	51026	GOLT1B	http://www.ncbi.nlm.nih.gov/gene/?term=51026	"CGI-141, GCT2, GOT1, GOT1B, YMR292W "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014308	51026	GOLT1B	http://www.ncbi.nlm.nih.gov/gene/?term=51026	"CGI-141, GCT2, GOT1, GOT1B, YMR292W "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014309	51027	BOLA1	http://www.ncbi.nlm.nih.gov/gene/?term=51027	CGI-143	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014310	51028	VPS36	http://www.ncbi.nlm.nih.gov/gene/?term=51028	"C13orf9, CGI-145, EAP45 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014311	51028	VPS36	http://www.ncbi.nlm.nih.gov/gene/?term=51028	"C13orf9, CGI-145, EAP45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014312	51029	DESI2	http://www.ncbi.nlm.nih.gov/gene/?term=51029	"C1orf121, CGI-146, DESI, DESI1, DeSI-2, FAM152A, PNAS-4, PPPDE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014313	51029	DESI2	http://www.ncbi.nlm.nih.gov/gene/?term=51029	"C1orf121, CGI-146, DESI, DESI1, DeSI-2, FAM152A, PNAS-4, PPPDE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014314	51030	TVP23B	http://www.ncbi.nlm.nih.gov/gene/?term=51030	"CGI-148, FAM18B, FAM18B1, NPD008, YDR084C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014315	51031	GLOD4	http://www.ncbi.nlm.nih.gov/gene/?term=51031	"C17orf25, CGI-150, HC71 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014316	51031	GLOD4	http://www.ncbi.nlm.nih.gov/gene/?term=51031	"C17orf25, CGI-150, HC71 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014317	51035	UBXN1	http://www.ncbi.nlm.nih.gov/gene/?term=51035	"2B28, SAKS1, UBXD10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014318	51035	UBXN1	http://www.ncbi.nlm.nih.gov/gene/?term=51035	"2B28, SAKS1, UBXD10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014319	51035	UBXN1	http://www.ncbi.nlm.nih.gov/gene/?term=51035	"2B28, SAKS1, UBXD10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014320	51042	ZNF593	http://www.ncbi.nlm.nih.gov/gene/?term=51042	ZT86	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014321	51042	ZNF593	http://www.ncbi.nlm.nih.gov/gene/?term=51042	ZT86	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014322	51053	GMNN	http://www.ncbi.nlm.nih.gov/gene/?term=51053	"Gem, MGORS6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014323	51053	GMNN	http://www.ncbi.nlm.nih.gov/gene/?term=51053	Gem	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014324	51056	LAP3	http://www.ncbi.nlm.nih.gov/gene/?term=51056	"HEL-S-106, LAP, LAPEP, PEPS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014325	51056	LAP3	http://www.ncbi.nlm.nih.gov/gene/?term=51056	"HEL-S-106, LAP, LAPEP, PEPS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014326	51056	LAP3	http://www.ncbi.nlm.nih.gov/gene/?term=51056	"HEL-S-106, LAP, LAPEP, PEPS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014327	51057	WDPCP	http://www.ncbi.nlm.nih.gov/gene/?term=51057	"BBS15, C2orf86, CHDTHP, FRITZ, FRTZ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014328	51058	ZNF691	http://www.ncbi.nlm.nih.gov/gene/?term=51058	Zfp691	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014329	51060	TXNDC12	http://www.ncbi.nlm.nih.gov/gene/?term=51060	"AG1, AGR1, ERP16, ERP18, ERP19, PDIA16, TLP19, hAG-1, hTLP19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014330	51065	RPS27L	http://www.ncbi.nlm.nih.gov/gene/?term=51065		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014331	51065	RPS27L	http://www.ncbi.nlm.nih.gov/gene/?term=51065		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014332	51065	RPS27L	http://www.ncbi.nlm.nih.gov/gene/?term=51065		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014333	51065	RPS27L	http://www.ncbi.nlm.nih.gov/gene/?term=51065		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014334	51067	YARS2	http://www.ncbi.nlm.nih.gov/gene/?term=51067	"CGI-04, MLASA2, MT-TYRRS, TYRRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014335	51067	YARS2	http://www.ncbi.nlm.nih.gov/gene/?term=51067	"CGI-04, MLASA2, MT-TYRRS, TYRRS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014336	51068	NMD3	http://www.ncbi.nlm.nih.gov/gene/?term=51068	CGI-07	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014337	51069	MRPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51069	"CGI-22, MRP-L14, RPML14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014338	51069	MRPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51069	"CGI-22, MRP-L14, RPML14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014339	51069	MRPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51069	"CGI-22, MRP-L14, RPML14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014340	5106	PCK2	http://www.ncbi.nlm.nih.gov/gene/?term=5106	"PEPCK, PEPCK-M, PEPCK2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014341	51070	NOSIP	http://www.ncbi.nlm.nih.gov/gene/?term=51070	CGI-25	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014342	51070	NOSIP	http://www.ncbi.nlm.nih.gov/gene/?term=51070	CGI-25	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014343	51070	NOSIP	http://www.ncbi.nlm.nih.gov/gene/?term=51070	CGI-25	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014344	51071	DERA	http://www.ncbi.nlm.nih.gov/gene/?term=51071	"CGI-26, DEOC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014345	51071	DERA	http://www.ncbi.nlm.nih.gov/gene/?term=51071	"CGI-26, DEOC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014346	51071	DERA	http://www.ncbi.nlm.nih.gov/gene/?term=51071	"CGI-26, DEOC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014347	51073	MRPL4	http://www.ncbi.nlm.nih.gov/gene/?term=51073	"CGI-28, L4mt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014348	51074	APIP	http://www.ncbi.nlm.nih.gov/gene/?term=51074	"APIP2, CGI-29, CGI29, MMRP19, hAPIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014349	51075	TMX2	http://www.ncbi.nlm.nih.gov/gene/?term=51075	"CGI-31, PDIA12, PIG26, TXNDC14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014350	51076	CUTC	http://www.ncbi.nlm.nih.gov/gene/?term=51076	CGI-32	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014351	51076	CUTC	http://www.ncbi.nlm.nih.gov/gene/?term=51076	CGI-32	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014352	51077	FCF1	http://www.ncbi.nlm.nih.gov/gene/?term=51077	"Bka, C14orf111, CGI-35, UTP24 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014353	51077	FCF1	http://www.ncbi.nlm.nih.gov/gene/?term=51077	"Bka, C14orf111, CGI-35, UTP24 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014354	51077	FCF1	http://www.ncbi.nlm.nih.gov/gene/?term=51077	"Bka, C14orf111, CGI-35, UTP24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014355	51078	THAP4	http://www.ncbi.nlm.nih.gov/gene/?term=51078	"CGI-36, PP238 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014356	51079	NDUFA13	http://www.ncbi.nlm.nih.gov/gene/?term=51079	"B16.6, CDA016, CGI-39, GRIM-19, GRIM19 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014357	51081	MRPS7	http://www.ncbi.nlm.nih.gov/gene/?term=51081	"MRP-S, MRP-S7, RP-S7, RPMS7, S7mt, bMRP27a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014358	51081	MRPS7	http://www.ncbi.nlm.nih.gov/gene/?term=51081	"MRP-S, MRP-S7, RP-S7, RPMS7, S7mt, bMRP27a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014359	51082	POLR1D	http://www.ncbi.nlm.nih.gov/gene/?term=51082	"AC19, POLR1C, RPA16, RPA9, RPAC2, RPC16, RPO1-3, TCS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014360	51082	POLR1D	http://www.ncbi.nlm.nih.gov/gene/?term=51082	"AC19, POLR1C, RPA16, RPA9, RPAC2, RPC16, RPO1-3, TCS2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014361	51083	GAL	http://www.ncbi.nlm.nih.gov/gene/?term=51083	"ETL8-GMAP, GALN, GLNN, GMAP, GAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014362	51083	GAL	http://www.ncbi.nlm.nih.gov/gene/?term=51083	"ETL8-GMAP, GALN, GLNN, GMAP, GAL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014363	51084	CRYL1	http://www.ncbi.nlm.nih.gov/gene/?term=51084	"GDH, HEL30, lambda-CRY "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014364	51085	MLXIPL	http://www.ncbi.nlm.nih.gov/gene/?term=51085	"CHREBP, MIO, MONDOB, WBSCR14, WS-bHLH, bHLHd14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014365	5108	PCM1	http://www.ncbi.nlm.nih.gov/gene/?term=5108	"PTC4, RET/PCM-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014366	5108	PCM1	http://www.ncbi.nlm.nih.gov/gene/?term=5108	"PTC4, RET/PCM-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014367	5108	PCM1	http://www.ncbi.nlm.nih.gov/gene/?term=5108	"PTC4, RET/PCM-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014368	51090	PLLP	http://www.ncbi.nlm.nih.gov/gene/?term=51090	"PMLP, TM4SF11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014369	51090	PLLP	http://www.ncbi.nlm.nih.gov/gene/?term=51090	"PMLP, TM4SF11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014370	51091	SEPSECS	http://www.ncbi.nlm.nih.gov/gene/?term=51091	"LP, PCH2D, SLA, SLA/LP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014371	51092	SIDT2	http://www.ncbi.nlm.nih.gov/gene/?term=51092	CGI-40	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014372	51092	SIDT2	http://www.ncbi.nlm.nih.gov/gene/?term=51092	CGI-40	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014373	51094	ADIPOR1	http://www.ncbi.nlm.nih.gov/gene/?term=51094	"ACDCR1, CGI-45, CGI45, PAQR1, TESBP1A "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014374	51094	ADIPOR1	http://www.ncbi.nlm.nih.gov/gene/?term=51094	"ACDCR1, CGI-45, CGI45, PAQR1, TESBP1A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014375	51095	TRNT1	http://www.ncbi.nlm.nih.gov/gene/?term=51095	"CCA1, CGI-47, MtCCA, SIFD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014376	51096	UTP18	http://www.ncbi.nlm.nih.gov/gene/?term=51096	"CGI-48, WDR50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014377	51096	UTP18	http://www.ncbi.nlm.nih.gov/gene/?term=51096	"CGI-48, WDR50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014378	51097	SCCPDH	http://www.ncbi.nlm.nih.gov/gene/?term=51097	"CGI-49, NET11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014379	51097	SCCPDH	http://www.ncbi.nlm.nih.gov/gene/?term=51097	"CGI-49, NET11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014380	51099	ABHD5	http://www.ncbi.nlm.nih.gov/gene/?term=51099	"CDS, CGI58, IECN2, NCIE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014381	51099	ABHD5	http://www.ncbi.nlm.nih.gov/gene/?term=51099	"CDS, CGI58, IECN2, NCIE2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014382	51099	ABHD5	http://www.ncbi.nlm.nih.gov/gene/?term=51099	"CDS, CGI58, IECN2, NCIE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014383	51100	SH3GLB1	http://www.ncbi.nlm.nih.gov/gene/?term=51100	"Bif-1, CGI-61, PPP1R70, dJ612B15.2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014384	51100	SH3GLB1	http://www.ncbi.nlm.nih.gov/gene/?term=51100	"Bif-1, CGI-61, PPP1R70, dJ612B15.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014385	51102	MECR	http://www.ncbi.nlm.nih.gov/gene/?term=51102	"CGI-63, FASN2B, NRBF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014386	51103	NDUFAF1	http://www.ncbi.nlm.nih.gov/gene/?term=51103	"CGI-65, CGI65, CIA30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014387	51104	ABHD17B	http://www.ncbi.nlm.nih.gov/gene/?term=51104	"C9orf77, CGI-67, FAM108B1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014388	51104	ABHD17B	http://www.ncbi.nlm.nih.gov/gene/?term=51104	"C9orf77, CGI-67, FAM108B1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014389	51104	ABHD17B	http://www.ncbi.nlm.nih.gov/gene/?term=51104	"C9orf77, CGI-67, FAM108B1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014390	51104	ABHD17B	http://www.ncbi.nlm.nih.gov/gene/?term=51104	"C9orf77, CGI-67, FAM108B1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014391	51105	PHF20L1	http://www.ncbi.nlm.nih.gov/gene/?term=51105	"CGI-72, TDRD20B, URLC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014392	51105	PHF20L1	http://www.ncbi.nlm.nih.gov/gene/?term=51105	"CGI-72, TDRD20B, URLC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014393	51106	TFB1M	http://www.ncbi.nlm.nih.gov/gene/?term=51106	"CGI-75, CGI75, mtTFB, mtTFB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014394	51107	APH1A	http://www.ncbi.nlm.nih.gov/gene/?term=51107	"6530402N02Rik, APH-1, APH-1A, CGI-78 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014395	51107	APH1A	http://www.ncbi.nlm.nih.gov/gene/?term=51107	"6530402N02Rik, APH-1, APH-1A, CGI-78 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014396	51107	APH1A	http://www.ncbi.nlm.nih.gov/gene/?term=51107	"6530402N02Rik, APH-1, APH-1A, CGI-78 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014397	51108	METTL9	http://www.ncbi.nlm.nih.gov/gene/?term=51108	"CGI-81, DREV, DREV1, PAP1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014398	51108	METTL9	http://www.ncbi.nlm.nih.gov/gene/?term=51108	"CGI-81, DREV, DREV1, PAP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014399	51108	METTL9	http://www.ncbi.nlm.nih.gov/gene/?term=51108	"CGI-81, DREV, DREV1, PAP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014400	51108	METTL9	http://www.ncbi.nlm.nih.gov/gene/?term=51108	"CGI-81, DREV, DREV1, PAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014401	51109	RDH11	http://www.ncbi.nlm.nih.gov/gene/?term=51109	"ARSDR1, CGI82, HCBP12, MDT1, PSDR1, RALR1, RDJCSS, SCALD, SDR7C1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014402	5110	PCMT1	http://www.ncbi.nlm.nih.gov/gene/?term=5110	PIMT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014403	5110	PCMT1	http://www.ncbi.nlm.nih.gov/gene/?term=5110	PIMT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014404	5110	PCMT1	http://www.ncbi.nlm.nih.gov/gene/?term=5110	PIMT	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014405	51110	LACTB2	http://www.ncbi.nlm.nih.gov/gene/?term=51110	CGI-83	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014406	51110	LACTB2	http://www.ncbi.nlm.nih.gov/gene/?term=51110	CGI-83	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014407	51112	TRAPPC12	http://www.ncbi.nlm.nih.gov/gene/?term=51112	"CGI-87, TTC-15, TTC15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014408	51114	ZDHHC9	http://www.ncbi.nlm.nih.gov/gene/?term=51114	"CGI89, CXorf11, DHHC9, MMSA1, MRXSZ, ZDHHC10, ZNF379, ZNF380 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014409	51114	ZDHHC9	http://www.ncbi.nlm.nih.gov/gene/?term=51114	"CGI89, CXorf11, DHHC9, MMSA1, MRXSZ, ZDHHC10, ZNF379, ZNF380 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014410	51115	RMDN1	http://www.ncbi.nlm.nih.gov/gene/?term=51115	"CGI-90, FAM82B, RMD-1, RMD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014411	51115	RMDN1	http://www.ncbi.nlm.nih.gov/gene/?term=51115	"CGI-90, FAM82B, RMD-1, RMD1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014412	51115	RMDN1	http://www.ncbi.nlm.nih.gov/gene/?term=51115	"CGI-90, FAM82B, RMD-1, RMD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014413	51116	MRPS2	http://www.ncbi.nlm.nih.gov/gene/?term=51116	"CGI-91, MRP-S2, S2mt "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014414	51116	MRPS2	http://www.ncbi.nlm.nih.gov/gene/?term=51116	"CGI-91, MRP-S2, S2mt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014415	51117	COQ4	http://www.ncbi.nlm.nih.gov/gene/?term=51117	"CGI-92, COQ10D7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014416	51118	UTP11	http://www.ncbi.nlm.nih.gov/gene/?term=51118	"CGI-94, CGI94L, UTP11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014417	51118	UTP11	http://www.ncbi.nlm.nih.gov/gene/?term=51118	"CGI-94, CGI94L, UTP11 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014418	51118	UTP11	http://www.ncbi.nlm.nih.gov/gene/?term=51118	"CGI-94, CGI94L, UTP11 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014419	51119	SBDS	http://www.ncbi.nlm.nih.gov/gene/?term=51119	"CGI-97, SDS, SWDS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014420	5111	PCNA	http://www.ncbi.nlm.nih.gov/gene/?term=5111	ATLD2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014421	5111	PCNA	http://www.ncbi.nlm.nih.gov/gene/?term=5111	ATLD2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014422	51121	RPL26L1	http://www.ncbi.nlm.nih.gov/gene/?term=51121	RPL26P1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014423	51122	COMMD2	http://www.ncbi.nlm.nih.gov/gene/?term=51122	HSPC042	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014424	51122	COMMD2	http://www.ncbi.nlm.nih.gov/gene/?term=51122	HSPC042	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014425	51123	ZNF706	http://www.ncbi.nlm.nih.gov/gene/?term=51123	"HSPC038, PNAS-106, PNAS-113 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014426	51123	ZNF706	http://www.ncbi.nlm.nih.gov/gene/?term=51123	"HSPC038, PNAS-106, PNAS-113 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014427	51124	IER3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=51124	"HSPC039, MEDS, PRO2309 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014428	51124	IER3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=51124	"HSPC039, MEDS, PRO2309 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014429	51125	GOLGA7	http://www.ncbi.nlm.nih.gov/gene/?term=51125	"GCP16, GOLGA3AP1A, HSPC041, GOLGA7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014430	51126	NAA20	http://www.ncbi.nlm.nih.gov/gene/?term=51126	"NAT3, NAT3P, NAT5, NAT5P, dJ1002M8.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014431	51128	SAR1B	http://www.ncbi.nlm.nih.gov/gene/?term=51128	"ANDD, CMRD, GTBPB, SARA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014432	51128	SAR1B	http://www.ncbi.nlm.nih.gov/gene/?term=51128	"ANDD, CMRD, GTBPB, SARA2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014433	51128	SAR1B	http://www.ncbi.nlm.nih.gov/gene/?term=51128	"ANDD, CMRD, GTBPB, SARA2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014434	51129	ANGPTL4	http://www.ncbi.nlm.nih.gov/gene/?term=51129	"ARP4, FIAF, HARP, HFARP, NL2, PGAR, TGQTL, UNQ171, pp1158 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014435	51131	PHF11	http://www.ncbi.nlm.nih.gov/gene/?term=51131	"APY, BCAP, IGEL, IGER, IGHER, NY-REN-34, NYREN34 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014436	51131	PHF11	http://www.ncbi.nlm.nih.gov/gene/?term=51131	"APY, BCAP, IGEL, IGER, IGHER, NY-REN-34, NYREN34 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014437	51132	RLIM	http://www.ncbi.nlm.nih.gov/gene/?term=51132	"NY-REN-43, RNF12 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014438	51133	KCTD3	http://www.ncbi.nlm.nih.gov/gene/?term=51133	NY-REN-45	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014439	51133	KCTD3	http://www.ncbi.nlm.nih.gov/gene/?term=51133	NY-REN-45	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014440	51135	IRAK4	http://www.ncbi.nlm.nih.gov/gene/?term=51135	"IPD1, IRAK-4, NY-REN-64, REN64 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014441	51138	COPS4	http://www.ncbi.nlm.nih.gov/gene/?term=51138	CSN4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014442	51141	INSIG2	http://www.ncbi.nlm.nih.gov/gene/?term=51141	INSIG-2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014443	51141	INSIG2	http://www.ncbi.nlm.nih.gov/gene/?term=51141		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014444	51142	CHCHD2	http://www.ncbi.nlm.nih.gov/gene/?term=51142	"C7orf17, MNRR1, NS2TP, PARK22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014445	51142	CHCHD2	http://www.ncbi.nlm.nih.gov/gene/?term=51142	"C7orf17, MNRR1, NS2TP, PARK22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014446	51143	DYNC1LI1	http://www.ncbi.nlm.nih.gov/gene/?term=51143	"DNCLI1, LIC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014447	51144	HSD17B12	http://www.ncbi.nlm.nih.gov/gene/?term=51144	"KAR, SDR12C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014448	51144	HSD17B12	http://www.ncbi.nlm.nih.gov/gene/?term=51144	"KAR, SDR12C1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014449	51147	ING4	http://www.ncbi.nlm.nih.gov/gene/?term=51147	"my036, p29ING4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014450	51150	SDF4	http://www.ncbi.nlm.nih.gov/gene/?term=51150	"Cab45, SDF-4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014451	51154	MRTO4	http://www.ncbi.nlm.nih.gov/gene/?term=51154	"C1orf33, MRT4, dJ657E11.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014452	51154	MRTO4	http://www.ncbi.nlm.nih.gov/gene/?term=51154	"C1orf33, MRT4, dJ657E11.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014453	51155	HN1	http://www.ncbi.nlm.nih.gov/gene/?term=51155	"ARM2A, HN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014454	51155	HN1	http://www.ncbi.nlm.nih.gov/gene/?term=51155	"ARM2, HN1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014455	51160	VPS28	http://www.ncbi.nlm.nih.gov/gene/?term=51160		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014456	51162	EGFL7	http://www.ncbi.nlm.nih.gov/gene/?term=51162	"NEU1, VE-STATIN, ZNEU1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014457	51163	DBR1	http://www.ncbi.nlm.nih.gov/gene/?term=51163		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014458	51163	DBR1	http://www.ncbi.nlm.nih.gov/gene/?term=51163		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014459	51163	DBR1	http://www.ncbi.nlm.nih.gov/gene/?term=51163		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014460	51164	DCTN4	http://www.ncbi.nlm.nih.gov/gene/?term=51164	"DYN4, P62 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014461	51164	DCTN4	http://www.ncbi.nlm.nih.gov/gene/?term=51164	"DYN4, P62 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014462	51164	DCTN4	http://www.ncbi.nlm.nih.gov/gene/?term=51164	"DYN4, P62 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014463	51166	AADAT	http://www.ncbi.nlm.nih.gov/gene/?term=51166	"KAT2, KATII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014464	51167	CYB5R4	http://www.ncbi.nlm.nih.gov/gene/?term=51167	"NCB5OR, cb5/cb5R, dJ676J13.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014465	51167	CYB5R4	http://www.ncbi.nlm.nih.gov/gene/?term=51167	"NCB5OR, cb5/cb5R, dJ676J13.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014466	5116	PCNT	http://www.ncbi.nlm.nih.gov/gene/?term=5116	"KEN, MOPD2, PCN2, PCNTB, PCTN2, SCKL4, PCNT "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00014467	5116	PCNT	http://www.ncbi.nlm.nih.gov/gene/?term=5116	"KEN, MOPD2, PCN2, PCNTB, PCTN2, SCKL4, PCNT "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014468	5116	PCNT	http://www.ncbi.nlm.nih.gov/gene/?term=5116	"KEN, MOPD2, PCN, PCNT2, PCNTB, PCTN2, SCKL4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014469	51170	HSD17B11	http://www.ncbi.nlm.nih.gov/gene/?term=51170	"17-BETA-HSD11, 17-BETA-HSDXI, 17BHSD11, DHRS8, PAN1B, RETSDR2, SDR16C2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014470	51170	HSD17B11	http://www.ncbi.nlm.nih.gov/gene/?term=51170	"17-BETA-HSD11, 17-BETA-HSDXI, 17BHSD11, DHRS8, PAN1B, RETSDR2, SDR16C2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014471	51171	HSD17B14	http://www.ncbi.nlm.nih.gov/gene/?term=51171	"DHRS10, SDR47C1, retSDR3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014472	51174	TUBD1	http://www.ncbi.nlm.nih.gov/gene/?term=51174	TUBD	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014473	51174	TUBD1	http://www.ncbi.nlm.nih.gov/gene/?term=51174	TUBD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014474	51175	TUBE1	http://www.ncbi.nlm.nih.gov/gene/?term=51175	"TUBE, dJ142L7.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014475	51176	LEF1	http://www.ncbi.nlm.nih.gov/gene/?term=51176	"LEF-1, TCF10, TCF1ALPHA, TCF7L3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014476	51177	PLEKHO1	http://www.ncbi.nlm.nih.gov/gene/?term=51177	"CKIP-1, CKIP1, JBP, OC120 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014477	51177	PLEKHO1	http://www.ncbi.nlm.nih.gov/gene/?term=51177	"CKIP-1, CKIP1, JBP, OC120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014478	51181	DCXR	http://www.ncbi.nlm.nih.gov/gene/?term=51181	"DCR, HCR2, HCRII, KIDCR, P34H, PNTSU, SDR20C1, XR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014479	51182	HSPA14	http://www.ncbi.nlm.nih.gov/gene/?term=51182	"HSP70-4, HSP70L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014480	51184	GPN3	http://www.ncbi.nlm.nih.gov/gene/?term=51184	ATPBD1C	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014481	51185	CRBN	http://www.ncbi.nlm.nih.gov/gene/?term=51185	"MRT2, MRT2A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014482	51185	CRBN	http://www.ncbi.nlm.nih.gov/gene/?term=51185	"MRT2, MRT2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014483	51186	TCEAL9	http://www.ncbi.nlm.nih.gov/gene/?term=51186	"WBP5, WEX6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014484	51187	RSL24D1	http://www.ncbi.nlm.nih.gov/gene/?term=51187	"C15orf15, HRP-L30-iso, L30, RLP24, RPL24, RPL24L, TVAS3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014485	51188	SS18L2	http://www.ncbi.nlm.nih.gov/gene/?term=51188	KIAA-iso	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014486	51188	SS18L2	http://www.ncbi.nlm.nih.gov/gene/?term=51188	KIAA-iso	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014487	5118	PCOLCE	http://www.ncbi.nlm.nih.gov/gene/?term=5118	"PCPE, PCPE-1, PCPE1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014488	51192	CKLF	http://www.ncbi.nlm.nih.gov/gene/?term=51192	"C321, CKLF2, CKLF3, CKLF4, HSPC224, UCK-1, CKLF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014489	51192	CKLF	http://www.ncbi.nlm.nih.gov/gene/?term=51192	"C321, CKLF2, CKLF3, CKLF4, HSPC224, UCK-1, CKLF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014490	51192	CKLF	http://www.ncbi.nlm.nih.gov/gene/?term=51192	"C32, CKLF1, CKLF2, CKLF3, CKLF4, HSPC224, UCK-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014491	51193	ZNF639	http://www.ncbi.nlm.nih.gov/gene/?term=51193	"ANC-2H01, ANC_2H01, ZASC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014492	51193	ZNF639	http://www.ncbi.nlm.nih.gov/gene/?term=51193	"ANC-2H01, ANC_2H01, ZASC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014493	51194	IPO11	http://www.ncbi.nlm.nih.gov/gene/?term=51194	RanBP11	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014494	51194	IPO11	http://www.ncbi.nlm.nih.gov/gene/?term=51194	RanBP11	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014495	51199	NIN	http://www.ncbi.nlm.nih.gov/gene/?term=51199	SCKL7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014496	51199	NIN	http://www.ncbi.nlm.nih.gov/gene/?term=51199	SCKL7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014497	5119	CHMP1A	http://www.ncbi.nlm.nih.gov/gene/?term=5119	"CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014498	5119	CHMP1A	http://www.ncbi.nlm.nih.gov/gene/?term=5119	"CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014499	5119	CHMP1A	http://www.ncbi.nlm.nih.gov/gene/?term=5119	"CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014500	51200	CPA4	http://www.ncbi.nlm.nih.gov/gene/?term=51200	CPA3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014501	51201	ZDHHC2	http://www.ncbi.nlm.nih.gov/gene/?term=51201	"DHHC2, ZNF372 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014502	51203	NUSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51203	"ANKT, BM037, LNP, NUSAP, PRO0310p1, Q0310, SAPL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014503	51203	NUSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51203	"ANKT, BM037, LNP, NUSAP, PRO0310p1, Q0310, SAPL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014504	51203	NUSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51203	"ANKT, BM037, LNP, NUSAP, PRO0310p1, Q0310, SAPL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014505	51204	TACO1	http://www.ncbi.nlm.nih.gov/gene/?term=51204	CCDC44	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014506	51205	ACP6	http://www.ncbi.nlm.nih.gov/gene/?term=51205	"ACPL1, LPAP, PACPL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014507	51205	ACP6	http://www.ncbi.nlm.nih.gov/gene/?term=51205	"ACPL1, LPAP, PACPL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014508	51205	ACP6	http://www.ncbi.nlm.nih.gov/gene/?term=51205	"ACPL1, LPAP, PACPL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014509	51207	DUSP13	http://www.ncbi.nlm.nih.gov/gene/?term=51207	"BEDPA, DUSP13B, MDSP, SKRP4, TMDP, DUSP13 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00014510	51208	CLDN18	http://www.ncbi.nlm.nih.gov/gene/?term=51208	"SFTA5, SFTPJ "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014511	51218	GLRX5	http://www.ncbi.nlm.nih.gov/gene/?term=51218	"C14orf87, FLB4739, GRX5, PR01238, PRO1238, PRSA, SIDBA3, SPAHGC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014512	5121	PCP4	http://www.ncbi.nlm.nih.gov/gene/?term=5121	PEP-19	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014513	51222	ZNF219	http://www.ncbi.nlm.nih.gov/gene/?term=51222	ZFP219	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014514	51222	ZNF219	http://www.ncbi.nlm.nih.gov/gene/?term=51222	ZFP219	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014515	51227	PIGP	http://www.ncbi.nlm.nih.gov/gene/?term=51227	"DCRC, DCRC-S, DSCR5, DSRC, PIG-P "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014516	51227	PIGP	http://www.ncbi.nlm.nih.gov/gene/?term=51227	"DCRC, DCRC-S, DSCR5, DSRC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014517	51228	GLTP	http://www.ncbi.nlm.nih.gov/gene/?term=51228		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014518	51231	VRK3	http://www.ncbi.nlm.nih.gov/gene/?term=51231		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014519	51232	CRIM1	http://www.ncbi.nlm.nih.gov/gene/?term=51232	"CRIM-1, S52 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014520	51232	CRIM1	http://www.ncbi.nlm.nih.gov/gene/?term=51232	"CRIM-1, S52 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014521	51232	CRIM1	http://www.ncbi.nlm.nih.gov/gene/?term=51232	"CRIM-1, S52 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014522	51232	CRIM1	http://www.ncbi.nlm.nih.gov/gene/?term=51232	"CRIM-1, S52 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014523	51234	EMC4	http://www.ncbi.nlm.nih.gov/gene/?term=51234	"PIG17, TMEM85 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014524	51236	HGH1	http://www.ncbi.nlm.nih.gov/gene/?term=51236	"BRP16, BRP16L, C8orf30A, C8orf30B, FAM203A, FAM203B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014525	51239	ANKRD39	http://www.ncbi.nlm.nih.gov/gene/?term=51239		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014526	51241	COX16	http://www.ncbi.nlm.nih.gov/gene/?term=51241	"C14orf112, HSPC203 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014527	51241	COX16	http://www.ncbi.nlm.nih.gov/gene/?term=51241	"C14orf112, HSPC203 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014528	51241	COX16	http://www.ncbi.nlm.nih.gov/gene/?term=51241	"C14orf112, HSPC203 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014529	51244	CCDC174	http://www.ncbi.nlm.nih.gov/gene/?term=51244	"C3orf19, HSPC212, IHPMR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014530	51246	SHISA5	http://www.ncbi.nlm.nih.gov/gene/?term=51246	SCOTIN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014531	51246	SHISA5	http://www.ncbi.nlm.nih.gov/gene/?term=51246	SCOTIN	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014532	51247	PAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=51247	"PAIP-2A, PAIP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014533	51247	PAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=51247	"PAIP-2A, PAIP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014534	51247	PAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=51247	"PAIP-2, PAIP2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014535	51248	PDZD11	http://www.ncbi.nlm.nih.gov/gene/?term=51248	"AIPP1, PDZK11, PISP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014536	51248	PDZD11	http://www.ncbi.nlm.nih.gov/gene/?term=51248	"AIPP1, PDZK11, PISP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014537	51248	PDZD11	http://www.ncbi.nlm.nih.gov/gene/?term=51248	"AIPP1, PDZK11, PISP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014538	51249	TMEM69	http://www.ncbi.nlm.nih.gov/gene/?term=51249	C1orf154	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014539	51249	TMEM69	http://www.ncbi.nlm.nih.gov/gene/?term=51249	C1orf154	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014540	51250	C6orf203	http://www.ncbi.nlm.nih.gov/gene/?term=51250	"HSPC230, PRED31 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014541	51251	NT5C3A	http://www.ncbi.nlm.nih.gov/gene/?term=51251	"NT5C3, P5'N-1, P5N-1, PN-I, POMP, PSN1, UMPH, UMPH1, cN-III, hUMP1, p36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014542	51251	NT5C3A	http://www.ncbi.nlm.nih.gov/gene/?term=51251	"NT5C3, P5'N-1, P5N-1, PN-I, POMP, PSN1, UMPH, UMPH1, cN-III, hUMP1, p36 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014543	51253	MRPL37	http://www.ncbi.nlm.nih.gov/gene/?term=51253	"L37mt, MRP-L2, MRP-L37, MRPL2, RPML2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014544	51253	MRPL37	http://www.ncbi.nlm.nih.gov/gene/?term=51253	"L37mt, MRP-L2, MRP-L37, MRPL2, RPML2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014545	51255	RNF181	http://www.ncbi.nlm.nih.gov/gene/?term=51255	HSPC238	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014546	51256	TBC1D7	http://www.ncbi.nlm.nih.gov/gene/?term=51256	"MGCPH, PIG51, TBC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014547	51257	MARCH2	http://www.ncbi.nlm.nih.gov/gene/?term=51257	"HSPC240, MARCH-II, RNF172 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014548	51257	MARCH2	http://www.ncbi.nlm.nih.gov/gene/?term=51257	"HSPC240, MARCH-II, RNF172 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014549	51257	MARCH2	http://www.ncbi.nlm.nih.gov/gene/?term=51257	"HSPC240, MARCH-II, RNF172 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014550	51258	MRPL51	http://www.ncbi.nlm.nih.gov/gene/?term=51258	"CDA09, HSPC241, MRP64, bMRP64 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014551	51259	TMEM216	http://www.ncbi.nlm.nih.gov/gene/?term=51259	HSPC244	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014552	51263	MRPL30	http://www.ncbi.nlm.nih.gov/gene/?term=51263	"L28MT, L30MT, MRP-L28, MRP-L30, MRPL28, MRPL28M, RPML28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014553	51264	MRPL27	http://www.ncbi.nlm.nih.gov/gene/?term=51264	L27mt	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014554	51266	CLEC1B	http://www.ncbi.nlm.nih.gov/gene/?term=51266	"1810061I13Rik, CLEC2, CLEC2B, PRO1384, QDED721 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014555	5126	PCSK2	http://www.ncbi.nlm.nih.gov/gene/?term=5126	"NEC 2, NEC-2, NEC2, PC2, SPC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014556	51271	UBAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51271	"NAG20, UAP, UBAP, UBAP-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014557	51271	UBAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51271	"NAG20, UAP, UBAP, UBAP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014558	51272	BET1L	http://www.ncbi.nlm.nih.gov/gene/?term=51272	"BET1L1, GOLIM3, GS15, HSPC197 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014559	51272	BET1L	http://www.ncbi.nlm.nih.gov/gene/?term=51272	"BET1L1, GOLIM3, GS15, HSPC197 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014560	51274	KLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51274	BKLF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014561	51275	MAPKAPK5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=51275	C12orf47	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014562	51277	DNAJC27	http://www.ncbi.nlm.nih.gov/gene/?term=51277	"RBJ, RabJS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014563	51279	C1RL	http://www.ncbi.nlm.nih.gov/gene/?term=51279	"C1RL1P, C1r-LP, CLSPa, C1RL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014564	51279	C1RL	http://www.ncbi.nlm.nih.gov/gene/?term=51279	"C1RL1, C1RLP, C1r-LP, CLSPa "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014565	5127	CDK16	http://www.ncbi.nlm.nih.gov/gene/?term=5127	"PCTAIRE, PCTAIRE1, PCTGAIRE, PCTK1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014566	5127	CDK16	http://www.ncbi.nlm.nih.gov/gene/?term=5127	"PCTAIRE, PCTAIRE1, PCTGAIRE, PCTK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014567	51280	GOLM1	http://www.ncbi.nlm.nih.gov/gene/?term=51280	"C9orf155, GOLPH2, GP73, HEL46, PSEC0257, bA379P1.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014568	51280	GOLM1	http://www.ncbi.nlm.nih.gov/gene/?term=51280	"C9orf155, GOLPH2, GP73, HEL46, PSEC0257, bA379P1.3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014569	51280	GOLM1	http://www.ncbi.nlm.nih.gov/gene/?term=51280	"C9orf155, GOLPH2, GP73, HEL46, PSEC0257, bA379P1.3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014570	51280	GOLM1	http://www.ncbi.nlm.nih.gov/gene/?term=51280	"C9orf155, GOLPH2, GP73, HEL46, PSEC0257, bA379P1.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014571	51282	SCAND1	http://www.ncbi.nlm.nih.gov/gene/?term=51282	"RAZ1, SDP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014572	51282	SCAND1	http://www.ncbi.nlm.nih.gov/gene/?term=51282	"RAZ1, SDP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014573	51283	BFAR	http://www.ncbi.nlm.nih.gov/gene/?term=51283	"BAR, RNF47 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014574	51283	BFAR	http://www.ncbi.nlm.nih.gov/gene/?term=51283	"BAR, RNF47 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014575	51287	COA4	http://www.ncbi.nlm.nih.gov/gene/?term=51287	"CHCHD8, CMC3, E2IG2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014576	51290	ERGIC2	http://www.ncbi.nlm.nih.gov/gene/?term=51290	"CDA14, Erv41, PTX1, cd002 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014577	51290	ERGIC2	http://www.ncbi.nlm.nih.gov/gene/?term=51290	"CDA14, Erv41, PTX1, cd002 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014578	51292	GMPR2	http://www.ncbi.nlm.nih.gov/gene/?term=51292	GMPR 2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014579	51293	CD320	http://www.ncbi.nlm.nih.gov/gene/?term=51293	"8D6, 8D6A, TCBLR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014580	51295	ECSIT	http://www.ncbi.nlm.nih.gov/gene/?term=51295	SITPEC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014581	51295	ECSIT	http://www.ncbi.nlm.nih.gov/gene/?term=51295	SITPEC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014582	51299	NRN1	http://www.ncbi.nlm.nih.gov/gene/?term=51299	"NRN, dJ380B8.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014583	51300	TIMMDC1	http://www.ncbi.nlm.nih.gov/gene/?term=51300	C3orf1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014584	51300	TIMMDC1	http://www.ncbi.nlm.nih.gov/gene/?term=51300	C3orf1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014585	51302	CYP39A1	http://www.ncbi.nlm.nih.gov/gene/?term=51302		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014586	51303	FKBP11	http://www.ncbi.nlm.nih.gov/gene/?term=51303	FKBP19	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014587	51304	ZDHHC3	http://www.ncbi.nlm.nih.gov/gene/?term=51304	"DHHC-3, GODZ, ZNF373 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014588	51304	ZDHHC3	http://www.ncbi.nlm.nih.gov/gene/?term=51304	"DHHC-3, GODZ, ZNF373 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014589	51306	FAM13B	http://www.ncbi.nlm.nih.gov/gene/?term=51306	"ARHGAP49, C5orf5, FAM13B1, KHCHP, N61 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014590	5130	PCYT1A	http://www.ncbi.nlm.nih.gov/gene/?term=5130	"CCTA, CT, CTA, CTPCT, PCYT1, SMDCRD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014591	5130	PCYT1A	http://www.ncbi.nlm.nih.gov/gene/?term=5130	"CCTA, CT, CTA, CTPCT, PCYT1, SMDCRD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014592	5130	PCYT1A	http://www.ncbi.nlm.nih.gov/gene/?term=5130	"CCTA, CT, CTA, CTPCT, PCYT1, SMDCRD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014593	51312	SLC25A37	http://www.ncbi.nlm.nih.gov/gene/?term=51312	"HT015, MFRN, MFRN1, MSC, MSCP, PRO1278, PRO1584, PRO2217 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014594	51312	SLC25A37	http://www.ncbi.nlm.nih.gov/gene/?term=51312	"HT015, MFRN, MFRN1, MSC, MSCP, PRO1278, PRO1584, PRO2217 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014595	51313	FAM198B	http://www.ncbi.nlm.nih.gov/gene/?term=51313	"AD021, AD036, C4orf18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014596	51315	KRCC1	http://www.ncbi.nlm.nih.gov/gene/?term=51315	CHBP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014597	51316	PLAC8	http://www.ncbi.nlm.nih.gov/gene/?term=51316	"C15, DGIC, PNAS-144, onzin "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014598	51316	PLAC8	http://www.ncbi.nlm.nih.gov/gene/?term=51316	"C15, DGIC, PNAS-144, onzin "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014599	51317	PHF21A	http://www.ncbi.nlm.nih.gov/gene/?term=51317	"BHC80, BM-006 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014600	51318	MRPL35	http://www.ncbi.nlm.nih.gov/gene/?term=51318	"L35mt, MRP-L35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014601	51318	MRPL35	http://www.ncbi.nlm.nih.gov/gene/?term=51318	"L35mt, MRP-L35 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014602	51318	MRPL35	http://www.ncbi.nlm.nih.gov/gene/?term=51318	"L35mt, MRP-L35 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014603	51318	MRPL35	http://www.ncbi.nlm.nih.gov/gene/?term=51318	"L35mt, MRP-L35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014604	51319	RSRC1	http://www.ncbi.nlm.nih.gov/gene/?term=51319	"BM-011, SFRS21, SRrp53 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014605	51319	RSRC1	http://www.ncbi.nlm.nih.gov/gene/?term=51319	"BM-011, SFRS21, SRrp53 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014606	51321	AMZ2	http://www.ncbi.nlm.nih.gov/gene/?term=51321		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014607	51322	WAC	http://www.ncbi.nlm.nih.gov/gene/?term=51322	"BM-016, DESSH, PRO1741, Wwp4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014608	51324	SPG21	http://www.ncbi.nlm.nih.gov/gene/?term=51324	"ACP33, BM-019, GL010, MAST "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014609	51324	SPG21	http://www.ncbi.nlm.nih.gov/gene/?term=51324	"ACP33, BM-019, GL010, MAST "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014610	51324	SPG21	http://www.ncbi.nlm.nih.gov/gene/?term=51324	"ACP33, BM-019, GL010, MAST "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014611	51327	AHSP	http://www.ncbi.nlm.nih.gov/gene/?term=51327	"EDRF, ERAF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014612	51329	ARL6IP4	http://www.ncbi.nlm.nih.gov/gene/?term=51329	"SFRS20, SR-25, SRp25, SRrp37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014613	51330	TNFRSF12A	http://www.ncbi.nlm.nih.gov/gene/?term=51330	"CD266, FN14, TWEAKR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014614	51330	TNFRSF12A	http://www.ncbi.nlm.nih.gov/gene/?term=51330	"CD266, FN14, TWEAKR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014615	51333	ZNF771	http://www.ncbi.nlm.nih.gov/gene/?term=51333	DSC43	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014616	51334	PRR16	http://www.ncbi.nlm.nih.gov/gene/?term=51334	"DSC54, LARGEN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014617	51335	NGRN	http://www.ncbi.nlm.nih.gov/gene/?term=51335	DSC92	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014618	51337	THEM6	http://www.ncbi.nlm.nih.gov/gene/?term=51337	"C8orf55, DSCD75 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014619	51338	MS4A4A	http://www.ncbi.nlm.nih.gov/gene/?term=51338	"4SPAN1, CD20-L1, CD20L1, HDCME31P, MS4A4, MS4A7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014620	51341	ZBTB7A	http://www.ncbi.nlm.nih.gov/gene/?term=51341	"FBI-1, FBI1, LRF, TIP21, ZBTB7, ZNF857A, pokemon "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014621	51341	ZBTB7A	http://www.ncbi.nlm.nih.gov/gene/?term=51341	"FBI-1, FBI1, LRF, TIP21, ZBTB7, ZNF857A, pokemon "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014622	51341	ZBTB7A	http://www.ncbi.nlm.nih.gov/gene/?term=51341	"FBI-1, FBI1, LRF, TIP21, ZBTB7, ZNF857A, pokemon "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014623	51343	FZR1	http://www.ncbi.nlm.nih.gov/gene/?term=51343	"CDC20C, CDH1, FZR, FZR2, HCDH, HCDH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014624	51343	FZR1	http://www.ncbi.nlm.nih.gov/gene/?term=51343	"CDC20C, CDH1, FZR, FZR2, HCDH, HCDH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014625	5134	PDCD2	http://www.ncbi.nlm.nih.gov/gene/?term=5134	"RP8, ZMYND7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014626	5134	PDCD2	http://www.ncbi.nlm.nih.gov/gene/?term=5134	"RP8, ZMYND7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014627	5134	PDCD2	http://www.ncbi.nlm.nih.gov/gene/?term=5134	"RP8, ZMYND7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014628	51351	ZNF117	http://www.ncbi.nlm.nih.gov/gene/?term=51351	"H-plk, HPF9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014629	51351	ZNF117	http://www.ncbi.nlm.nih.gov/gene/?term=51351	"H-plk, HPF9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014630	51351	ZNF117	http://www.ncbi.nlm.nih.gov/gene/?term=51351	"H-plk, HPF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014631	51360	MBTPS2	http://www.ncbi.nlm.nih.gov/gene/?term=51360	"BRESEK, IFAP, KFSD, KFSDX, OLMSX, S2P "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014632	51366	UBR5	http://www.ncbi.nlm.nih.gov/gene/?term=51366	"DD5, EDD, EDD1, HYD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014633	51366	UBR5	http://www.ncbi.nlm.nih.gov/gene/?term=51366	"DD5, EDD, EDD1, HYD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014634	51367	POP5	http://www.ncbi.nlm.nih.gov/gene/?term=51367	"HSPC004, RPP2, RPP20, hPop5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014635	51368	TEX264	http://www.ncbi.nlm.nih.gov/gene/?term=51368	ZSIG11	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014636	51368	TEX264	http://www.ncbi.nlm.nih.gov/gene/?term=51368	ZSIG11	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014637	51371	POMP	http://www.ncbi.nlm.nih.gov/gene/?term=51371	"C13orf12, HSPC014, PNAS-110, UMP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014638	51371	POMP	http://www.ncbi.nlm.nih.gov/gene/?term=51371	"C13orf12, HSPC014, PNAS-110, UMP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014639	51371	POMP	http://www.ncbi.nlm.nih.gov/gene/?term=51371	"C13orf12, HSPC014, PNAS-110, UMP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014640	51372	TMA7	http://www.ncbi.nlm.nih.gov/gene/?term=51372	"CCDC72, HSPC016 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014641	51374	ATRAID	http://www.ncbi.nlm.nih.gov/gene/?term=51374	"APR--3, APR-3, APR3, C2orf28, HSPC013, PRO240, p18 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014642	51375	SNX7	http://www.ncbi.nlm.nih.gov/gene/?term=51375		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014643	51377	UCHL5	http://www.ncbi.nlm.nih.gov/gene/?term=51377	"CGI-70, INO80R, UCH-L5, UCH37 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014644	51379	CRLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51379	"CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014645	51379	CRLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51379	"CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014646	51379	CRLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51379	"CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014647	51379	CRLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51379	"CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014648	51382	ATP6V1D	http://www.ncbi.nlm.nih.gov/gene/?term=51382	"ATP6M, VATD, VMA8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014649	51382	ATP6V1D	http://www.ncbi.nlm.nih.gov/gene/?term=51382	"ATP6M, VATD, VMA8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014650	51385	ZNF589	http://www.ncbi.nlm.nih.gov/gene/?term=51385	SZF1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014651	51386	EIF3L	http://www.ncbi.nlm.nih.gov/gene/?term=51386	"EIF3EIP, EIF3S11, EIF3S6IP, HSPC021, HSPC025, MSTP005 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014652	51386	EIF3L	http://www.ncbi.nlm.nih.gov/gene/?term=51386	"EIF3EIP, EIF3S11, EIF3S6IP, HSPC021, HSPC025, MSTP005 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014653	51388	NIP7	http://www.ncbi.nlm.nih.gov/gene/?term=51388	"CGI-37, HSPC031, KD93 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014654	51389	RWDD1	http://www.ncbi.nlm.nih.gov/gene/?term=51389	"CGI-24, PTD013 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014655	51389	RWDD1	http://www.ncbi.nlm.nih.gov/gene/?term=51389	"CGI-24, PTD013 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014656	51390	AIG1	http://www.ncbi.nlm.nih.gov/gene/?term=51390	"AIG-1, dJ95L4.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014657	51393	TRPV2	http://www.ncbi.nlm.nih.gov/gene/?term=51393	"VRL, VRL-1, VRL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014658	51397	COMMD10	http://www.ncbi.nlm.nih.gov/gene/?term=51397	PTD002	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014659	51398	WDR83OS	http://www.ncbi.nlm.nih.gov/gene/?term=51398	"C19orf56, PTD008 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014660	51398	WDR83OS	http://www.ncbi.nlm.nih.gov/gene/?term=51398	"C19orf56, PTD008 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014661	51399	TRAPPC4	http://www.ncbi.nlm.nih.gov/gene/?term=51399	"CGI-104, HSPC172, PTD009, SBDN, SYNBINDIN, TRS23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014662	513	ATP5D	http://www.ncbi.nlm.nih.gov/gene/?term=513		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014663	513	ATP5D	http://www.ncbi.nlm.nih.gov/gene/?term=513		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014664	51400	PPME1	http://www.ncbi.nlm.nih.gov/gene/?term=51400	PME-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014665	51400	PPME1	http://www.ncbi.nlm.nih.gov/gene/?term=51400	PME-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014666	51406	NOL7	http://www.ncbi.nlm.nih.gov/gene/?term=51406	"C6orf90, PQBP3, RARG-1, dJ223E5.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014667	51406	NOL7	http://www.ncbi.nlm.nih.gov/gene/?term=51406	"C6orf90, PQBP3, RARG-1, dJ223E5.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014668	51409	HEMK1	http://www.ncbi.nlm.nih.gov/gene/?term=51409	"HEMK, MTQ1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014669	51421	AMOTL2	http://www.ncbi.nlm.nih.gov/gene/?term=51421	LCCP	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014670	51421	AMOTL2	http://www.ncbi.nlm.nih.gov/gene/?term=51421	LCCP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014671	51422	PRKAG2	http://www.ncbi.nlm.nih.gov/gene/?term=51422	"AAKG, AAKG2, CMH6, H91620p, WPWS "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014672	51422	PRKAG2	http://www.ncbi.nlm.nih.gov/gene/?term=51422	"AAKG, AAKG2, CMH6, H91620p, WPWS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014673	51427	ZNF107	http://www.ncbi.nlm.nih.gov/gene/?term=51427	"Y8, ZFD25, ZNF588, smap-7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014674	51427	ZNF107	http://www.ncbi.nlm.nih.gov/gene/?term=51427	"Y8, ZFD25, ZNF588, smap-7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014675	51428	DDX41	http://www.ncbi.nlm.nih.gov/gene/?term=51428	"ABS, MPLPF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014676	51428	DDX41	http://www.ncbi.nlm.nih.gov/gene/?term=51428	ABS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014677	51429	SNX9	http://www.ncbi.nlm.nih.gov/gene/?term=51429	"SDP1, SH3PX1, SH3PXD3A, WISP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014678	51429	SNX9	http://www.ncbi.nlm.nih.gov/gene/?term=51429	"SDP1, SH3PX1, SH3PXD3A, WISP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014679	51430	SUCO	http://www.ncbi.nlm.nih.gov/gene/?term=51430	"C1orf9, CH1, OPT, SLP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014680	51430	SUCO	http://www.ncbi.nlm.nih.gov/gene/?term=51430	"C1orf9, CH1, OPT, SLP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014681	51433	ANAPC5	http://www.ncbi.nlm.nih.gov/gene/?term=51433	APC5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014682	51434	ANAPC7	http://www.ncbi.nlm.nih.gov/gene/?term=51434	APC7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014683	51434	ANAPC7	http://www.ncbi.nlm.nih.gov/gene/?term=51434	APC7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014684	51435	SCARA3	http://www.ncbi.nlm.nih.gov/gene/?term=51435	"APC7, CSR, CSR1, MSLR1, MSRL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014685	51439	FAM8A1	http://www.ncbi.nlm.nih.gov/gene/?term=51439	AHCP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014686	5143	PDE4C	http://www.ncbi.nlm.nih.gov/gene/?term=5143	DPDE1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014687	51441	YTHDF2	http://www.ncbi.nlm.nih.gov/gene/?term=51441	"CAHL, HGRG8, NY-REN-2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014688	51441	YTHDF2	http://www.ncbi.nlm.nih.gov/gene/?term=51441	"CAHL, HGRG8, NY-REN-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014689	51444	RNF138	http://www.ncbi.nlm.nih.gov/gene/?term=51444	"HSD-4, NARF, STRIN, hNARF "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014690	51444	RNF138	http://www.ncbi.nlm.nih.gov/gene/?term=51444	"HSD-4, NARF, STRIN, hNARF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014691	51449	PCYOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51449	PCL1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014692	51449	PCYOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51449	PCL1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014693	51449	PCYOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51449	PCL1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014694	51449	PCYOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51449	PCL1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014695	51451	LCMT1	http://www.ncbi.nlm.nih.gov/gene/?term=51451	"CGI-68, LCMT, PPMT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014696	51454	GULP1	http://www.ncbi.nlm.nih.gov/gene/?term=51454	"CED-6, CED6, GULP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014697	51454	GULP1	http://www.ncbi.nlm.nih.gov/gene/?term=51454	"CED-6, CED6, GULP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014698	51455	REV1	http://www.ncbi.nlm.nih.gov/gene/?term=51455	"AIBP80L, REV1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014699	51455	REV1	http://www.ncbi.nlm.nih.gov/gene/?term=51455	REV1L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014700	5145	PDE6A	http://www.ncbi.nlm.nih.gov/gene/?term=5145	"CGPR-A, PDEA, RP43 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014701	5145	PDE6A	http://www.ncbi.nlm.nih.gov/gene/?term=5145	"CGPR-A, PDEA, RP43 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014702	51460	SFMBT1	http://www.ncbi.nlm.nih.gov/gene/?term=51460	"RU1, SFMBT, hSFMBT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014703	51460	SFMBT1	http://www.ncbi.nlm.nih.gov/gene/?term=51460	"RU1, SFMBT, hSFMBT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014704	51465	UBE2J1	http://www.ncbi.nlm.nih.gov/gene/?term=51465	"CGI-76, HSPC153, HSPC205, HSU93243, NCUBE-1, NCUBE1, UBC6, UBC6E, Ubc6p "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014705	51465	UBE2J1	http://www.ncbi.nlm.nih.gov/gene/?term=51465	"CGI-76, HSPC153, HSPC205, HSU93243, NCUBE-1, NCUBE1, UBC6, UBC6E, Ubc6p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014706	51474	LIMA1	http://www.ncbi.nlm.nih.gov/gene/?term=51474	"EPLIN, SREBP3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014707	51474	LIMA1	http://www.ncbi.nlm.nih.gov/gene/?term=51474	"EPLIN, SREBP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014708	51477	ISYNA1	http://www.ncbi.nlm.nih.gov/gene/?term=51477	"INO1, INOS, IPS, IPS 1, IPS-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014709	51478	HSD17B7	http://www.ncbi.nlm.nih.gov/gene/?term=51478	"PRAP, SDR37C1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014710	51479	ANKFY1	http://www.ncbi.nlm.nih.gov/gene/?term=51479	"ANKHZN, BTBD23, ZFYVE14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014711	51479	ANKFY1	http://www.ncbi.nlm.nih.gov/gene/?term=51479	"ANKHZN, BTBD23, ZFYVE14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014712	5147	PDE6D	http://www.ncbi.nlm.nih.gov/gene/?term=5147	"JBTS22, PDED "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014713	51481	VCX3A	http://www.ncbi.nlm.nih.gov/gene/?term=51481	"VCX-8r, VCX-A, VCX3, VCX8R, VCXA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014714	51490	C9orf114	http://www.ncbi.nlm.nih.gov/gene/?term=51490	"CENP-32, HSPC109 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014715	51491	NOP16	http://www.ncbi.nlm.nih.gov/gene/?term=51491	"HSPC111, HSPC185 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014716	51493	RTCB	http://www.ncbi.nlm.nih.gov/gene/?term=51493	"C22orf28, DJ149A16.6, FAAP, HSPC117 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014717	51493	RTCB	http://www.ncbi.nlm.nih.gov/gene/?term=51493	"C22orf28, DJ149A16.6, FAAP, HSPC117 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014718	51495	HACD3	http://www.ncbi.nlm.nih.gov/gene/?term=51495	"B-IND1, BIND1, HSPC121, PTPLAD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014719	51495	HACD3	http://www.ncbi.nlm.nih.gov/gene/?term=51495	"B-IND1, BIND1, HSPC121, PTPLAD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014720	51496	CTDSPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51496	"HSPC058, HSPC129 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014721	51496	CTDSPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51496	"HSPC058, HSPC129 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014722	51497	NELFCD	http://www.ncbi.nlm.nih.gov/gene/?term=51497	"HSPC130, NELF-C, NELF-D, TH1, TH1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014723	51499	TRIAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51499	"HSPC132, MDM35, P53CSV, WF-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014724	514	ATP5E	http://www.ncbi.nlm.nih.gov/gene/?term=514	"ATPE, MC5DN3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014725	514	ATP5E	http://www.ncbi.nlm.nih.gov/gene/?term=514	"ATPE, MC5DN3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014726	51501	C11orf73	http://www.ncbi.nlm.nih.gov/gene/?term=51501	"HLD13, HSPC138, HSPC179, Hikeshi, L7RN6, OPI10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014727	51503	CWC15	http://www.ncbi.nlm.nih.gov/gene/?term=51503	"AD002, C11orf5, Cwf15, HSPC148, ORF5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014728	51503	CWC15	http://www.ncbi.nlm.nih.gov/gene/?term=51503	"AD002, C11orf5, Cwf15, HSPC148, ORF5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014729	51504	TRMT112	http://www.ncbi.nlm.nih.gov/gene/?term=51504	"HSPC152, HSPC170, TRM112, TRMT11-2, hTrm112 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014730	51506	UFC1	http://www.ncbi.nlm.nih.gov/gene/?term=51506	HSPC155	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014731	51507	RTFDC1	http://www.ncbi.nlm.nih.gov/gene/?term=51507	"C20orf43, CDAO5, HSPC164, SHUJUN-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014732	51507	RTFDC1	http://www.ncbi.nlm.nih.gov/gene/?term=51507	"C20orf43, CDAO5, HSPC164, SHUJUN-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014733	51510	CHMP5	http://www.ncbi.nlm.nih.gov/gene/?term=51510	"C9orf83, CGI-34, HSPC177, PNAS-2, SNF7DC2, Vps60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014734	51512	GTSE1	http://www.ncbi.nlm.nih.gov/gene/?term=51512	B99	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014735	51512	GTSE1	http://www.ncbi.nlm.nih.gov/gene/?term=51512	B99	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014736	51514	DTL	http://www.ncbi.nlm.nih.gov/gene/?term=51514	"CDT2, DCAF2, L2DTL, RAMP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014737	51514	DTL	http://www.ncbi.nlm.nih.gov/gene/?term=51514	"CDT2, DCAF2, L2DTL, RAMP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014738	51514	DTL	http://www.ncbi.nlm.nih.gov/gene/?term=51514	"CDT2, DCAF2, L2DTL, RAMP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014739	51517	NCKIPSD	http://www.ncbi.nlm.nih.gov/gene/?term=51517	"AF3P21, DIP, DIP1, ORF1, SPIN90, VIP54, WASLBP, WISH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014740	5151	PDE8A	http://www.ncbi.nlm.nih.gov/gene/?term=5151	HsT19550	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014741	5151	PDE8A	http://www.ncbi.nlm.nih.gov/gene/?term=5151	HsT19550	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014742	51520	LARS	http://www.ncbi.nlm.nih.gov/gene/?term=51520	"HSPC192, ILFS11, LEURS, LEUS, LFIS, LRS, PIG44, RNTLS, hr025Cl, LARS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014743	51522	TMEM14C	http://www.ncbi.nlm.nih.gov/gene/?term=51522	"C6orf53, HSPC194, MSTP073, NET26, bA421M1.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014744	51523	CXXC5	http://www.ncbi.nlm.nih.gov/gene/?term=51523	"CF5, HSPC195, RINF, WID "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014745	51523	CXXC5	http://www.ncbi.nlm.nih.gov/gene/?term=51523	"CF5, HSPC195, RINF, WID "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014746	51524	TMEM138	http://www.ncbi.nlm.nih.gov/gene/?term=51524	HSPC196	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014747	51526	OSER1	http://www.ncbi.nlm.nih.gov/gene/?term=51526	"C20orf111, HSPC207, Osr1, Perit1, dJ1183I21.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014748	51527	GSKIP	http://www.ncbi.nlm.nih.gov/gene/?term=51527	"C14orf129, HSPC210 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014749	51527	GSKIP	http://www.ncbi.nlm.nih.gov/gene/?term=51527	"C14orf129, HSPC210 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014750	51528	JKAMP	http://www.ncbi.nlm.nih.gov/gene/?term=51528	"C14orf100, CDA06, HSPC213, HSPC327, JAMP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014751	51529	ANAPC11	http://www.ncbi.nlm.nih.gov/gene/?term=51529	"APC11, Apc11p, HSPC214 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014752	51530	ZC3HC1	http://www.ncbi.nlm.nih.gov/gene/?term=51530	"HSPC216, NIPA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014753	51534	VTA1	http://www.ncbi.nlm.nih.gov/gene/?term=51534	"C6orf55, DRG-1, DRG1, HSPC228, LIP5, My012, SBP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014754	51534	VTA1	http://www.ncbi.nlm.nih.gov/gene/?term=51534	"C6orf55, DRG-1, DRG1, HSPC228, LIP5, My012, SBP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014755	51534	VTA1	http://www.ncbi.nlm.nih.gov/gene/?term=51534	"C6orf55, DRG-1, DRG1, HSPC228, LIP5, My012, SBP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014756	51535	PPHLN1	http://www.ncbi.nlm.nih.gov/gene/?term=51535	"CR, HSPC206, HSPC232 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014757	51535	PPHLN1	http://www.ncbi.nlm.nih.gov/gene/?term=51535	"CR, HSPC206, HSPC232 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014758	51535	PPHLN1	http://www.ncbi.nlm.nih.gov/gene/?term=51535	"CR, HSPC206, HSPC232 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014759	51537	MTFP1	http://www.ncbi.nlm.nih.gov/gene/?term=51537	"HSPC242, MTP18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014760	51538	ZCCHC17	http://www.ncbi.nlm.nih.gov/gene/?term=51538	"HSPC251, PS1D, pNO40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014761	51538	ZCCHC17	http://www.ncbi.nlm.nih.gov/gene/?term=51538	"HSPC251, PS1D, pNO40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014762	51540	SCLY	http://www.ncbi.nlm.nih.gov/gene/?term=51540	"SCL, hSCL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014763	51540	SCLY	http://www.ncbi.nlm.nih.gov/gene/?term=51540	"SCL, hSCL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014764	51545	ZNF581	http://www.ncbi.nlm.nih.gov/gene/?term=51545	HSPC189	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014765	51548	SIRT6	http://www.ncbi.nlm.nih.gov/gene/?term=51548	SIR2L6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014766	51550	CINP	http://www.ncbi.nlm.nih.gov/gene/?term=51550		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014767	51552	RAB14	http://www.ncbi.nlm.nih.gov/gene/?term=51552	"FBP, RAB-14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014768	51552	RAB14	http://www.ncbi.nlm.nih.gov/gene/?term=51552	"FBP, RAB-14 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014769	51559	NT5DC3	http://www.ncbi.nlm.nih.gov/gene/?term=51559	"TU12B1-TY, TU12B1TY "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014770	51559	NT5DC3	http://www.ncbi.nlm.nih.gov/gene/?term=51559	"TU12B1-TY, TU12B1TY "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014771	51559	NT5DC3	http://www.ncbi.nlm.nih.gov/gene/?term=51559	"TU12B1-TY, TU12B1TY "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014772	51561	IL23A	http://www.ncbi.nlm.nih.gov/gene/?term=51561	"IL-23, IL-23A, IL23P19, P19, SGRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014773	51562	MBIP	http://www.ncbi.nlm.nih.gov/gene/?term=51562		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014774	51562	MBIP	http://www.ncbi.nlm.nih.gov/gene/?term=51562		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014775	51564	HDAC7	http://www.ncbi.nlm.nih.gov/gene/?term=51564	"HD7, HD7A, HDAC7A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014776	51566	ARMCX3	http://www.ncbi.nlm.nih.gov/gene/?term=51566	"ALEX3, GASP6, dJ545K15.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014777	51567	TDP2	http://www.ncbi.nlm.nih.gov/gene/?term=51567	"AD022, EAP2, EAPII, TTRAP, dJ30M3.3, hTDP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014778	51567	TDP2	http://www.ncbi.nlm.nih.gov/gene/?term=51567	"AD022, EAP2, EAPII, TTRAP, dJ30M3.3, hTDP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014779	51569	UFM1	http://www.ncbi.nlm.nih.gov/gene/?term=51569	"BM-002, C13orf20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014780	51569	UFM1	http://www.ncbi.nlm.nih.gov/gene/?term=51569	"BM-002, C13orf20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014781	51569	UFM1	http://www.ncbi.nlm.nih.gov/gene/?term=51569	"BM-002, C13orf20 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014782	51569	UFM1	http://www.ncbi.nlm.nih.gov/gene/?term=51569	"BM-002, C13orf20 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014783	51569	UFM1	http://www.ncbi.nlm.nih.gov/gene/?term=51569	"BM-002, C13orf20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014784	51571	FAM49B	http://www.ncbi.nlm.nih.gov/gene/?term=51571	"BM-009, L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014785	51573	GDE1	http://www.ncbi.nlm.nih.gov/gene/?term=51573	"363E6.2, MIR16 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014786	51573	GDE1	http://www.ncbi.nlm.nih.gov/gene/?term=51573	"363E6.2, MIR16 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014787	51582	AZIN1	http://www.ncbi.nlm.nih.gov/gene/?term=51582	"AZI, AZIA1, OAZI, OAZIN, ODC1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014788	51585	PCF11	http://www.ncbi.nlm.nih.gov/gene/?term=51585		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014789	51585	PCF11	http://www.ncbi.nlm.nih.gov/gene/?term=51585		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014790	51586	MED15	http://www.ncbi.nlm.nih.gov/gene/?term=51586	"ARC105, CAG7A, CTG7A, PCQAP, TIG-1, TIG1, TNRC7 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014791	51586	MED15	http://www.ncbi.nlm.nih.gov/gene/?term=51586	"ARC105, CAG7A, CTG7A, PCQAP, TIG-1, TIG1, TNRC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014792	5158	PDE6B	http://www.ncbi.nlm.nih.gov/gene/?term=5158	"CSNB3, CSNBAD2, PDEB, RP40, rd1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014793	5158	PDE6B	http://www.ncbi.nlm.nih.gov/gene/?term=5158	"CSNB3, CSNBAD2, PDEB, RP40, rd1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014794	51592	TRIM33	http://www.ncbi.nlm.nih.gov/gene/?term=51592	"ECTO, PTC7, RFG7, TF1G, TIF1G, TIF1GAMMA, TIFGAMMA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014795	51593	SRRT	http://www.ncbi.nlm.nih.gov/gene/?term=51593	"ARS2, ASR2, serrate "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014796	51593	SRRT	http://www.ncbi.nlm.nih.gov/gene/?term=51593	"ARS2, ASR2, serrate "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014797	51594	NBAS	http://www.ncbi.nlm.nih.gov/gene/?term=51594	"ILFS2, NAG, SOPH "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014798	51594	NBAS	http://www.ncbi.nlm.nih.gov/gene/?term=51594	"ILFS2, NAG, SOPH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014799	51596	CUTA	http://www.ncbi.nlm.nih.gov/gene/?term=51596	"ACHAP, C6orf82 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014800	51596	CUTA	http://www.ncbi.nlm.nih.gov/gene/?term=51596	"ACHAP, C6orf82 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014801	515	ATP5F1	http://www.ncbi.nlm.nih.gov/gene/?term=515	PIG47	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014802	515	ATP5F1	http://www.ncbi.nlm.nih.gov/gene/?term=515	PIG47	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014803	51602	NOP58	http://www.ncbi.nlm.nih.gov/gene/?term=51602	"HSPC120, NOP5, NOP5/NOP58 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014804	51603	METTL13	http://www.ncbi.nlm.nih.gov/gene/?term=51603	"5630401D24Rik, CGI-01, KIAA0859, feat "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014805	51604	PIGT	http://www.ncbi.nlm.nih.gov/gene/?term=51604	"CGI-06, MCAHS3, NDAP, PNH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014806	51604	PIGT	http://www.ncbi.nlm.nih.gov/gene/?term=51604	"CGI-06, MCAHS3, NDAP, PNH2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014807	51606	ATP6V1H	http://www.ncbi.nlm.nih.gov/gene/?term=51606	"CGI-11, MSTP042, NBP1, SFD, SFDalpha, SFDbeta, VMA13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014808	51608	GET4	http://www.ncbi.nlm.nih.gov/gene/?term=51608	"C7orf20, CEE, CGI-20, TRC35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014809	5160	PDHA1	http://www.ncbi.nlm.nih.gov/gene/?term=5160	"PDHA, PDHAD, PDHCE1A, PHE1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014810	5160	PDHA1	http://www.ncbi.nlm.nih.gov/gene/?term=5160	"PDHA, PDHAD, PDHCE1A, PHE1A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014811	5160	PDHA1	http://www.ncbi.nlm.nih.gov/gene/?term=5160	"PDHA, PDHAD, PDHCE1A, PHE1A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014812	5160	PDHA1	http://www.ncbi.nlm.nih.gov/gene/?term=5160	"PDHA, PDHAD, PDHCE1A, PHE1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014813	51611	DPH5	http://www.ncbi.nlm.nih.gov/gene/?term=51611	"AD-018, CGI-30, HSPC143, NPD015 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014814	51614	ERGIC3	http://www.ncbi.nlm.nih.gov/gene/?term=51614	"C20orf47, CGI-54, Erv46, NY-BR-84, PRO0989, SDBCAG84, dJ477O4.2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014815	51614	ERGIC3	http://www.ncbi.nlm.nih.gov/gene/?term=51614	"C20orf47, CGI-54, Erv46, NY-BR-84, PRO0989, SDBCAG84, dJ477O4.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014816	51616	TAF9B	http://www.ncbi.nlm.nih.gov/gene/?term=51616	"DN-7, DN7, TAF9L, TAFII31L, TFIID-31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014817	51619	UBE2D4	http://www.ncbi.nlm.nih.gov/gene/?term=51619	HBUCE1	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014818	51621	KLF13	http://www.ncbi.nlm.nih.gov/gene/?term=51621	"BTEB3, FKLF2, NSLP1, RFLAT-1, RFLAT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014819	51621	KLF13	http://www.ncbi.nlm.nih.gov/gene/?term=51621	"BTEB3, FKLF2, NSLP1, RFLAT-1, RFLAT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014820	51622	CCZ1	http://www.ncbi.nlm.nih.gov/gene/?term=51622	"C7orf28AA, CGI-43, H_DJ1163J12.2, CCZ1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014821	51622	CCZ1	http://www.ncbi.nlm.nih.gov/gene/?term=51622	"C7orf28A, CCZ1A, CGI-43, H_DJ1163J12.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014822	51629	SLC25A39	http://www.ncbi.nlm.nih.gov/gene/?term=51629	"CGI-69, CGI69 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014823	5162	PDHB	http://www.ncbi.nlm.nih.gov/gene/?term=5162	"PDHBD, PDHE1-B, PHE1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014824	51631	LUC7L2	http://www.ncbi.nlm.nih.gov/gene/?term=51631	"CGI-59, CGI-74, LUC7B2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014825	51633	OTUD6B	http://www.ncbi.nlm.nih.gov/gene/?term=51633	"CGI-77, DUBA-5, DUBA5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014826	51633	OTUD6B	http://www.ncbi.nlm.nih.gov/gene/?term=51633	"CGI-77, DUBA-5, DUBA5 "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00014827	51635	DHRS7	http://www.ncbi.nlm.nih.gov/gene/?term=51635	"CGI-86, SDR34C1, retDSR4, retSDR4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014828	51635	DHRS7	http://www.ncbi.nlm.nih.gov/gene/?term=51635	"CGI-86, SDR34C1, retDSR4, retSDR4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014829	51637	C14orf166	http://www.ncbi.nlm.nih.gov/gene/?term=51637	"CGI-99, CGI99, CLE, CLE7, LCRP369, RLLM1, hCLE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014830	51637	C14orf166	http://www.ncbi.nlm.nih.gov/gene/?term=51637	"CGI-99, CGI99, CLE, CLE7, LCRP369, RLLM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014831	51639	SF3B6	http://www.ncbi.nlm.nih.gov/gene/?term=51639	"CGI-110, HSPC175, Ht006, P14, SAP14, SAP14a, SF3B14, SF3B14a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014832	51639	SF3B6	http://www.ncbi.nlm.nih.gov/gene/?term=51639	"CGI-110, HSPC175, Ht006, P14, SAP14, SAP14a, SF3B14, SF3B14a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014833	5163	PDK1	http://www.ncbi.nlm.nih.gov/gene/?term=5163		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014834	5163	PDK1	http://www.ncbi.nlm.nih.gov/gene/?term=5163		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014835	5163	PDK1	http://www.ncbi.nlm.nih.gov/gene/?term=5163		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014836	5163	PDK1	http://www.ncbi.nlm.nih.gov/gene/?term=5163		mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00014837	51642	MRPL48	http://www.ncbi.nlm.nih.gov/gene/?term=51642	"CGI-118, HSPC290, L48MT, MRP-L48 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014838	51642	MRPL48	http://www.ncbi.nlm.nih.gov/gene/?term=51642	"CGI-118, HSPC290, L48MT, MRP-L48 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014839	51643	TMBIM4	http://www.ncbi.nlm.nih.gov/gene/?term=51643	"CGI-119, GAAP, LFG4, S1R, ZPRO "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014840	51645	PPIL1	http://www.ncbi.nlm.nih.gov/gene/?term=51645	"CGI-124, CYPL1, PPIase, hCyPX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014841	51646	YPEL5	http://www.ncbi.nlm.nih.gov/gene/?term=51646	CGI-127	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014842	51647	FAM96B	http://www.ncbi.nlm.nih.gov/gene/?term=51647	"CGI-128, MIP18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014843	51649	MRPS23	http://www.ncbi.nlm.nih.gov/gene/?term=51649	"CGI-138, HSPC329, MRP-S23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014844	5164	PDK2	http://www.ncbi.nlm.nih.gov/gene/?term=5164	"PDHK2, PDKII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014845	5164	PDK2	http://www.ncbi.nlm.nih.gov/gene/?term=5164	"PDHK2, PDKII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014846	51650	MRPS33	http://www.ncbi.nlm.nih.gov/gene/?term=51650	"CGI-139, MRP-S33, PTD003, S33mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014847	51650	MRPS33	http://www.ncbi.nlm.nih.gov/gene/?term=51650	"CGI-139, MRP-S33, PTD003, S33mt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014848	51651	PTRH2	http://www.ncbi.nlm.nih.gov/gene/?term=51651	"BIT1, CFAP37, CGI-147, IMNEPD, PTH, PTH 2, PTH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014849	51652	CHMP3	http://www.ncbi.nlm.nih.gov/gene/?term=51652	"CGI-149, NEDF, VPS24 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014850	51652	CHMP3	http://www.ncbi.nlm.nih.gov/gene/?term=51652	"CGI-149, NEDF, VPS24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014851	51659	GINS2	http://www.ncbi.nlm.nih.gov/gene/?term=51659	"HSPC037, PSF2, Pfs2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014852	51660	MPC1	http://www.ncbi.nlm.nih.gov/gene/?term=51660	"BRP44L, CGI-129, MPYCD, dJ68L15.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014853	51660	MPC1	http://www.ncbi.nlm.nih.gov/gene/?term=51660	"BRP44L, CGI-129, MPYCD, dJ68L15.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014854	51663	ZFR	http://www.ncbi.nlm.nih.gov/gene/?term=51663	"SPG711, ZFR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014855	51663	ZFR	http://www.ncbi.nlm.nih.gov/gene/?term=51663	"SPG711, ZFR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014856	51663	ZFR	http://www.ncbi.nlm.nih.gov/gene/?term=51663	"SPG71, ZFR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014857	51665	ASB1	http://www.ncbi.nlm.nih.gov/gene/?term=51665	ASB-1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014858	51665	ASB1	http://www.ncbi.nlm.nih.gov/gene/?term=51665	ASB-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014859	51667	NUB1	http://www.ncbi.nlm.nih.gov/gene/?term=51667	"BS4L, NYREN18, NUB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014860	51667	NUB1	http://www.ncbi.nlm.nih.gov/gene/?term=51667	"BS4, NUB1L, NYREN18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014861	51668	HSPB11	http://www.ncbi.nlm.nih.gov/gene/?term=51668	"C1orf41, HSPCO34, IFT25, PP25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014862	51668	HSPB11	http://www.ncbi.nlm.nih.gov/gene/?term=51668	"C1orf41, HSPCO34, IFT25, PP25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014863	51669	SARAF	http://www.ncbi.nlm.nih.gov/gene/?term=51669	"FOAP-7, HSPC035, TMEM66, XTP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014864	51678	MPP6	http://www.ncbi.nlm.nih.gov/gene/?term=51678	"PALS2, VAM-1, VAM1, p55T "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014865	51678	MPP6	http://www.ncbi.nlm.nih.gov/gene/?term=51678	"PALS2, VAM-1, VAM1, p55T "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014866	5167	ENPP1	http://www.ncbi.nlm.nih.gov/gene/?term=5167	"ARHR2, COLED, M6S1, NPP1, NPPS, PC-1, PCA1, PDNP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014867	5167	ENPP1	http://www.ncbi.nlm.nih.gov/gene/?term=5167	"ARHR2, COLED, M6S1, NPP1, NPPS, PC-1, PCA1, PDNP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014868	51690	LSM7	http://www.ncbi.nlm.nih.gov/gene/?term=51690	YNL147W	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014869	51691	LSM8	http://www.ncbi.nlm.nih.gov/gene/?term=51691	NAA38	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014870	51692	CPSF3	http://www.ncbi.nlm.nih.gov/gene/?term=51692	"CPSF-73, CPSF73 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014871	51693	TRAPPC2L	http://www.ncbi.nlm.nih.gov/gene/?term=51693	HSPC176	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014872	51696	HECA	http://www.ncbi.nlm.nih.gov/gene/?term=51696	"HDC, HDCL, HHDC, dJ225E12.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014873	51696	HECA	http://www.ncbi.nlm.nih.gov/gene/?term=51696	"HDC, HDCL, HHDC, dJ225E12.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014874	51696	HECA	http://www.ncbi.nlm.nih.gov/gene/?term=51696	"HDC, HDCL, HHDC, dJ225E12.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014875	51699	VPS29	http://www.ncbi.nlm.nih.gov/gene/?term=51699	"DC15, DC7, PEP11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014876	5169	ENPP3	http://www.ncbi.nlm.nih.gov/gene/?term=5169	"B10, CD203c, NPP3, PD-IBETA, PDNP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014877	516	ATP5G1	http://www.ncbi.nlm.nih.gov/gene/?term=516	"ATP5A, ATP5G "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014878	516	ATP5G1	http://www.ncbi.nlm.nih.gov/gene/?term=516	"ATP5A, ATP5G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014879	51700	CYB5R2	http://www.ncbi.nlm.nih.gov/gene/?term=51700	B5R.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014880	51701	NLK	http://www.ncbi.nlm.nih.gov/gene/?term=51701		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014881	51701	NLK	http://www.ncbi.nlm.nih.gov/gene/?term=51701		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014882	51703	ACSL5	http://www.ncbi.nlm.nih.gov/gene/?term=51703	"ACS2, ACS5, FACL5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014883	51704	GPRC5B	http://www.ncbi.nlm.nih.gov/gene/?term=51704	"RAIG-2, RAIG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014884	51706	CYB5R1	http://www.ncbi.nlm.nih.gov/gene/?term=51706	"B5R.1, B5R1, B5R2, NQO3A2, humb5R2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014885	5170	PDPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5170	"PDK1, PDPK2, PDPK2P, PRO0461 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014886	5170	PDPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5170	"PDK1, PDPK2, PDPK2P, PRO0461 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014887	5170	PDPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5170	"PDK1, PDPK2, PDPK2P, PRO0461 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014888	51714	SELT	http://www.ncbi.nlm.nih.gov/gene/?term=51714		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014889	51714	SELT	http://www.ncbi.nlm.nih.gov/gene/?term=51714		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014890	51715	RAB23	http://www.ncbi.nlm.nih.gov/gene/?term=51715	HSPC137	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014891	51719	CAB39	http://www.ncbi.nlm.nih.gov/gene/?term=51719	"CGI-66, MO25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014892	51719	CAB39	http://www.ncbi.nlm.nih.gov/gene/?term=51719	"CGI-66, MO25 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014893	51719	CAB39	http://www.ncbi.nlm.nih.gov/gene/?term=51719	"CGI-66, MO25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014894	51720	UIMC1	http://www.ncbi.nlm.nih.gov/gene/?term=51720	"RAP80, X2HRIP110 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014895	51726	DNAJB11	http://www.ncbi.nlm.nih.gov/gene/?term=51726	"ABBP-2, ABBP2, DJ9, Dj-9, EDJ, ERdj3, ERj3, ERj3p, PRO1080, UNQ537 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014896	51728	POLR3K	http://www.ncbi.nlm.nih.gov/gene/?term=51728	"C11, C11-RNP3, My010, RPC10, RPC11, RPC12.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014897	51728	POLR3K	http://www.ncbi.nlm.nih.gov/gene/?term=51728	"C11, C11-RNP3, My010, RPC10, RPC11, RPC12.5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014898	51728	POLR3K	http://www.ncbi.nlm.nih.gov/gene/?term=51728	"C11, C11-RNP3, My010, RPC10, RPC11, RPC12.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014899	51729	WBP11	http://www.ncbi.nlm.nih.gov/gene/?term=51729	"NPWBP, PPP1R165, SIPP1, WBP-11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014900	51729	WBP11	http://www.ncbi.nlm.nih.gov/gene/?term=51729	"NPWBP, PPP1R165, SIPP1, WBP-11 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014901	5172	SLC26A4	http://www.ncbi.nlm.nih.gov/gene/?term=5172	"DFNB4, EVA, PDS, TDH2B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014902	5172	SLC26A4	http://www.ncbi.nlm.nih.gov/gene/?term=5172	"DFNB4, EVA, PDS, TDH2B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014903	51734	MSRB1	http://www.ncbi.nlm.nih.gov/gene/?term=51734	"HSPC270, SELR, SELX, SEPX1, SepR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014904	51741	WWOX	http://www.ncbi.nlm.nih.gov/gene/?term=51741	"D16S432E, EIEE28, FOR, FRA16D, HHCMA56, PRO0128, SCAR12, SDR41C1, WOX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014905	51742	ARID4B	http://www.ncbi.nlm.nih.gov/gene/?term=51742	"BCAA, BRCAA1, RBBP1L1, RBP1L1, SAP180 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014906	51742	ARID4B	http://www.ncbi.nlm.nih.gov/gene/?term=51742	"BCAA, BRCAA1, RBBP1L1, RBP1L1, SAP180 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014907	51747	LUC7L3	http://www.ncbi.nlm.nih.gov/gene/?term=51747	"CRA, CREAP-1, CROP, LUC7A, OA48-18, hLuc7A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014908	5174	PDZK1	http://www.ncbi.nlm.nih.gov/gene/?term=5174	"CAP70, CLAMP, NHERF-3, NHERF3, PDZD1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014909	5174	PDZK1	http://www.ncbi.nlm.nih.gov/gene/?term=5174	"CAP70, CLAMP, NHERF-3, NHERF3, PDZD1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014910	51752	ERAP1	http://www.ncbi.nlm.nih.gov/gene/?term=51752	"A-LAP, ALAP, APPILS, ARTS-1, ARTS1, ERAAP, ERAAP1, PILS-AP, PILSAP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014911	51755	CDK12	http://www.ncbi.nlm.nih.gov/gene/?term=51755	"CRK7, CRKR, CRKRS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014912	51755	CDK12	http://www.ncbi.nlm.nih.gov/gene/?term=51755	"CRK7, CRKR, CRKRS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014913	51759	C9orf78	http://www.ncbi.nlm.nih.gov/gene/?term=51759	"HCA59, HSPC220, bA409K20.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014914	51759	C9orf78	http://www.ncbi.nlm.nih.gov/gene/?term=51759	"HCA59, HSPC220, bA409K20.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014915	5175	PECAM1	http://www.ncbi.nlm.nih.gov/gene/?term=5175	"CD31, CD31/EndoCAM, GPIIA', PECA1, PECAM-1, endoCAM "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014916	51762	RAB8B	http://www.ncbi.nlm.nih.gov/gene/?term=51762		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014917	51762	RAB8B	http://www.ncbi.nlm.nih.gov/gene/?term=51762		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014918	51763	INPP5K	http://www.ncbi.nlm.nih.gov/gene/?term=51763	"PPS, SKIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014919	51765	STK26	http://www.ncbi.nlm.nih.gov/gene/?term=51765	"MASK, MST4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014920	51765	STK26	http://www.ncbi.nlm.nih.gov/gene/?term=51765	"MASK, MST4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014921	51768	TM7SF3	http://www.ncbi.nlm.nih.gov/gene/?term=51768		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014922	51768	TM7SF3	http://www.ncbi.nlm.nih.gov/gene/?term=51768		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014923	51773	RSF1	http://www.ncbi.nlm.nih.gov/gene/?term=51773	"HBXAP, RSF-1, XAP8, p325 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014924	51773	RSF1	http://www.ncbi.nlm.nih.gov/gene/?term=51773	"HBXAP, RSF-1, XAP8, p325 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014925	51776	ZAK	http://www.ncbi.nlm.nih.gov/gene/?term=51776	"AZK, MLK7, MLT, MLTK, MRK, SFMMP, mlklak, pk "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014926	51780	KDM3B	http://www.ncbi.nlm.nih.gov/gene/?term=51780	"5qNCA, C5orf7, JMJD1B, NET22 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014927	51780	KDM3B	http://www.ncbi.nlm.nih.gov/gene/?term=51780	"5qNCA, C5orf7, JMJD1B, NET22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014928	51786	Cpsf2	http://www.ncbi.nlm.nih.gov/gene/?term=51786	"100kDa, 2610024B04Rik, AI662483, Cpsf, MCPSF, mKIAA1367 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014929	51788	H2afz	http://www.ncbi.nlm.nih.gov/gene/?term=51788	"H2A.Z, H2a.z-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014930	51788	H2afz	http://www.ncbi.nlm.nih.gov/gene/?term=51788	"H2A.Z, H2a.z-1 "	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00014931	51793	Ddah2	http://www.ncbi.nlm.nih.gov/gene/?term=51793	"1110003M04Rik, AU019324, AW413173, DDAH-2, DDAHII, Ddah, G6a, NG30 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014932	51797	Ctps	http://www.ncbi.nlm.nih.gov/gene/?term=51797	Ctps1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014933	517	ATP5G2	http://www.ncbi.nlm.nih.gov/gene/?term=517	ATP5A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014934	517	ATP5G2	http://www.ncbi.nlm.nih.gov/gene/?term=517	ATP5A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014935	51804	SIX4	http://www.ncbi.nlm.nih.gov/gene/?term=51804	AREC3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014936	51804	SIX4	http://www.ncbi.nlm.nih.gov/gene/?term=51804	AREC3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014937	51805	COQ3	http://www.ncbi.nlm.nih.gov/gene/?term=51805	"DHHBMT, DHHBMTASE, UG0215E05, bA9819.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014938	51808	PHAX	http://www.ncbi.nlm.nih.gov/gene/?term=51808	RNUXA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014939	51810	Hnrnpu	http://www.ncbi.nlm.nih.gov/gene/?term=51810	"AA408410, AI256620, AL024194, AL024437, AW557595, C86794, Hnrpu, SAFA, Sp120, hnRNP U "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014940	51813	Ccnc	http://www.ncbi.nlm.nih.gov/gene/?term=51813	"AI451004, AU020987, CG1C "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014941	51816	CECR1	http://www.ncbi.nlm.nih.gov/gene/?term=51816	"ADA2, ADGF, IDGFL, PAN, SNEDS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014942	51816	CECR1	http://www.ncbi.nlm.nih.gov/gene/?term=51816	"ADA2, ADGF, IDGFL, PAN, SNEDS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014943	51816	CECR1	http://www.ncbi.nlm.nih.gov/gene/?term=51816	"ADA2, ADGF, IDGFL, PAN, SNEDS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014944	51845	D2Ertd63e	http://www.ncbi.nlm.nih.gov/gene/?term=51845		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014945	5184	PEPD	http://www.ncbi.nlm.nih.gov/gene/?term=5184	PROLIDASE	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014946	51864	D2Ertd173e	http://www.ncbi.nlm.nih.gov/gene/?term=51864		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014947	51869	Rif1	http://www.ncbi.nlm.nih.gov/gene/?term=51869	"5730435J01Rik, 6530403D07Rik, AU016181, AW549474, D2Ertd145e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014948	51875	Tmem141	http://www.ncbi.nlm.nih.gov/gene/?term=51875	"1110065P14Rik, AI663999, D2Ertd217e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014949	51880	D2Ertd239e	http://www.ncbi.nlm.nih.gov/gene/?term=51880		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014950	51885	Tubgcp4	http://www.ncbi.nlm.nih.gov/gene/?term=51885	"4932441P04Rik, 76p, D2Ertd435e, GCP-4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014951	51885	Tubgcp4	http://www.ncbi.nlm.nih.gov/gene/?term=51885	"4932441P04Rik, 76p, D2Ertd435e, GCP-4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00014952	51886	Fubp1	http://www.ncbi.nlm.nih.gov/gene/?term=51886	"9530027K12Rik, D3Ertd330e, FBP, Fubp, Fubp4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014953	5188	GATB	http://www.ncbi.nlm.nih.gov/gene/?term=5188	"HSPC199, PET112, PET112L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014954	5189	PEX1	http://www.ncbi.nlm.nih.gov/gene/?term=5189	"HMLR1, PBD1A, PBD1B, ZWS, ZWS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014955	5189	PEX1	http://www.ncbi.nlm.nih.gov/gene/?term=5189	"HMLR1, PBD1A, PBD1B, ZWS, ZWS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014956	518	ATP5G3	http://www.ncbi.nlm.nih.gov/gene/?term=518	P3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014957	518	ATP5G3	http://www.ncbi.nlm.nih.gov/gene/?term=518	P3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014958	5190	PEX6	http://www.ncbi.nlm.nih.gov/gene/?term=5190	"HMLR2, PAF-2, PAF2, PBD4A, PDB4B, PXAAA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014959	5191	PEX7	http://www.ncbi.nlm.nih.gov/gene/?term=5191	"PBD9B, PTS2R, RCDP1, RD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014960	5192	PEX10	http://www.ncbi.nlm.nih.gov/gene/?term=5192	"NALD, PBD6A, PBD6B, RNF69 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014961	5193	PEX12	http://www.ncbi.nlm.nih.gov/gene/?term=5193	"PAF-3, PBD3A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014962	51944	Knstrn	http://www.ncbi.nlm.nih.gov/gene/?term=51944	"1700025D04Rik, C15orf23, D2Ertd750e, SKAP, Traf4af1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014963	5194	PEX13	http://www.ncbi.nlm.nih.gov/gene/?term=5194	"NALD, PBD11A, PBD11B, ZWS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014964	5194	PEX13	http://www.ncbi.nlm.nih.gov/gene/?term=5194	"NALD, PBD11A, PBD11B, ZWS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014965	5194	PEX13	http://www.ncbi.nlm.nih.gov/gene/?term=5194	"NALD, PBD11A, PBD11B, ZWS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014966	5194	PEX13	http://www.ncbi.nlm.nih.gov/gene/?term=5194	"NALD, PBD11A, PBD11B, ZWS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014967	5195	PEX14	http://www.ncbi.nlm.nih.gov/gene/?term=5195	"NAPP2, PBD13A, Pex14p, dJ734G22.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014968	51960	Kctd18	http://www.ncbi.nlm.nih.gov/gene/?term=51960	"4932411A20Rik, 6530404F10Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014969	5198	PFAS	http://www.ncbi.nlm.nih.gov/gene/?term=5198	"FGAMS, FGAR-AT, FGARAT, PURL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014970	5198	PFAS	http://www.ncbi.nlm.nih.gov/gene/?term=5198	"FGAMS, FGAR-AT, FGARAT, PURL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014971	5198	PFAS	http://www.ncbi.nlm.nih.gov/gene/?term=5198	"FGAMS, FGAR-AT, FGARAT, PURL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014972	51	ACOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51	"ACOX, PALMCOX, SCOX "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014973	51	ACOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51	"ACOX, PALMCOX, SCOX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014974	51	ACOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51	"ACOX, PALMCOX, SCOX "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014975	51	ACOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51	"ACOX, PALMCOX, SCOX "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00014976	51	ACOX1	http://www.ncbi.nlm.nih.gov/gene/?term=51	"ACOX, PALMCOX, SCOX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014977	52004	Cdk2ap2	http://www.ncbi.nlm.nih.gov/gene/?term=52004	"5830466O21Rik, D19Ertd144e, Doc-1r "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014978	52013	R3hcc1l	http://www.ncbi.nlm.nih.gov/gene/?term=52013	"1700036B12Rik, AI450607, C10orf28, D19Ertd386e, GIDRP86, Gidrp88 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014979	5201	PFDN1	http://www.ncbi.nlm.nih.gov/gene/?term=5201	"PDF, PFD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014980	52020	Umodl1	http://www.ncbi.nlm.nih.gov/gene/?term=52020	D17Ertd488e	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014981	5202	PFDN2	http://www.ncbi.nlm.nih.gov/gene/?term=5202	PFD2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014982	52033	Pbk	http://www.ncbi.nlm.nih.gov/gene/?term=52033	"2810434B10Rik, AW538537, D14Ertd732e, TOPK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014983	52036	Ppp6r3	http://www.ncbi.nlm.nih.gov/gene/?term=52036	"4930528G08Rik, 9130026N02Rik, D19Bwg1430e, D19Ertd703e, Pp6r3, Ppcs3, Pptcs3, Sapl, Saps3, mKIAA1558 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014984	5203	PFDN4	http://www.ncbi.nlm.nih.gov/gene/?term=5203	"C1, PFD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014985	5204	PFDN5	http://www.ncbi.nlm.nih.gov/gene/?term=5204	"MM-1, MM1, PFD5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014986	5204	PFDN5	http://www.ncbi.nlm.nih.gov/gene/?term=5204	"MM-1, MM1, PFD5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014987	5204	PFDN5	http://www.ncbi.nlm.nih.gov/gene/?term=5204	"MM-1, MM1, PFD5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014988	5205	ATP8B1	http://www.ncbi.nlm.nih.gov/gene/?term=5205	"ATPIC, BRIC, FIC1, ICP1, PFIC, PFIC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014989	5207	PFKFB1	http://www.ncbi.nlm.nih.gov/gene/?term=5207	"F6PK, HL2K, PFRX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014990	5208	PFKFB2	http://www.ncbi.nlm.nih.gov/gene/?term=5208	PFK-2/FBPase-2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014991	5208	PFKFB2	http://www.ncbi.nlm.nih.gov/gene/?term=5208	PFK-2/FBPase-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014992	5209	PFKFB3	http://www.ncbi.nlm.nih.gov/gene/?term=5209	"IPFK2, PFK2, iPFK-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014993	5209	PFKFB3	http://www.ncbi.nlm.nih.gov/gene/?term=5209	"IPFK2, PFK2, iPFK-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014994	5210	PFKFB4	http://www.ncbi.nlm.nih.gov/gene/?term=5210		mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00014995	5211	PFKL	http://www.ncbi.nlm.nih.gov/gene/?term=5211	"ATP-PFK, PFK-B, PFK-L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00014996	5211	PFKL	http://www.ncbi.nlm.nih.gov/gene/?term=5211	"ATP-PFK, PFK-B, PFK-L "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00014997	5211	PFKL	http://www.ncbi.nlm.nih.gov/gene/?term=5211	"ATP-PFK, PFK-B, PFK-L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00014998	52120	Hgsnat	http://www.ncbi.nlm.nih.gov/gene/?term=52120	"9430010M12Rik, AW208455, D8Ertd354e, Tmem76 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00014999	52123	Agpat5	http://www.ncbi.nlm.nih.gov/gene/?term=52123	"1110013A05Rik, D8Ertd319e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015000	5213	PFKM	http://www.ncbi.nlm.nih.gov/gene/?term=5213	"ATP-PFK, GSD7, PFK-1, PFK1, PFKA, PFKX, PPP1R122 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015001	5213	PFKM	http://www.ncbi.nlm.nih.gov/gene/?term=5213	"ATP-PFK, GSD7, PFK-1, PFK1, PFKA, PFKX, PPP1R122 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015002	5213	PFKM	http://www.ncbi.nlm.nih.gov/gene/?term=5213	"ATP-PFK, GSD7, PFK-1, PFK1, PFKA, PFKX, PPP1R122 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00015003	5213	PFKM	http://www.ncbi.nlm.nih.gov/gene/?term=5213	"ATP-PFK, GSD7, PFK-1, PFK1, PFKA, PFKX, PPP1R122 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015004	5214	PFKP	http://www.ncbi.nlm.nih.gov/gene/?term=5214	"ATP-PFK, PFK-C, PFK-P, PFKF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015005	5214	PFKP	http://www.ncbi.nlm.nih.gov/gene/?term=5214	"ATP-PFK, PFK-C, PFK-P, PFKF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015006	52164	D4Ertd117e	http://www.ncbi.nlm.nih.gov/gene/?term=52164	D4Ertd41e	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015007	5216	PFN1	http://www.ncbi.nlm.nih.gov/gene/?term=5216	ALS18	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015008	5216	PFN1	http://www.ncbi.nlm.nih.gov/gene/?term=5216	ALS18	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015009	5216	PFN1	http://www.ncbi.nlm.nih.gov/gene/?term=5216	ALS18	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015010	5217	PFN2	http://www.ncbi.nlm.nih.gov/gene/?term=5217	"D3S1319E, PFL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015011	52184	Odf2l	http://www.ncbi.nlm.nih.gov/gene/?term=52184	"4733401D09Rik, 9630045K08Rik, D3Ertd250e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015012	5218	CDK14	http://www.ncbi.nlm.nih.gov/gene/?term=5218	"PFTAIRE1, PFTK1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015013	5218	CDK14	http://www.ncbi.nlm.nih.gov/gene/?term=5218	"PFTAIRE1, PFTK1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015014	5218	CDK14	http://www.ncbi.nlm.nih.gov/gene/?term=5218	"PFTAIRE1, PFTK1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015015	521	ATP5I	http://www.ncbi.nlm.nih.gov/gene/?term=521	ATP5K	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015016	521	ATP5I	http://www.ncbi.nlm.nih.gov/gene/?term=521	ATP5K	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015017	52223	D6Ertd160e	http://www.ncbi.nlm.nih.gov/gene/?term=52223		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015018	5223	PGAM1	http://www.ncbi.nlm.nih.gov/gene/?term=5223	"HEL-S-35, PGAM-B, PGAMA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015019	52252	D3Ertd162e	http://www.ncbi.nlm.nih.gov/gene/?term=52252		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015020	5226	PGD	http://www.ncbi.nlm.nih.gov/gene/?term=5226	6PGD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015021	5228	PGF	http://www.ncbi.nlm.nih.gov/gene/?term=5228	"D12S1900, PGFL, PLGF, PlGF-2, SHGC-10760 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015022	522	ATP5J	http://www.ncbi.nlm.nih.gov/gene/?term=522	"ATP5, ATP5A, ATPM, CF6, F6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015023	522	ATP5J	http://www.ncbi.nlm.nih.gov/gene/?term=522	"ATP5, ATP5A, ATPM, CF6, F6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015024	5230	PGK1	http://www.ncbi.nlm.nih.gov/gene/?term=5230	"HEL-S-68p, MIG10, PGKA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015025	5230	PGK1	http://www.ncbi.nlm.nih.gov/gene/?term=5230	"HEL-S-68p, MIG10, PGKA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015026	5230	PGK1	http://www.ncbi.nlm.nih.gov/gene/?term=5230	"HEL-S-68p, MIG10, PGKA "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00015027	5230	PGK1	http://www.ncbi.nlm.nih.gov/gene/?term=5230	"HEL-S-68p, MIG10, PGKA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015028	52331	Stbd1	http://www.ncbi.nlm.nih.gov/gene/?term=52331	"D530019K15Rik, D5Ertd593e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015029	5236	PGM1	http://www.ncbi.nlm.nih.gov/gene/?term=5236	"CDG1T, GSD14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015030	5236	PGM1	http://www.ncbi.nlm.nih.gov/gene/?term=5236	"CDG1T, GSD14 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00015031	5236	PGM1	http://www.ncbi.nlm.nih.gov/gene/?term=5236	"CDG1T, GSD14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015032	5238	PGM3	http://www.ncbi.nlm.nih.gov/gene/?term=5238	"AGM1, IMD23, PAGM, PGM 3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015033	5238	PGM3	http://www.ncbi.nlm.nih.gov/gene/?term=5238	"AGM1, IMD23, PAGM, PGM 3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015034	52398	Sept11	http://www.ncbi.nlm.nih.gov/gene/?term=52398	"6230410I01Rik, AW548875, D5Ertd606e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015035	523	ATP6V1A	http://www.ncbi.nlm.nih.gov/gene/?term=523	"ATP6A11, HO68, VA68, VPP2, Vma1, ATP6V1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015036	523	ATP6V1A	http://www.ncbi.nlm.nih.gov/gene/?term=523	"ATP6A1, ATP6V1A1, HO68, VA68, VPP2, Vma1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015037	5243	ABCB1	http://www.ncbi.nlm.nih.gov/gene/?term=5243	"ABC20, CD243, CLCS, GP170, MDR1, P-GP, PGY1 "	mRNA	Homo sapiens	20453113	Endoplasmic reticulum	NCI/ADR-RES cell	qRT-PCR	"The relative partitioning of both cytosolic (ACTB, H3.3) and ER-bound (MDR1, CANX) transcripts between both fractions was marked, despite the small carryover of cytosol in the ER fraction (Fig. 2B). Polysome profile analyses from the isolated fractions indicated that these transcripts migrated in polyribosome-containing fractions (Fig. 2C). Notably, the distribution of ER-bound transcripts between the ER and cytosol did not change on arsenite treatment of NCI/ADR-RES cells (Fig. 2D). Data are collected from Figure 2. "
RLID00015038	5243	ABCB1	http://www.ncbi.nlm.nih.gov/gene/?term=5243	"ABC20, CD243, CLCS, GP170, MDR1, P-GP, PGY1 "	mRNA	Homo sapiens	20453113	Ribosome	NCI/ADR-RES cell	qRT-PCR	"The relative partitioning of both cytosolic (ACTB, H3.3) and ER-bound (MDR1, CANX) transcripts between both fractions was marked, despite the small carryover of cytosol in the ER fraction (Fig. 2B). Polysome profile analyses from the isolated fractions indicated that these transcripts migrated in polyribosome-containing fractions (Fig. 2C). Notably, the distribution of ER-bound transcripts between the ER and cytosol did not change on arsenite treatment of NCI/ADR-RES cells (Fig. 2D). Data are collected from Figure 2. "
RLID00015039	52440	Tax1bp1	http://www.ncbi.nlm.nih.gov/gene/?term=52440	"1200003J11Rik, 1700069J21Rik, AA930106, D6Ertd404e, D6Ertd772e, T6bp, TXBP151 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015040	52455	D11Ertd49e	http://www.ncbi.nlm.nih.gov/gene/?term=52455		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015041	5245	PHB	http://www.ncbi.nlm.nih.gov/gene/?term=5245	"HEL-215, HEL-S-54e1, PHB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015042	5245	PHB	http://www.ncbi.nlm.nih.gov/gene/?term=5245	"HEL-215, HEL-S-54e, PHB1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015043	52463	Tet1	http://www.ncbi.nlm.nih.gov/gene/?term=52463	"2510010B09Rik, AA517754, BB001228, Cxxc6, D10Ertd17e, LCX, mKIAA1676 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015044	52480	Snhg14	http://www.ncbi.nlm.nih.gov/gene/?term=52480	"AU018661, D7Ertd715e, Lncat "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015045	52480	Snhg14	http://www.ncbi.nlm.nih.gov/gene/?term=52480	"AU018661, D7Ertd715e, Lncat "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015046	52495	D12Ertd208e	http://www.ncbi.nlm.nih.gov/gene/?term=52495		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015047	52502	Carhsp1	http://www.ncbi.nlm.nih.gov/gene/?term=52502	"1200011K09Rik, Crhsp-24, D16Ertd465e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015048	5250	SLC25A3	http://www.ncbi.nlm.nih.gov/gene/?term=5250	"OK/SW-cl.48, PHC, PTP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015049	5250	SLC25A3	http://www.ncbi.nlm.nih.gov/gene/?term=5250	"OK/SW-cl.48, PHC, PTP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015050	5252	PHF1	http://www.ncbi.nlm.nih.gov/gene/?term=5252	"MTF2L2, PCL1, PHF2, TDRD19C, hPHF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015051	52538	Acaa2	http://www.ncbi.nlm.nih.gov/gene/?term=52538	"0610011L04Rik, AI255831, AI265397, D18Ertd240e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015052	52538	Acaa2	http://www.ncbi.nlm.nih.gov/gene/?term=52538	"0610011L04Rik, AI255831, AI265397, D18Ertd240e "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00015053	52552	Parp8	http://www.ncbi.nlm.nih.gov/gene/?term=52552	"2810430O08Rik, ARTD16, D13Ertd275e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015054	52563	Cdc23	http://www.ncbi.nlm.nih.gov/gene/?term=52563	"6030435O18, D18Ertd243e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015055	52565	D12Ertd125e	http://www.ncbi.nlm.nih.gov/gene/?term=52565		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015056	5256	PHKA2	http://www.ncbi.nlm.nih.gov/gene/?term=5256	"GSD9A, PHK, PYK, PYKL, XLG, XLG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015057	52575	Trmt10c	http://www.ncbi.nlm.nih.gov/gene/?term=52575	"1300018J16Rik, D16Ertd454e, Rg9mtd1, Rnmtd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015058	5257	PHKB	http://www.ncbi.nlm.nih.gov/gene/?term=5257		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015059	52585	Dhrs1	http://www.ncbi.nlm.nih.gov/gene/?term=52585	"1110029G07Rik, AW112170, D14Ertd484e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015060	525	ATP6V1B1	http://www.ncbi.nlm.nih.gov/gene/?term=525	"ATP6B1, RTA1B, VATB, VMA2, VPP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015061	5260	PHKG1	http://www.ncbi.nlm.nih.gov/gene/?term=5260	PHKG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015062	52615	Suz12	http://www.ncbi.nlm.nih.gov/gene/?term=52615	"2610028O16Rik, AI195385, AU016842, AW536442, D11Ertd530e, mKIAA0160 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015063	5261	PHKG2	http://www.ncbi.nlm.nih.gov/gene/?term=5261	GSD9C	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015064	5261	PHKG2	http://www.ncbi.nlm.nih.gov/gene/?term=5261	GSD9C	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015065	52635	Esyt2	http://www.ncbi.nlm.nih.gov/gene/?term=52635	"2410017M09Rik, 4921504I16Rik, CHR2SYT, D12Ertd551e, Fam62b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015066	52639	Wipi1	http://www.ncbi.nlm.nih.gov/gene/?term=52639	"4930533H01Rik, AW411817, D11Ertd498e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015067	5264	PHYH	http://www.ncbi.nlm.nih.gov/gene/?term=5264	"LN1, LNAP1, PAHX1, RD, PHYH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015068	5264	PHYH	http://www.ncbi.nlm.nih.gov/gene/?term=5264	"LN1, LNAP1, PAHX, PHYH1, RD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015069	52653	Nudcd2	http://www.ncbi.nlm.nih.gov/gene/?term=52653		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015070	5265	SERPINA1	http://www.ncbi.nlm.nih.gov/gene/?term=5265	"A1A, A1AT, AAT, PI, PI1, PRO2275, alpha1AT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015071	52665	Echdc1	http://www.ncbi.nlm.nih.gov/gene/?term=52665	"1700028A24Rik, AI314462, AI930038, D10Ertd667e, MMCD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015072	526937	DCXR	http://www.ncbi.nlm.nih.gov/gene/?term=526937		mRNA	Bos taurus	25815750	Cytoplasm	Epithelial cell	qRT-PCR|In situ hybridization	"In situ hybridization was used to localize the DCXR gene expression pattern at the histological level. In agreement with the PCR results, antisense DCXR cRNA hybridization increases from the caput to the cauda epididymidis, with expression being in the majority, located to the epithelial cells. Some faint staining can be found in some blood vessels endothelial cells (S1 Fig.). The mRNA is uniformly located in the cytoplasm of caput epithelial cells (Fig. 3A). "
RLID00015073	5269	SERPINB6	http://www.ncbi.nlm.nih.gov/gene/?term=5269	"CAP, DFNB91, MSTP057, PI-6, PI6, PTI, SPI3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015074	5269	SERPINB6	http://www.ncbi.nlm.nih.gov/gene/?term=5269	"CAP, DFNB91, MSTP057, PI-6, PI6, PTI, SPI3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015075	5269	SERPINB6	http://www.ncbi.nlm.nih.gov/gene/?term=5269	"CAP, DFNB91, MSTP057, PI-6, PI6, PTI, SPI3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015076	526	ATP6V1B2	http://www.ncbi.nlm.nih.gov/gene/?term=526	"ATP6B1B2, ATP6B2, HO57, VATB, VPP3, Vma2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015077	526	ATP6V1B2	http://www.ncbi.nlm.nih.gov/gene/?term=526	"ATP6B1B2, ATP6B2, HO57, VATB, VPP3, Vma2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015078	52704	D11Ertd717e	http://www.ncbi.nlm.nih.gov/gene/?term=52704		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015079	52705	Krr1	http://www.ncbi.nlm.nih.gov/gene/?term=52705	"2610511F02Rik, AI255219, AI428520, D10Ertd773e, Hrb2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015080	5270	SERPINE2	http://www.ncbi.nlm.nih.gov/gene/?term=5270	"GDN, GDNPF, PI-7, PI7, PN-1, PN1, PNI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015081	5270	SERPINE2	http://www.ncbi.nlm.nih.gov/gene/?term=5270	"GDN, GDNPF, PI-7, PI7, PN-1, PN1, PNI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015082	5270	SERPINE2	http://www.ncbi.nlm.nih.gov/gene/?term=5270	"GDN, GDNPF, PI-7, PI7, PN-1, PN1, PNI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015083	5272	SERPINB9	http://www.ncbi.nlm.nih.gov/gene/?term=5272	"CAP-3, CAP3, PI-9, PI9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015084	5272	SERPINB9	http://www.ncbi.nlm.nih.gov/gene/?term=5272	"CAP-3, CAP3, PI-9, PI9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015085	5272	SERPINB9	http://www.ncbi.nlm.nih.gov/gene/?term=5272	"CAP-3, CAP3, PI-9, PI9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015086	5274	SERPINI1	http://www.ncbi.nlm.nih.gov/gene/?term=5274	"PI12, neuroserpin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015087	5277	PIGA	http://www.ncbi.nlm.nih.gov/gene/?term=5277	"GPI3, MCAHS2, PIG-A, PNH1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015088	5277	PIGA	http://www.ncbi.nlm.nih.gov/gene/?term=5277	"GPI3, MCAHS2, PIG-A, PNH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015089	5279	PIGC	http://www.ncbi.nlm.nih.gov/gene/?term=5279	GPI2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015090	5279	PIGC	http://www.ncbi.nlm.nih.gov/gene/?term=5279	GPI2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015091	5279	PIGC	http://www.ncbi.nlm.nih.gov/gene/?term=5279	GPI2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015092	527	ATP6V0C	http://www.ncbi.nlm.nih.gov/gene/?term=527	"ATP6C, ATP6L, ATPL, VATL, VPPC, Vma3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015093	52808	Tspyl2	http://www.ncbi.nlm.nih.gov/gene/?term=52808	"CDA1, CINAP, DENTT, DXBwg1396e, DXHXS1008E, E130307F10Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015094	5281	PIGF	http://www.ncbi.nlm.nih.gov/gene/?term=5281		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015095	5281	PIGF	http://www.ncbi.nlm.nih.gov/gene/?term=5281		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015096	52822	Rufy3	http://www.ncbi.nlm.nih.gov/gene/?term=52822	"2810428M05Rik, 6330416M07Rik, AW455998, AW538594, D5Bwg0860e, Ripx, Rpipx "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015097	52837	Tmx4	http://www.ncbi.nlm.nih.gov/gene/?term=52837	"2810417D04Rik, 4930500L08Rik, AI843224, AW046784, D2Bwg1356e, Txndc13, mKIAA1162 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015098	52838	Dnlz	http://www.ncbi.nlm.nih.gov/gene/?term=52838	"1110034G11Rik, D2Bwg1335e, HEP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015099	5283	PIGH	http://www.ncbi.nlm.nih.gov/gene/?term=5283	GPI-H	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015100	52840	Dbndd2	http://www.ncbi.nlm.nih.gov/gene/?term=52840	"1110017A21Rik, 2900022J10Rik, AU041050, AW048677, D2Bwg0891e, Nkip, R74724 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015101	5284	PIGR	http://www.ncbi.nlm.nih.gov/gene/?term=5284		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015102	5284	PIGR	http://www.ncbi.nlm.nih.gov/gene/?term=5284		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015103	5284	PIGR	http://www.ncbi.nlm.nih.gov/gene/?term=5284		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015104	52856	Mtg2	http://www.ncbi.nlm.nih.gov/gene/?term=52856	"1810011P19Rik, 2900056P18Rik, D2Bwg0647e, Gtpbp5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015105	52856	Mtg2	http://www.ncbi.nlm.nih.gov/gene/?term=52856	"1810011P19Rik, 2900056P18Rik, D2Bwg0647e, Gtpbp5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015106	5286	PIK3C2A	http://www.ncbi.nlm.nih.gov/gene/?term=5286	"CPK, PI3-K-C2(ALPHA), PI3-K-C2A, PI3K-C2-alpha, PI3K-C2alpha "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015107	5286	PIK3C2A	http://www.ncbi.nlm.nih.gov/gene/?term=5286	"CPK, PI3-K-C2(ALPHA), PI3-K-C2A, PI3K-C2-alpha, PI3K-C2alpha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015108	5286	PIK3C2A	http://www.ncbi.nlm.nih.gov/gene/?term=5286	"CPK, PI3-K-C2(ALPHA), PI3-K-C2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015109	5287	PIK3C2B	http://www.ncbi.nlm.nih.gov/gene/?term=5287	C2-PI3K	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015110	5287	PIK3C2B	http://www.ncbi.nlm.nih.gov/gene/?term=5287	C2-PI3K	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015111	5287	PIK3C2B	http://www.ncbi.nlm.nih.gov/gene/?term=5287	C2-PI3K	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015112	5289	PIK3C3	http://www.ncbi.nlm.nih.gov/gene/?term=5289	"VPS34, Vps34, hVps34 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015113	528	ATP6V1C1	http://www.ncbi.nlm.nih.gov/gene/?term=528	"ATP6C, ATP6D, VATC, Vma5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015114	528	ATP6V1C1	http://www.ncbi.nlm.nih.gov/gene/?term=528	"ATP6C, ATP6D, VATC, Vma5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015115	52902	D10Bwg1070e	http://www.ncbi.nlm.nih.gov/gene/?term=52902	5730421K10Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015116	52906	Ahi1	http://www.ncbi.nlm.nih.gov/gene/?term=52906	"1700015F03Rik, Ahi-1, D10Bwg0629e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015117	5290	PIK3CA	http://www.ncbi.nlm.nih.gov/gene/?term=5290	"CLOVE, CWS5, MCAP, MCM, MCMTC, PI3K, p110-alpha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015118	5290	PIK3CA	http://www.ncbi.nlm.nih.gov/gene/?term=5290	"CLOVE, CWS5, MCAP, MCM, MCMTC, PI3K, p110-alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015119	5291	PIK3CB	http://www.ncbi.nlm.nih.gov/gene/?term=5291	"P110BETA, PI3K, PI3KBETA, PIK3C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015120	5292	PIM1	http://www.ncbi.nlm.nih.gov/gene/?term=5292	PIM	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015121	5292	PIM1	http://www.ncbi.nlm.nih.gov/gene/?term=5292	PIM	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015122	5292	PIM1	http://www.ncbi.nlm.nih.gov/gene/?term=5292	PIM	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015123	5292	PIM1	http://www.ncbi.nlm.nih.gov/gene/?term=5292	PIM	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015124	5292	PIM1	http://www.ncbi.nlm.nih.gov/gene/?term=5292	PIM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015125	5293	PIK3CD	http://www.ncbi.nlm.nih.gov/gene/?term=5293	"APDS, IMD14, P110DELTA, PI3K, p110D "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015126	5293	PIK3CD	http://www.ncbi.nlm.nih.gov/gene/?term=5293	"APDS, IMD14, P110DELTA, PI3K, p110D "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015127	5293	PIK3CD	http://www.ncbi.nlm.nih.gov/gene/?term=5293	"APDS, IMD14, P110DELTA, PI3K, p110D "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015128	5294	PIK3CG	http://www.ncbi.nlm.nih.gov/gene/?term=5294	"PI3CG, PI3K, PI3Kgamma, PIK3, p110gamma, p120-PI3K "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015129	5295	PIK3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5295	"AGM7, GRB1, IMD36, p85, p85-ALPHA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015130	5295	PIK3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5295	"AGM7, GRB1, IMD36, p85, p85-ALPHA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015131	5295	PIK3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5295	"AGM7, GRB1, IMD36, p85, p85-ALPHA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015132	5296	PIK3R2	http://www.ncbi.nlm.nih.gov/gene/?term=5296	"MPPH, MPPH1, P85B, p85, p85-BETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015133	5297	PI4KA	http://www.ncbi.nlm.nih.gov/gene/?term=5297	"PI4K-ALPHA, PIK4CA, PMGYCHA, pi4K230 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015134	5298	PI4KB	http://www.ncbi.nlm.nih.gov/gene/?term=5298	"NPIK, PI4K-BETA, PI4K92ETA, PI4KIIIBETA, PIK4CB, PI4KB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015135	5298	PI4KB	http://www.ncbi.nlm.nih.gov/gene/?term=5298	"NPIK, PI4K-BETA, PI4K92, PI4KBETA, PI4KIIIBETA, PIK4CB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015136	529	ATP6V1E1	http://www.ncbi.nlm.nih.gov/gene/?term=529	"ATP6E, ATP6E2, ATP6V1E, P31, Vma4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015137	52	ACP1	http://www.ncbi.nlm.nih.gov/gene/?term=52	"HAAP, LMW-PTP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015138	5300	PIN1	http://www.ncbi.nlm.nih.gov/gene/?term=5300	"DOD, UBL5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015139	5301	PIN1P1	http://www.ncbi.nlm.nih.gov/gene/?term=5301	PIN1L	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015140	5303	PIN4	http://www.ncbi.nlm.nih.gov/gene/?term=5303	"EPVH, PAR14, PAR17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015141	5303	PIN4	http://www.ncbi.nlm.nih.gov/gene/?term=5303	"EPVH, PAR14, PAR17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015142	5305	PIP4K2A	http://www.ncbi.nlm.nih.gov/gene/?term=5305	"PI5P4KA, PIP5K2A, PIP5KII-alpha, PIP5KIIA, PIPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015143	5306	PITPNA	http://www.ncbi.nlm.nih.gov/gene/?term=5306	"HEL-S-36, PI-TPalpha, PITPN, VIB1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015144	5306	PITPNA	http://www.ncbi.nlm.nih.gov/gene/?term=5306	"HEL-S-36, PI-TPalpha, PITPN, VIB1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015145	5306	PITPNA	http://www.ncbi.nlm.nih.gov/gene/?term=5306	"HEL-S-36, PI-TPalpha, PITPN, VIB1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015146	5307	PITX1	http://www.ncbi.nlm.nih.gov/gene/?term=5307	"BFT, CCF, LBNBG, POTX, PTX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015147	5310	PKD1	http://www.ncbi.nlm.nih.gov/gene/?term=5310	"PBP, Pc-1, TRPP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015148	5311	PKD2	http://www.ncbi.nlm.nih.gov/gene/?term=5311	"APKD2, PC2, PKD4, Pc-2, TRPP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015149	5313	PKLR	http://www.ncbi.nlm.nih.gov/gene/?term=5313	"PK1, PKL, PKR, PKRL, RPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015150	5315	PKM	http://www.ncbi.nlm.nih.gov/gene/?term=5315	"CTHBP, HEL-S-30, OIP3, PK32, TCB, THBP1, PKM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015151	5316	PKNOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5316	"PREP1, pkonx1c "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015152	5316	PKNOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5316	"PREP1, pkonx1c "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015153	5316	PKNOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5316	"PREP1, pkonx1c "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015154	5316	PKNOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5316	"PREP1, pkonx1c "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015155	5316	PKNOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5316	"PREP1, pkonx1c "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015156	5318	PKP2	http://www.ncbi.nlm.nih.gov/gene/?term=5318	ARVD9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015157	5320	PLA2G2A	http://www.ncbi.nlm.nih.gov/gene/?term=5320	"MOM1, PLA2, PLA2B, PLA2L, PLA2S, PLAS1, sPLA2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015158	5325	PLAGL1	http://www.ncbi.nlm.nih.gov/gene/?term=5325	"LOT1, ZAC, ZAC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015159	5326	PLAGL2	http://www.ncbi.nlm.nih.gov/gene/?term=5326	ZNF900	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015160	5326	PLAGL2	http://www.ncbi.nlm.nih.gov/gene/?term=5326	ZNF900	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015161	5327	PLAT	http://www.ncbi.nlm.nih.gov/gene/?term=5327	"T-PA, TPA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015162	5328	PLAU	http://www.ncbi.nlm.nih.gov/gene/?term=5328	"ATF, BDPLT5, QPD, UPA, URK, u-PA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015163	5329	PLAUR	http://www.ncbi.nlm.nih.gov/gene/?term=5329	"CD87, U-PAR, UPAR, URKR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015164	5330	PLCB2	http://www.ncbi.nlm.nih.gov/gene/?term=5330	PLC-beta-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015165	53312	Nub1	http://www.ncbi.nlm.nih.gov/gene/?term=53312	"4931404D21Rik, 6330412F12Rik, BS4, NY-REN-18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015166	53319	Nxf1	http://www.ncbi.nlm.nih.gov/gene/?term=53319	"Mex67, Mvb1, Tap "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015167	5331	PLCB3	http://www.ncbi.nlm.nih.gov/gene/?term=5331		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015168	53320	Folh1	http://www.ncbi.nlm.nih.gov/gene/?term=53320	"GCP2, mopsm "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015169	53322	Nucb2	http://www.ncbi.nlm.nih.gov/gene/?term=53322	"AI607786, Calnuc, Nefa, Nesfatin-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015170	53328	Pgrmc1	http://www.ncbi.nlm.nih.gov/gene/?term=53328	"AA415812, HPR6.6, PPMR, Vema "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015171	53334	Gosr1	http://www.ncbi.nlm.nih.gov/gene/?term=53334	"AI414660, AI426320, BB145494, GOS-28, GOSRI, GS28 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015172	53339	BTBD1	http://www.ncbi.nlm.nih.gov/gene/?term=53339	"C15orf1, NS5ATP8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015173	53339	BTBD1	http://www.ncbi.nlm.nih.gov/gene/?term=53339	"C15orf1, NS5ATP8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015174	53339	BTBD1	http://www.ncbi.nlm.nih.gov/gene/?term=53339	"C15orf1, NS5ATP8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015175	5333	PLCD1	http://www.ncbi.nlm.nih.gov/gene/?term=5333	"NDNC3, PLC-III "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015176	53340	SPA17	http://www.ncbi.nlm.nih.gov/gene/?term=53340	"CT22, SP17, SP17-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015177	53349	ZFYVE1	http://www.ncbi.nlm.nih.gov/gene/?term=53349	"DFCP1, PPP1R172, SR3, TAFF1, ZNFN2A1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015178	5334	PLCL1	http://www.ncbi.nlm.nih.gov/gene/?term=5334	"PLCE, PLCL, PLDL1, PPP1R127, PRIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015179	53354	PANK1	http://www.ncbi.nlm.nih.gov/gene/?term=53354	PANK	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015180	53357	Pla2g6	http://www.ncbi.nlm.nih.gov/gene/?term=53357	"BB112799, PNPLA9, iPLA(2)beta, iPLA2, iPLA2beta "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015181	5335	PLCG1	http://www.ncbi.nlm.nih.gov/gene/?term=5335	"NCKAP3, PLC-II, PLC1, PLC148, PLCgamma1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015182	5336	PLCG2	http://www.ncbi.nlm.nih.gov/gene/?term=5336	"APLAID, FCAS3, PLC-IV, PLC-gamma-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015183	53371	NUP54	http://www.ncbi.nlm.nih.gov/gene/?term=53371		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015184	53375	Mtx2	http://www.ncbi.nlm.nih.gov/gene/?term=53375	1500012G02Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015185	53378	Sdcbp	http://www.ncbi.nlm.nih.gov/gene/?term=53378	"MDA-9, Sycl, syntenin-1 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015186	53378	Sdcbp	http://www.ncbi.nlm.nih.gov/gene/?term=53378	"MDA-9, Sycl, syntenin-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015187	53379	Hnrnpa2b1	http://www.ncbi.nlm.nih.gov/gene/?term=53379	"9130414A06Rik, Hnrpa2, Hnrpa2b1, hnrnp-A "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015188	5338	PLD2	http://www.ncbi.nlm.nih.gov/gene/?term=5338		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015189	5339	PLEC	http://www.ncbi.nlm.nih.gov/gene/?term=5339	"EBS1, EBSMD, EBSND, EBSO, EBSOG, EBSPA, HD1, LGMD2Q, PCN1, PLEC1b, PLTN, PLEC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015190	5339	PLEC	http://www.ncbi.nlm.nih.gov/gene/?term=5339	"EBS1, EBSMD, EBSND, EBSO, EBSOG, EBSPA, HD1, LGMD2Q, PCN, PLEC1, PLEC1b, PLTN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015191	533	ATP6V0B	http://www.ncbi.nlm.nih.gov/gene/?term=533	"ATP6F, HATPL, VMA16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015192	533	ATP6V0B	http://www.ncbi.nlm.nih.gov/gene/?term=533	"ATP6F, HATPL, VMA16 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015193	53407	STX18	http://www.ncbi.nlm.nih.gov/gene/?term=53407	Ufe1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015194	53414	Bysl	http://www.ncbi.nlm.nih.gov/gene/?term=53414	"Bys, Enp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015195	53418	B4galt2	http://www.ncbi.nlm.nih.gov/gene/?term=53418	Ggtb2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015196	53421	Sec61a1	http://www.ncbi.nlm.nih.gov/gene/?term=53421	"AA408394, AA410007, Sec61a "	mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. As depicted in Figure 4, Sec61a and calnexin were highly enriched in the membrane-bound fraction, as may be predicted for those mRNAs encoding signal sequences. "
RLID00015197	53421	Sec61a1	http://www.ncbi.nlm.nih.gov/gene/?term=53421	"Sec61a, AA408394, AA410007 "	mRNA	Mus musculus	12923260	Ribosome	J558 cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 μg of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00015198	5342	PLGLB2	http://www.ncbi.nlm.nih.gov/gene/?term=5342	PLGP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015199	5345	SERPINF2	http://www.ncbi.nlm.nih.gov/gene/?term=5345	"A2AP, AAP, ALPHA-2-PI, API, PLI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015200	5346	PLIN1	http://www.ncbi.nlm.nih.gov/gene/?term=5346	"FPLD4, PERI, PLIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015201	5347	PLK1	http://www.ncbi.nlm.nih.gov/gene/?term=5347	"PLK, STPK13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015202	5347	PLK1	http://www.ncbi.nlm.nih.gov/gene/?term=5347	"PLK, STPK13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015203	5348	FXYD1	http://www.ncbi.nlm.nih.gov/gene/?term=5348	PLM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015204	5349	FXYD3	http://www.ncbi.nlm.nih.gov/gene/?term=5349	"MAT8, PLML "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015205	5349	FXYD3	http://www.ncbi.nlm.nih.gov/gene/?term=5349	"MAT8, PLML "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015206	5350	PLN	http://www.ncbi.nlm.nih.gov/gene/?term=5350	"CMD1P, CMH18, PLB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015207	53510	Ugt86Da	http://www.ncbi.nlm.nih.gov/gene/?term=53510	"Dmel_CG18578, AC 006491A, BEST:GM04645, CG18578, Dmel\CG18578, GM04645, ugt86Da "	mRNA	Drosophila melanogaster	25838129	Perinuclear	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00015208	53510	Ugt86Da	http://www.ncbi.nlm.nih.gov/gene/?term=53510	"Dmel_CG18578, AC 006491A, BEST:GM04645, CG18578, Dmel\CG18578, GM04645, ugt86Da "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00015209	5351	PLOD1	http://www.ncbi.nlm.nih.gov/gene/?term=5351	"EDS6, LH, LH1, LLH, PLOD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015210	5351	PLOD1	http://www.ncbi.nlm.nih.gov/gene/?term=5351	"EDS6, LH, LH1, LLH, PLOD "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00015211	5351	PLOD1	http://www.ncbi.nlm.nih.gov/gene/?term=5351	"EDS6, LH, LH1, LLH, PLOD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015212	5352	PLOD2	http://www.ncbi.nlm.nih.gov/gene/?term=5352	"BRKS2, LH2, TLH "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00015213	5352	PLOD2	http://www.ncbi.nlm.nih.gov/gene/?term=5352	"BRKS2, LH2, TLH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015214	5354	PLP1	http://www.ncbi.nlm.nih.gov/gene/?term=5354	"GPM6C, HLD1, MMPL, PLP, PLP/DM20, PMD, SPG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015215	5355	PLP2	http://www.ncbi.nlm.nih.gov/gene/?term=5355	"A4, A4LSB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015216	5355	PLP2	http://www.ncbi.nlm.nih.gov/gene/?term=5355	"A4, A4LSB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015217	53563	gukh	http://www.ncbi.nlm.nih.gov/gene/?term=53563	"Dmel_CG31043, CG14287, CG14288, CG31043, CG5456, CG6003, Dmel\CG31043, GUKH, GUKh, GukH, Gukh, anon-WO0118547.205 "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00015218	53563	gukh	http://www.ncbi.nlm.nih.gov/gene/?term=53563	"Dmel_CG31043, CG14287, CG14288, CG31043, CG5456, CG6003, Dmel\CG31043, GUKH, GUKh, GukH, Gukh, anon-WO0118547.205 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00015219	5356	PLRG1	http://www.ncbi.nlm.nih.gov/gene/?term=5356	"Cwc1, PRL1, PRP46, PRPF46, TANGO4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015220	5357	PLS1	http://www.ncbi.nlm.nih.gov/gene/?term=5357		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015221	5357	PLS1	http://www.ncbi.nlm.nih.gov/gene/?term=5357		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015222	5357	PLS1	http://www.ncbi.nlm.nih.gov/gene/?term=5357		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015223	53581	Gclc	http://www.ncbi.nlm.nih.gov/gene/?term=53581	"Dmel_CG2259, 2259, CG2259, DmGCLC, DmGCS, DmGCSh, Dmel\CG2259, GCL, GCLC, GCLc, GCSh, Gcs, Gcsh, gclc "	mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00015224	5358	PLS3	http://www.ncbi.nlm.nih.gov/gene/?term=5358	"BMND18, T-plastin "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015225	53599	Cd164	http://www.ncbi.nlm.nih.gov/gene/?term=53599	"A115, A24, AA589639, AW540279, MGC-24, MSSP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015226	5359	PLSCR1	http://www.ncbi.nlm.nih.gov/gene/?term=5359	MMTRA1B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015227	5359	PLSCR1	http://www.ncbi.nlm.nih.gov/gene/?term=5359	MMTRA1B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015228	535	ATP6V0A1	http://www.ncbi.nlm.nih.gov/gene/?term=535	"ATP6N1, ATP6N1A, Stv1, VPP1, Vph1, a1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015229	53600	Timm23	http://www.ncbi.nlm.nih.gov/gene/?term=53600	Tim23	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015230	53604	Zpbp	http://www.ncbi.nlm.nih.gov/gene/?term=53604	"4930486K01Rik, Iam38, Sp38 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015231	53607	Snrpa	http://www.ncbi.nlm.nih.gov/gene/?term=53607	"C430021M15Rik, Rnu1a-1, Rnu1a1, U1-A, U1A "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015232	53609	Clasrp	http://www.ncbi.nlm.nih.gov/gene/?term=53609	"Clasp, Sfrs16, Srsf16, Swap2 "	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00015233	5360	PLTP	http://www.ncbi.nlm.nih.gov/gene/?term=5360	"BPIFE, HDLCQ9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015234	53610	Nono	http://www.ncbi.nlm.nih.gov/gene/?term=53610	"AA407051, AV149256, NRB54, P54NRB, nonA "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015235	53612	Vti1b	http://www.ncbi.nlm.nih.gov/gene/?term=53612	"AU015348, GES30, MVti1b, SNARE, Vti1-rp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015236	53614	Reck	http://www.ncbi.nlm.nih.gov/gene/?term=53614	"St15, mRECK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015237	53615	MBD3	http://www.ncbi.nlm.nih.gov/gene/?term=53615		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015238	53618	Fut8	http://www.ncbi.nlm.nih.gov/gene/?term=53618		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015239	53618	Fut8	http://www.ncbi.nlm.nih.gov/gene/?term=53618		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015240	5361	PLXNA1	http://www.ncbi.nlm.nih.gov/gene/?term=5361	"NOV, NOVP, PLEXIN-A1, PLXN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015241	53620	Vamp5	http://www.ncbi.nlm.nih.gov/gene/?term=53620	"AF119384, Camp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015242	53620	Vamp5	http://www.ncbi.nlm.nih.gov/gene/?term=53620	"AF119384, Camp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015243	53621	Cnot4	http://www.ncbi.nlm.nih.gov/gene/?term=53621	"Not4, Not4h, Not4hp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015244	53625	B3gnt2	http://www.ncbi.nlm.nih.gov/gene/?term=53625	"AA408337, AA409404, AW260308, B3Galt6, B3gnt1, BGnT-1, BGnT-2, BGnT1, BGnT2, Beta3gnt "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015245	5362	PLXNA2	http://www.ncbi.nlm.nih.gov/gene/?term=5362	"OCT, PLXN2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015246	53635	PTOV1	http://www.ncbi.nlm.nih.gov/gene/?term=53635	"ACID2, PTOV-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015247	53635	PTOV1	http://www.ncbi.nlm.nih.gov/gene/?term=53635	"ACID2, PTOV-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015248	53635	PTOV1	http://www.ncbi.nlm.nih.gov/gene/?term=53635	"ACID2, PTOV-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015249	5364	PLXNB1	http://www.ncbi.nlm.nih.gov/gene/?term=5364	"PLEXIN-B1, PLXN5, SEP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015250	5364	PLXNB1	http://www.ncbi.nlm.nih.gov/gene/?term=5364	"PLEXIN-B1, PLXN5, SEP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015251	5365	PLXNB3	http://www.ncbi.nlm.nih.gov/gene/?term=5365	"PLEXB3, PLEXR, PLXN6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015252	5366	PMAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=5366	"APR, NOXA "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015253	5366	PMAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=5366	"APR, NOXA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015254	5366	PMAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=5366	"APR, NOXA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015255	5366	PMAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=5366	"APR, NOXA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015256	5371	PML	http://www.ncbi.nlm.nih.gov/gene/?term=5371	"MYL, PP8675, RNF71, TRIM19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015257	5372	PMM1	http://www.ncbi.nlm.nih.gov/gene/?term=5372	Sec53	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015258	5372	PMM1	http://www.ncbi.nlm.nih.gov/gene/?term=5372	Sec53	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015259	5373	PMM2	http://www.ncbi.nlm.nih.gov/gene/?term=5373	"CDG1, CDG1a, CDGS, PMI, PMI1, PMM 2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015260	5373	PMM2	http://www.ncbi.nlm.nih.gov/gene/?term=5373	"CDG1, CDG1a, CDGS, PMI, PMI1, PMM 2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015261	5373	PMM2	http://www.ncbi.nlm.nih.gov/gene/?term=5373	"CDG1, CDG1a, CDGS, PMI, PMI1, PMM 2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015262	5376	PMP22	http://www.ncbi.nlm.nih.gov/gene/?term=5376	"CMT1A, CMT1E, DSS, GAS-3, GAS3, HMSNIA, HNPP, Sp110 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00015263	5376	PMP22	http://www.ncbi.nlm.nih.gov/gene/?term=5376	"CMT1A, CMT1E, DSS, GAS-3, GAS3, HMSNIA, HNPP, Sp110 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015264	5376	PMP22	http://www.ncbi.nlm.nih.gov/gene/?term=5376	"DSS, GAS3, HNPP, CMT1A, CMT1E, GAS-3, Sp110, HMSNIA "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00015265	5379	PMS2P1	http://www.ncbi.nlm.nih.gov/gene/?term=5379	"PMS2L1, PMS2L13, PMS2L6, PMS2L7, PMS2L8, PMS3, PMS8, PMSR1, PMSR2 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015266	537	ATP6AP1	http://www.ncbi.nlm.nih.gov/gene/?term=537	"16A, ATP6IP1, ATP6S1, Ac45, CF2, VATPS1, XAP-3, XAP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015267	537	ATP6AP1	http://www.ncbi.nlm.nih.gov/gene/?term=537	"16A, ATP6IP1, ATP6S1, Ac45, CF2, VATPS1, XAP-3, XAP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015268	53820	RIPPLY3	http://www.ncbi.nlm.nih.gov/gene/?term=53820	DSCR6	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015269	53820	RIPPLY3	http://www.ncbi.nlm.nih.gov/gene/?term=53820	DSCR6	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015270	53827	FXYD5	http://www.ncbi.nlm.nih.gov/gene/?term=53827	"DYSAD, HSPC113, IWU1, KCT1, OIT2, PRO6241, RIC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015271	5382	PMS2P4	http://www.ncbi.nlm.nih.gov/gene/?term=5382	"PMS2L4, PMS6 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015272	53834	FGFRL1	http://www.ncbi.nlm.nih.gov/gene/?term=53834	"FGFR5, FHFR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015273	53834	FGFRL1	http://www.ncbi.nlm.nih.gov/gene/?term=53834	"FGFR5, FHFR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015274	53838	C11orf24	http://www.ncbi.nlm.nih.gov/gene/?term=53838	DM4E3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015275	53840	TRIM34	http://www.ncbi.nlm.nih.gov/gene/?term=53840	"IFP1, RNF21 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015276	53840	TRIM34	http://www.ncbi.nlm.nih.gov/gene/?term=53840	"IFP1, RNF21 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015277	53857	Tuba8	http://www.ncbi.nlm.nih.gov/gene/?term=53857		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015278	53861	Zranb2	http://www.ncbi.nlm.nih.gov/gene/?term=53861	"AI227013, Zfp265, Zis, Znf265 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015279	53872	Caprin1	http://www.ncbi.nlm.nih.gov/gene/?term=53872	"AL022980, Caprin-1, Gpiap, Gpiap1, Mmgpip137, P137, rng105 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015280	53872	Caprin1	http://www.ncbi.nlm.nih.gov/gene/?term=53872	"AL022980, Caprin-1, Gpiap, Gpiap1, Mmgpip137, P137, rng105 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015281	538	ATP7A	http://www.ncbi.nlm.nih.gov/gene/?term=538	"DSMAX, MK, MNK, SMAX3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015282	538	ATP7A	http://www.ncbi.nlm.nih.gov/gene/?term=538	"DSMAX, MK, MNK, SMAX3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015283	538	ATP7A	http://www.ncbi.nlm.nih.gov/gene/?term=538	"DSMAX, MK, MNK, SMAX3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015284	538	ATP7A	http://www.ncbi.nlm.nih.gov/gene/?term=538	"DSMAX, MK, MNK, SMAX3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015285	53902	Rcan3	http://www.ncbi.nlm.nih.gov/gene/?term=53902	"AU041093, Csp3, Dscr1l2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015286	53916	RAB4B	http://www.ncbi.nlm.nih.gov/gene/?term=53916		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015287	53917	RAB24	http://www.ncbi.nlm.nih.gov/gene/?term=53917		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015288	53918	PELO	http://www.ncbi.nlm.nih.gov/gene/?term=53918	"CGI-17, PRO1770 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015289	53918	PELO	http://www.ncbi.nlm.nih.gov/gene/?term=53918	"CGI-17, PRO1770 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015290	53918	PELO	http://www.ncbi.nlm.nih.gov/gene/?term=53918	"CGI-17, PRO1770 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015291	53938	PPIL3	http://www.ncbi.nlm.nih.gov/gene/?term=53938	CYPJ	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015292	53938	PPIL3	http://www.ncbi.nlm.nih.gov/gene/?term=53938	CYPJ	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015293	5393	EXOSC9	http://www.ncbi.nlm.nih.gov/gene/?term=5393	"PM/Scl-75, PMSCL1, RRP45, Rrp45p, p5, p6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015294	53942	CNTN5	http://www.ncbi.nlm.nih.gov/gene/?term=53942	"HNB-2s, NB-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015295	5394	EXOSC10	http://www.ncbi.nlm.nih.gov/gene/?term=5394	"PM-Scl, PM/Scl-100, PMSCL, PMSCL2, RRP6, Rrp6p, p2, p3, p4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015296	5394	EXOSC10	http://www.ncbi.nlm.nih.gov/gene/?term=5394	"PM-Scl, PM/Scl-100, PMSCL, PMSCL2, RRP6, Rrp6p, p2, p3, p4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015297	5394	EXOSC10	http://www.ncbi.nlm.nih.gov/gene/?term=5394	"PM-Scl, PM/Scl-100, PMSCL, PMSCL2, RRP6, Rrp6p, p2, p3, p4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015298	53951	Gpatch11	http://www.ncbi.nlm.nih.gov/gene/?term=53951	"2310002B06Rik, C80922, Ccdc75, L26697 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015299	5395	PMS2	http://www.ncbi.nlm.nih.gov/gene/?term=5395	"HNPCC4, MLH4CL, PMSL2, PMS2 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00015300	5395	PMS2	http://www.ncbi.nlm.nih.gov/gene/?term=5395	"MLH4, PMSL2, HNPCC4, PMS2CL "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00015301	53960	AA066038	http://www.ncbi.nlm.nih.gov/gene/?term=53960		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015302	53975	Ddx20	http://www.ncbi.nlm.nih.gov/gene/?term=53975	"GEMIN3, dp103 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015303	53981	CPSF2	http://www.ncbi.nlm.nih.gov/gene/?term=53981	CPSF100	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015304	53981	CPSF2	http://www.ncbi.nlm.nih.gov/gene/?term=53981	CPSF100	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015305	53981	CPSF2	http://www.ncbi.nlm.nih.gov/gene/?term=53981	CPSF100	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015306	53981	CPSF2	http://www.ncbi.nlm.nih.gov/gene/?term=53981	CPSF100	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015307	53981	CPSF2	http://www.ncbi.nlm.nih.gov/gene/?term=53981	CPSF100	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015308	539	ATP5O	http://www.ncbi.nlm.nih.gov/gene/?term=539	"ATPO, HMC08D05, OSCP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015309	539	ATP5O	http://www.ncbi.nlm.nih.gov/gene/?term=539	"ATPO, HMC08D05, OSCP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015310	53	ACP2	http://www.ncbi.nlm.nih.gov/gene/?term=53	LAP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015311	53	ACP2	http://www.ncbi.nlm.nih.gov/gene/?term=53	LAP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015312	54004	Diaph2	http://www.ncbi.nlm.nih.gov/gene/?term=54004	"Dia3, Diap2, Drf2, E430022I22Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015313	54014	BRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=54014	"C21orf107, DCAF19, N143, WDR9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015314	54014	BRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=54014	"C21orf107, DCAF19, N143, WDR9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015315	54014	BRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=54014	"C21orf107, DCAF19, N143, WDR9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015316	54065	SMIM11A	http://www.ncbi.nlm.nih.gov/gene/?term=54065	"C21orf51, FAM165B, SMIM11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015317	54065	SMIM11A	http://www.ncbi.nlm.nih.gov/gene/?term=54065	"C21orf51, FAM165B, SMIM11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015318	54067	C21orf62-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=54067	C21orf49	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00015319	54069	MIS18A	http://www.ncbi.nlm.nih.gov/gene/?term=54069	"B28, C21orf45, C21orf46, FASP1, MIS18alpha, hMis18alpha "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015320	54069	MIS18A	http://www.ncbi.nlm.nih.gov/gene/?term=54069	"B28, C21orf45, C21orf46, FASP1, MIS18alpha, hMis18alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015321	54093	SETD4	http://www.ncbi.nlm.nih.gov/gene/?term=54093	"C21orf18, C21orf27 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015322	54097	FAM3B	http://www.ncbi.nlm.nih.gov/gene/?term=54097	"2-21, C21orf11, C21orf76, ORF9, PANDER, PRED44 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015323	5409	PNMT	http://www.ncbi.nlm.nih.gov/gene/?term=5409	"PENT, PNMTase "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015324	540	ATP7B	http://www.ncbi.nlm.nih.gov/gene/?term=540	"PWD, WC1, WD, WND "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015325	54107	POLE3	http://www.ncbi.nlm.nih.gov/gene/?term=54107	"CHARAC17, CHRAC17, YBL1, p17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015326	54107	POLE3	http://www.ncbi.nlm.nih.gov/gene/?term=54107	"CHARAC17, CHRAC17, YBL1, p17 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015327	54107	POLE3	http://www.ncbi.nlm.nih.gov/gene/?term=54107	"CHARAC17, CHRAC17, YBL1, p17 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015328	54107	POLE3	http://www.ncbi.nlm.nih.gov/gene/?term=54107	"CHARAC17, CHRAC17, YBL1, p17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015329	54108	CHRAC1	http://www.ncbi.nlm.nih.gov/gene/?term=54108	"CHARC1, CHARC15, CHRAC-1, CHRAC-155, YCL1, CHRAC1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015330	5411	PNN	http://www.ncbi.nlm.nih.gov/gene/?term=5411	"DRS, DRSP, SDK3, memA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015331	5411	PNN	http://www.ncbi.nlm.nih.gov/gene/?term=5411	"DRS, DRSP, SDK3, memA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015332	5411	PNN	http://www.ncbi.nlm.nih.gov/gene/?term=5411	"DRS, DRSP, SDK3, memA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015333	54127	Rps28	http://www.ncbi.nlm.nih.gov/gene/?term=54127		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015334	5412	UBL3	http://www.ncbi.nlm.nih.gov/gene/?term=5412	"HCG-1, PNSC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015335	54130	Actr1a	http://www.ncbi.nlm.nih.gov/gene/?term=54130	"Arp1, alpha-Arp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015336	54131	Irf3	http://www.ncbi.nlm.nih.gov/gene/?term=54131	"C920001K05Rik, IRF-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015337	54137	Acrbp	http://www.ncbi.nlm.nih.gov/gene/?term=54137	"OY-TES-1, sp32 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015338	54141	Spag5	http://www.ncbi.nlm.nih.gov/gene/?term=54141	"AI874642, D11Bhm180e, Deepest, MAP126, Mastrin, S17 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015339	541463	Tex24	http://www.ncbi.nlm.nih.gov/gene/?term=541463	"1700108N07Rik, TESF-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015340	541471	MIR4435-2HG	http://www.ncbi.nlm.nih.gov/gene/?term=541471	"AGD2, AK001796, LINC00978, MIR4435-1HG "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015341	541471	MIR4435-2HG	http://www.ncbi.nlm.nih.gov/gene/?term=541471	"AGD2, AK001796, LINC00978, MIR4435-1HG "	lncRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00015342	541471	MIR4435-2HG	http://www.ncbi.nlm.nih.gov/gene/?term=541471	"AGD2, AK001796, LINC00978, MIR4435-1HG "	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00015343	541471	MIR4435-2HG	http://www.ncbi.nlm.nih.gov/gene/?term=541471	"AGD2, AK001796, LINC00978, MIR4435-1HG "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00015344	54148	MRPL39	http://www.ncbi.nlm.nih.gov/gene/?term=54148	"C21orf92, L39mt, MRP-L5, MRPL5, MSTP003, PRED22, PRED66, RPML5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015345	54150	Rdh7	http://www.ncbi.nlm.nih.gov/gene/?term=54150	"AI194929, CRAD2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015346	54152	Dnal4	http://www.ncbi.nlm.nih.gov/gene/?term=54152	"D15Ertd424e, Dnalc4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015347	541578	CXorf40B	http://www.ncbi.nlm.nih.gov/gene/?term=541578		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015348	541578	CXorf40B	http://www.ncbi.nlm.nih.gov/gene/?term=541578		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015349	54161	Copg1	http://www.ncbi.nlm.nih.gov/gene/?term=54161	"AU019265, BC056168, Copg, D6Ertd71e, D6Wsu16e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015350	541640	leg1	http://www.ncbi.nlm.nih.gov/gene/?term=541640	"ZEAMMB73_079584, GRMZM2G174883, cb "	mRNA	Zea mays	15653801	Endoplasmic reticulum	Endosperm	RT-PCR	"Indeed, in situ RT-PCR and confocal microscopy analysis showed that legumin-1 RNAs are distributed in a pattern markedly distinct from that observed for the zein RNAs. Instead of the punctate pattern indicative of the localization of zein RNAs to the zein PBs, legumin-1 RNAs were distributed as large fluorescent patches. The size and shape of these fluorescent patches and their close proximity to the zein PBs is consistent with the location of legumin-1 RNAs on lamellar membranes of the cis-ER (Fig. 4). "
RLID00015351	54165	DCUN1D1	http://www.ncbi.nlm.nih.gov/gene/?term=54165	"DCNL1, DCUN1L1, RP42, SCCRO, SCRO, Tes3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015352	54165	DCUN1D1	http://www.ncbi.nlm.nih.gov/gene/?term=54165	"DCNL1, DCUN1L1, RP42, SCCRO, SCRO, Tes3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015353	54187	NANS	http://www.ncbi.nlm.nih.gov/gene/?term=54187	"HEL-S-100, SAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015354	54187	NANS	http://www.ncbi.nlm.nih.gov/gene/?term=54187	"HEL-S-100, SAS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015355	54188	Cpsf4	http://www.ncbi.nlm.nih.gov/gene/?term=54188	"30kDa, C79664 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015356	54189	Rabep1	http://www.ncbi.nlm.nih.gov/gene/?term=54189	"Rab5ep, rabaptin-5, rabaptin-5alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015357	541922	dzs10	http://www.ncbi.nlm.nih.gov/gene/?term=541922		mRNA	Zea mays	15653801	Endoplasmic reticulum	Endosperm	RT-PCR	"RNAs coding for 22 kDa alpha-zein, 15 kDa beta-zein, 27 kDa gamma-zein and 10 kDa delta-zein were localized to ER-bounded zein protein bodies, whereas 51 kDa legumin-1 RNAs were distributed on adjacent cisternal ER proximal to the zein protein bodies. "
RLID00015358	541926	az22z5	http://www.ncbi.nlm.nih.gov/gene/?term=541926	"ZEAMMB73_710866, GRMZM2G088365 "	mRNA	Zea mays	15653801	Endoplasmic reticulum	Endosperm	RT-PCR	"RNAs coding for 22 kDa alpha-zein, 15 kDa beta-zein, 27 kDa gamma-zein and 10 kDa delta-zein were localized to ER-bounded zein protein bodies, whereas 51 kDa legumin-1 RNAs were distributed on adjacent cisternal ER proximal to the zein protein bodies "
RLID00015359	54195	Gucy1b3	http://www.ncbi.nlm.nih.gov/gene/?term=54195	"GC-S-beta-1, GCbeta1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015360	54196	Pabpn1	http://www.ncbi.nlm.nih.gov/gene/?term=54196	"PAB2, Pabp3, mPABII "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015361	54205	CYCS	http://www.ncbi.nlm.nih.gov/gene/?term=54205	"CYC, HCS, THC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015362	54205	CYCS	http://www.ncbi.nlm.nih.gov/gene/?term=54205	"CYC, HCS, THC4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015363	54205	CYCS	http://www.ncbi.nlm.nih.gov/gene/?term=54205	"CYC, HCS, THC4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015364	54205	CYCS	http://www.ncbi.nlm.nih.gov/gene/?term=54205	"CYC, HCS, THC4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015365	54206	ERRFI1	http://www.ncbi.nlm.nih.gov/gene/?term=54206	"GENE-33, MIG-6, MIG6, RALT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015366	54206	ERRFI1	http://www.ncbi.nlm.nih.gov/gene/?term=54206	"GENE-33, MIG-6, MIG6, RALT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015367	54208	Arl6ip1	http://www.ncbi.nlm.nih.gov/gene/?term=54208	"AIP-6, AL022945, ARMER, AU042858, Aip-1, Arl6ip, C85138, mKIAA0069 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015368	5420	PODXL	http://www.ncbi.nlm.nih.gov/gene/?term=5420	"Gp200, PC, PCLP, PCLP-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015369	54217	Rpl36	http://www.ncbi.nlm.nih.gov/gene/?term=54217		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015370	54217	Rpl36	http://www.ncbi.nlm.nih.gov/gene/?term=54217		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00015371	542296	LOC542296	http://www.ncbi.nlm.nih.gov/gene/?term=542296	"ZEAMMB73_835432, GRMZM2G138727 "	mRNA	Zea mays	15653801	Endoplasmic reticulum	Endosperm	RT-PCR	"RNAs coding for 22 kDa alpha-zein, 15 kDa beta-zein, 27 kDa gamma-zein and 10 kDa delta-zein were localized to ER-bounded zein protein bodies, whereas 51 kDa legumin-1 RNAs were distributed on adjacent cisternal ER proximal to the zein protein bodies. "
RLID00015372	5423	POLB	http://www.ncbi.nlm.nih.gov/gene/?term=5423		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015373	5423	POLB	http://www.ncbi.nlm.nih.gov/gene/?term=5423		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015374	5423	POLB	http://www.ncbi.nlm.nih.gov/gene/?term=5423		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015375	5424	POLD1	http://www.ncbi.nlm.nih.gov/gene/?term=5424	"CDC2, CRCS10, MDPL, POLD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015376	5424	POLD1	http://www.ncbi.nlm.nih.gov/gene/?term=5424	"CDC2, CRCS10, MDPL, POLD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015377	5425	POLD2	http://www.ncbi.nlm.nih.gov/gene/?term=5425		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015378	5425	POLD2	http://www.ncbi.nlm.nih.gov/gene/?term=5425		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015379	5426	POLE	http://www.ncbi.nlm.nih.gov/gene/?term=5426	"CRCS12, FILS1, POLE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015380	5426	POLE	http://www.ncbi.nlm.nih.gov/gene/?term=5426	"CRCS12, FILS, POLE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015381	542732	crt2	http://www.ncbi.nlm.nih.gov/gene/?term=542732	"ZEAMMB73_853300, CRH, GRMZM2G358059 "	mRNA	Zea mays	17882422	Endoplasmic reticulum	Callus	In situ hybridization	"Calreticulin mRNAs were selectively targeted to the endoplasmic reticulum (ER) subdomains surrounding protein bodies. These data suggest that calreticulin mRNA is targeted towards protein body forming subdomains of the ER, and that calreticulin is localized and enriched in these protein bodies. High levels of calreticulin mRNAs were observed in these callus cells (Fig. 2a). D "
RLID00015382	542760	zp15	http://www.ncbi.nlm.nih.gov/gene/?term=542760	"ZEAMMB73_427631, bz15, zein-2 "	mRNA	Zea mays	15653801	Endoplasmic reticulum	Endosperm	RT-PCR	"RNAs coding for 22 kDa alpha-zein, 15 kDa beta-zein, 27 kDa gamma-zein and 10 kDa delta-zein were localized to ER-bounded zein protein bodies, whereas 51 kDa legumin-1 RNAs were distributed on adjacent cisternal ER proximal to the zein protein bodies. "
RLID00015383	5428	POLG	http://www.ncbi.nlm.nih.gov/gene/?term=5428	"MDP1, MIRAS, MTDPS4A, MTDPS4B, PEO1, POLGA, SANDO, SCAE, POLG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015384	5429	POLH	http://www.ncbi.nlm.nih.gov/gene/?term=5429	"RAD30, RAD30A, XP-V, XPV "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015385	5429	POLH	http://www.ncbi.nlm.nih.gov/gene/?term=5429	"RAD30, RAD30A, XP-V, XPV "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015386	5430	POLR2A	http://www.ncbi.nlm.nih.gov/gene/?term=5430	"POLR2, POLRA, RPB1, RPBh1, RPO2, RPOL2, RpIILS, hRPB220, hsRPB1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015387	5430	POLR2A	http://www.ncbi.nlm.nih.gov/gene/?term=5430	"POLR2, POLRA, RPB1, RPBh1, RPO2, RPOL2, RpIILS, hRPB220, hsRPB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015388	54315	Ucp2	http://www.ncbi.nlm.nih.gov/gene/?term=54315		mRNA	Rattus norvegicus	15485813	Nucleus	Hepatoma cell	qRT-PCR	The three-hybrid screen and the co-IP results show that the K protein interaction with ucp2 mRNA is specific. These results (Fig. 2) also show that K protein-ucp2 mRNA complexes are found in multiple subcellular compartments. Data are collected from Figure 2.
RLID00015389	54315	Ucp2	http://www.ncbi.nlm.nih.gov/gene/?term=54315		mRNA	Rattus norvegicus	15485813	Cytoplasm	Hepatoma cell	qRT-PCR	The three-hybrid screen and the co-IP results show that the K protein interaction with ucp2 mRNA is specific. These results (Fig. 2) also show that K protein-ucp2 mRNA complexes are found in multiple subcellular compartments. Data are collected from Figure 2.
RLID00015390	54315	Ucp2	http://www.ncbi.nlm.nih.gov/gene/?term=54315		mRNA	Rattus norvegicus	15485813	Mitochondrion	Hepatoma cell	qRT-PCR	The three-hybrid screen and the co-IP results show that the K protein interaction with ucp2 mRNA is specific. These results (Fig. 2) also show that K protein-ucp2 mRNA complexes are found in multiple subcellular compartments. Data are collected from Figure 2.
RLID00015391	5431	POLR2B	http://www.ncbi.nlm.nih.gov/gene/?term=5431	"POL2RB, RPB2, hRPB140 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015392	5431	POLR2B	http://www.ncbi.nlm.nih.gov/gene/?term=5431	"POL2RB, RPB2, hRPB140 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015393	54323	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=54323	rg3.1	mRNA	Rattus norvegicus	7857651	Dendrite	Hippocampus	In situ hybridization	"In situ studies provided evidence of an unusual cellular localization of Arc mRNA. Figure 5. Arc mRNA Is Expressed in the Molecular Layer of the Hippocampus, Suggesting Dendritic Localization. "
RLID00015394	54323	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=54323	rg3.1	mRNA	Rattus norvegicus	17765733	Dendrite	Hippocampus	-	Arc mRNA is strongly induced and transported to dendritic processes following high-frequency stimulation (HFS) that induces LTP in the rat dentate gyrus in vivo.
RLID00015395	54323	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=54323	rg3.1	mRNA	Rattus norvegicus	22350812	Dendrite	Cortical neuron	GFP-labeling|Live imaging	"In the course of our studies of Arc mRNA transport in dendrites, we noticed that apparently stationary Arc/MS2 mRNA particles were often precisely localized beneath the base of dendritic spines. In these images, many stationary Arc/MS2 mRNA particles were localized at or near the base of dendritic spines and many spines had underlying Arc/MS2 particles (Fig. 1D,G-K).   "
RLID00015396	54323	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=54323	rg3.1	mRNA	Rattus norvegicus	24671994	Synapse	-	Fluorescence in situ hybridization	Here we show in vivo in rats that newly synthesized Arc mRNA accumulates at activated synapses and that synaptic activity simultaneously triggers mRNA decay that eliminates Arc mRNA from inactive dendritic domains.
RLID00015397	54323	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=54323	rg3.1	mRNA	Rattus norvegicus	25628532	Dendrite	Brain	In situ hybridizationqRT-PCR	"Subsequent studies revealed that Arc/MS2 mRNA localized with remarkable precision at the base of dendritic spines (Figures 1G,H). "
RLID00015398	54323	Arc	http://www.ncbi.nlm.nih.gov/gene/?term=54323	rg3.1	mRNA	Rattus norvegicus	7773006	Dendrite	Neuron	In situ hybridization	"Table 1. As of 1994, mRNAs that have been localized within dendrites by in situ hybridization.  Data are collected from Table 1. "
RLID00015399	54326	Elovl2	http://www.ncbi.nlm.nih.gov/gene/?term=54326	"AI317360, Ssc2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015400	5432	POLR2C	http://www.ncbi.nlm.nih.gov/gene/?term=5432	"RPB3, RPB31, hRPB33, hsRPB3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015401	5432	POLR2C	http://www.ncbi.nlm.nih.gov/gene/?term=5432	"RPB3, RPB31, hRPB33, hsRPB3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015402	5432	POLR2C	http://www.ncbi.nlm.nih.gov/gene/?term=5432	"RPB3, RPB31, hRPB33, hsRPB3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015403	54331	GNG2	http://www.ncbi.nlm.nih.gov/gene/?term=54331		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015404	5433	POLR2D	http://www.ncbi.nlm.nih.gov/gene/?term=5433	"HSRBP4, HSRPB4, RBP4, RPB16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015405	54343	Atf7ip	http://www.ncbi.nlm.nih.gov/gene/?term=54343	"2610204M12Rik, AM, Mcaf1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015406	54344	DPM3	http://www.ncbi.nlm.nih.gov/gene/?term=54344	CDG1O	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015407	5434	POLR2E	http://www.ncbi.nlm.nih.gov/gene/?term=5434	"RPABC1, RPB5, XAP4, hRPB25, hsRPB5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015408	5434	POLR2E	http://www.ncbi.nlm.nih.gov/gene/?term=5434	"RPABC1, RPB5, XAP4, hRPB25, hsRPB5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015409	54352	Irx5	http://www.ncbi.nlm.nih.gov/gene/?term=54352		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015410	5435	POLR2F	http://www.ncbi.nlm.nih.gov/gene/?term=5435	"HRBP14.4, POLRF, RPABC14.4, RPABC2, RPB14.4, RPB6, RPC15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015411	5435	POLR2F	http://www.ncbi.nlm.nih.gov/gene/?term=5435	"HRBP14.4, POLRF, RPABC14.4, RPABC2, RPB14.4, RPB6, RPC15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015412	54363	HAO1	http://www.ncbi.nlm.nih.gov/gene/?term=54363	"GOX, GOX1, HAOX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015413	54364	Rpp30	http://www.ncbi.nlm.nih.gov/gene/?term=54364	"Rnasep2, TSG15 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015414	54367	Zfp326	http://www.ncbi.nlm.nih.gov/gene/?term=54367	"5730470H14Rik, ZAN75, Znf326 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015415	54369	Nme6	http://www.ncbi.nlm.nih.gov/gene/?term=54369	nm23-M6	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015416	5436	POLR2G	http://www.ncbi.nlm.nih.gov/gene/?term=5436	"RPB19, RPB7, hRPB19, hsRPB7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015417	5436	POLR2G	http://www.ncbi.nlm.nih.gov/gene/?term=5436	"RPB19, RPB7, hRPB19, hsRPB7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015418	54375	Azin1	http://www.ncbi.nlm.nih.gov/gene/?term=54375	"1700085L02Rik, AZI, Oazi, Oazin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015419	5437	POLR2H	http://www.ncbi.nlm.nih.gov/gene/?term=5437	"RPABC3, RPB17, RPB8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015420	54383	Phc2	http://www.ncbi.nlm.nih.gov/gene/?term=54383	"A3galt2, AA415044, D130050K19Rik, D4Ertd810e, Edr2, Mph2, p36 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015421	54386	TERF2IP	http://www.ncbi.nlm.nih.gov/gene/?term=54386	"DRIP5, RAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015422	54386	TERF2IP	http://www.ncbi.nlm.nih.gov/gene/?term=54386	"DRIP5, RAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015423	54386	TERF2IP	http://www.ncbi.nlm.nih.gov/gene/?term=54386	"DRIP5, RAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015424	5438	POLR2I	http://www.ncbi.nlm.nih.gov/gene/?term=5438	"RPB9, hRPB14.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015425	5438	POLR2I	http://www.ncbi.nlm.nih.gov/gene/?term=5438	"RPB9, hRPB14.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015426	5439	POLR2J	http://www.ncbi.nlm.nih.gov/gene/?term=5439	"POLR2J1, RPB11, RPB11A, RPB11m, hRPB14 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015427	5439	POLR2J	http://www.ncbi.nlm.nih.gov/gene/?term=5439	"POLR2J1, RPB11, RPB11A, RPB11m, hRPB14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015428	54401	Ywhab	http://www.ncbi.nlm.nih.gov/gene/?term=54401	1300003C17Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015429	54407	SLC38A2	http://www.ncbi.nlm.nih.gov/gene/?term=54407	"ATA2, PRO1068, SAT2, SNAT2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015430	54407	SLC38A2	http://www.ncbi.nlm.nih.gov/gene/?term=54407	"ATA2, PRO1068, SAT2, SNAT2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015431	54407	SLC38A2	http://www.ncbi.nlm.nih.gov/gene/?term=54407	"ATA2, PRO1068, SAT2, SNAT2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015432	54407	SLC38A2	http://www.ncbi.nlm.nih.gov/gene/?term=54407	"ATA2, PRO1068, SAT2, SNAT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015433	5440	POLR2K	http://www.ncbi.nlm.nih.gov/gene/?term=5440	"ABC10-alpha, RPABC4, RPB10alpha, RPB12, RPB7.0, hRPB7.0, hsRPB10a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015434	5440	POLR2K	http://www.ncbi.nlm.nih.gov/gene/?term=5440	"ABC10-alpha, RPABC4, RPB10alpha, RPB12, RPB7.0, hRPB7.0, hsRPB10a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015435	54414	SIAE	http://www.ncbi.nlm.nih.gov/gene/?term=54414	"AIS6, CSE-C, CSEC, LSE, YSG2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015436	5441	POLR2L	http://www.ncbi.nlm.nih.gov/gene/?term=5441	"RBP10, RPABC5, RPB10, RPB10beta, RPB7.6, hRPB7.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015437	5441	POLR2L	http://www.ncbi.nlm.nih.gov/gene/?term=5441	"RBP10, RPABC5, RPB10, RPB10beta, RPB7.6, hRPB7.6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015438	5442	POLRMT	http://www.ncbi.nlm.nih.gov/gene/?term=5442	"APOLMT, MTRNAP, MTRPOL, h-mtRPOL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015439	5442	POLRMT	http://www.ncbi.nlm.nih.gov/gene/?term=5442	"APOLMT, MTRNAP, MTRPOL, h-mtRPOL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015440	54431	DNAJC10	http://www.ncbi.nlm.nih.gov/gene/?term=54431	"ERdj5, JPDI, MTHr, PDIA19 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015441	54431	DNAJC10	http://www.ncbi.nlm.nih.gov/gene/?term=54431	"ERdj5, JPDI, MTHr, PDIA19 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015442	54434	SSH1	http://www.ncbi.nlm.nih.gov/gene/?term=54434	SSH1L	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015443	54434	SSH1	http://www.ncbi.nlm.nih.gov/gene/?term=54434	SSH1L	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015444	54439	RBM27	http://www.ncbi.nlm.nih.gov/gene/?term=54439	"ARRS1, Psc1, ZC3H18, ZC3H20 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015445	54439	RBM27	http://www.ncbi.nlm.nih.gov/gene/?term=54439	"ARRS1, Psc1, ZC3H18, ZC3H20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015446	54439	RBM27	http://www.ncbi.nlm.nih.gov/gene/?term=54439	"ARRS1, Psc1, ZC3H18, ZC3H20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015447	5443	POMC	http://www.ncbi.nlm.nih.gov/gene/?term=5443	"ACTH, CLIP, LPH, MSH, NPP, POC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015448	54441	STAG3L1	http://www.ncbi.nlm.nih.gov/gene/?term=54441	"STAG3L1P, STAG3L2, STAG3L3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015449	54441	STAG3L1	http://www.ncbi.nlm.nih.gov/gene/?term=54441	"STAG3L1P, STAG3L2, STAG3L3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015450	54442	KCTD5	http://www.ncbi.nlm.nih.gov/gene/?term=54442		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015451	54442	KCTD5	http://www.ncbi.nlm.nih.gov/gene/?term=54442		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015452	54442	KCTD5	http://www.ncbi.nlm.nih.gov/gene/?term=54442		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015453	54443	ANLN	http://www.ncbi.nlm.nih.gov/gene/?term=54443	"FSGS8, Scraps, scra "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015454	54446	Nfat5	http://www.ncbi.nlm.nih.gov/gene/?term=54446	"AI225870, B130038B15Rik, CAG-8, CAG80, NFATL1, OREBP, TonEBP, mKIAA0827, nfatz "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015455	54447	Asah2	http://www.ncbi.nlm.nih.gov/gene/?term=54447	AI585898	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015456	5444	PON1	http://www.ncbi.nlm.nih.gov/gene/?term=5444	"ESA, MVCD5, PON "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015457	5444	PON1	http://www.ncbi.nlm.nih.gov/gene/?term=5444	"ESA, MVCD5, PON "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015458	54451	Cpsf3	http://www.ncbi.nlm.nih.gov/gene/?term=54451		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015459	54454	ATAD2B	http://www.ncbi.nlm.nih.gov/gene/?term=54454		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015460	54455	FBXO42	http://www.ncbi.nlm.nih.gov/gene/?term=54455	"Fbx42, JFK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015461	54455	FBXO42	http://www.ncbi.nlm.nih.gov/gene/?term=54455	"Fbx42, JFK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015462	54457	TAF7L	http://www.ncbi.nlm.nih.gov/gene/?term=54457	"CT40, TAF2Q "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015463	54458	PRR13	http://www.ncbi.nlm.nih.gov/gene/?term=54458	TXR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015464	5445	PON2	http://www.ncbi.nlm.nih.gov/gene/?term=5445		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015465	5445	PON2	http://www.ncbi.nlm.nih.gov/gene/?term=5445		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015466	54460	MRPS21	http://www.ncbi.nlm.nih.gov/gene/?term=54460	"MDS016, MRP-S21, RPMS21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015467	54461	FBXW5	http://www.ncbi.nlm.nih.gov/gene/?term=54461	Fbw5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015468	54462	CCSER2	http://www.ncbi.nlm.nih.gov/gene/?term=54462	"FAM190B, Gcap14, KIAA1128, bA486O22.1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015469	54462	CCSER2	http://www.ncbi.nlm.nih.gov/gene/?term=54462	"FAM190B, Gcap14, KIAA1128, bA486O22.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015470	54462	CCSER2	http://www.ncbi.nlm.nih.gov/gene/?term=54462	"FAM190B, Gcap14, KIAA1128, bA486O22.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015471	54463	FAM134B	http://www.ncbi.nlm.nih.gov/gene/?term=54463	"JK-1, JK1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015472	54464	XRN1	http://www.ncbi.nlm.nih.gov/gene/?term=54464	42614	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015473	54464	XRN1	http://www.ncbi.nlm.nih.gov/gene/?term=54464	42614	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015474	54467	ANKIB1	http://www.ncbi.nlm.nih.gov/gene/?term=54467		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015475	54468	MIOS	http://www.ncbi.nlm.nih.gov/gene/?term=54468	MIO	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015476	544696	Tbc1d32	http://www.ncbi.nlm.nih.gov/gene/?term=544696	"Bromi, D630037F22Rik, b2b2284Clo "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015477	544696	Tbc1d32	http://www.ncbi.nlm.nih.gov/gene/?term=544696	"Bromi, D630037F22Rik, b2b2284Clo "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015478	54469	ZFAND6	http://www.ncbi.nlm.nih.gov/gene/?term=54469	"AWP1, ZA20D3, ZFAND5B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015479	54470	ARMCX6	http://www.ncbi.nlm.nih.gov/gene/?term=54470	GASP10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015480	54472	TOLLIP	http://www.ncbi.nlm.nih.gov/gene/?term=54472	IL-1RAcPIP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015481	54472	TOLLIP	http://www.ncbi.nlm.nih.gov/gene/?term=54472	IL-1RAcPIP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015482	544730	LOC544730	http://www.ncbi.nlm.nih.gov/gene/?term=544730		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015483	54475	NLE1	http://www.ncbi.nlm.nih.gov/gene/?term=54475	Nle	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015484	54476	RNF216	http://www.ncbi.nlm.nih.gov/gene/?term=54476	"CAHH, TRIAD3, U7I1, UBCE7IP1, ZIN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015485	54476	RNF216	http://www.ncbi.nlm.nih.gov/gene/?term=54476	"CAHH, TRIAD3, U7I1, UBCE7IP1, ZIN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015486	54476	RNF216	http://www.ncbi.nlm.nih.gov/gene/?term=54476	"CAHH, TRIAD3, U7I1, UBCE7IP1, ZIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015487	54478	FAM64A	http://www.ncbi.nlm.nih.gov/gene/?term=54478	"CATS, RCS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015488	54478	FAM64A	http://www.ncbi.nlm.nih.gov/gene/?term=54478	"CATS, RCS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015489	5447	POR	http://www.ncbi.nlm.nih.gov/gene/?term=5447	"CPR, CYPOR, P450R "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015490	5447	POR	http://www.ncbi.nlm.nih.gov/gene/?term=5447	"CPR, CYPOR, P450R "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015491	5447	POR	http://www.ncbi.nlm.nih.gov/gene/?term=5447	"CPR, CYPOR, P450R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015492	544800	Gm12346	http://www.ncbi.nlm.nih.gov/gene/?term=544800	"EG544800, OTTMUSG00000006249 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015493	54480	CHPF2	http://www.ncbi.nlm.nih.gov/gene/?term=54480	"CSGLCA-T, CSGlcAT, ChSy-3, chPF-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015494	54480	CHPF2	http://www.ncbi.nlm.nih.gov/gene/?term=54480	"CSGLCA-T, CSGlcAT, ChSy-3, chPF-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015495	54487	DGCR8	http://www.ncbi.nlm.nih.gov/gene/?term=54487	"C22orf12, DGCRK6, Gy1, pasha "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015496	54487	DGCR8	http://www.ncbi.nlm.nih.gov/gene/?term=54487	"C22orf12, DGCRK6, Gy1, pasha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015497	544944	Cbx3-ps5	http://www.ncbi.nlm.nih.gov/gene/?term=544944	"EG544944, Gm5792 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015498	54494	C11orf71	http://www.ncbi.nlm.nih.gov/gene/?term=54494	URLC7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015499	54494	C11orf71	http://www.ncbi.nlm.nih.gov/gene/?term=54494	URLC7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015500	54495	TMX3	http://www.ncbi.nlm.nih.gov/gene/?term=54495	"PDIA13, TXNDC10 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015501	544963	Iqgap2	http://www.ncbi.nlm.nih.gov/gene/?term=544963	"4933417J23Rik, A630053O10, AI788777 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015502	54496	PRMT7	http://www.ncbi.nlm.nih.gov/gene/?term=54496		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015503	54496	PRMT7	http://www.ncbi.nlm.nih.gov/gene/?term=54496		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015504	54496	PRMT7	http://www.ncbi.nlm.nih.gov/gene/?term=54496		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015505	54496	PRMT7	http://www.ncbi.nlm.nih.gov/gene/?term=54496		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015506	54496	PRMT7	http://www.ncbi.nlm.nih.gov/gene/?term=54496		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015507	54497	HEATR5B	http://www.ncbi.nlm.nih.gov/gene/?term=54497		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015508	54497	HEATR5B	http://www.ncbi.nlm.nih.gov/gene/?term=54497		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015509	54498	SMOX	http://www.ncbi.nlm.nih.gov/gene/?term=54498	"C20orf16, PAO, PAO-1, PAO1, PAOH, PAOH1, SMO "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015510	54498	SMOX	http://www.ncbi.nlm.nih.gov/gene/?term=54498	"C20orf16, PAO, PAO-1, PAO1, PAOH, PAOH1, SMO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015511	54499	TMCO1	http://www.ncbi.nlm.nih.gov/gene/?term=54499	"HP10122, PCIA3, PNAS-136, TMCC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015512	54499	TMCO1	http://www.ncbi.nlm.nih.gov/gene/?term=54499	"HP10122, PCIA3, PNAS-136, TMCC4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015513	54499	TMCO1	http://www.ncbi.nlm.nih.gov/gene/?term=54499	"HP10122, PCIA3, PNAS-136, TMCC4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015514	54502	RBM47	http://www.ncbi.nlm.nih.gov/gene/?term=54502	NET18	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015515	545039	Gm5799	http://www.ncbi.nlm.nih.gov/gene/?term=545039	EG545039	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015516	54503	ZDHHC13	http://www.ncbi.nlm.nih.gov/gene/?term=54503	"HIP14L, HIP3RP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015517	54503	ZDHHC13	http://www.ncbi.nlm.nih.gov/gene/?term=54503	"HIP14L, HIP3RP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015518	54507	ADAMTSL4	http://www.ncbi.nlm.nih.gov/gene/?term=54507	"ADAMTSL-4, ECTOL2, TSRC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015519	54509	RHOF	http://www.ncbi.nlm.nih.gov/gene/?term=54509	"ARHF, RIF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015520	54509	RHOF	http://www.ncbi.nlm.nih.gov/gene/?term=54509	"ARHF, RIF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015521	54509	RHOF	http://www.ncbi.nlm.nih.gov/gene/?term=54509	"ARHF, RIF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015522	545124	Tdg-ps	http://www.ncbi.nlm.nih.gov/gene/?term=545124	"EG545124, Gm5806 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015523	54512	EXOSC4	http://www.ncbi.nlm.nih.gov/gene/?term=54512	"RRP41, RRP41A, Rrp41p, SKI6, Ski6p, hRrp41p, p12A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015524	54516	MTRF1L	http://www.ncbi.nlm.nih.gov/gene/?term=54516	"HMRF1L, MRF1L, mtRF1a "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015525	54516	MTRF1L	http://www.ncbi.nlm.nih.gov/gene/?term=54516	"HMRF1L, MRF1L, mtRF1a "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015526	54517	PUS7	http://www.ncbi.nlm.nih.gov/gene/?term=54517		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015527	54517	PUS7	http://www.ncbi.nlm.nih.gov/gene/?term=54517		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015528	54519	Apbb1ip	http://www.ncbi.nlm.nih.gov/gene/?term=54519	"9930118P07Rik, Prp48 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015529	5451	POU2F1	http://www.ncbi.nlm.nih.gov/gene/?term=5451	"OCT1, OTF1, oct-1B "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015530	5451	POU2F1	http://www.ncbi.nlm.nih.gov/gene/?term=5451	"OCT1, OTF1, oct-1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015531	54520	CCDC93	http://www.ncbi.nlm.nih.gov/gene/?term=54520		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015532	54520	CCDC93	http://www.ncbi.nlm.nih.gov/gene/?term=54520		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015533	54521	WDR44	http://www.ncbi.nlm.nih.gov/gene/?term=54521	"RAB11BP, RPH11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015534	54521	WDR44	http://www.ncbi.nlm.nih.gov/gene/?term=54521	"RAB11BP, RPH11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015535	54522	ANKRD16	http://www.ncbi.nlm.nih.gov/gene/?term=54522		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015536	54522	ANKRD16	http://www.ncbi.nlm.nih.gov/gene/?term=54522		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015537	54524	Syt6	http://www.ncbi.nlm.nih.gov/gene/?term=54524	"3110037A08Rik, AW048930, sytVI "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015538	54532	USP53	http://www.ncbi.nlm.nih.gov/gene/?term=54532		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015539	54532	USP53	http://www.ncbi.nlm.nih.gov/gene/?term=54532		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015540	54534	MRPL50	http://www.ncbi.nlm.nih.gov/gene/?term=54534	MRP-L50	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015541	54536	EXOC6	http://www.ncbi.nlm.nih.gov/gene/?term=54536	"EXOC6A, SEC15, SEC15L, SEC15L1, SEC15L3, Sec15p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015542	54537	FAM35A	http://www.ncbi.nlm.nih.gov/gene/?term=54537	"FAM35A1, bA163M19.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015543	545389	Cep170	http://www.ncbi.nlm.nih.gov/gene/?term=545389	"4933426L22Rik, A330004A13Rik, AI195353 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015544	54539	NDUFB11	http://www.ncbi.nlm.nih.gov/gene/?term=54539	"CI-ESSS, ESSS, LSDMCA3, NP17.3, Np15, P17.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015545	54540	FAM193B	http://www.ncbi.nlm.nih.gov/gene/?term=54540	IRIZIO	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015546	54541	DDIT4	http://www.ncbi.nlm.nih.gov/gene/?term=54541	"Dig2, REDD-1, REDD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015547	54541	DDIT4	http://www.ncbi.nlm.nih.gov/gene/?term=54541	"Dig2, REDD-1, REDD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015548	54542	RC3H2	http://www.ncbi.nlm.nih.gov/gene/?term=54542	"MNAB, RNF164 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015549	54542	RC3H2	http://www.ncbi.nlm.nih.gov/gene/?term=54542	"MNAB, RNF164 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015550	54543	TOMM7	http://www.ncbi.nlm.nih.gov/gene/?term=54543	TOM7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015551	54543	TOMM7	http://www.ncbi.nlm.nih.gov/gene/?term=54543	TOM7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015552	54545	MTMR12	http://www.ncbi.nlm.nih.gov/gene/?term=54545	"3-PAP, PIP3AP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015553	54545	MTMR12	http://www.ncbi.nlm.nih.gov/gene/?term=54545	"3-PAP, PIP3AP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015554	54546	RNF186	http://www.ncbi.nlm.nih.gov/gene/?term=54546		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015555	545486	Tubb1	http://www.ncbi.nlm.nih.gov/gene/?term=545486	"2810484G07Rik, M(beta)1 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015556	54549	SDK2	http://www.ncbi.nlm.nih.gov/gene/?term=54549		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015557	545508	Gm5844	http://www.ncbi.nlm.nih.gov/gene/?term=545508	EG545508	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015558	54552	GNL3L	http://www.ncbi.nlm.nih.gov/gene/?term=54552	GNL3B	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015559	54552	GNL3L	http://www.ncbi.nlm.nih.gov/gene/?term=54552	GNL3B	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015560	545536	Gm10704	http://www.ncbi.nlm.nih.gov/gene/?term=545536	ENSMUSG00000074479	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015561	54554	WDR5B	http://www.ncbi.nlm.nih.gov/gene/?term=54554		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015562	54554	WDR5B	http://www.ncbi.nlm.nih.gov/gene/?term=54554		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015563	54555	DDX49	http://www.ncbi.nlm.nih.gov/gene/?term=54555	R27090_2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015564	54556	ING3	http://www.ncbi.nlm.nih.gov/gene/?term=54556	"Eaf4, ING2, MEAF4, p47ING3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015565	54557	SGTB	http://www.ncbi.nlm.nih.gov/gene/?term=54557	SGT2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015566	54557	SGTB	http://www.ncbi.nlm.nih.gov/gene/?term=54557	SGT2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015567	54557	SGTB	http://www.ncbi.nlm.nih.gov/gene/?term=54557	SGT2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015568	54558	SPATA6	http://www.ncbi.nlm.nih.gov/gene/?term=54558	"HASH, SRF-1, SRF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015569	545611	Fam205a2	http://www.ncbi.nlm.nih.gov/gene/?term=545611	"Fam205a, Gm13298, OTTMUSG00000011339 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015570	54561	Nap1l3	http://www.ncbi.nlm.nih.gov/gene/?term=54561	MB20	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015571	545640	Gm14138	http://www.ncbi.nlm.nih.gov/gene/?term=545640	OTTMUSG00000015767	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015572	54566	EPB41L4B	http://www.ncbi.nlm.nih.gov/gene/?term=54566	"CG1, EHM2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015573	545677	Gm12888	http://www.ncbi.nlm.nih.gov/gene/?term=545677	OTTMUSG00000008911	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015574	54567	DLL4	http://www.ncbi.nlm.nih.gov/gene/?term=54567	"AOS6, hdelta2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015575	5457	POU4F1	http://www.ncbi.nlm.nih.gov/gene/?term=5457	"BRN3A, Oct-T1, RDC-1, brn-3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015576	54583	EGLN1	http://www.ncbi.nlm.nih.gov/gene/?term=54583	"C1orf12, ECYT3, HALAH, HIF-PH2, HIFPH2, HPH-2, HPH2, PHD2, SM20, ZMYND6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015577	54583	EGLN1	http://www.ncbi.nlm.nih.gov/gene/?term=54583	"C1orf12, ECYT3, HALAH, HIF-PH2, HIFPH2, HPH-2, HPH2, PHD2, SM20, ZMYND6 "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00015578	54584	GNB1L	http://www.ncbi.nlm.nih.gov/gene/?term=54584	"DGCRK3, FKSG1, GY2, WDR14, WDVCF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015579	54584	GNB1L	http://www.ncbi.nlm.nih.gov/gene/?term=54584	"DGCRK3, FKSG1, GY2, WDR14, WDVCF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015580	54585	LZTFL1	http://www.ncbi.nlm.nih.gov/gene/?term=54585	BBS17	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015581	54585	LZTFL1	http://www.ncbi.nlm.nih.gov/gene/?term=54585	BBS17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015582	545913	Zscan4d	http://www.ncbi.nlm.nih.gov/gene/?term=545913	EG545913	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015583	545938	Zfp607	http://www.ncbi.nlm.nih.gov/gene/?term=545938	4732475C15Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015584	54596	L1TD1	http://www.ncbi.nlm.nih.gov/gene/?term=54596	ECAT11	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015585	54596	L1TD1	http://www.ncbi.nlm.nih.gov/gene/?term=54596	ECAT11	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015586	545	ATR	http://www.ncbi.nlm.nih.gov/gene/?term=545	"FCTCS, FRP1, MEC1, SCKL, SCKL1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015587	545	ATR	http://www.ncbi.nlm.nih.gov/gene/?term=545	"FCTCS, FRP1, MEC1, SCKL, SCKL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015588	546024	Crxos	http://www.ncbi.nlm.nih.gov/gene/?term=546024	"AA606869, AY5908911, Egam1, Crxos "	mRNA	Mus musculus	15703187	Nucleus	Embryonic tissue	In situ hybridization|RT-PCR	"We detected the expression in adult retina (postnatal day 30, P30) of Six3OS, Six6OS, Otx2OS, CrxOS and RaxOS (Fig. 3 and data not shown). In general, these transcripts were all expressed at higher levels in the inner nuclear layer (INL) and in the ganglion cell layer (GCL).  "
RLID00015589	54602	NDFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=54602	N4WBP5A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015590	54602	NDFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=54602	N4WBP5A	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015591	54604	Pcnx	http://www.ncbi.nlm.nih.gov/gene/?term=54604	"2900024E21Rik, 3526401J03Rik, AF096286, AI327143, AI413187l1, Pcnx "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015592	54606	DDX56	http://www.ncbi.nlm.nih.gov/gene/?term=54606	"DDX21, DDX26, NOH61 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015593	54606	DDX56	http://www.ncbi.nlm.nih.gov/gene/?term=54606	"DDX21, DDX26, NOH61 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015594	54609	Ubqln2	http://www.ncbi.nlm.nih.gov/gene/?term=54609	"Chap1, Dsk2, HRIHFB2157, Plic-2, Plic2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015595	54614	Prpf40b	http://www.ncbi.nlm.nih.gov/gene/?term=54614	"2610317D23Rik, Hypc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015596	546157	7420426K07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=546157		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015597	546165	Gm10608	http://www.ncbi.nlm.nih.gov/gene/?term=546165	"EG546165, ENSMUSG00000074029 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015598	54617	INO80	http://www.ncbi.nlm.nih.gov/gene/?term=54617	"INO80A, INOC1, hINO80 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015599	54617	INO80	http://www.ncbi.nlm.nih.gov/gene/?term=54617	"INO80A, INOC1, hINO80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015600	54622	ARL15	http://www.ncbi.nlm.nih.gov/gene/?term=54622	ARFRP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015601	54623	PAF1	http://www.ncbi.nlm.nih.gov/gene/?term=54623	"F23149_1, PD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015602	54625	PARP14	http://www.ncbi.nlm.nih.gov/gene/?term=54625	"ARTD8, BAL2, PARP-14, pART8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015603	54625	PARP14	http://www.ncbi.nlm.nih.gov/gene/?term=54625	"ARTD8, BAL2, PARP-14, pART8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015604	54625	PARP14	http://www.ncbi.nlm.nih.gov/gene/?term=54625	"ARTD8, BAL2, PARP-14, pART8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015605	54629	FAM63B	http://www.ncbi.nlm.nih.gov/gene/?term=54629		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015606	546321	Gm15365	http://www.ncbi.nlm.nih.gov/gene/?term=546321	"EG546321, OTTMUSG00000020738 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015607	54633	Pqbp1	http://www.ncbi.nlm.nih.gov/gene/?term=54633	"PQBP-1, Sfc2, npw38 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015608	54644	Otud5	http://www.ncbi.nlm.nih.gov/gene/?term=54644	"AA407879, AI553596, BB114028, DUBA, DXImx46e, Sfc7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015609	54646	Ppp1r3f	http://www.ncbi.nlm.nih.gov/gene/?term=54646	"DXImx48e, R3F, RF3, Sfc15 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015610	5464	PPA1	http://www.ncbi.nlm.nih.gov/gene/?term=5464	"HEL-S-66p, IOPPP, PP, PP1, SID6-8061 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015611	5464	PPA1	http://www.ncbi.nlm.nih.gov/gene/?term=5464	"HEL-S-66p, IOPPP, PP, PP1, SID6-8061 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015612	5464	PPA1	http://www.ncbi.nlm.nih.gov/gene/?term=5464	"HEL-S-66p, IOPPP, PP, PP1, SID6-8061 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015613	54662	TBC1D13	http://www.ncbi.nlm.nih.gov/gene/?term=54662		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015614	54663	WDR74	http://www.ncbi.nlm.nih.gov/gene/?term=54663		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015615	54663	WDR74	http://www.ncbi.nlm.nih.gov/gene/?term=54663		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015616	54664	TMEM106B	http://www.ncbi.nlm.nih.gov/gene/?term=54664		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015617	54675	CRLS1	http://www.ncbi.nlm.nih.gov/gene/?term=54675	"C20orf155, CLS, CLS1, GCD10, dJ967N21.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015618	54675	CRLS1	http://www.ncbi.nlm.nih.gov/gene/?term=54675	"C20orf155, CLS, CLS1, GCD10, dJ967N21.6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015619	54676	GTPBP2	http://www.ncbi.nlm.nih.gov/gene/?term=54676		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015620	5467	PPARD	http://www.ncbi.nlm.nih.gov/gene/?term=5467	"FAAR, NR1C2, NUC1, NUCI, NUCII, PPARB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015621	54681	P4HTM	http://www.ncbi.nlm.nih.gov/gene/?term=54681	"EGLN4, HIFPH4, P4H-TM, PH-4, PH4, PHD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015622	5468	PPARG	http://www.ncbi.nlm.nih.gov/gene/?term=5468	"CIMT1, GLM1, NR1C31, PPARG2, PPARgamma, PPARG "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015623	54700	RRN3	http://www.ncbi.nlm.nih.gov/gene/?term=54700	"A-270G1.2, TIFIA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015624	54704	PDP1	http://www.ncbi.nlm.nih.gov/gene/?term=54704	"PDH, PDP, PDPC, PPM2A, PPM2C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015625	54707	GPN2	http://www.ncbi.nlm.nih.gov/gene/?term=54707	ATPBD1B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015626	54708	MARCH5	http://www.ncbi.nlm.nih.gov/gene/?term=54708	"MARCH-V, MITOL, RNF153 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015627	54709	Eif3i	http://www.ncbi.nlm.nih.gov/gene/?term=54709	"36kDa, D4Ertd632e, Eif3s2, Trip1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015628	54715	RBFOX1	http://www.ncbi.nlm.nih.gov/gene/?term=54715	"2BP1, A2BP1, FOX-1, FOX1, HRNBP1 "	mRNA	Homo sapiens	26687839	Cytoplasm	Hippocampus cortex	Microarray	"To investigate the function of cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. "
RLID00015629	54715	RBFOX1	http://www.ncbi.nlm.nih.gov/gene/?term=54715	"2BP1, A2BP1, FOX-1, FOX1, HRNBP1 "	mRNA	Homo sapiens	26687839	Nucleus	Hippocampus cortex	Microarray	"To investigate the function of cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. "
RLID00015630	54716	SLC6A20	http://www.ncbi.nlm.nih.gov/gene/?term=54716	"SIT1, XT3, Xtrp3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015631	5471	PPAT	http://www.ncbi.nlm.nih.gov/gene/?term=5471	"ATASE, GPAT, PRAT "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015632	54720	Rcan1	http://www.ncbi.nlm.nih.gov/gene/?term=54720	"Adapt78, CALP1L, CSP1, DSC1, Dscr1, MCIP1, RCN1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015633	54723	Tfip11	http://www.ncbi.nlm.nih.gov/gene/?term=54723	"2810002G02Rik, AF097181, AW046167, Srr1, TIP33, Tip39 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015634	54725	Cadm1	http://www.ncbi.nlm.nih.gov/gene/?term=54725	"2900073G06Rik, 3100001I08Rik, AI987920, Bl2, Igsf4, Igsf4a, Necl2, RA175, RA175A, RA175B, RA175C, RA175N, ST17, SgIGSF, SynCam, Tslc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015635	54725	Cadm1	http://www.ncbi.nlm.nih.gov/gene/?term=54725	"2900073G06Rik, 3100001I08Rik, AI987920, Bl2, Igsf4, Igsf4a, Necl2, RA175, RA175A, RA175B, RA175C, RA175N, ST17, SgIGSF, SynCam, Tslc1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00015636	54726	OTUD4	http://www.ncbi.nlm.nih.gov/gene/?term=54726	"DUBA6, HIN1, HSHIN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015637	54732	TMED9	http://www.ncbi.nlm.nih.gov/gene/?term=54732	"GMP25, HSGP25L2G, p24a2, p25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015638	54732	TMED9	http://www.ncbi.nlm.nih.gov/gene/?term=54732	"GMP25, HSGP25L2G, p24a2, p25 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015639	54732	TMED9	http://www.ncbi.nlm.nih.gov/gene/?term=54732	"GMP25, HSGP25L2G, p24a2, p25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015640	54733	SLC35F2	http://www.ncbi.nlm.nih.gov/gene/?term=54733	HSNOV1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015641	54734	RAB39A	http://www.ncbi.nlm.nih.gov/gene/?term=54734	RAB39	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015642	54734	RAB39A	http://www.ncbi.nlm.nih.gov/gene/?term=54734	RAB39	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015643	54737	MPHOSPH8	http://www.ncbi.nlm.nih.gov/gene/?term=54737	"HSMPP8, TWA3, mpp8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015644	54737	MPHOSPH8	http://www.ncbi.nlm.nih.gov/gene/?term=54737	"HSMPP8, TWA3, mpp8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015645	54741	LEPROT	http://www.ncbi.nlm.nih.gov/gene/?term=54741	"LEPR, OB-RGRP, OBRGRP, VPS55 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015646	54741	LEPROT	http://www.ncbi.nlm.nih.gov/gene/?term=54741	"LEPR, OB-RGRP, OBRGRP, VPS55 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015647	54749	EPDR1	http://www.ncbi.nlm.nih.gov/gene/?term=54749	"EPDR, MERP-1, MERP1, UCC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015648	54751	FBLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=54751	"CAL, FBLP-1, FBLP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015649	54751	FBLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=54751	"CAL, FBLP-1, FBLP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015650	54756	IL17RD	http://www.ncbi.nlm.nih.gov/gene/?term=54756	"HH18, IL-17RD, IL17RLM, SEF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015651	54756	IL17RD	http://www.ncbi.nlm.nih.gov/gene/?term=54756	"HH18, IL-17RD, IL17RLM, SEF "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015652	54758	KLHDC4	http://www.ncbi.nlm.nih.gov/gene/?term=54758		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015653	54758	KLHDC4	http://www.ncbi.nlm.nih.gov/gene/?term=54758		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015654	54760	PCSK4	http://www.ncbi.nlm.nih.gov/gene/?term=54760	"PC4, SPC5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015655	54764	ZRANB1	http://www.ncbi.nlm.nih.gov/gene/?term=54764	TRABID	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015656	54764	ZRANB1	http://www.ncbi.nlm.nih.gov/gene/?term=54764	TRABID	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015657	54765	TRIM44	http://www.ncbi.nlm.nih.gov/gene/?term=54765	"DIPB, HSA249128, MC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015658	54765	TRIM44	http://www.ncbi.nlm.nih.gov/gene/?term=54765	"DIPB, HSA249128, MC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015659	5476	CTSA	http://www.ncbi.nlm.nih.gov/gene/?term=5476	"GLB2, GSL, NGBE, PPCA, PPGB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015660	5476	CTSA	http://www.ncbi.nlm.nih.gov/gene/?term=5476	"GLB2, GSL, NGBE, PPCA, PPGB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015661	5476	CTSA	http://www.ncbi.nlm.nih.gov/gene/?term=5476	"GLB2, GSL, NGBE, PPCA, PPGB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015662	54776	PPP1R12C	http://www.ncbi.nlm.nih.gov/gene/?term=54776	"LENG3, MBS85, p84, p85 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015663	54778	RNF111	http://www.ncbi.nlm.nih.gov/gene/?term=54778	ARK	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015664	54778	RNF111	http://www.ncbi.nlm.nih.gov/gene/?term=54778	ARK	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015665	547814	FAD2-1	http://www.ncbi.nlm.nih.gov/gene/?term=547814	GLYMA_10G278000	mRNA	Glycine max	21173264	Nucleus	Seedling	Next-generation sequencing	"However, expression of an inverted-repeat double-stranded RNA corresponding to the soybean FAD2-1A desaturase intron is sufficient to silence FAD2-1, implicating nuclear precursor mRNA (pre-mRNA) rather than cytosolic mRNA as the target of PTGS. "
RLID00015666	54784	ALKBH4	http://www.ncbi.nlm.nih.gov/gene/?term=54784	ABH4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015667	54785	BORCS6	http://www.ncbi.nlm.nih.gov/gene/?term=54785	"C17orf59, PRO2472 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015668	54788	DNAJB12	http://www.ncbi.nlm.nih.gov/gene/?term=54788	DJ10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015669	54788	DNAJB12	http://www.ncbi.nlm.nih.gov/gene/?term=54788	DJ10	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015670	5478	PPIA	http://www.ncbi.nlm.nih.gov/gene/?term=5478	"CYPA, CYPH, HEL-S-69p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015671	5478	PPIA	http://www.ncbi.nlm.nih.gov/gene/?term=5478	"CYPA, CYPH, HEL-S-69p "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015672	54790	TET2	http://www.ncbi.nlm.nih.gov/gene/?term=54790	"KIAA1546, MDS "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015673	54797	MED18	http://www.ncbi.nlm.nih.gov/gene/?term=54797	p28b	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015674	54797	MED18	http://www.ncbi.nlm.nih.gov/gene/?term=54797	p28b	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015675	54797	MED18	http://www.ncbi.nlm.nih.gov/gene/?term=54797	p28b	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015676	54799	MBTD1	http://www.ncbi.nlm.nih.gov/gene/?term=54799	SA49P01	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015677	5479	PPIB	http://www.ncbi.nlm.nih.gov/gene/?term=5479	"CYP-S1, CYPB, HEL-S-39, OI9, SCYLP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015678	5479	PPIB	http://www.ncbi.nlm.nih.gov/gene/?term=5479	"CYP-S1, CYPB, HEL-S-39, OI9, SCYLP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015679	54800	KLHL24	http://www.ncbi.nlm.nih.gov/gene/?term=54800	"DRE1, KRIP6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015680	54800	KLHL24	http://www.ncbi.nlm.nih.gov/gene/?term=54800	"DRE1, KRIP6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015681	54800	KLHL24	http://www.ncbi.nlm.nih.gov/gene/?term=54800	"DRE1, KRIP6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015682	54800	KLHL24	http://www.ncbi.nlm.nih.gov/gene/?term=54800	"DRE1, KRIP6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015683	54801	HAUS6	http://www.ncbi.nlm.nih.gov/gene/?term=54801	"Dgt6, FAM29A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015684	54801	HAUS6	http://www.ncbi.nlm.nih.gov/gene/?term=54801	"Dgt6, FAM29A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015685	54802	TRIT1	http://www.ncbi.nlm.nih.gov/gene/?term=54802	"GRO1, IPPT, IPT, IPTase, MOD5, hGRO1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015686	54802	TRIT1	http://www.ncbi.nlm.nih.gov/gene/?term=54802	"GRO1, IPPT, IPT, IPTase, MOD5, hGRO1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015687	54802	TRIT1	http://www.ncbi.nlm.nih.gov/gene/?term=54802	"GRO1, IPPT, IPT, IPTase, MOD5, hGRO1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015688	54805	CNNM2	http://www.ncbi.nlm.nih.gov/gene/?term=54805	"ACDP2, HOMG6, HOMGSMR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015689	54805	CNNM2	http://www.ncbi.nlm.nih.gov/gene/?term=54805	"ACDP2, HOMG6, HOMGSMR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015690	54806	AHI1	http://www.ncbi.nlm.nih.gov/gene/?term=54806	"AHI-1, JBTS3, ORF1, dJ71N10.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015691	54808	DYM	http://www.ncbi.nlm.nih.gov/gene/?term=54808	"DMC, SMC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015692	5480	PPIC	http://www.ncbi.nlm.nih.gov/gene/?term=5480	CYPC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015693	5480	PPIC	http://www.ncbi.nlm.nih.gov/gene/?term=5480	CYPC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015694	54811	ZNF562	http://www.ncbi.nlm.nih.gov/gene/?term=54811		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015695	54812	AFTPH	http://www.ncbi.nlm.nih.gov/gene/?term=54812	Nbla10388	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015696	54815	GATAD2A	http://www.ncbi.nlm.nih.gov/gene/?term=54815	p66alpha	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015697	54816	ZNF280D	http://www.ncbi.nlm.nih.gov/gene/?term=54816	"SUHW4, ZNF634 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015698	54819	ZCCHC10	http://www.ncbi.nlm.nih.gov/gene/?term=54819		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015699	5481	PPID	http://www.ncbi.nlm.nih.gov/gene/?term=5481	"CYP-40, CYPD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015700	5481	PPID	http://www.ncbi.nlm.nih.gov/gene/?term=5481	"CYP-40, CYPD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015701	5481	PPID	http://www.ncbi.nlm.nih.gov/gene/?term=5481	"CYP-40, CYPD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015702	5481	PPID	http://www.ncbi.nlm.nih.gov/gene/?term=5481	"CYP-40, CYPD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015703	5481	PPID	http://www.ncbi.nlm.nih.gov/gene/?term=5481	"CYP-40, CYPD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015704	54822	TRPM7	http://www.ncbi.nlm.nih.gov/gene/?term=54822	"ALSPDC, CHAK, CHAK1, LTRPC7, LTrpC-7, TRP-PLIK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015705	54825	CDHR2	http://www.ncbi.nlm.nih.gov/gene/?term=54825	"PCDH24, PCLKC "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00015706	54828	BCAS3	http://www.ncbi.nlm.nih.gov/gene/?term=54828	"GAOB1, MAAB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015707	548313	SSX4B	http://www.ncbi.nlm.nih.gov/gene/?term=548313	CT5.4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015708	54832	VPS13C	http://www.ncbi.nlm.nih.gov/gene/?term=54832	PARK23	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015709	54832	VPS13C	http://www.ncbi.nlm.nih.gov/gene/?term=54832		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015710	54834	GDAP2	http://www.ncbi.nlm.nih.gov/gene/?term=54834	MACROD3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015711	54834	GDAP2	http://www.ncbi.nlm.nih.gov/gene/?term=54834	MACROD3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015712	54834	GDAP2	http://www.ncbi.nlm.nih.gov/gene/?term=54834	MACROD3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015713	54836	BSPRY	http://www.ncbi.nlm.nih.gov/gene/?term=54836		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015714	54836	BSPRY	http://www.ncbi.nlm.nih.gov/gene/?term=54836		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015715	54841	BIVM	http://www.ncbi.nlm.nih.gov/gene/?term=54841		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015716	54841	BIVM	http://www.ncbi.nlm.nih.gov/gene/?term=54841		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015717	54841	BIVM	http://www.ncbi.nlm.nih.gov/gene/?term=54841		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015718	54841	BIVM	http://www.ncbi.nlm.nih.gov/gene/?term=54841		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015719	54842	MFSD6	http://www.ncbi.nlm.nih.gov/gene/?term=54842	"MMR2, hMMR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015720	54845	ESRP1	http://www.ncbi.nlm.nih.gov/gene/?term=54845	"RBM35A, RMB35A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015721	54849	DEF8	http://www.ncbi.nlm.nih.gov/gene/?term=54849		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015722	54849	DEF8	http://www.ncbi.nlm.nih.gov/gene/?term=54849		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015723	54850	FBXL12	http://www.ncbi.nlm.nih.gov/gene/?term=54850	Fbl12	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015724	54850	FBXL12	http://www.ncbi.nlm.nih.gov/gene/?term=54850	Fbl12	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015725	54852	PAQR5	http://www.ncbi.nlm.nih.gov/gene/?term=54852	MPRG	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015726	54852	PAQR5	http://www.ncbi.nlm.nih.gov/gene/?term=54852	MPRG	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015727	54852	PAQR5	http://www.ncbi.nlm.nih.gov/gene/?term=54852	MPRG	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015728	54853	WDR55	http://www.ncbi.nlm.nih.gov/gene/?term=54853		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015729	54853	WDR55	http://www.ncbi.nlm.nih.gov/gene/?term=54853		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015730	54855	FAM46C	http://www.ncbi.nlm.nih.gov/gene/?term=54855		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015731	54856	GON4L	http://www.ncbi.nlm.nih.gov/gene/?term=54856	"GON-4, GON4, YARP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015732	54856	GON4L	http://www.ncbi.nlm.nih.gov/gene/?term=54856	"GON-4, GON4, YARP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015733	54856	GON4L	http://www.ncbi.nlm.nih.gov/gene/?term=54856	"GON-4, GON4, YARP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015734	54858	PGPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=54858	"PAP-I, PGP, PGP-I, PGPI, Pcp "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015735	54858	PGPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=54858	"PAP-I, PGP, PGP-I, PGPI, Pcp "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015736	54858	PGPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=54858	"PAP-I, PGP, PGP-I, PGPI, Pcp "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015737	54859	ELP6	http://www.ncbi.nlm.nih.gov/gene/?term=54859	"C3orf75, TMEM103 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015738	54859	ELP6	http://www.ncbi.nlm.nih.gov/gene/?term=54859	"C3orf75, TMEM103 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015739	54861	SNRK	http://www.ncbi.nlm.nih.gov/gene/?term=54861	HSNFRK	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015740	54863	TOR4A	http://www.ncbi.nlm.nih.gov/gene/?term=54863	C9orf167	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015741	54863	TOR4A	http://www.ncbi.nlm.nih.gov/gene/?term=54863	C9orf167	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015742	54863	TOR4A	http://www.ncbi.nlm.nih.gov/gene/?term=54863	C9orf167	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015743	548644	POLR2J3	http://www.ncbi.nlm.nih.gov/gene/?term=548644	"POLR2J2, RPB11b1, RPB11b2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015744	548644	POLR2J3	http://www.ncbi.nlm.nih.gov/gene/?term=548644	"POLR2J2, RPB11b1, RPB11b2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015745	548644	POLR2J3	http://www.ncbi.nlm.nih.gov/gene/?term=548644	"POLR2J2, RPB11b1, RPB11b2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015746	54865	GPATCH4	http://www.ncbi.nlm.nih.gov/gene/?term=54865	GPATC4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015747	54865	GPATCH4	http://www.ncbi.nlm.nih.gov/gene/?term=54865	GPATC4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015748	54866	PPP1R14D	http://www.ncbi.nlm.nih.gov/gene/?term=54866	"CPI17-like, GBPI-1, GBPI1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015749	54866	PPP1R14D	http://www.ncbi.nlm.nih.gov/gene/?term=54866	"CPI17-like, GBPI-1, GBPI1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015750	54867	TMEM214	http://www.ncbi.nlm.nih.gov/gene/?term=54867		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015751	54867	TMEM214	http://www.ncbi.nlm.nih.gov/gene/?term=54867		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015752	54868	TMEM104	http://www.ncbi.nlm.nih.gov/gene/?term=54868		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015753	54869	EPS8L1	http://www.ncbi.nlm.nih.gov/gene/?term=54869	"DRC3, EPS8R1, PP10566 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015754	54870	QRICH1	http://www.ncbi.nlm.nih.gov/gene/?term=54870		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015755	54870	QRICH1	http://www.ncbi.nlm.nih.gov/gene/?term=54870		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015756	54872	PIGG	http://www.ncbi.nlm.nih.gov/gene/?term=54872	"GPI7, LAS21, PRO4405, RLGS1930 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015757	54872	PIGG	http://www.ncbi.nlm.nih.gov/gene/?term=54872	"GPI7, LAS21, PRO4405, RLGS1930 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015758	54873	PALMD	http://www.ncbi.nlm.nih.gov/gene/?term=54873	"C1orf11, PALML "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015759	54874	FNBP1L	http://www.ncbi.nlm.nih.gov/gene/?term=54874	"C1orf39, TOCA1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015760	54876	DCAF16	http://www.ncbi.nlm.nih.gov/gene/?term=54876	C4orf30	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015761	54876	DCAF16	http://www.ncbi.nlm.nih.gov/gene/?term=54876	C4orf30	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015762	54878	DPP8	http://www.ncbi.nlm.nih.gov/gene/?term=54878	"DP8, DPRP-1, DPRP1, MST097, MSTP097, MSTP135, MSTP141 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015763	54879	ST7L	http://www.ncbi.nlm.nih.gov/gene/?term=54879	"FAM4B, ST7R, STLR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015764	54881	TEX10	http://www.ncbi.nlm.nih.gov/gene/?term=54881	"Ipi1, bA208F1.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015765	54882	ANKHD1	http://www.ncbi.nlm.nih.gov/gene/?term=54882	"MASK, MASK1, PP2500, VBARP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015766	54882	ANKHD1	http://www.ncbi.nlm.nih.gov/gene/?term=54882	"MASK, MASK1, PP2500, VBARP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015767	54883	CWC25	http://www.ncbi.nlm.nih.gov/gene/?term=54883	CCDC49	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00015768	54884	RETSAT	http://www.ncbi.nlm.nih.gov/gene/?term=54884		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015769	54884	RETSAT	http://www.ncbi.nlm.nih.gov/gene/?term=54884		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015770	54884	RETSAT	http://www.ncbi.nlm.nih.gov/gene/?term=54884		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015771	54887	UHRF1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=54887	"C6orf107, ICBP90, dJ349A12.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015772	54888	NSUN2	http://www.ncbi.nlm.nih.gov/gene/?term=54888	"MISU, MRT5, SAKI, TRM4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015773	54890	ALKBH5	http://www.ncbi.nlm.nih.gov/gene/?term=54890	"ABH5, OFOXD, OFOXD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015774	54892	NCAPG2	http://www.ncbi.nlm.nih.gov/gene/?term=54892	"CAP-G2, CAPG2, LUZP5, MTB, hCAP-G2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015775	54892	NCAPG2	http://www.ncbi.nlm.nih.gov/gene/?term=54892	"CAP-G2, CAPG2, LUZP5, MTB, hCAP-G2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015776	54893	MTMR10	http://www.ncbi.nlm.nih.gov/gene/?term=54893		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015777	54894	RNF43	http://www.ncbi.nlm.nih.gov/gene/?term=54894	"RNF124, URCC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015778	54898	ELOVL2	http://www.ncbi.nlm.nih.gov/gene/?term=54898	SSC2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015779	54899	PXK	http://www.ncbi.nlm.nih.gov/gene/?term=54899	MONaKA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015780	54899	PXK	http://www.ncbi.nlm.nih.gov/gene/?term=54899	MONaKA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015781	54902	TTC19	http://www.ncbi.nlm.nih.gov/gene/?term=54902	"2010204O13Rik, MC3DN2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015782	54902	TTC19	http://www.ncbi.nlm.nih.gov/gene/?term=54902	"2010204O13Rik, MC3DN2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015783	54903	MKS1	http://www.ncbi.nlm.nih.gov/gene/?term=54903	"BBS13, MES, MKS, POC12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015784	54904	WHSC1L1	http://www.ncbi.nlm.nih.gov/gene/?term=54904	"NSD3, WHISTLE, pp14328 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015785	54906	FAM208B	http://www.ncbi.nlm.nih.gov/gene/?term=54906	"C10orf18, bA318E3.2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015786	54906	FAM208B	http://www.ncbi.nlm.nih.gov/gene/?term=54906	"C10orf18, bA318E3.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015787	54913	RPP25	http://www.ncbi.nlm.nih.gov/gene/?term=54913		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015788	54913	RPP25	http://www.ncbi.nlm.nih.gov/gene/?term=54913		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015789	54914	FOCAD	http://www.ncbi.nlm.nih.gov/gene/?term=54914	KIAA1797	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015790	54916	TMEM260	http://www.ncbi.nlm.nih.gov/gene/?term=54916	C14orf101	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015791	54918	CMTM6	http://www.ncbi.nlm.nih.gov/gene/?term=54918	"CKLFSF6, PRO2219 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015792	54919	DNAAF5	http://www.ncbi.nlm.nih.gov/gene/?term=54919	"CILD18, HEATR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015793	54919	DNAAF5	http://www.ncbi.nlm.nih.gov/gene/?term=54919	"CILD18, HEATR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015794	54920	DUS2	http://www.ncbi.nlm.nih.gov/gene/?term=54920	"DUS2L, SMM1, URLC8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015795	54920	DUS2	http://www.ncbi.nlm.nih.gov/gene/?term=54920	"DUS2L, SMM1, URLC8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015796	54921	CHTF8	http://www.ncbi.nlm.nih.gov/gene/?term=54921	"CTF8, DERPC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015797	54921	CHTF8	http://www.ncbi.nlm.nih.gov/gene/?term=54921	"CTF8, DERPC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015798	54925	ZSCAN32	http://www.ncbi.nlm.nih.gov/gene/?term=54925	"HCCS-5, ZNF434 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015799	54926	UBE2R2	http://www.ncbi.nlm.nih.gov/gene/?term=54926	"CDC34B, E2-CDC34B, UBC3B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015800	54928	IMPAD1	http://www.ncbi.nlm.nih.gov/gene/?term=54928	"GPAPP, IMP 3, IMP-3, IMPA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015801	54928	IMPAD1	http://www.ncbi.nlm.nih.gov/gene/?term=54928	"GPAPP, IMP 3, IMP-3, IMPA3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015802	54930	HAUS4	http://www.ncbi.nlm.nih.gov/gene/?term=54930	C14orf94	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015803	54931	TRMT10C	http://www.ncbi.nlm.nih.gov/gene/?term=54931	"HNYA, MRPP1, RG9MTD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015804	54931	TRMT10C	http://www.ncbi.nlm.nih.gov/gene/?term=54931	"HNYA, MRPP1, RG9MTD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015805	54935	DUSP23	http://www.ncbi.nlm.nih.gov/gene/?term=54935	"DUSP25, LDP-3, MOSP, VHZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015806	54936	ADPRHL2	http://www.ncbi.nlm.nih.gov/gene/?term=54936	ARH3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015807	54938	SARS2	http://www.ncbi.nlm.nih.gov/gene/?term=54938	"SARS, SARSM, SERS, SYS, SerRS, SerRSmt, mtSerRS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015808	54939	COMMD4	http://www.ncbi.nlm.nih.gov/gene/?term=54939		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015809	54939	COMMD4	http://www.ncbi.nlm.nih.gov/gene/?term=54939		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015810	54939	COMMD4	http://www.ncbi.nlm.nih.gov/gene/?term=54939		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015811	54940	OCIAD1	http://www.ncbi.nlm.nih.gov/gene/?term=54940	"ASRIJ, OCIA, TPA018 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015812	54940	OCIAD1	http://www.ncbi.nlm.nih.gov/gene/?term=54940	"ASRIJ, OCIA, TPA018 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015813	54941	RNF125	http://www.ncbi.nlm.nih.gov/gene/?term=54941	"TNORS, TRAC-1, TRAC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015814	54941	RNF125	http://www.ncbi.nlm.nih.gov/gene/?term=54941	"TNORS, TRAC-1, TRAC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015815	54942	FAM206A	http://www.ncbi.nlm.nih.gov/gene/?term=54942	"C9orf6, CG-8, Simiate "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015816	54942	FAM206A	http://www.ncbi.nlm.nih.gov/gene/?term=54942	"C9orf6, CG-8, Simiate "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015817	54946	SLC41A3	http://www.ncbi.nlm.nih.gov/gene/?term=54946	SLC41A1-L2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015818	54947	LPCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=54947	"AGPAT11, AYTL1, LysoPAFAT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015819	54947	LPCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=54947	"AGPAT11, AYTL1, LysoPAFAT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015820	54947	LPCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=54947	"AGPAT11, AYTL1, LysoPAFAT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015821	54948	MRPL16	http://www.ncbi.nlm.nih.gov/gene/?term=54948	"L16mt, MRP-L16, PNAS-111 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015822	54948	MRPL16	http://www.ncbi.nlm.nih.gov/gene/?term=54948	"L16mt, MRP-L16, PNAS-111 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015823	54951	COMMD8	http://www.ncbi.nlm.nih.gov/gene/?term=54951		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015824	54952	TRNAU1AP	http://www.ncbi.nlm.nih.gov/gene/?term=54952	"PRO1902, SECP43, TRSPAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015825	54952	TRNAU1AP	http://www.ncbi.nlm.nih.gov/gene/?term=54952	"PRO1902, SECP43, TRSPAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015826	54952	TRNAU1AP	http://www.ncbi.nlm.nih.gov/gene/?term=54952	"PRO1902, SECP43, TRSPAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015827	54955	C1orf109	http://www.ncbi.nlm.nih.gov/gene/?term=54955		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015828	549573	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=549573	"dvr-1, dvr1, gdf-1, gdf3, vg-1, vg1 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00015829	54957	TXNL4B	http://www.ncbi.nlm.nih.gov/gene/?term=54957	"DLP, Dim2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015830	54957	TXNL4B	http://www.ncbi.nlm.nih.gov/gene/?term=54957	"DLP, Dim2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015831	54957	TXNL4B	http://www.ncbi.nlm.nih.gov/gene/?term=54957	"DLP, Dim2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015832	54958	TMEM160	http://www.ncbi.nlm.nih.gov/gene/?term=54958		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015833	5495	PPM1B	http://www.ncbi.nlm.nih.gov/gene/?term=5495	"PP2C-beta, PP2C-beta-X, PP2CB, PP2CBETA, PPC2BETAX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015834	54960	GEMIN8	http://www.ncbi.nlm.nih.gov/gene/?term=54960	FAM51A1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015835	54960	GEMIN8	http://www.ncbi.nlm.nih.gov/gene/?term=54960	FAM51A1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015836	54962	TIPIN	http://www.ncbi.nlm.nih.gov/gene/?term=54962		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015837	54962	TIPIN	http://www.ncbi.nlm.nih.gov/gene/?term=54962		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015838	54963	UCKL1	http://www.ncbi.nlm.nih.gov/gene/?term=54963	"UCK1L, URKL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015839	54964	C1orf56	http://www.ncbi.nlm.nih.gov/gene/?term=54964	MENT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015840	54965	PIGX	http://www.ncbi.nlm.nih.gov/gene/?term=54965	PIG-X	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015841	54965	PIGX	http://www.ncbi.nlm.nih.gov/gene/?term=54965	PIG-X	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015842	54965	PIGX	http://www.ncbi.nlm.nih.gov/gene/?term=54965	PIG-X	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015843	54968	TMEM70	http://www.ncbi.nlm.nih.gov/gene/?term=54968	MC5DN2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015844	54968	TMEM70	http://www.ncbi.nlm.nih.gov/gene/?term=54968	MC5DN2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015845	54969	HPF1	http://www.ncbi.nlm.nih.gov/gene/?term=54969		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015846	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015847	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015848	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015849	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015850	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015851	54971	BANP	http://www.ncbi.nlm.nih.gov/gene/?term=54971	"BEND1, SMAR1, SMARBP1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015852	54972	TMEM132A	http://www.ncbi.nlm.nih.gov/gene/?term=54972	"GBP, HSPA5BP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015853	54974	THG1L	http://www.ncbi.nlm.nih.gov/gene/?term=54974	"ICF45, IHG-1, hTHG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015854	54974	THG1L	http://www.ncbi.nlm.nih.gov/gene/?term=54974	"ICF45, IHG-1, hTHG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015855	54974	THG1L	http://www.ncbi.nlm.nih.gov/gene/?term=54974	"ICF45, IHG-1, hTHG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015856	54976	C20orf27	http://www.ncbi.nlm.nih.gov/gene/?term=54976		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015857	54977	SLC25A38	http://www.ncbi.nlm.nih.gov/gene/?term=54977	SIDBA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015858	54977	SLC25A38	http://www.ncbi.nlm.nih.gov/gene/?term=54977		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015859	54978	SLC35F6	http://www.ncbi.nlm.nih.gov/gene/?term=54978	"ANT2BP, C2orf18, TANGO9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015860	54978	SLC35F6	http://www.ncbi.nlm.nih.gov/gene/?term=54978	"ANT2BP, C2orf18, TANGO9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015861	54978	SLC35F6	http://www.ncbi.nlm.nih.gov/gene/?term=54978	"ANT2BP, C2orf18, TANGO9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015862	54978	SLC35F6	http://www.ncbi.nlm.nih.gov/gene/?term=54978	"ANT2BP, C2orf18, TANGO9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015863	54982	CLN6	http://www.ncbi.nlm.nih.gov/gene/?term=54982	"CLN4A, HsT18960, nclf "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015864	54985	HCFC1R1	http://www.ncbi.nlm.nih.gov/gene/?term=54985	HPIP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015865	54985	HCFC1R1	http://www.ncbi.nlm.nih.gov/gene/?term=54985	HPIP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015866	54987	C1orf123	http://www.ncbi.nlm.nih.gov/gene/?term=54987		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015867	54987	C1orf123	http://www.ncbi.nlm.nih.gov/gene/?term=54987		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015868	54989	ZNF770	http://www.ncbi.nlm.nih.gov/gene/?term=54989	PRO1914	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015869	54989	ZNF770	http://www.ncbi.nlm.nih.gov/gene/?term=54989	PRO1914	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015870	5498	PPOX	http://www.ncbi.nlm.nih.gov/gene/?term=5498	"PPO, V290M, VP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015871	54991	C1orf159	http://www.ncbi.nlm.nih.gov/gene/?term=54991		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015872	54993	ZSCAN2	http://www.ncbi.nlm.nih.gov/gene/?term=54993	"ZFP29, ZNF854 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015873	54993	ZSCAN2	http://www.ncbi.nlm.nih.gov/gene/?term=54993	"ZFP29, ZNF854 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015874	54994	GID8	http://www.ncbi.nlm.nih.gov/gene/?term=54994	"C20orf11, TWA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015875	54994	GID8	http://www.ncbi.nlm.nih.gov/gene/?term=54994	"C20orf11, TWA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015876	54995	OXSM	http://www.ncbi.nlm.nih.gov/gene/?term=54995	"FASN2D, KASI, KS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015877	54995	OXSM	http://www.ncbi.nlm.nih.gov/gene/?term=54995	"FASN2D, KASI, KS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015878	54997	TESC	http://www.ncbi.nlm.nih.gov/gene/?term=54997	"CHP3, TSC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015879	54998	AURKAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=54998	"AIP, AKIP, MRP-S38 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015880	5499	PPP1CA	http://www.ncbi.nlm.nih.gov/gene/?term=5499	"PP-1A, PP1A, PP1alpha, PPP1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015881	5499	PPP1CA	http://www.ncbi.nlm.nih.gov/gene/?term=5499	"PP-1A, PP1A, PP1alpha, PPP1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015882	5499	PPP1CA	http://www.ncbi.nlm.nih.gov/gene/?term=5499	"PP-1A, PP1A, PP1alpha, PPP1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015883	54	ACP5	http://www.ncbi.nlm.nih.gov/gene/?term=54	"HPAP, SPENCDI, TRAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015884	55000	TUG1	http://www.ncbi.nlm.nih.gov/gene/?term=55000	"LINC00080, NCRNA00080, TI-227H "	lncRNA	Homo sapiens	19571010	Nucleus	HFF|HLF|HeLa cell	Fluorescence in situ hybridization	"Figure 3b: Subcellular localization analysis of lincRNAs by RNA FISH demonstrates localization of lincRNAs to the nucleus. Each panel represents the in situ hybridization of �0 fluorescently labeled DNA oligos with complementarity to the interrogated lincRNA. RNA FISH experiments were performed in male hFF for each represented lincRNA (XIST, HOTAIR, TUG-1, lincMKLN-1, lincFOXF1, and lincSFPQ), and also in female hLF for XIST (XX). White “speckles�indicate the subcellular localization of each lincRNA. The nuclear compartment is demarked by DAPI staining (purple). "
RLID00015885	55000	TUG1	http://www.ncbi.nlm.nih.gov/gene/?term=55000	"LINC00080, NCRNA00080, TI-227H "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015886	55000	TUG1	http://www.ncbi.nlm.nih.gov/gene/?term=55000	"LINC00080, NCRNA00080, TI-227H "	lncRNA	Homo sapiens	22078878	Nucleus	HeLa cell|Kidney|Lung fibroblast	In situ hybridizationq|RT-PCR 	"While Pc2 methylation appears to be the key determinant for relocation of growth control genes, based on a methylation/demethylation dependent switch in preference for TUG1 or NEAT2 interactions, respectively, we are tempted to speculate that other ncRNAs recognize covalent modifications of other gene-associated proteins, exerting their ncRNA scaffold functions in distinct subnuclear compartments to act as sensors for many regulated signaling pathways, and as modulators of 'reading' marks on histone tails for a variety of chromodomain-containing proteins and other histone code 'readers'. "
RLID00015887	55000	TUG1	http://www.ncbi.nlm.nih.gov/gene/?term=55000	"LINC00080, NCRNA00080, TI-227H "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00015888	55002	TMCO3	http://www.ncbi.nlm.nih.gov/gene/?term=55002	C13orf11	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015889	55003	PAK1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=55003	"MAK11, PIP1, WDR84, bA421M1.5, hPIP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015890	55003	PAK1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=55003	"MAK11, PIP1, WDR84, bA421M1.5, hPIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015891	55004	LAMTOR1	http://www.ncbi.nlm.nih.gov/gene/?term=55004	"C11orf59, PDRO, Ragulator1, p18, p27RF-Rho "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015892	55006	TRMT61B	http://www.ncbi.nlm.nih.gov/gene/?term=55006		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015893	55006	TRMT61B	http://www.ncbi.nlm.nih.gov/gene/?term=55006		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015894	55007	FAM118A	http://www.ncbi.nlm.nih.gov/gene/?term=55007	C22orf8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015895	55008	HERC6	http://www.ncbi.nlm.nih.gov/gene/?term=55008		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015896	55009	C19orf24	http://www.ncbi.nlm.nih.gov/gene/?term=55009		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015897	5500	PPP1CB	http://www.ncbi.nlm.nih.gov/gene/?term=5500	"HEL-S-80p, PP-1B, PP1B, PP1beta, PPP1CD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015898	5500	PPP1CB	http://www.ncbi.nlm.nih.gov/gene/?term=5500	"HEL-S-80p, PP-1B, PP1B, PP1beta, PPP1CD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015899	55011	PIH1D1	http://www.ncbi.nlm.nih.gov/gene/?term=55011	NOP17	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015900	55011	PIH1D1	http://www.ncbi.nlm.nih.gov/gene/?term=55011	NOP17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015901	55013	CCDC109B	http://www.ncbi.nlm.nih.gov/gene/?term=55013	MCUb	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015902	55014	STX17	http://www.ncbi.nlm.nih.gov/gene/?term=55014		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015903	55017	C14orf119	http://www.ncbi.nlm.nih.gov/gene/?term=55017		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015904	55017	C14orf119	http://www.ncbi.nlm.nih.gov/gene/?term=55017		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015905	55017	C14orf119	http://www.ncbi.nlm.nih.gov/gene/?term=55017		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015906	55017	C14orf119	http://www.ncbi.nlm.nih.gov/gene/?term=55017		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015907	5501	PPP1CC	http://www.ncbi.nlm.nih.gov/gene/?term=5501	"PP-1G, PP1C, PPP1G "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015908	5501	PPP1CC	http://www.ncbi.nlm.nih.gov/gene/?term=5501	"PP-1G, PP1C, PPP1G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015909	55020	TTC38	http://www.ncbi.nlm.nih.gov/gene/?term=55020	LL22NC03-5H6.5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015910	55020	TTC38	http://www.ncbi.nlm.nih.gov/gene/?term=55020	LL22NC03-5H6.5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015911	55023	PHIP	http://www.ncbi.nlm.nih.gov/gene/?term=55023	"BRWD2, DCAF14, WDR11, ndrp "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015912	55027	HEATR3	http://www.ncbi.nlm.nih.gov/gene/?term=55027	SYO1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015913	55031	USP47	http://www.ncbi.nlm.nih.gov/gene/?term=55031	TRFP	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015914	55031	USP47	http://www.ncbi.nlm.nih.gov/gene/?term=55031	TRFP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015915	55033	FKBP14	http://www.ncbi.nlm.nih.gov/gene/?term=55033	"EDSKMH, FKBP22, IPBP12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015916	55034	MOCOS	http://www.ncbi.nlm.nih.gov/gene/?term=55034	"HMCS, MCS, MOS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015917	55035	NOL8	http://www.ncbi.nlm.nih.gov/gene/?term=55035	"C9orf34, NOP132, bA62C3.3, bA62C3.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015918	55037	PTCD3	http://www.ncbi.nlm.nih.gov/gene/?term=55037	MRP-S39	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015919	55037	PTCD3	http://www.ncbi.nlm.nih.gov/gene/?term=55037	MRP-S39	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015920	55039	TRMT12	http://www.ncbi.nlm.nih.gov/gene/?term=55039	"TRM12, TYW2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015921	55041	PLEKHB2	http://www.ncbi.nlm.nih.gov/gene/?term=55041	EVT2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015922	55041	PLEKHB2	http://www.ncbi.nlm.nih.gov/gene/?term=55041	EVT2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015923	55041	PLEKHB2	http://www.ncbi.nlm.nih.gov/gene/?term=55041	EVT2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015924	55041	PLEKHB2	http://www.ncbi.nlm.nih.gov/gene/?term=55041	EVT2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015925	55048	VPS37C	http://www.ncbi.nlm.nih.gov/gene/?term=55048		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015926	55048	VPS37C	http://www.ncbi.nlm.nih.gov/gene/?term=55048		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015927	55049	C19orf60	http://www.ncbi.nlm.nih.gov/gene/?term=55049		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015928	5504	PPP1R2	http://www.ncbi.nlm.nih.gov/gene/?term=5504	"IPP-2, IPP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015929	5504	PPP1R2	http://www.ncbi.nlm.nih.gov/gene/?term=5504	"IPP-2, IPP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015930	55052	MRPL20	http://www.ncbi.nlm.nih.gov/gene/?term=55052	"L20mt, MRP-L20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015931	55054	ATG16L1	http://www.ncbi.nlm.nih.gov/gene/?term=55054	"APG16L, ATG16A, ATG16L, IBD10, WDR30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015932	55055	ZWILCH	http://www.ncbi.nlm.nih.gov/gene/?term=55055	"KNTC1AP, hZwilch "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015933	55055	ZWILCH	http://www.ncbi.nlm.nih.gov/gene/?term=55055	"KNTC1AP, hZwilch "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015934	550619	Arid3c	http://www.ncbi.nlm.nih.gov/gene/?term=550619	OTTMUSG00000006683	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00015935	55062	WIPI1	http://www.ncbi.nlm.nih.gov/gene/?term=55062	"ATG18, ATG18A, WIPI49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015936	55062	WIPI1	http://www.ncbi.nlm.nih.gov/gene/?term=55062	"ATG18, ATG18A, WIPI49 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015937	55062	WIPI1	http://www.ncbi.nlm.nih.gov/gene/?term=55062	"ATG18, ATG18A, WIPI49 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015938	550643	LINC01420	http://www.ncbi.nlm.nih.gov/gene/?term=550643		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015939	55065	SLC52A1	http://www.ncbi.nlm.nih.gov/gene/?term=55065	"GPCR42, GPR172B, PAR2, RBFVD, RFT1, RFVT1, hRFT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015940	55065	SLC52A1	http://www.ncbi.nlm.nih.gov/gene/?term=55065	"GPCR42, GPR172B, PAR2, RBFVD, RFT1, RFVT1, hRFT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015941	55066	PDPR	http://www.ncbi.nlm.nih.gov/gene/?term=55066	PDP3	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015942	55066	PDPR	http://www.ncbi.nlm.nih.gov/gene/?term=55066	PDP3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015943	55066	PDPR	http://www.ncbi.nlm.nih.gov/gene/?term=55066	PDP3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015944	55069	TMEM248	http://www.ncbi.nlm.nih.gov/gene/?term=55069	C7orf42	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015945	55069	TMEM248	http://www.ncbi.nlm.nih.gov/gene/?term=55069	C7orf42	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015946	55069	TMEM248	http://www.ncbi.nlm.nih.gov/gene/?term=55069	C7orf42	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015947	55070	DET1	http://www.ncbi.nlm.nih.gov/gene/?term=55070		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015948	55071	C9orf40	http://www.ncbi.nlm.nih.gov/gene/?term=55071		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015949	55072	RNF31	http://www.ncbi.nlm.nih.gov/gene/?term=55072	"HOIP, ZIBRA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015950	55072	RNF31	http://www.ncbi.nlm.nih.gov/gene/?term=55072	"HOIP, ZIBRA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015951	55075	UACA	http://www.ncbi.nlm.nih.gov/gene/?term=55075	NUCLING	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015952	55076	TMEM45A	http://www.ncbi.nlm.nih.gov/gene/?term=55076	DERP7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015953	55082	ARGLU1	http://www.ncbi.nlm.nih.gov/gene/?term=55082		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015954	55088	CCDC186	http://www.ncbi.nlm.nih.gov/gene/?term=55088	C10orf118	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015955	55088	CCDC186	http://www.ncbi.nlm.nih.gov/gene/?term=55088	C10orf118	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015956	55088	CCDC186	http://www.ncbi.nlm.nih.gov/gene/?term=55088	C10orf118	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015957	55090	MED9	http://www.ncbi.nlm.nih.gov/gene/?term=55090	MED25	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015958	55090	MED9	http://www.ncbi.nlm.nih.gov/gene/?term=55090	MED25	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015959	55093	WDYHV1	http://www.ncbi.nlm.nih.gov/gene/?term=55093	C8orf32	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015960	55094	GPATCH1	http://www.ncbi.nlm.nih.gov/gene/?term=55094	"ECGP, GPATC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015961	55095	SAMD4B	http://www.ncbi.nlm.nih.gov/gene/?term=55095	"SMGB, Smaug2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015962	55095	SAMD4B	http://www.ncbi.nlm.nih.gov/gene/?term=55095	"SMGB, Smaug2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015963	550	AUP1	http://www.ncbi.nlm.nih.gov/gene/?term=550		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015964	550	AUP1	http://www.ncbi.nlm.nih.gov/gene/?term=550		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015965	55101	ATP5SL	http://www.ncbi.nlm.nih.gov/gene/?term=55101		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015966	55102	ATG2B	http://www.ncbi.nlm.nih.gov/gene/?term=55102	C14orf103	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015967	55103	RALGPS2	http://www.ncbi.nlm.nih.gov/gene/?term=55103	dJ595C2.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015968	55107	ANO1	http://www.ncbi.nlm.nih.gov/gene/?term=55107	"DOG1, ORAOV2, TAOS2, TMEM16A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015969	55108	BSDC1	http://www.ncbi.nlm.nih.gov/gene/?term=55108		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015970	55109	AGGF1	http://www.ncbi.nlm.nih.gov/gene/?term=55109	"GPATC7, GPATCH7, HSU84971, HUS84971, VG5Q "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015971	55109	AGGF1	http://www.ncbi.nlm.nih.gov/gene/?term=55109	"GPATC7, GPATCH7, HSU84971, HUS84971, VG5Q "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015972	5510	PPP1R7	http://www.ncbi.nlm.nih.gov/gene/?term=5510	SDS22	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015973	5510	PPP1R7	http://www.ncbi.nlm.nih.gov/gene/?term=5510	SDS22	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015974	5510	PPP1R7	http://www.ncbi.nlm.nih.gov/gene/?term=5510	SDS22	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015975	55110	MAGOHB	http://www.ncbi.nlm.nih.gov/gene/?term=55110	"MGN2, mago, magoh "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015976	55111	PLEKHJ1	http://www.ncbi.nlm.nih.gov/gene/?term=55111	GNRPX	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015977	55113	XKR8	http://www.ncbi.nlm.nih.gov/gene/?term=55113	"XRG8, hXkr8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015978	55114	ARHGAP17	http://www.ncbi.nlm.nih.gov/gene/?term=55114	"MST066, MST110, MSTP038, MSTP066, MSTP110, NADRIN, PP367, PP4534, RICH-1, RICH1, WBP15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015979	55114	ARHGAP17	http://www.ncbi.nlm.nih.gov/gene/?term=55114	"MST066, MST110, MSTP038, MSTP066, MSTP110, NADRIN, PP367, PP4534, RICH-1, RICH1, WBP15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015980	55117	SLC6A15	http://www.ncbi.nlm.nih.gov/gene/?term=55117	"NTT73, SBAT1, V7-3, hv7-3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015981	55117	SLC6A15	http://www.ncbi.nlm.nih.gov/gene/?term=55117	"NTT73, SBAT1, V7-3, hv7-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015982	55119	PRPF38B	http://www.ncbi.nlm.nih.gov/gene/?term=55119	NET1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015983	55119	PRPF38B	http://www.ncbi.nlm.nih.gov/gene/?term=55119	NET1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015984	5511	PPP1R8	http://www.ncbi.nlm.nih.gov/gene/?term=5511	"ARD-1, ARD1, NIPP-1, NIPP1, PRO2047 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015985	5511	PPP1R8	http://www.ncbi.nlm.nih.gov/gene/?term=5511	"ARD-1, ARD1, NIPP-1, NIPP1, PRO2047 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015986	5511	PPP1R8	http://www.ncbi.nlm.nih.gov/gene/?term=5511	"ARD-1, ARD1, NIPP-1, NIPP1, PRO2047 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015987	55120	FANCL	http://www.ncbi.nlm.nih.gov/gene/?term=55120	"FAAP43, PHF9, POG "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015988	55122	AKIRIN2	http://www.ncbi.nlm.nih.gov/gene/?term=55122	"C6orf166, FBI1, dJ486L4.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015989	55125	CEP192	http://www.ncbi.nlm.nih.gov/gene/?term=55125	PPP1R62	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015990	55125	CEP192	http://www.ncbi.nlm.nih.gov/gene/?term=55125	PPP1R62	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015991	55127	HEATR1	http://www.ncbi.nlm.nih.gov/gene/?term=55127	"BAP28, UTP10 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015992	55128	TRIM68	http://www.ncbi.nlm.nih.gov/gene/?term=55128	"GC109, RNF137, SS-56, SS56 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015993	55128	TRIM68	http://www.ncbi.nlm.nih.gov/gene/?term=55128	"GC109, RNF137, SS-56, SS56 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015994	55131	RBM28	http://www.ncbi.nlm.nih.gov/gene/?term=55131	ANES	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00015995	55132	LARP1B	http://www.ncbi.nlm.nih.gov/gene/?term=55132	LARP2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015996	55135	WRAP53	http://www.ncbi.nlm.nih.gov/gene/?term=55135	"DKCB3, TCAB1, WDR79 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00015997	55140	ELP3	http://www.ncbi.nlm.nih.gov/gene/?term=55140	KAT9	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00015998	55140	ELP3	http://www.ncbi.nlm.nih.gov/gene/?term=55140	KAT9	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00015999	55140	ELP3	http://www.ncbi.nlm.nih.gov/gene/?term=55140	KAT9	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016000	55140	ELP3	http://www.ncbi.nlm.nih.gov/gene/?term=55140	KAT9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016001	55142	HAUS2	http://www.ncbi.nlm.nih.gov/gene/?term=55142	"C15orf25, CEP27, HsT17025 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016002	55143	CDCA8	http://www.ncbi.nlm.nih.gov/gene/?term=55143	"BOR, BOREALIN, DasraB, MESRGP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016003	55143	CDCA8	http://www.ncbi.nlm.nih.gov/gene/?term=55143	"BOR, BOREALIN, DasraB, MESRGP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016004	55143	CDCA8	http://www.ncbi.nlm.nih.gov/gene/?term=55143	"BOR, BOREALIN, DasraB, MESRGP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016005	55146	ZDHHC4	http://www.ncbi.nlm.nih.gov/gene/?term=55146	ZNF374	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016006	55146	ZDHHC4	http://www.ncbi.nlm.nih.gov/gene/?term=55146	ZNF374	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016007	55147	RBM23	http://www.ncbi.nlm.nih.gov/gene/?term=55147	"CAPERbeta, PP239, RNPC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016008	55148	UBR7	http://www.ncbi.nlm.nih.gov/gene/?term=55148	C14orf130	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016009	55148	UBR7	http://www.ncbi.nlm.nih.gov/gene/?term=55148	C14orf130	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016010	55149	MTPAP	http://www.ncbi.nlm.nih.gov/gene/?term=55149	"PAPD1, SPAX4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016011	55149	MTPAP	http://www.ncbi.nlm.nih.gov/gene/?term=55149	"PAPD1, SPAX4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016012	55149	MTPAP	http://www.ncbi.nlm.nih.gov/gene/?term=55149	"PAPD1, SPAX4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016013	5514	PPP1R10	http://www.ncbi.nlm.nih.gov/gene/?term=5514	"CAT53, FB19, PNUTS, PP1R10, R111, p99 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016014	5514	PPP1R10	http://www.ncbi.nlm.nih.gov/gene/?term=5514	"CAT53, FB19, PNUTS, PP1R10, R111, p99 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016015	55151	TMEM38B	http://www.ncbi.nlm.nih.gov/gene/?term=55151	"C9orf87, D4Ertd89e, OI14, TRIC-B, TRICB, bA219P18.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016016	55151	TMEM38B	http://www.ncbi.nlm.nih.gov/gene/?term=55151	"C9orf87, D4Ertd89e, OI14, TRIC-B, TRICB, bA219P18.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016017	55154	MSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=55154	"LST005, MST "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016018	55154	MSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=55154	"LST005, MST "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016019	55156	ARMC1	http://www.ncbi.nlm.nih.gov/gene/?term=55156	Arcp	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016020	55156	ARMC1	http://www.ncbi.nlm.nih.gov/gene/?term=55156	Arcp	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016021	5515	PPP2CA	http://www.ncbi.nlm.nih.gov/gene/?term=5515	"PP2Ac, PP2CA, PP2Calpha, RP-C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016022	5515	PPP2CA	http://www.ncbi.nlm.nih.gov/gene/?term=5515	"PP2Ac, PP2CA, PP2Calpha, RP-C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016023	5515	PPP2CA	http://www.ncbi.nlm.nih.gov/gene/?term=5515	"PP2Ac, PP2CA, PP2Calpha, RP-C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016024	55161	TMEM33	http://www.ncbi.nlm.nih.gov/gene/?term=55161	"1600019D15Rik, SHINC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016025	55163	PNPO	http://www.ncbi.nlm.nih.gov/gene/?term=55163	"HEL-S-302, PDXPO "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016026	55163	PNPO	http://www.ncbi.nlm.nih.gov/gene/?term=55163	"HEL-S-302, PDXPO "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016027	55163	PNPO	http://www.ncbi.nlm.nih.gov/gene/?term=55163	"HEL-S-302, PDXPO "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016028	55163	PNPO	http://www.ncbi.nlm.nih.gov/gene/?term=55163	"HEL-S-302, PDXPO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016029	55164	SHQ1	http://www.ncbi.nlm.nih.gov/gene/?term=55164	"GRIM-1, Shq1p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016030	55164	SHQ1	http://www.ncbi.nlm.nih.gov/gene/?term=55164	"GRIM-1, Shq1p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016031	55165	CEP55	http://www.ncbi.nlm.nih.gov/gene/?term=55165	"C10orf3, CT111, URCC6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016032	55165	CEP55	http://www.ncbi.nlm.nih.gov/gene/?term=55165	"C10orf3, CT111, URCC6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016033	55166	CENPQ	http://www.ncbi.nlm.nih.gov/gene/?term=55166	"C6orf139, CENP-Q "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016034	55168	MRPS18A	http://www.ncbi.nlm.nih.gov/gene/?term=55168	"HumanS18b, MRP-S18-3, MRPS18-3, S18bmt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016035	5516	PPP2CB	http://www.ncbi.nlm.nih.gov/gene/?term=5516	"PP2Abeta, PP2CB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016036	5516	PPP2CB	http://www.ncbi.nlm.nih.gov/gene/?term=5516	"PP2Abeta, PP2CB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016037	5516	PPP2CB	http://www.ncbi.nlm.nih.gov/gene/?term=5516	"PP2Abeta, PP2CB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016038	55170	PRMT6	http://www.ncbi.nlm.nih.gov/gene/?term=55170	HRMT1L6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016039	55170	PRMT6	http://www.ncbi.nlm.nih.gov/gene/?term=55170	HRMT1L6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016040	55171	TBCCD1	http://www.ncbi.nlm.nih.gov/gene/?term=55171		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016041	55171	TBCCD1	http://www.ncbi.nlm.nih.gov/gene/?term=55171		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016042	55172	DNAAF2	http://www.ncbi.nlm.nih.gov/gene/?term=55172	"C14orf104, CILD10, KTU, PF13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016043	55172	DNAAF2	http://www.ncbi.nlm.nih.gov/gene/?term=55172	"C14orf104, CILD10, KTU, PF13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016044	55173	MRPS10	http://www.ncbi.nlm.nih.gov/gene/?term=55173	"MRP-S10, PNAS-122 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016045	55173	MRPS10	http://www.ncbi.nlm.nih.gov/gene/?term=55173	"MRP-S10, PNAS-122 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016046	55174	INTS10	http://www.ncbi.nlm.nih.gov/gene/?term=55174	"C8orf35, INT10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016047	55175	KLHL11	http://www.ncbi.nlm.nih.gov/gene/?term=55175		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016048	55176	SEC61A2	http://www.ncbi.nlm.nih.gov/gene/?term=55176		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016049	55176	SEC61A2	http://www.ncbi.nlm.nih.gov/gene/?term=55176		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016050	55177	RMDN3	http://www.ncbi.nlm.nih.gov/gene/?term=55177	"FAM82A2, FAM82C, RMD-3, RMD3, ptpip51 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016051	55178	RNMTL1	http://www.ncbi.nlm.nih.gov/gene/?term=55178	"MRM3, RMTL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016052	55179	FAIM	http://www.ncbi.nlm.nih.gov/gene/?term=55179	FAIM1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016053	55179	FAIM	http://www.ncbi.nlm.nih.gov/gene/?term=55179	FAIM1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016054	55179	FAIM	http://www.ncbi.nlm.nih.gov/gene/?term=55179	FAIM1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016055	55180	LINS1	http://www.ncbi.nlm.nih.gov/gene/?term=55180	"LINS, MRT27, WINS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016056	55182	RNF220	http://www.ncbi.nlm.nih.gov/gene/?term=55182	C1orf164	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016057	55183	RIF1	http://www.ncbi.nlm.nih.gov/gene/?term=55183		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016058	55186	SLC25A36	http://www.ncbi.nlm.nih.gov/gene/?term=55186	PNC2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016059	55186	SLC25A36	http://www.ncbi.nlm.nih.gov/gene/?term=55186	PNC2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016060	55187	VPS13D	http://www.ncbi.nlm.nih.gov/gene/?term=55187		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016061	55187	VPS13D	http://www.ncbi.nlm.nih.gov/gene/?term=55187		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016062	5518	PPP2R1A	http://www.ncbi.nlm.nih.gov/gene/?term=5518	"MRD36, PP2A-Aalpha, PP2AAALPHA, PR65A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016063	5518	PPP2R1A	http://www.ncbi.nlm.nih.gov/gene/?term=5518	"MRD36, PP2A-Aalpha, PP2AAALPHA, PR65A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016064	55191	NADSYN1	http://www.ncbi.nlm.nih.gov/gene/?term=55191		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016065	55193	PBRM1	http://www.ncbi.nlm.nih.gov/gene/?term=55193	"BAF180, PB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016066	55196	KIAA1551	http://www.ncbi.nlm.nih.gov/gene/?term=55196	"C12orf35, UTA2-1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016067	55197	RPRD1A	http://www.ncbi.nlm.nih.gov/gene/?term=55197	"HsT3101, P15RS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016068	55198	APPL2	http://www.ncbi.nlm.nih.gov/gene/?term=55198	DIP13B	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016069	55198	APPL2	http://www.ncbi.nlm.nih.gov/gene/?term=55198	DIP13B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016070	55199	FAM86C1	http://www.ncbi.nlm.nih.gov/gene/?term=55199	FAM86C	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016071	5519	PPP2R1B	http://www.ncbi.nlm.nih.gov/gene/?term=5519	"PP2A-Abeta, PR65B "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016072	5519	PPP2R1B	http://www.ncbi.nlm.nih.gov/gene/?term=5519	"PP2A-Abeta, PR65B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016073	55201	MAP1S	http://www.ncbi.nlm.nih.gov/gene/?term=55201	"BPY2IP1, C19orf5, MAP8, VCY2IP-1, VCY2IP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016074	55205	ZNF532	http://www.ncbi.nlm.nih.gov/gene/?term=55205		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016075	55206	SBNO1	http://www.ncbi.nlm.nih.gov/gene/?term=55206	"MOP3, Sno "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016076	55206	SBNO1	http://www.ncbi.nlm.nih.gov/gene/?term=55206	"MOP3, Sno "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016077	55206	SBNO1	http://www.ncbi.nlm.nih.gov/gene/?term=55206	"MOP3, Sno "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016078	55206	SBNO1	http://www.ncbi.nlm.nih.gov/gene/?term=55206	"MOP3, Sno "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016079	55207	ARL8B	http://www.ncbi.nlm.nih.gov/gene/?term=55207	"ARL10C, Gie1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016080	55207	ARL8B	http://www.ncbi.nlm.nih.gov/gene/?term=55207	"ARL10C, Gie1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016081	55207	ARL8B	http://www.ncbi.nlm.nih.gov/gene/?term=55207	"ARL10C, Gie1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016082	55209	SETD5	http://www.ncbi.nlm.nih.gov/gene/?term=55209		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016083	55209	SETD5	http://www.ncbi.nlm.nih.gov/gene/?term=55209		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016084	5520	PPP2R2A	http://www.ncbi.nlm.nih.gov/gene/?term=5520	"B55A, B55ALPHA, PR52A, PR55A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016085	55210	ATAD3A	http://www.ncbi.nlm.nih.gov/gene/?term=55210		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016086	55210	ATAD3A	http://www.ncbi.nlm.nih.gov/gene/?term=55210		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016087	55211	DPPA4	http://www.ncbi.nlm.nih.gov/gene/?term=55211	2410091M23Rik	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016088	55211	DPPA4	http://www.ncbi.nlm.nih.gov/gene/?term=55211	2410091M23Rik	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016089	55212	BBS7	http://www.ncbi.nlm.nih.gov/gene/?term=55212	BBS2L1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016090	55212	BBS7	http://www.ncbi.nlm.nih.gov/gene/?term=55212	BBS2L1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016091	55213	RCBTB1	http://www.ncbi.nlm.nih.gov/gene/?term=55213	"CLLD7, CLLL7, GLP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016092	55213	RCBTB1	http://www.ncbi.nlm.nih.gov/gene/?term=55213	"CLLD7, CLLL7, GLP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016093	55213	RCBTB1	http://www.ncbi.nlm.nih.gov/gene/?term=55213	"CLLD7, CLLL7, GLP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016094	55215	FANCI	http://www.ncbi.nlm.nih.gov/gene/?term=55215	KIAA1794	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016095	55215	FANCI	http://www.ncbi.nlm.nih.gov/gene/?term=55215	KIAA1794	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016096	55216	C11orf57	http://www.ncbi.nlm.nih.gov/gene/?term=55216		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016097	55217	TMLHE	http://www.ncbi.nlm.nih.gov/gene/?term=55217	"AUTSX6, BBOX2, TMLD, TMLH, TMLHED, XAP130 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016098	55218	EXD2	http://www.ncbi.nlm.nih.gov/gene/?term=55218	"C14orf114, EXDL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016099	55219	TMEM57	http://www.ncbi.nlm.nih.gov/gene/?term=55219	MACOILIN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016100	55219	TMEM57	http://www.ncbi.nlm.nih.gov/gene/?term=55219	MACOILIN	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016101	55220	KLHDC8A	http://www.ncbi.nlm.nih.gov/gene/?term=55220		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016102	55222	LRRC20	http://www.ncbi.nlm.nih.gov/gene/?term=55222		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016103	55225	RAVER2	http://www.ncbi.nlm.nih.gov/gene/?term=55225		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016104	55227	LRRC1	http://www.ncbi.nlm.nih.gov/gene/?term=55227	"LANO, dJ523E19.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016105	55227	LRRC1	http://www.ncbi.nlm.nih.gov/gene/?term=55227	"LANO, dJ523E19.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016106	55230	USP40	http://www.ncbi.nlm.nih.gov/gene/?term=55230		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016107	55230	USP40	http://www.ncbi.nlm.nih.gov/gene/?term=55230		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016108	55233	MOB1A	http://www.ncbi.nlm.nih.gov/gene/?term=55233	"C2orf6, MATS1, MOB1, MOBK1B, MOBKL1B, Mob4B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016109	55234	SMU1	http://www.ncbi.nlm.nih.gov/gene/?term=55234	"BWD, SMU-1, fSAP57 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016110	55234	SMU1	http://www.ncbi.nlm.nih.gov/gene/?term=55234	"BWD, SMU-1, fSAP57 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016111	55234	SMU1	http://www.ncbi.nlm.nih.gov/gene/?term=55234	"BWD, SMU-1, fSAP57 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016112	55234	SMU1	http://www.ncbi.nlm.nih.gov/gene/?term=55234	"BWD, SMU-1, fSAP57 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016113	55236	UBA6	http://www.ncbi.nlm.nih.gov/gene/?term=55236	"E1-L2, MOP-4, UBE1L2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016114	55236	UBA6	http://www.ncbi.nlm.nih.gov/gene/?term=55236	"E1-L2, MOP-4, UBE1L2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016115	55236	UBA6	http://www.ncbi.nlm.nih.gov/gene/?term=55236	"E1-L2, MOP-4, UBE1L2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016116	55238	SLC38A7	http://www.ncbi.nlm.nih.gov/gene/?term=55238	SNAT7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016117	55239	OGFOD1	http://www.ncbi.nlm.nih.gov/gene/?term=55239	TPA1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016118	55239	OGFOD1	http://www.ncbi.nlm.nih.gov/gene/?term=55239	TPA1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016119	55239	OGFOD1	http://www.ncbi.nlm.nih.gov/gene/?term=55239	TPA1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016120	55240	STEAP3	http://www.ncbi.nlm.nih.gov/gene/?term=55240	"AHMIO2, STMP3, TSAP6, dudlin-2, dudulin-2, pHyde "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016121	55244	SLC47A1	http://www.ncbi.nlm.nih.gov/gene/?term=55244	MATE1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016122	55245	UQCC1	http://www.ncbi.nlm.nih.gov/gene/?term=55245	"BFZB, C20orf44, CBP3, UQCC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016123	55246	CCDC25	http://www.ncbi.nlm.nih.gov/gene/?term=55246		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016124	55248	TMEM206	http://www.ncbi.nlm.nih.gov/gene/?term=55248	C1orf75	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016125	55248	TMEM206	http://www.ncbi.nlm.nih.gov/gene/?term=55248	C1orf75	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016126	55249	YY1AP1	http://www.ncbi.nlm.nih.gov/gene/?term=55249	"HCCA1, HCCA2, YAP, YY1AP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016127	55249	YY1AP1	http://www.ncbi.nlm.nih.gov/gene/?term=55249	"HCCA1, HCCA2, YAP, YY1AP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016128	5524	PPP2R4	http://www.ncbi.nlm.nih.gov/gene/?term=5524	"PP2A, PR53, PTPA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016129	55250	ELP2	http://www.ncbi.nlm.nih.gov/gene/?term=55250	"SHINC-2, STATIP1, StIP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016130	55250	ELP2	http://www.ncbi.nlm.nih.gov/gene/?term=55250	"SHINC-2, STATIP1, StIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016131	55250	ELP2	http://www.ncbi.nlm.nih.gov/gene/?term=55250	"SHINC-2, STATIP1, StIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016132	55251	PCMTD2	http://www.ncbi.nlm.nih.gov/gene/?term=55251	C20orf36	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016133	55252	ASXL2	http://www.ncbi.nlm.nih.gov/gene/?term=55252	ASXH2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016134	55252	ASXL2	http://www.ncbi.nlm.nih.gov/gene/?term=55252	ASXH2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016135	55253	TYW1	http://www.ncbi.nlm.nih.gov/gene/?term=55253	"RSAFD1, TYW1A, YPL207W "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016136	55254	TMEM39A	http://www.ncbi.nlm.nih.gov/gene/?term=55254		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016137	55254	TMEM39A	http://www.ncbi.nlm.nih.gov/gene/?term=55254		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016138	55255	WDR41	http://www.ncbi.nlm.nih.gov/gene/?term=55255	MSTP048	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016139	55256	ADI1	http://www.ncbi.nlm.nih.gov/gene/?term=55256	"APL1, ARD, Fe-ARD, HMFT1638, MTCBP1, Ni-ARD, SIPL, mtnD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016140	55256	ADI1	http://www.ncbi.nlm.nih.gov/gene/?term=55256	"APL1, ARD, Fe-ARD, HMFT1638, MTCBP1, Ni-ARD, SIPL, mtnD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016141	55256	ADI1	http://www.ncbi.nlm.nih.gov/gene/?term=55256	"APL1, ARD, Fe-ARD, HMFT1638, MTCBP1, Ni-ARD, SIPL, mtnD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016142	55257	MRGBP	http://www.ncbi.nlm.nih.gov/gene/?term=55257	"C20orf20, Eaf7, MRG15BP, URCC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016143	5525	PPP2R5A	http://www.ncbi.nlm.nih.gov/gene/?term=5525	"B56A, PR61A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016144	5525	PPP2R5A	http://www.ncbi.nlm.nih.gov/gene/?term=5525	"B56A, PR61A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016145	55260	TMEM143	http://www.ncbi.nlm.nih.gov/gene/?term=55260		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016146	55266	TMEM19	http://www.ncbi.nlm.nih.gov/gene/?term=55266		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016147	55269	PSPC1	http://www.ncbi.nlm.nih.gov/gene/?term=55269	PSP1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016148	55269	PSPC1	http://www.ncbi.nlm.nih.gov/gene/?term=55269	PSP1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016149	55269	PSPC1	http://www.ncbi.nlm.nih.gov/gene/?term=55269	PSP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016150	5526	PPP2R5B	http://www.ncbi.nlm.nih.gov/gene/?term=5526	"B56B, PR61B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016151	5526	PPP2R5B	http://www.ncbi.nlm.nih.gov/gene/?term=5526	"B56B, PR61B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016152	55270	NUDT15	http://www.ncbi.nlm.nih.gov/gene/?term=55270	MTH2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016153	55270	NUDT15	http://www.ncbi.nlm.nih.gov/gene/?term=55270	MTH2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016154	55272	IMP3	http://www.ncbi.nlm.nih.gov/gene/?term=55272	"BRMS2, C15orf12, MRPS4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016155	55272	IMP3	http://www.ncbi.nlm.nih.gov/gene/?term=55272	"BRMS2, C15orf12, MRPS4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016156	55274	PHF10	http://www.ncbi.nlm.nih.gov/gene/?term=55274	"BAF45A, XAP135 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016157	55275	VPS53	http://www.ncbi.nlm.nih.gov/gene/?term=55275	"HCCS1, PCH2E, hVps53L, pp13624 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016158	55275	VPS53	http://www.ncbi.nlm.nih.gov/gene/?term=55275	"HCCS1, PCH2E, hVps53L, pp13624 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016159	55276	PGM2	http://www.ncbi.nlm.nih.gov/gene/?term=55276	MSTP006	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016160	55276	PGM2	http://www.ncbi.nlm.nih.gov/gene/?term=55276	MSTP006	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016161	55276	PGM2	http://www.ncbi.nlm.nih.gov/gene/?term=55276	MSTP006	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016162	55277	FGGY	http://www.ncbi.nlm.nih.gov/gene/?term=55277		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016163	55278	QRSL1	http://www.ncbi.nlm.nih.gov/gene/?term=55278	GatA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016164	5527	PPP2R5C	http://www.ncbi.nlm.nih.gov/gene/?term=5527	"B56G, PR61G "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016165	5527	PPP2R5C	http://www.ncbi.nlm.nih.gov/gene/?term=5527	"B56G, PR61G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016166	55280	CWF19L1	http://www.ncbi.nlm.nih.gov/gene/?term=55280	"C19L1, SCAR17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016167	55284	UBE2W	http://www.ncbi.nlm.nih.gov/gene/?term=55284	"UBC-16, UBC16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016168	55286	C4orf19	http://www.ncbi.nlm.nih.gov/gene/?term=55286		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016169	552889	ATXN7L3B	http://www.ncbi.nlm.nih.gov/gene/?term=552889	lnc-SCA7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016170	55288	RHOT1	http://www.ncbi.nlm.nih.gov/gene/?term=55288	"ARHT1, MIRO-1, MIRO1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016171	5528	PPP2R5D	http://www.ncbi.nlm.nih.gov/gene/?term=5528	"B56D, MRD35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016172	552900	BOLA2	http://www.ncbi.nlm.nih.gov/gene/?term=552900	"BOLA2A, My016 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016173	552902	LOC552902	http://www.ncbi.nlm.nih.gov/gene/?term=552902		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016174	55290	BRF2	http://www.ncbi.nlm.nih.gov/gene/?term=55290	"BRFU, TFIIIB50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016175	55291	PPP6R3	http://www.ncbi.nlm.nih.gov/gene/?term=55291	"C11orf23, PP6R3, SAP190, SAPL, SAPLa, SAPS3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016176	55291	PPP6R3	http://www.ncbi.nlm.nih.gov/gene/?term=55291	"C11orf23, PP6R3, SAP190, SAPL, SAPLa, SAPS3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016177	55293	UEVLD	http://www.ncbi.nlm.nih.gov/gene/?term=55293	"ATTP, UEV3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016178	55294	FBXW7	http://www.ncbi.nlm.nih.gov/gene/?term=55294	"AGO, CDC4, FBW6, FBW7, FBX30, FBXO30, FBXW6, SEL-10, SEL10, hAgo, hCdc4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016179	55296	TBC1D19	http://www.ncbi.nlm.nih.gov/gene/?term=55296		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016180	55297	CCDC91	http://www.ncbi.nlm.nih.gov/gene/?term=55297	"HSD8, p56 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016181	55299	BRIX1	http://www.ncbi.nlm.nih.gov/gene/?term=55299	"BRIX, BXDC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016182	55299	BRIX1	http://www.ncbi.nlm.nih.gov/gene/?term=55299	"BRIX, BXDC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016183	5529	PPP2R5E	http://www.ncbi.nlm.nih.gov/gene/?term=5529		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016184	5529	PPP2R5E	http://www.ncbi.nlm.nih.gov/gene/?term=5529		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016185	55300	PI4K2B	http://www.ncbi.nlm.nih.gov/gene/?term=55300	"PI4KIIB, PIK42B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016186	55308	DDX19A	http://www.ncbi.nlm.nih.gov/gene/?term=55308	"DDX19-DDX19L, DDX19L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016187	5530	PPP3CA	http://www.ncbi.nlm.nih.gov/gene/?term=5530	"CALN, CALNA, CALNA1, CCN1, CNA1, PPP2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016188	5530	PPP3CA	http://www.ncbi.nlm.nih.gov/gene/?term=5530	"CALN, CALNA, CALNA1, CCN1, CNA1, PPP2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016189	553115	PEF1	http://www.ncbi.nlm.nih.gov/gene/?term=553115	"ABP32A, PEF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016190	553115	PEF1	http://www.ncbi.nlm.nih.gov/gene/?term=553115	"ABP32A, PEF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016191	553115	PEF1	http://www.ncbi.nlm.nih.gov/gene/?term=553115	"ABP32, PEF1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016192	55311	ZNF444	http://www.ncbi.nlm.nih.gov/gene/?term=55311	"EZF-2, EZF2, ZSCAN17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016193	55312	RFK	http://www.ncbi.nlm.nih.gov/gene/?term=55312	RIFK	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016194	55312	RFK	http://www.ncbi.nlm.nih.gov/gene/?term=55312	RIFK	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016195	55312	RFK	http://www.ncbi.nlm.nih.gov/gene/?term=55312	RIFK	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016196	55313	CPPED1	http://www.ncbi.nlm.nih.gov/gene/?term=55313	CSTP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016197	55313	CPPED1	http://www.ncbi.nlm.nih.gov/gene/?term=55313	CSTP1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016198	55313	CPPED1	http://www.ncbi.nlm.nih.gov/gene/?term=55313	CSTP1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016199	55314	TMEM144	http://www.ncbi.nlm.nih.gov/gene/?term=55314		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016200	55316	RSAD1	http://www.ncbi.nlm.nih.gov/gene/?term=55316		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016201	55316	RSAD1	http://www.ncbi.nlm.nih.gov/gene/?term=55316		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016202	55317	AP5S1	http://www.ncbi.nlm.nih.gov/gene/?term=55317	C20orf29	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016203	55319	TMA16	http://www.ncbi.nlm.nih.gov/gene/?term=55319	C4orf43	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016204	55319	TMA16	http://www.ncbi.nlm.nih.gov/gene/?term=55319	C4orf43	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016205	5531	PPP4C	http://www.ncbi.nlm.nih.gov/gene/?term=5531	"PP-X, PP4, PP4C, PPH3, PPP4, PPX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016206	5531	PPP4C	http://www.ncbi.nlm.nih.gov/gene/?term=5531	"PP-X, PP4, PP4C, PPH3, PPP4, PPX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016207	5531	PPP4C	http://www.ncbi.nlm.nih.gov/gene/?term=5531	"PP-X, PP4, PP4C, PPH3, PPP4, PPX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016208	55320	MIS18BP1	http://www.ncbi.nlm.nih.gov/gene/?term=55320	"C14orf106, HSA242977, KNL2, M18BP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016209	55322	C5orf22	http://www.ncbi.nlm.nih.gov/gene/?term=55322		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016210	55322	C5orf22	http://www.ncbi.nlm.nih.gov/gene/?term=55322		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016211	55323	LARP6	http://www.ncbi.nlm.nih.gov/gene/?term=55323	ACHN	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016212	55323	LARP6	http://www.ncbi.nlm.nih.gov/gene/?term=55323	ACHN	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016213	55324	ABCF3	http://www.ncbi.nlm.nih.gov/gene/?term=55324	EST201864	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016214	55326	AGPAT5	http://www.ncbi.nlm.nih.gov/gene/?term=55326	"1AGPAT5, LPAATE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016215	55327	LIN7C	http://www.ncbi.nlm.nih.gov/gene/?term=55327	"LIN-7-C, LIN-7C, MALS-3, MALS3, VELI3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016216	55327	LIN7C	http://www.ncbi.nlm.nih.gov/gene/?term=55327	"LIN-7-C, LIN-7C, MALS-3, MALS3, VELI3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016217	5532	PPP3CB	http://www.ncbi.nlm.nih.gov/gene/?term=5532	"CALNA2, CALNB, CNA2, PP2Bbeta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016218	5532	PPP3CB	http://www.ncbi.nlm.nih.gov/gene/?term=5532	"CALNA2, CALNB, CNA2, PP2Bbeta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016219	55330	BLOC1S4	http://www.ncbi.nlm.nih.gov/gene/?term=55330	"BCAS4L, BLOS4, CNO "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016220	55331	ACER3	http://www.ncbi.nlm.nih.gov/gene/?term=55331	"APHC, PHCA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016221	55332	DRAM1	http://www.ncbi.nlm.nih.gov/gene/?term=55332	DRAM	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016222	55333	SYNJ2BP	http://www.ncbi.nlm.nih.gov/gene/?term=55333	"ARIP2, OMP25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016223	55333	SYNJ2BP	http://www.ncbi.nlm.nih.gov/gene/?term=55333	"ARIP2, OMP25 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016224	55333	SYNJ2BP	http://www.ncbi.nlm.nih.gov/gene/?term=55333	"ARIP2, OMP25 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016225	55334	SLC39A9	http://www.ncbi.nlm.nih.gov/gene/?term=55334	"ZIP-9, ZIP9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016226	55337	C19orf66	http://www.ncbi.nlm.nih.gov/gene/?term=55337	RyDEN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016227	55337	C19orf66	http://www.ncbi.nlm.nih.gov/gene/?term=55337	RyDEN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016228	55339	WDR33	http://www.ncbi.nlm.nih.gov/gene/?term=55339	"NET14, WDC146 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016229	55339	WDR33	http://www.ncbi.nlm.nih.gov/gene/?term=55339	"NET14, WDC146 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016230	5533	PPP3CC	http://www.ncbi.nlm.nih.gov/gene/?term=5533	"CALNA3, CNA3, PP2Bgamma "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016231	55341	LSG1	http://www.ncbi.nlm.nih.gov/gene/?term=55341		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016232	55342	STRBP	http://www.ncbi.nlm.nih.gov/gene/?term=55342	"HEL162, ILF3L, SPNR, p74 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016233	55342	STRBP	http://www.ncbi.nlm.nih.gov/gene/?term=55342	"HEL162, ILF3L, SPNR, p74 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016234	55342	STRBP	http://www.ncbi.nlm.nih.gov/gene/?term=55342	"HEL162, ILF3L, SPNR, p74 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016235	55343	SLC35C1	http://www.ncbi.nlm.nih.gov/gene/?term=55343	"CDG2C, FUCT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016236	55344	PLCXD1	http://www.ncbi.nlm.nih.gov/gene/?term=55344	LL0XNC01-136G2.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016237	55346	TCP11L1	http://www.ncbi.nlm.nih.gov/gene/?term=55346	dJ85M6.3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016238	55346	TCP11L1	http://www.ncbi.nlm.nih.gov/gene/?term=55346	dJ85M6.3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016239	55347	ABHD10	http://www.ncbi.nlm.nih.gov/gene/?term=55347		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016240	55347	ABHD10	http://www.ncbi.nlm.nih.gov/gene/?term=55347		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016241	55349	CHDH	http://www.ncbi.nlm.nih.gov/gene/?term=55349		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016242	5534	PPP3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5534	"CALNB1, CNB, CNB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016243	5534	PPP3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5534	"CALNB1, CNB, CNB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016244	55352	COPRS	http://www.ncbi.nlm.nih.gov/gene/?term=55352	"C17orf79, COPR5, HSA272196, TTP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016245	55353	LAPTM4B	http://www.ncbi.nlm.nih.gov/gene/?term=55353	"LAPTM4beta, LC27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016246	55353	LAPTM4B	http://www.ncbi.nlm.nih.gov/gene/?term=55353	"LAPTM4beta, LC27 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016247	55355	HJURP	http://www.ncbi.nlm.nih.gov/gene/?term=55355	"FAKTS, URLC9, hFLEG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016248	55355	HJURP	http://www.ncbi.nlm.nih.gov/gene/?term=55355	"FAKTS, URLC9, hFLEG1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016249	55355	HJURP	http://www.ncbi.nlm.nih.gov/gene/?term=55355	"FAKTS, URLC9, hFLEG1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016250	55355	HJURP	http://www.ncbi.nlm.nih.gov/gene/?term=55355	"FAKTS, URLC9, hFLEG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016251	55361	PI4K2A	http://www.ncbi.nlm.nih.gov/gene/?term=55361	"PI4KII, PIK42A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016252	55362	TMEM63B	http://www.ncbi.nlm.nih.gov/gene/?term=55362	C6orf110	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016253	55362	TMEM63B	http://www.ncbi.nlm.nih.gov/gene/?term=55362	C6orf110	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016254	55363	HEMGN	http://www.ncbi.nlm.nih.gov/gene/?term=55363	"CT155, EDAG, EDAG-1, NDR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016255	55364	IMPACT	http://www.ncbi.nlm.nih.gov/gene/?term=55364	RWDD5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016256	55364	IMPACT	http://www.ncbi.nlm.nih.gov/gene/?term=55364	RWDD5	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016257	55364	IMPACT	http://www.ncbi.nlm.nih.gov/gene/?term=55364	RWDD5	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016258	55364	IMPACT	http://www.ncbi.nlm.nih.gov/gene/?term=55364	RWDD5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016259	55366	LGR4	http://www.ncbi.nlm.nih.gov/gene/?term=55366	"BNMD17, GPR48 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016260	55366	LGR4	http://www.ncbi.nlm.nih.gov/gene/?term=55366	"BNMD17, GPR48 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016261	5536	PPP5C	http://www.ncbi.nlm.nih.gov/gene/?term=5536	"PP5, PPP5, PPT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016262	5536	PPP5C	http://www.ncbi.nlm.nih.gov/gene/?term=5536	"PP5, PPP5, PPT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016263	5536	PPP5C	http://www.ncbi.nlm.nih.gov/gene/?term=5536	"PP5, PPP5, PPT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016264	553718	nefma	http://www.ncbi.nlm.nih.gov/gene/?term=553718	zgc:112359	mRNA	Danio rerio	24089481	Axon	Embryoneuron	Whole mount in situ hybridization	"Here, we provide direct evidence of the presence of mRNAs of the tubb5, nefma, and stmnb2 genes in several types of axons in the developing zebrafish (Danio rerio) embryo, with frequent accumulation at the growth cone. We further show that axonal localization of mRNA is a specific property of a subset of genes, as mRNAs of the huc and neurod genes, abundantly expressed in neurons, were not found in axons. "
RLID00016265	55379	LRRC59	http://www.ncbi.nlm.nih.gov/gene/?term=55379	"PRO1855, p34 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016266	5537	PPP6C	http://www.ncbi.nlm.nih.gov/gene/?term=5537	"PP6, PP6C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016267	5537	PPP6C	http://www.ncbi.nlm.nih.gov/gene/?term=5537	"PP6, PP6C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016268	5537	PPP6C	http://www.ncbi.nlm.nih.gov/gene/?term=5537	"PP6, PP6C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016269	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1 "	lncRNA	Homo sapiens	21625215	Cytoplasm	Hepatoma cell	In situ hybridization	RNA in situ hybridization showed intense cytoplasmic expression of MEG3 in non-neoplastic liver with absent or very weak expression in HCC tissues.
RLID00016270	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1 "	lncRNA	Homo sapiens	21128942	Nucleus	Brain tissue	qRT-PCR|Microarray	Table 2: Long noncoding RNAs represented on Affymetrix U133 arrays that were reliably detected in human nucleus accumbens. An lncRNA was considered reliably detected in human NAcc if at least one probe corresponding to the transcript gave a specific signal in all control subjects. No transcripts undetected in the controls were consistently detected in drug abusers. Data are collected from Talbe 2.
RLID00016271	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1 "	lncRNA	Homo sapiens	22955988	Nucleus	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00016272	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1 "	lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00016273	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1 "	lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00016274	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1 "	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016275	55388	MCM10	http://www.ncbi.nlm.nih.gov/gene/?term=55388	"CNA43, DNA43, PRO2249 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016276	5538	PPT1	http://www.ncbi.nlm.nih.gov/gene/?term=5538	"CLN1, INCL, PPT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016277	5538	PPT1	http://www.ncbi.nlm.nih.gov/gene/?term=5538	"CLN1, INCL, PPT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016278	5538	PPT1	http://www.ncbi.nlm.nih.gov/gene/?term=5538	"CLN1, INCL, PPT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016279	554161	AA438147	http://www.ncbi.nlm.nih.gov/gene/?term=554161		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016280	554202	MIR31HG	http://www.ncbi.nlm.nih.gov/gene/?term=554202		lncRNA	Homo sapiens	25908244	Cytoplasm	TIG3 cell|BJ cell	qRT-PCR	"Under normal conditions, MIR31HG is found in both nucleus and cytoplasm, but following B-RAF expression MIR31HG is located mainly in the cytoplasm. Under normal conditions MIR31HG is located in both the nucleus and the cytoplasm, whereas upon B-RAF expression MIR31HG is almost exclusively localized in the cytoplasm.  "
RLID00016281	554202	MIR31HG	http://www.ncbi.nlm.nih.gov/gene/?term=554202		lncRNA	Homo sapiens	25908244	Nucleus	TIG3 cell|BJ cell	qRT-PCR	"Under normal conditions, MIR31HG is found in both nucleus and cytoplasm, but following B-RAF expression MIR31HG is located mainly in the cytoplasm. Under normal conditions MIR31HG is located in both the nucleus and the cytoplasm, whereas upon B-RAF expression MIR31HG is almost exclusively localized in the cytoplasm.  "
RLID00016282	55421	NCBP3	http://www.ncbi.nlm.nih.gov/gene/?term=55421	"C17orf85, ELG, HSA277841 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016283	554226	ANKRD30BL	http://www.ncbi.nlm.nih.gov/gene/?term=554226	"ANKRD30BP3, NCRNA00164 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016284	55422	ZNF331	http://www.ncbi.nlm.nih.gov/gene/?term=55422	"RITA, ZNF361, ZNF463 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016285	55422	ZNF331	http://www.ncbi.nlm.nih.gov/gene/?term=55422	"RITA, ZNF361, ZNF463 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016286	554313	HIST2H4B	http://www.ncbi.nlm.nih.gov/gene/?term=554313	H4/o	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016287	554327	2610042L04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=554327	"Tksn, takusan "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016288	55435	AP1AR	http://www.ncbi.nlm.nih.gov/gene/?term=55435	"2C18, C4orf16, GBAR, PRO0971, gamma-BAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016289	55437	STRADB	http://www.ncbi.nlm.nih.gov/gene/?term=55437	"ALS2CR2, CALS-21, ILPIP, ILPIPA, PAPK, PRO1038 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016290	55437	STRADB	http://www.ncbi.nlm.nih.gov/gene/?term=55437	"ALS2CR2, CALS-21, ILPIP, ILPIPA, PAPK, PRO1038 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016291	55437	STRADB	http://www.ncbi.nlm.nih.gov/gene/?term=55437	"ALS2CR2, CALS-21, ILPIP, ILPIPA, PAPK, PRO1038 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016292	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, PRO1488 "	lncRNA	Homo sapiens	22891334	Cytoplasm	HL7702 cell|HepG2 cell	qRT-PCR	"QPCR analysis of nuclear and cytoplasmic RNA extracts from HL7702 and HepG2 cells found that AS1DHRS4 was distributed more in the cytoplasm (60.47%) and less in the nucleus (39.53%) (SI Appendix, Fig. S3C). "
RLID00016293	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, PRO1488 "	lncRNA	Homo sapiens	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/dhrs4-as1/
RLID00016294	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, PRO1488 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016295	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, PRO1488 "	lncRNA	Homo sapiens	22891334	Nucleus	HL7702 cell|HepG2 cell	qRT-PCR	"QPCR analysis of nuclear and cytoplasmic RNA extracts from HL7702 and HepG2 cells found that AS1DHRS4 was distributed more in the cytoplasm (60.47%) and less in the nucleus (39.53%) (SI Appendix, Fig. S3C). "
RLID00016296	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, PRO1488 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016297	55450	CAMK2N1	http://www.ncbi.nlm.nih.gov/gene/?term=55450	PRO1489	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016298	55450	CAMK2N1	http://www.ncbi.nlm.nih.gov/gene/?term=55450	PRO1489	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016299	55454	CSGALNACT2	http://www.ncbi.nlm.nih.gov/gene/?term=55454	"CHGN2, ChGn-2, GALNACT-2, GALNACT2, PRO0082, beta4GalNAcT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016300	55466	DNAJA4	http://www.ncbi.nlm.nih.gov/gene/?term=55466	"MST104, MSTP104, PRO1472 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016301	55466	DNAJA4	http://www.ncbi.nlm.nih.gov/gene/?term=55466	"MST104, MSTP104, PRO1472 "	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00016302	5546	PRCC	http://www.ncbi.nlm.nih.gov/gene/?term=5546	"RCCP1, TPRC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016303	5546	PRCC	http://www.ncbi.nlm.nih.gov/gene/?term=5546	"RCCP1, TPRC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016304	5547	PRCP	http://www.ncbi.nlm.nih.gov/gene/?term=5547	"HUMPCP, PCP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016305	55486	PARL	http://www.ncbi.nlm.nih.gov/gene/?term=55486	"PRO2207, PSARL, PSARL1, PSENIP2, RHBDS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016306	55500	ETNK1	http://www.ncbi.nlm.nih.gov/gene/?term=55500	"EKI, EKI 1, EKI1, Nbla10396 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016307	55500	ETNK1	http://www.ncbi.nlm.nih.gov/gene/?term=55500	"EKI, EKI 1, EKI1, Nbla10396 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016308	55502	HES6	http://www.ncbi.nlm.nih.gov/gene/?term=55502	"C-HAIRY1, HES-6, bHLHb41, bHLHc23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016309	55503	TRPV6	http://www.ncbi.nlm.nih.gov/gene/?term=55503	"ABP/ZF, CAT1, CATL, ECAC2, HSA277909, LP6728, ZFAB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016310	55505	NOP10	http://www.ncbi.nlm.nih.gov/gene/?term=55505	"DKCB1, NOLA3P, NOP10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016311	55505	NOP10	http://www.ncbi.nlm.nih.gov/gene/?term=55505	"DKCB1, NOLA3, NOP10P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016312	55506	H2AFY2	http://www.ncbi.nlm.nih.gov/gene/?term=55506	macroH2A2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016313	5550	PREP	http://www.ncbi.nlm.nih.gov/gene/?term=5550	"PE, PEP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016314	5550	PREP	http://www.ncbi.nlm.nih.gov/gene/?term=5550	"PE, PEP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016315	5550	PREP	http://www.ncbi.nlm.nih.gov/gene/?term=5550	"PE, PEP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016316	55511	SAGE1	http://www.ncbi.nlm.nih.gov/gene/?term=55511	"CT14, SAGE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016317	55512	SMPD3	http://www.ncbi.nlm.nih.gov/gene/?term=55512	NSMASE2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016318	55520	ELAC1	http://www.ncbi.nlm.nih.gov/gene/?term=55520	D29	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016319	55520	ELAC1	http://www.ncbi.nlm.nih.gov/gene/?term=55520	D29	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016320	55526	DHTKD1	http://www.ncbi.nlm.nih.gov/gene/?term=55526	"AMOXAD, CMT2Q "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016321	55527	FEM1A	http://www.ncbi.nlm.nih.gov/gene/?term=55527	EPRAP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016322	55527	FEM1A	http://www.ncbi.nlm.nih.gov/gene/?term=55527	EPRAP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016323	55527	FEM1A	http://www.ncbi.nlm.nih.gov/gene/?term=55527	EPRAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016324	5552	SRGN	http://www.ncbi.nlm.nih.gov/gene/?term=5552	"PPG, PRG, PRG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016325	55530	SVOP	http://www.ncbi.nlm.nih.gov/gene/?term=55530		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016326	55530	SVOP	http://www.ncbi.nlm.nih.gov/gene/?term=55530		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016327	55532	SLC30A10	http://www.ncbi.nlm.nih.gov/gene/?term=55532	"HMDPC, ZNT10, ZNT8, ZRC1, ZnT-10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016328	55536	CDCA7L	http://www.ncbi.nlm.nih.gov/gene/?term=55536	"JPO2, R1, RAM2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016329	5553	PRG2	http://www.ncbi.nlm.nih.gov/gene/?term=5553	"BMPG, MBP, MBP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016330	55540	IL17RB	http://www.ncbi.nlm.nih.gov/gene/?term=55540	"CRL4, EVI27, IL17BR, IL17RH1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016331	55544	RBM38	http://www.ncbi.nlm.nih.gov/gene/?term=55544	"HSRNASEB, RNPC1, SEB4B, SEB4D, dJ800J21.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016332	55544	RBM38	http://www.ncbi.nlm.nih.gov/gene/?term=55544	"HSRNASEB, RNPC1, SEB4B, SEB4D, dJ800J21.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016333	55552	ZNF823	http://www.ncbi.nlm.nih.gov/gene/?term=55552	HSZFP36	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016334	55553	SOX6	http://www.ncbi.nlm.nih.gov/gene/?term=55553	"HSSOX6, SOXD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016335	55556	ENOSF1	http://www.ncbi.nlm.nih.gov/gene/?term=55556	"RTS, TYMSAS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016336	55556	ENOSF1	http://www.ncbi.nlm.nih.gov/gene/?term=55556	"RTS, TYMSAS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016337	55558	PLXNA3	http://www.ncbi.nlm.nih.gov/gene/?term=55558	"6.3, HSSEXGENE, PLXN3, PLXN4, XAP-6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016338	55565	ZNF821	http://www.ncbi.nlm.nih.gov/gene/?term=55565		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016339	55568	GALNT10	http://www.ncbi.nlm.nih.gov/gene/?term=55568	"GALNACT10, PPGALNACT10, PPGANTASE10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016340	55568	GALNT10	http://www.ncbi.nlm.nih.gov/gene/?term=55568	"GALNACT10, PPGALNACT10, PPGANTASE10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016341	55568	GALNT10	http://www.ncbi.nlm.nih.gov/gene/?term=55568	"GALNACT10, PPGALNACT10, PPGANTASE10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016342	55571	CNOT11	http://www.ncbi.nlm.nih.gov/gene/?term=55571	"C2orf29, C40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016343	55571	CNOT11	http://www.ncbi.nlm.nih.gov/gene/?term=55571	"C2orf29, C40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016344	55572	FOXRED1	http://www.ncbi.nlm.nih.gov/gene/?term=55572	"FP634, H17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016345	55572	FOXRED1	http://www.ncbi.nlm.nih.gov/gene/?term=55572	"FP634, H17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016346	55573	CDV3	http://www.ncbi.nlm.nih.gov/gene/?term=55573	H41	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016347	55573	CDV3	http://www.ncbi.nlm.nih.gov/gene/?term=55573	H41	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016348	55573	CDV3	http://www.ncbi.nlm.nih.gov/gene/?term=55573	H41	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016349	55578	SUPT20H	http://www.ncbi.nlm.nih.gov/gene/?term=55578	"C13, C13orf19, FAM48A, FP757, P38IP, SPT20 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016350	5557	PRIM1	http://www.ncbi.nlm.nih.gov/gene/?term=5557	p49	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016351	55585	UBE2Q1	http://www.ncbi.nlm.nih.gov/gene/?term=55585	"GTAP, NICE-5, PRO3094, UBE2Q "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016352	55585	UBE2Q1	http://www.ncbi.nlm.nih.gov/gene/?term=55585	"GTAP, NICE-5, PRO3094, UBE2Q "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016353	55588	MED29	http://www.ncbi.nlm.nih.gov/gene/?term=55588	"IXL, MED2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016354	55589	BMP2K	http://www.ncbi.nlm.nih.gov/gene/?term=55589	"BIKE, HRIHFB2017 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016355	5558	PRIM2	http://www.ncbi.nlm.nih.gov/gene/?term=5558	"PRIM2A, p58 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016356	55591	VEZT	http://www.ncbi.nlm.nih.gov/gene/?term=55591	VEZATIN	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016357	55592	GOLGA2P5	http://www.ncbi.nlm.nih.gov/gene/?term=55592	"GOLGA2B, GOLGA2L1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016358	55593	OTUD5	http://www.ncbi.nlm.nih.gov/gene/?term=55593	DUBA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016359	55599	RNPC3	http://www.ncbi.nlm.nih.gov/gene/?term=55599	"RBM40, RNP, SNRNP65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016360	55601	DDX60	http://www.ncbi.nlm.nih.gov/gene/?term=55601		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016361	55601	DDX60	http://www.ncbi.nlm.nih.gov/gene/?term=55601		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016362	55602	CDKN2AIP	http://www.ncbi.nlm.nih.gov/gene/?term=55602	CARF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016363	55604	LRRC16A	http://www.ncbi.nlm.nih.gov/gene/?term=55604	"CARMIL, CARMIL1, CARMIL1a, LRRC16, dJ501N12.1, dJ501N12.5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016364	55607	PPP1R9A	http://www.ncbi.nlm.nih.gov/gene/?term=55607	"NRB1, NRBI, Neurabin-I "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016365	55607	PPP1R9A	http://www.ncbi.nlm.nih.gov/gene/?term=55607	"NRB1, NRBI, Neurabin-I "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016366	55607	PPP1R9A	http://www.ncbi.nlm.nih.gov/gene/?term=55607	"NRB1, NRBI, Neurabin-I "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016367	55608	ANKRD10	http://www.ncbi.nlm.nih.gov/gene/?term=55608		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016368	55609	ZNF280C	http://www.ncbi.nlm.nih.gov/gene/?term=55609	"SUHW3, ZNF633 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016369	55609	ZNF280C	http://www.ncbi.nlm.nih.gov/gene/?term=55609	"SUHW3, ZNF633 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016370	55610	VPS50	http://www.ncbi.nlm.nih.gov/gene/?term=55610	"CCDC132, VPS54L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016371	55611	OTUB1	http://www.ncbi.nlm.nih.gov/gene/?term=55611	"HSPC263, OTB1, OTU1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016372	55612	FERMT1	http://www.ncbi.nlm.nih.gov/gene/?term=55612	"C20orf42, DTGCU2, KIND1, UNC112A, URP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016373	55614	KIF16B	http://www.ncbi.nlm.nih.gov/gene/?term=55614	"C20orf23, KISC20ORF, SNX23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016374	55615	PRR5	http://www.ncbi.nlm.nih.gov/gene/?term=55615	"FLJ20185k, PP610, PROTOR-1, PROTOR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016375	55620	STAP2	http://www.ncbi.nlm.nih.gov/gene/?term=55620	BKS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016376	55622	TTC27	http://www.ncbi.nlm.nih.gov/gene/?term=55622		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016377	55623	THUMPD1	http://www.ncbi.nlm.nih.gov/gene/?term=55623	Tan1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016378	55623	THUMPD1	http://www.ncbi.nlm.nih.gov/gene/?term=55623	Tan1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016379	55624	POMGNT1	http://www.ncbi.nlm.nih.gov/gene/?term=55624	"GNTI.2, GnT I.2, LGMD2O, MEB, MGAT1.2, gnT-I.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016380	55624	POMGNT1	http://www.ncbi.nlm.nih.gov/gene/?term=55624	"GNTI.2, GnT I.2, LGMD2O, MEB, MGAT1.2, gnT-I.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016381	55625	ZDHHC7	http://www.ncbi.nlm.nih.gov/gene/?term=55625	"DHHC7, SERZ-B, SERZ1, ZNF370 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016382	55626	AMBRA1	http://www.ncbi.nlm.nih.gov/gene/?term=55626	"DCAF3, WDR94 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016383	55626	AMBRA1	http://www.ncbi.nlm.nih.gov/gene/?term=55626	"DCAF3, WDR94 "	mRNA	Homo sapiens	26086269	Cytoplasm	HeLa cell|HEK-293 cell	Fluorescence in situ hybridization	Partial re-localization of Ambra1 mRNA to non-translating fractions and cytoplasmic P-bodies was further detected.
RLID00016384	55627	SMPD4	http://www.ncbi.nlm.nih.gov/gene/?term=55627	"NET13, NSMASE-3, NSMASE3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016385	55628	ZNF407	http://www.ncbi.nlm.nih.gov/gene/?term=55628		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016386	55629	PNRC2	http://www.ncbi.nlm.nih.gov/gene/?term=55629		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016387	5562	PRKAA1	http://www.ncbi.nlm.nih.gov/gene/?term=5562	"AMPK, AMPKa1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016388	5562	PRKAA1	http://www.ncbi.nlm.nih.gov/gene/?term=5562	"AMPK, AMPKa1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016389	55630	SLC39A4	http://www.ncbi.nlm.nih.gov/gene/?term=55630	"AEZ, AWMS2, ZIP4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016390	55631	LRRC40	http://www.ncbi.nlm.nih.gov/gene/?term=55631	dJ677H15.1	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016391	55632	G2E3	http://www.ncbi.nlm.nih.gov/gene/?term=55632	"KIAA1333, PHF7B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016392	55634	KRBOX4	http://www.ncbi.nlm.nih.gov/gene/?term=55634	ZNF673	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016393	55635	DEPDC1	http://www.ncbi.nlm.nih.gov/gene/?term=55635	"DEP.8-V2, DEPDC1A, SDP35, DEPDC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016394	55636	CHD7	http://www.ncbi.nlm.nih.gov/gene/?term=55636	"CRG, HH5, IS3, KAL5 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016395	5563	PRKAA2	http://www.ncbi.nlm.nih.gov/gene/?term=5563	"AMPK, AMPK2, AMPKa2, PRKAA "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00016396	55640	FLVCR2	http://www.ncbi.nlm.nih.gov/gene/?term=55640	"C14orf58, CCT, EPV, FLVCRL14q, MFSD7C, PVHH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016397	55644	OSGEP	http://www.ncbi.nlm.nih.gov/gene/?term=55644	"GCPL1, KAE11, PRSMG1, OSGEP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016398	55644	OSGEP	http://www.ncbi.nlm.nih.gov/gene/?term=55644	"GCPL1, KAE11, PRSMG1, OSGEP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016399	55644	OSGEP	http://www.ncbi.nlm.nih.gov/gene/?term=55644	"GCPL1, KAE1, OSGEP1, PRSMG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016400	55646	LYAR	http://www.ncbi.nlm.nih.gov/gene/?term=55646	"ZC2HC2, ZLYAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016401	55646	LYAR	http://www.ncbi.nlm.nih.gov/gene/?term=55646	"ZC2HC2, ZLYAR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016402	55647	RAB20	http://www.ncbi.nlm.nih.gov/gene/?term=55647		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016403	5564	PRKAB1	http://www.ncbi.nlm.nih.gov/gene/?term=5564	"AMPK, HAMPKb "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016404	5564	PRKAB1	http://www.ncbi.nlm.nih.gov/gene/?term=5564	"AMPK, HAMPKb "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016405	55650	PIGV	http://www.ncbi.nlm.nih.gov/gene/?term=55650	"GPI-MT-II, HPMRS1, PIG-V "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016406	55651	NHP2	http://www.ncbi.nlm.nih.gov/gene/?term=55651	"DKCB2P, NOLA2, NHP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016407	55652	SLC48A1	http://www.ncbi.nlm.nih.gov/gene/?term=55652	"HRG-1, HRG1, hHRG-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016408	55654	TMEM127	http://www.ncbi.nlm.nih.gov/gene/?term=55654		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016409	55654	TMEM127	http://www.ncbi.nlm.nih.gov/gene/?term=55654		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016410	55654	TMEM127	http://www.ncbi.nlm.nih.gov/gene/?term=55654		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016411	55654	TMEM127	http://www.ncbi.nlm.nih.gov/gene/?term=55654		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016412	55655	NLRP2	http://www.ncbi.nlm.nih.gov/gene/?term=55655	"CLR19.9, NALP2, NBS1, PAN1, PYPAF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016413	55656	INTS8	http://www.ncbi.nlm.nih.gov/gene/?term=55656	"C8orf52, INT8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016414	55657	ZNF692	http://www.ncbi.nlm.nih.gov/gene/?term=55657	"AREBP, Zfp692 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016415	55658	RNF126	http://www.ncbi.nlm.nih.gov/gene/?term=55658		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016416	55658	RNF126	http://www.ncbi.nlm.nih.gov/gene/?term=55658		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016417	5565	PRKAB2	http://www.ncbi.nlm.nih.gov/gene/?term=5565		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016418	55660	PRPF40A	http://www.ncbi.nlm.nih.gov/gene/?term=55660	"FBP-11, FBP11, FLAF1, FNBP3, HIP-10, HIP10, HYPA, NY-REN-6, Prp40 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016419	55660	PRPF40A	http://www.ncbi.nlm.nih.gov/gene/?term=55660	"FBP-11, FBP11, FLAF1, FNBP3, HIP-10, HIP10, HYPA, NY-REN-6, Prp40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016420	55662	HIF1AN	http://www.ncbi.nlm.nih.gov/gene/?term=55662	FIH1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016421	55662	HIF1AN	http://www.ncbi.nlm.nih.gov/gene/?term=55662	FIH1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016422	55664	CDC37L1	http://www.ncbi.nlm.nih.gov/gene/?term=55664	"CDC37B, HARC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016423	55664	CDC37L1	http://www.ncbi.nlm.nih.gov/gene/?term=55664	"CDC37B, HARC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016424	55665	URGCP	http://www.ncbi.nlm.nih.gov/gene/?term=55665	URG4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016425	55665	URGCP	http://www.ncbi.nlm.nih.gov/gene/?term=55665	URG4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016426	55666	NPLOC4	http://www.ncbi.nlm.nih.gov/gene/?term=55666	NPL4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016427	55667	DENND4C	http://www.ncbi.nlm.nih.gov/gene/?term=55667	"C9orf55, C9orf55B, bA513M16.3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016428	55667	DENND4C	http://www.ncbi.nlm.nih.gov/gene/?term=55667	"C9orf55, C9orf55B, bA513M16.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016429	55668	GPATCH2L	http://www.ncbi.nlm.nih.gov/gene/?term=55668	C14orf118	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016430	55668	GPATCH2L	http://www.ncbi.nlm.nih.gov/gene/?term=55668	C14orf118	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016431	55669	MFN1	http://www.ncbi.nlm.nih.gov/gene/?term=55669	"hfzo1, hfzo2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016432	55669	MFN1	http://www.ncbi.nlm.nih.gov/gene/?term=55669	"hfzo1, hfzo2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016433	55669	MFN1	http://www.ncbi.nlm.nih.gov/gene/?term=55669	"hfzo1, hfzo2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016434	55670	PEX26	http://www.ncbi.nlm.nih.gov/gene/?term=55670	"PBD7A, PBD7BM1T, Pex26pM1T, PEX26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016435	55671	PPP4R3A	http://www.ncbi.nlm.nih.gov/gene/?term=55671	"FLFL1, KIAA2010, MSTP033, PP4R3, PP4R3A, SMEK1, smk-1, smk1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016436	55671	PPP4R3A	http://www.ncbi.nlm.nih.gov/gene/?term=55671	"FLFL1, KIAA2010, MSTP033, PP4R3, PP4R3A, SMEK1, smk-1, smk1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016437	55671	PPP4R3A	http://www.ncbi.nlm.nih.gov/gene/?term=55671	"FLFL1, KIAA2010, MSTP033, PP4R3, PP4R3A, SMEK1, smk-1, smk1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016438	55672	NBPF1	http://www.ncbi.nlm.nih.gov/gene/?term=55672	"AB13, AB14, AB23, AD2, NBG, NBPF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016439	55672	NBPF1	http://www.ncbi.nlm.nih.gov/gene/?term=55672	"AB13, AB14, AB23, AD2, NBG, NBPF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016440	55676	SLC30A6	http://www.ncbi.nlm.nih.gov/gene/?term=55676	"MST103, MSTP103, ZNT6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016441	55676	SLC30A6	http://www.ncbi.nlm.nih.gov/gene/?term=55676	"MST103, MSTP103, ZNT6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016442	55677	IWS1	http://www.ncbi.nlm.nih.gov/gene/?term=55677		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016443	55677	IWS1	http://www.ncbi.nlm.nih.gov/gene/?term=55677		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016444	55683	KANSL3	http://www.ncbi.nlm.nih.gov/gene/?term=55683	"KIAA1310, NSL3, Rcd1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016445	55686	MREG	http://www.ncbi.nlm.nih.gov/gene/?term=55686	"DSU, WDT2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016446	55686	MREG	http://www.ncbi.nlm.nih.gov/gene/?term=55686	"DSU, WDT2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016447	55686	MREG	http://www.ncbi.nlm.nih.gov/gene/?term=55686	"DSU, WDT2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016448	55686	MREG	http://www.ncbi.nlm.nih.gov/gene/?term=55686	"DSU, WDT2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016449	55687	TRMU	http://www.ncbi.nlm.nih.gov/gene/?term=55687	"LCAL3, MTO2, MTU1, TRMT, TRMT1, TRNT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016450	55689	YEATS2	http://www.ncbi.nlm.nih.gov/gene/?term=55689		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016451	55690	PACS1	http://www.ncbi.nlm.nih.gov/gene/?term=55690	MRD17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016452	55692	LUC7L	http://www.ncbi.nlm.nih.gov/gene/?term=55692	"LUC7B1, Luc7, SR+89, hLuc7B1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016453	55696	RBM22	http://www.ncbi.nlm.nih.gov/gene/?term=55696	"Cwc2, ZC3H16, fSAP47 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016454	55696	RBM22	http://www.ncbi.nlm.nih.gov/gene/?term=55696	"Cwc2, ZC3H16, fSAP47 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016455	55696	RBM22	http://www.ncbi.nlm.nih.gov/gene/?term=55696	"Cwc2, ZC3H16, fSAP47 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016456	55697	VAC14	http://www.ncbi.nlm.nih.gov/gene/?term=55697	"ArPIKfyve, TAX1BP2, TRX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016457	55699	IARS2	http://www.ncbi.nlm.nih.gov/gene/?term=55699	"CAGSSS, ILERS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016458	5569	PKIA	http://www.ncbi.nlm.nih.gov/gene/?term=5569	PRKACN1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016459	5569	PKIA	http://www.ncbi.nlm.nih.gov/gene/?term=5569	PRKACN1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016460	55700	MAP7D1	http://www.ncbi.nlm.nih.gov/gene/?term=55700	"PARCC1, RPRC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016461	55700	MAP7D1	http://www.ncbi.nlm.nih.gov/gene/?term=55700	"PARCC1, RPRC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016462	55701	ARHGEF40	http://www.ncbi.nlm.nih.gov/gene/?term=55701	SOLO	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016463	55702	CCDC94	http://www.ncbi.nlm.nih.gov/gene/?term=55702		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016464	55704	CCDC88A	http://www.ncbi.nlm.nih.gov/gene/?term=55704	"APE, GIRDIN, GIV, GRDN, HkRP1, KIAA1212 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016465	55704	CCDC88A	http://www.ncbi.nlm.nih.gov/gene/?term=55704	"APE, GIRDIN, GIV, GRDN, HkRP1, KIAA1212 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016466	55705	IPO9	http://www.ncbi.nlm.nih.gov/gene/?term=55705	Imp9	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016467	55705	IPO9	http://www.ncbi.nlm.nih.gov/gene/?term=55705	Imp9	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016468	55705	IPO9	http://www.ncbi.nlm.nih.gov/gene/?term=55705	Imp9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016469	55707	NECAP2	http://www.ncbi.nlm.nih.gov/gene/?term=55707		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016470	5570	PKIB	http://www.ncbi.nlm.nih.gov/gene/?term=5570	PRKACN2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016471	5570	PKIB	http://www.ncbi.nlm.nih.gov/gene/?term=5570	PRKACN2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016472	55711	FAR2	http://www.ncbi.nlm.nih.gov/gene/?term=55711	"HEL-S-81, MLSTD1, SDR10E2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016473	55717	WDR11	http://www.ncbi.nlm.nih.gov/gene/?term=55717	"BRWD2, DR11, HH14, WDR15 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016474	55717	WDR11	http://www.ncbi.nlm.nih.gov/gene/?term=55717	"BRWD2, DR11, HH14, WDR15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016475	55718	POLR3E	http://www.ncbi.nlm.nih.gov/gene/?term=55718	"RPC5, SIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016476	55718	POLR3E	http://www.ncbi.nlm.nih.gov/gene/?term=55718	"RPC5, SIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016477	55719	SLF2	http://www.ncbi.nlm.nih.gov/gene/?term=55719	"C10orf6, FAM178A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016478	5571	PRKAG1	http://www.ncbi.nlm.nih.gov/gene/?term=5571	AMPKG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016479	5571	PRKAG1	http://www.ncbi.nlm.nih.gov/gene/?term=5571	AMPKG	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016480	55720	TSR1	http://www.ncbi.nlm.nih.gov/gene/?term=55720		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016481	55723	ASF1B	http://www.ncbi.nlm.nih.gov/gene/?term=55723	CIA-II	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016482	55723	ASF1B	http://www.ncbi.nlm.nih.gov/gene/?term=55723	CIA-II	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016483	55726	ASUN	http://www.ncbi.nlm.nih.gov/gene/?term=55726	"C12orf11, GCT1, Mat89Bb, NET48, SPATA30 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016484	55726	ASUN	http://www.ncbi.nlm.nih.gov/gene/?term=55726	"C12orf11, GCT1, Mat89Bb, NET48, SPATA30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016485	55727	BTBD7	http://www.ncbi.nlm.nih.gov/gene/?term=55727	FUP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016486	55728	N4BP2	http://www.ncbi.nlm.nih.gov/gene/?term=55728	B3BP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016487	55728	N4BP2	http://www.ncbi.nlm.nih.gov/gene/?term=55728	B3BP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016488	55729	ATF7IP	http://www.ncbi.nlm.nih.gov/gene/?term=55729	"AM, ATF-IP, MCAF, MCAF1, p621 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016489	55731	FAM222B	http://www.ncbi.nlm.nih.gov/gene/?term=55731	C17orf63	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016490	55732	C1orf112	http://www.ncbi.nlm.nih.gov/gene/?term=55732		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016491	55734	ZFP64	http://www.ncbi.nlm.nih.gov/gene/?term=55734	ZNF338	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016492	55734	ZFP64	http://www.ncbi.nlm.nih.gov/gene/?term=55734	ZNF338	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016493	55735	DNAJC11	http://www.ncbi.nlm.nih.gov/gene/?term=55735	dJ126A5.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016494	55735	DNAJC11	http://www.ncbi.nlm.nih.gov/gene/?term=55735	dJ126A5.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016495	55737	VPS35	http://www.ncbi.nlm.nih.gov/gene/?term=55737	"MEM3, PARK17 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016496	55737	VPS35	http://www.ncbi.nlm.nih.gov/gene/?term=55737	"MEM3, PARK17 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016497	55737	VPS35	http://www.ncbi.nlm.nih.gov/gene/?term=55737	"MEM3, PARK17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016498	55738	ARFGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=55738	"ARF1GAP, HRIHFB2281 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016499	55739	NAXD	http://www.ncbi.nlm.nih.gov/gene/?term=55739	LP3298	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016500	5573	PRKAR1A	http://www.ncbi.nlm.nih.gov/gene/?term=5573	"ACRDYS1, ADOHR, CAR, CNC, CNC1, PKR1, PPNAD1, PRKAR1, TSE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016501	5573	PRKAR1A	http://www.ncbi.nlm.nih.gov/gene/?term=5573	"ACRDYS1, ADOHR, CAR, CNC, CNC1, PKR1, PPNAD1, PRKAR1, TSE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016502	55740	ENAH	http://www.ncbi.nlm.nih.gov/gene/?term=55740	"ENA, MENA, NDPP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016503	55740	ENAH	http://www.ncbi.nlm.nih.gov/gene/?term=55740	"ENA, MENA, NDPP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016504	55740	ENAH	http://www.ncbi.nlm.nih.gov/gene/?term=55740	"ENA, MENA, NDPP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016505	55740	ENAH	http://www.ncbi.nlm.nih.gov/gene/?term=55740	"ENA, MENA, NDPP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016506	55741	EDEM2	http://www.ncbi.nlm.nih.gov/gene/?term=55741	"C20orf31, C20orf49, bA4204.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016507	55742	PARVA	http://www.ncbi.nlm.nih.gov/gene/?term=55742	"CH-ILKBP, MXRA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016508	55743	CHFR	http://www.ncbi.nlm.nih.gov/gene/?term=55743	"RNF116, RNF196 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016509	55744	COA1	http://www.ncbi.nlm.nih.gov/gene/?term=55744	"C7orf44, MITRAC15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016510	55744	COA1	http://www.ncbi.nlm.nih.gov/gene/?term=55744	"C7orf44, MITRAC15 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016511	55745	AP5M1	http://www.ncbi.nlm.nih.gov/gene/?term=55745	"C14orf108, MUDENG, Mu5, MuD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016512	55746	NUP133	http://www.ncbi.nlm.nih.gov/gene/?term=55746	hNUP133	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016513	55746	NUP133	http://www.ncbi.nlm.nih.gov/gene/?term=55746	hNUP133	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016514	55748	CNDP2	http://www.ncbi.nlm.nih.gov/gene/?term=55748	"CN2, CPGL, HEL-S-13, HsT2298, PEPA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016515	55749	CCAR1	http://www.ncbi.nlm.nih.gov/gene/?term=55749		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016516	55749	CCAR1	http://www.ncbi.nlm.nih.gov/gene/?term=55749		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016517	55750	AGK	http://www.ncbi.nlm.nih.gov/gene/?term=55750	"CATC5, CTRCT38, MTDPS10, MULK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016518	55751	TMEM184C	http://www.ncbi.nlm.nih.gov/gene/?term=55751	TMEM34	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016519	55751	TMEM184C	http://www.ncbi.nlm.nih.gov/gene/?term=55751	TMEM34	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016520	55751	TMEM184C	http://www.ncbi.nlm.nih.gov/gene/?term=55751	TMEM34	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016521	55752	SEPT11	http://www.ncbi.nlm.nih.gov/gene/?term=55752		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016522	55753	OGDHL	http://www.ncbi.nlm.nih.gov/gene/?term=55753		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016523	55754	TMEM30A	http://www.ncbi.nlm.nih.gov/gene/?term=55754	"C6orf67, CDC50A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016524	55754	TMEM30A	http://www.ncbi.nlm.nih.gov/gene/?term=55754	"C6orf67, CDC50A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016525	55757	UGGT2	http://www.ncbi.nlm.nih.gov/gene/?term=55757	"HUGT2, UGCGL2, UGT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016526	55758	RCOR3	http://www.ncbi.nlm.nih.gov/gene/?term=55758		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016527	55758	RCOR3	http://www.ncbi.nlm.nih.gov/gene/?term=55758		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016528	55759	WDR12	http://www.ncbi.nlm.nih.gov/gene/?term=55759	YTM1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016529	5575	PRKAR1B	http://www.ncbi.nlm.nih.gov/gene/?term=5575	PRKAR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016530	5575	PRKAR1B	http://www.ncbi.nlm.nih.gov/gene/?term=5575	PRKAR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016531	55760	DHX32	http://www.ncbi.nlm.nih.gov/gene/?term=55760	"DDX32, DHLP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016532	55761	TTC17	http://www.ncbi.nlm.nih.gov/gene/?term=55761		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016533	55761	TTC17	http://www.ncbi.nlm.nih.gov/gene/?term=55761		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016534	55763	EXOC1	http://www.ncbi.nlm.nih.gov/gene/?term=55763	"BM-102, SEC3, SEC3L1, SEC3P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016535	55766	H2AFJ	http://www.ncbi.nlm.nih.gov/gene/?term=55766	H2AJ	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016536	55768	NGLY1	http://www.ncbi.nlm.nih.gov/gene/?term=55768	"CDDG, CDG1V, PNG1, PNGase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016537	55769	ZNF83	http://www.ncbi.nlm.nih.gov/gene/?term=55769	"HPF1, ZNF816B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016538	55769	ZNF83	http://www.ncbi.nlm.nih.gov/gene/?term=55769	"HPF1, ZNF816B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016539	5576	PRKAR2A	http://www.ncbi.nlm.nih.gov/gene/?term=5576	"PKR2, PRKAR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016540	55771	PRR11	http://www.ncbi.nlm.nih.gov/gene/?term=55771		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016541	55773	TBC1D23	http://www.ncbi.nlm.nih.gov/gene/?term=55773	NS4ATP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016542	55773	TBC1D23	http://www.ncbi.nlm.nih.gov/gene/?term=55773	NS4ATP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016543	55776	SAYSD1	http://www.ncbi.nlm.nih.gov/gene/?term=55776	C6orf64	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016544	55776	SAYSD1	http://www.ncbi.nlm.nih.gov/gene/?term=55776	C6orf64	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016545	5577	PRKAR2B	http://www.ncbi.nlm.nih.gov/gene/?term=5577	"PRKAR2, RII-BETA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016546	5577	PRKAR2B	http://www.ncbi.nlm.nih.gov/gene/?term=5577	"PRKAR2, RII-BETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016547	55783	CMTR2	http://www.ncbi.nlm.nih.gov/gene/?term=55783	"AFT, FTSJD1, HMTr2, MTr2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016548	55783	CMTR2	http://www.ncbi.nlm.nih.gov/gene/?term=55783	"AFT, FTSJD1, HMTr2, MTr2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016549	55785	FGD6	http://www.ncbi.nlm.nih.gov/gene/?term=55785	ZFYVE24	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016550	55785	FGD6	http://www.ncbi.nlm.nih.gov/gene/?term=55785	ZFYVE24	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016551	55789	DEPDC1B	http://www.ncbi.nlm.nih.gov/gene/?term=55789	"BRCC3, XTP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016552	55789	DEPDC1B	http://www.ncbi.nlm.nih.gov/gene/?term=55789	"BRCC3, XTP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016553	5578	PRKCA	http://www.ncbi.nlm.nih.gov/gene/?term=5578	"AAG6, PKC-alpha, PKCA, PRKACA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016554	5578	PRKCA	http://www.ncbi.nlm.nih.gov/gene/?term=5578	"AAG6, PKC-alpha, PKCA, PRKACA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016555	5578	PRKCA	http://www.ncbi.nlm.nih.gov/gene/?term=5578	"AAG6, PKC-alpha, PKCA, PRKACA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016556	5578	PRKCA	http://www.ncbi.nlm.nih.gov/gene/?term=5578	"AAG6, PKC-alpha, PKCA, PRKACA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016557	55791	LRIF1	http://www.ncbi.nlm.nih.gov/gene/?term=55791	"C1orf103, RIF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016558	55793	FAM63A	http://www.ncbi.nlm.nih.gov/gene/?term=55793		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016559	55793	FAM63A	http://www.ncbi.nlm.nih.gov/gene/?term=55793		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016560	55793	FAM63A	http://www.ncbi.nlm.nih.gov/gene/?term=55793		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016561	55794	DDX28	http://www.ncbi.nlm.nih.gov/gene/?term=55794	MDDX28	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016562	55794	DDX28	http://www.ncbi.nlm.nih.gov/gene/?term=55794	MDDX28	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016563	55795	PCID2	http://www.ncbi.nlm.nih.gov/gene/?term=55795	F10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016564	55795	PCID2	http://www.ncbi.nlm.nih.gov/gene/?term=55795	F10	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016565	55796	MBNL3	http://www.ncbi.nlm.nih.gov/gene/?term=55796	"CHCR, MBLX, MBLX39, MBXL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016566	55798	METTL2B	http://www.ncbi.nlm.nih.gov/gene/?term=55798	"METL, METTL2, METTL2A, PSENIP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016567	5579	PRKCB	http://www.ncbi.nlm.nih.gov/gene/?term=5579	"PKC-beta, PKCB1, PRKCB2, PRKCB "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00016568	5579	PRKCB	http://www.ncbi.nlm.nih.gov/gene/?term=5579	"PKC-beta, PKCB, PRKCB1, PRKCB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016569	5579	PRKCB	http://www.ncbi.nlm.nih.gov/gene/?term=5579	"PKCB, PRKCB1, PRKCB2, PKC-beta "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00016570	55802	DCP1A	http://www.ncbi.nlm.nih.gov/gene/?term=55802	"HSA275986, Nbla00360, SMAD4IP1, SMIF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016571	55802	DCP1A	http://www.ncbi.nlm.nih.gov/gene/?term=55802	"HSA275986, Nbla00360, SMAD4IP1, SMIF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016572	55803	ADAP2	http://www.ncbi.nlm.nih.gov/gene/?term=55803	"CENTA2, HSA272195, cent-b "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016573	55803	ADAP2	http://www.ncbi.nlm.nih.gov/gene/?term=55803	"CENTA2, HSA272195, cent-b "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016574	55806	HR	http://www.ncbi.nlm.nih.gov/gene/?term=55806	"ALUNC, AU, HSA277165, HYPT4, MUHH, MUHH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016575	55806	HR	http://www.ncbi.nlm.nih.gov/gene/?term=55806	"ALUNC, AU, HSA277165, HYPT4, MUHH, MUHH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016576	5580	PRKCD	http://www.ncbi.nlm.nih.gov/gene/?term=5580	"ALPS3, CVID9, MAY1, PKCD, nPKC-delta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016577	55814	BDP1	http://www.ncbi.nlm.nih.gov/gene/?term=55814	"HSA238520, TAF3B1, TFC5, TFIIIB'', TFIIIB150, TFIIIB90, TFNR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016578	55819	RNF130	http://www.ncbi.nlm.nih.gov/gene/?term=55819	"G1RZFP, GOLIATH, GP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016579	55824	PAG1	http://www.ncbi.nlm.nih.gov/gene/?term=55824	"CBP, PAG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016580	55824	PAG1	http://www.ncbi.nlm.nih.gov/gene/?term=55824	"CBP, PAG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016581	55825	PECR	http://www.ncbi.nlm.nih.gov/gene/?term=55825	"DCRRP, HPDHASE, HSA250303, PVIARL, SDR29C1, TERP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016582	55827	DCAF6	http://www.ncbi.nlm.nih.gov/gene/?term=55827	"1200006M05Rik, ARCAP, IQWD1, MSTP055, NRIP, PC326 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016583	55829	VIMP	http://www.ncbi.nlm.nih.gov/gene/?term=55829	"AD-015, ADO15, SBBI8, SELS, SEPS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016584	55829	VIMP	http://www.ncbi.nlm.nih.gov/gene/?term=55829	"AD-015, ADO15, SBBI8, SELS, SEPS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016585	5582	PRKCG	http://www.ncbi.nlm.nih.gov/gene/?term=5582	"PKC-gamma, PKCC, PKCG, SCA14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016586	55830	GLT8D1	http://www.ncbi.nlm.nih.gov/gene/?term=55830	"AD-017, MSTP139 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016587	55831	EMC3	http://www.ncbi.nlm.nih.gov/gene/?term=55831	"POB, TMEM111 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016588	55832	CAND1	http://www.ncbi.nlm.nih.gov/gene/?term=55832	"TIP120, TIP120A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016589	55832	CAND1	http://www.ncbi.nlm.nih.gov/gene/?term=55832	"TIP120, TIP120A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016590	55833	UBAP2	http://www.ncbi.nlm.nih.gov/gene/?term=55833	UBAP-2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016591	55833	UBAP2	http://www.ncbi.nlm.nih.gov/gene/?term=55833	UBAP-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016592	55835	CENPJ	http://www.ncbi.nlm.nih.gov/gene/?term=55835	"BM032, CENP-J, CPAP, LAP, LIP1, MCPH6, SASS4, SCKL4, Sas-4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016593	55835	CENPJ	http://www.ncbi.nlm.nih.gov/gene/?term=55835	"BM032, CENP-J, CPAP, LAP, LIP1, MCPH6, SASS4, SCKL4, Sas-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016594	55837	EAPP	http://www.ncbi.nlm.nih.gov/gene/?term=55837	"BM036, C14orf11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016595	55837	EAPP	http://www.ncbi.nlm.nih.gov/gene/?term=55837	"BM036, C14orf11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016596	55837	EAPP	http://www.ncbi.nlm.nih.gov/gene/?term=55837	"BM036, C14orf11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016597	55839	CENPN	http://www.ncbi.nlm.nih.gov/gene/?term=55839	"BM039, C16orf60, CENP-N, ICEN32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016598	55839	CENPN	http://www.ncbi.nlm.nih.gov/gene/?term=55839	"BM039, C16orf60, CENP-N, ICEN32 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016599	5583	PRKCH	http://www.ncbi.nlm.nih.gov/gene/?term=5583	"PKC-L, PKCL, PRKCL, nPKC-eta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016600	55843	ARHGAP15	http://www.ncbi.nlm.nih.gov/gene/?term=55843	BM046	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016601	55845	BRK1	http://www.ncbi.nlm.nih.gov/gene/?term=55845	"C3orf10, HSPC300, MDS027, hHBrk1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016602	55845	BRK1	http://www.ncbi.nlm.nih.gov/gene/?term=55845	"C3orf10, HSPC300, MDS027, hHBrk1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016603	55847	CISD1	http://www.ncbi.nlm.nih.gov/gene/?term=55847	"C10orf70, MDS029, ZCD1, mitoNEET "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016604	55847	CISD1	http://www.ncbi.nlm.nih.gov/gene/?term=55847	"C10orf70, MDS029, ZCD1, mitoNEET "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016605	55848	PLGRKT	http://www.ncbi.nlm.nih.gov/gene/?term=55848	"AD025, C9orf46, MDS030, PLG-RKT, Plg-R(KT) "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016606	5584	PRKCI	http://www.ncbi.nlm.nih.gov/gene/?term=5584	"DXS1179E, PKCI, nPKC-iota "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016607	5584	PRKCI	http://www.ncbi.nlm.nih.gov/gene/?term=5584	"DXS1179E, PKCI, nPKC-iota "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016608	5584	PRKCI	http://www.ncbi.nlm.nih.gov/gene/?term=5584	"DXS1179E, PKCI, nPKC-iota "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016609	55850	USE1	http://www.ncbi.nlm.nih.gov/gene/?term=55850	"D12, MDS032, P31, SLT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016610	55851	PSENEN	http://www.ncbi.nlm.nih.gov/gene/?term=55851	"MDS033, MSTP064, PEN-2, PEN2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016611	55851	PSENEN	http://www.ncbi.nlm.nih.gov/gene/?term=55851	"MDS033, MSTP064, PEN-2, PEN2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016612	55851	PSENEN	http://www.ncbi.nlm.nih.gov/gene/?term=55851	"MDS033, MSTP064, PEN-2, PEN2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016613	55852	TEX2	http://www.ncbi.nlm.nih.gov/gene/?term=55852	"HT008, TMEM96 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016614	55854	ZC3H15	http://www.ncbi.nlm.nih.gov/gene/?term=55854	"HT010, LEREPO4, MSTP012 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016615	55854	ZC3H15	http://www.ncbi.nlm.nih.gov/gene/?term=55854	"HT010, LEREPO4, MSTP012 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016616	55854	ZC3H15	http://www.ncbi.nlm.nih.gov/gene/?term=55854	"HT010, LEREPO4, MSTP012 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016617	55856	ACOT13	http://www.ncbi.nlm.nih.gov/gene/?term=55856	"HT012, PNAS-27, THEM2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016618	55857	KIZ	http://www.ncbi.nlm.nih.gov/gene/?term=55857	"C20orf19, HT013, Kizuna, NCRNA00153, PLK1S1, RP69 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016619	55858	TMEM165	http://www.ncbi.nlm.nih.gov/gene/?term=55858	"CDG2K, FT27, GDT1, TMPT27, TPARL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016620	55858	TMEM165	http://www.ncbi.nlm.nih.gov/gene/?term=55858	"CDG2K, FT27, GDT1, TMPT27, TPARL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016621	55859	BEX1	http://www.ncbi.nlm.nih.gov/gene/?term=55859	"BEX2, HBEX2, HGR74-h "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016622	55859	BEX1	http://www.ncbi.nlm.nih.gov/gene/?term=55859	"BEX2, HBEX2, HGR74-h "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016623	5585	PKN1	http://www.ncbi.nlm.nih.gov/gene/?term=5585	"DBK, PAK-1, PAK1, PKN, PKN-ALPHA, PRK1, PRKCL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016624	55860	ACTR10	http://www.ncbi.nlm.nih.gov/gene/?term=55860	"ACTR11, Arp10, Arp11, HARP11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016625	55860	ACTR10	http://www.ncbi.nlm.nih.gov/gene/?term=55860	"ACTR11, Arp10, Arp11, HARP11 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016626	55860	ACTR10	http://www.ncbi.nlm.nih.gov/gene/?term=55860	"ACTR11, Arp10, Arp11, HARP11 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016627	55861	DBNDD2	http://www.ncbi.nlm.nih.gov/gene/?term=55861	"C20orf35, CK1BP, HSMNP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016628	55862	ECHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=55862	"HEL-S-76, MMCD, dJ351K20.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016629	55862	ECHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=55862	"HEL-S-76, MMCD, dJ351K20.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016630	55863	TMEM126B	http://www.ncbi.nlm.nih.gov/gene/?term=55863	HT007	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016631	55869	HDAC8	http://www.ncbi.nlm.nih.gov/gene/?term=55869	"CDA07, CDLS5, HD8, HDACL1, MRXS6, RPD3, WTS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016632	5586	PKN2	http://www.ncbi.nlm.nih.gov/gene/?term=5586	"PAK2, PRK2, PRKCL2, PRO2042, Pak-2, STK7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016633	55870	ASH1L	http://www.ncbi.nlm.nih.gov/gene/?term=55870	"ASH11, KMT2H, ASH1L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016634	55871	CBWD1	http://www.ncbi.nlm.nih.gov/gene/?term=55871	COBP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016635	55871	CBWD1	http://www.ncbi.nlm.nih.gov/gene/?term=55871	COBP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016636	55872	PBK	http://www.ncbi.nlm.nih.gov/gene/?term=55872	"CT84, HEL164, Nori-3, SPK, TOPK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016637	55872	PBK	http://www.ncbi.nlm.nih.gov/gene/?term=55872	"CT84, HEL164, Nori-3, SPK, TOPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016638	55884	WSB2	http://www.ncbi.nlm.nih.gov/gene/?term=55884	SBA2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016639	5588	PRKCQ	http://www.ncbi.nlm.nih.gov/gene/?term=5588	"PRKCT, nPKC-theta "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016640	55892	MYNN	http://www.ncbi.nlm.nih.gov/gene/?term=55892	"OSZF, SBBIZ1, ZBTB31, ZNF902 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016641	55892	MYNN	http://www.ncbi.nlm.nih.gov/gene/?term=55892	"OSZF, SBBIZ1, ZBTB31, ZNF902 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016642	55893	ZNF395	http://www.ncbi.nlm.nih.gov/gene/?term=55893	"HDBP-2, HDBP2, HDRF-2, PBF, PRF-1, PRF1, Si-1-8-14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016643	55893	ZNF395	http://www.ncbi.nlm.nih.gov/gene/?term=55893	"HDBP-2, HDBP2, HDRF-2, PBF, PRF-1, PRF1, Si-1-8-14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016644	55898	UNC45A	http://www.ncbi.nlm.nih.gov/gene/?term=55898	"GC-UNC45, GCUNC-45, GCUNC45, IRO039700, SMAP-1, SMAP1, UNC-45A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016645	55898	UNC45A	http://www.ncbi.nlm.nih.gov/gene/?term=55898	"GC-UNC45, GCUNC-45, GCUNC45, IRO039700, SMAP-1, SMAP1, UNC-45A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016646	55898	UNC45A	http://www.ncbi.nlm.nih.gov/gene/?term=55898	"GC-UNC45, GCUNC-45, GCUNC45, IRO039700, SMAP-1, SMAP1, UN, C-45A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016647	5589	PRKCSH	http://www.ncbi.nlm.nih.gov/gene/?term=5589	"AGE-R2, G19P1, GIIB, PCLD, PKCSH, PLD1, VASAP-60 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016648	5589	PRKCSH	http://www.ncbi.nlm.nih.gov/gene/?term=5589	"AGE-R2, G19P1, PCLD, PKCSH, PLD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016649	558	AXL	http://www.ncbi.nlm.nih.gov/gene/?term=558	"ARK, JTK11, Tyro7, UFO "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016650	558	AXL	http://www.ncbi.nlm.nih.gov/gene/?term=558	"ARK, JTK11, Tyro7, UFO "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016651	558	AXL	http://www.ncbi.nlm.nih.gov/gene/?term=558	"ARK, JTK11, Tyro7, UFO "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016652	55902	ACSS2	http://www.ncbi.nlm.nih.gov/gene/?term=55902	"ACAS2, ACECS, ACS, ACSA, dJ1161H23.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016653	55902	ACSS2	http://www.ncbi.nlm.nih.gov/gene/?term=55902	"ACAS2, ACECS, ACS, ACSA, dJ1161H23.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016654	55904	KMT2E	http://www.ncbi.nlm.nih.gov/gene/?term=55904	"HDCMC04P, MLL5, NKp44L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016655	55905	RNF114	http://www.ncbi.nlm.nih.gov/gene/?term=55905	"PSORS12, ZNF313 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016656	55905	RNF114	http://www.ncbi.nlm.nih.gov/gene/?term=55905	"PSORS12, ZNF313 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016657	55907	CMAS	http://www.ncbi.nlm.nih.gov/gene/?term=55907	CSS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016658	55907	CMAS	http://www.ncbi.nlm.nih.gov/gene/?term=55907	CSS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016659	55909	BIN3	http://www.ncbi.nlm.nih.gov/gene/?term=55909		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016660	55909	BIN3	http://www.ncbi.nlm.nih.gov/gene/?term=55909		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016661	5590	PRKCZ	http://www.ncbi.nlm.nih.gov/gene/?term=5590	"PKC-ZETA, PKC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016662	5590	PRKCZ	http://www.ncbi.nlm.nih.gov/gene/?term=5590	"PKC-ZETA, PKC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016663	55914	ERBIN	http://www.ncbi.nlm.nih.gov/gene/?term=55914	"ERBB2IP, HEL-S-78, LAP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016664	55915	LANCL2	http://www.ncbi.nlm.nih.gov/gene/?term=55915	"GPR69B, TASP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016665	55916	NXT2	http://www.ncbi.nlm.nih.gov/gene/?term=55916	P15-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016666	55917	CTTNBP2NL	http://www.ncbi.nlm.nih.gov/gene/?term=55917		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016667	5591	PRKDC	http://www.ncbi.nlm.nih.gov/gene/?term=5591	"DNA-PKcs, DNAPK, DNPK1, HYRC, HYRC1, IMD26, XRCC7, p350 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016668	5591	PRKDC	http://www.ncbi.nlm.nih.gov/gene/?term=5591	"DNA-PKcs, DNAPK, DNPK1, HYRC, HYRC1, IMD26, XRCC7, p350 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016669	55920	RCC2	http://www.ncbi.nlm.nih.gov/gene/?term=55920	TD-60	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016670	55920	RCC2	http://www.ncbi.nlm.nih.gov/gene/?term=55920	TD-60	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016671	55922	NKRF	http://www.ncbi.nlm.nih.gov/gene/?term=55922	"ITBA4, NRF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016672	55922	NKRF	http://www.ncbi.nlm.nih.gov/gene/?term=55922	"ITBA4, NRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016673	55924	FAM212B	http://www.ncbi.nlm.nih.gov/gene/?term=55924	C1orf183	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016674	55924	FAM212B	http://www.ncbi.nlm.nih.gov/gene/?term=55924	C1orf183	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016675	55927	Hes6	http://www.ncbi.nlm.nih.gov/gene/?term=55927	"AI326893, bHLHb41 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016676	55930	MYO5C	http://www.ncbi.nlm.nih.gov/gene/?term=55930		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016677	55930	MYO5C	http://www.ncbi.nlm.nih.gov/gene/?term=55930		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016678	55930	MYO5C	http://www.ncbi.nlm.nih.gov/gene/?term=55930		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016679	55934	Rp9	http://www.ncbi.nlm.nih.gov/gene/?term=55934	"PAP-1h, Rp9 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016680	55935	Fnbp4	http://www.ncbi.nlm.nih.gov/gene/?term=55935	"FBP30, Fnbp30, mKIAA1014 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016681	55937	APOM	http://www.ncbi.nlm.nih.gov/gene/?term=55937	"G3a, HSPC336, NG20, apo-M "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016682	55947	Dclre1a	http://www.ncbi.nlm.nih.gov/gene/?term=55947	"2810043H12Rik, AU022226, Pso2, Smn1a, Snm1, mKIAA0086 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016683	5594	MAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5594	"ERK, ERK-2, ERK2, ERT1, MAPK2, P42MAPK, PRKM1, PRKM2, p38, p40, p41, p41mapk, p42-MAPK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016684	5594	MAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5594	"ERK, ERK-2, ERK2, ERT1, MAPK2, P42MAPK, PRKM1, PRKM2, p38, p40, p41, p41mapk, p42-MAPK "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00016685	5594	MAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5594	"ERK, ERK-2, ERK2, ERT1, MAPK2, P42MAPK, PRKM1, PRKM2, p38, p40, p41, p41mapk, p42-MAPK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016686	5594	MAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5594	"ERK, ERK-2, ERK2, ERT1, MAPK2, P42MAPK, PRKM1, PRKM2, p38, p40, p41, p41mapk, p42-MAPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016687	5594	MAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=5594	"ERK, p38, p40, p41, ERK2, ERT1, ERK-2, MAPK2, PRKM1, PRKM2, P42MAPK, p41mapk, p42-MAPK "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00016688	55954	ZMAT5	http://www.ncbi.nlm.nih.gov/gene/?term=55954	"SNRNP20, U11/U12-20K, ZC3H19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016689	55954	ZMAT5	http://www.ncbi.nlm.nih.gov/gene/?term=55954	"SNRNP20, U11/U12-20K, ZC3H19 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016690	55954	ZMAT5	http://www.ncbi.nlm.nih.gov/gene/?term=55954	"SNRNP20, U11/U12-20K, ZC3H19 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016691	55957	LIN37	http://www.ncbi.nlm.nih.gov/gene/?term=55957	"F25965, ZK418.4, lin-37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016692	55958	KLHL9	http://www.ncbi.nlm.nih.gov/gene/?term=55958		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016693	55958	KLHL9	http://www.ncbi.nlm.nih.gov/gene/?term=55958		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016694	55963	Slc1a4	http://www.ncbi.nlm.nih.gov/gene/?term=55963	"ASCT-1, ASCT1, AW045657, SATT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016695	55967	NDUFA12	http://www.ncbi.nlm.nih.gov/gene/?term=55967	"B17.2, DAP13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016696	55968	NSFL1C	http://www.ncbi.nlm.nih.gov/gene/?term=55968	"P47, UBX1, UBXD10, UBXN2C, dJ776F14.1 "	lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00016697	55968	NSFL1C	http://www.ncbi.nlm.nih.gov/gene/?term=55968	"P47, UBX1, UBXD10, UBXN2C, dJ776F14.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016698	55969	C20orf24	http://www.ncbi.nlm.nih.gov/gene/?term=55969	"PNAS-11, RIP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016699	55970	GNG12	http://www.ncbi.nlm.nih.gov/gene/?term=55970		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016700	55970	GNG12	http://www.ncbi.nlm.nih.gov/gene/?term=55970		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016701	55971	BAIAP2L1	http://www.ncbi.nlm.nih.gov/gene/?term=55971	IRTKS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016702	55973	BCAP29	http://www.ncbi.nlm.nih.gov/gene/?term=55973	BAP29	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016703	55978	Ift20	http://www.ncbi.nlm.nih.gov/gene/?term=55978	"0610009H04Rik, AU015496 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016704	55979	Agpat1	http://www.ncbi.nlm.nih.gov/gene/?term=55979	"1-AGP, 1-AGPAT, AW047140 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016705	5597	MAPK6	http://www.ncbi.nlm.nih.gov/gene/?term=5597	"ERK3, HsT17250, PRKM6, p97MAPK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016706	5597	MAPK6	http://www.ncbi.nlm.nih.gov/gene/?term=5597	"ERK3, HsT17250, PRKM6, p97MAPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016707	55980	Impa1	http://www.ncbi.nlm.nih.gov/gene/?term=55980	"2610002K09Rik, 2900059K10Rik, AI325909 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016708	55982	Paxip1	http://www.ncbi.nlm.nih.gov/gene/?term=55982	"D5Ertd149e, PTIP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016709	55989	Nop58	http://www.ncbi.nlm.nih.gov/gene/?term=55989	"MSSP, Nol5, SIK, nop5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016710	5599	MAPK8	http://www.ncbi.nlm.nih.gov/gene/?term=5599	"JNK, JNK-46, JNK1, JNK1A2, JNK21B1/2, PRKM8, SAPK1, SAPK1c "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016711	55	ACPP	http://www.ncbi.nlm.nih.gov/gene/?term=55	"5'-NT, ACP-3, ACP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016712	56005	MYDGF	http://www.ncbi.nlm.nih.gov/gene/?term=56005	"C19orf10, EUROIMAGE1875335, IL25, IL27, IL27w, R33729_1, SF20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016713	56018	Stard10	http://www.ncbi.nlm.nih.gov/gene/?term=56018	"AV048538, CGI-52, NY-C0-28, PC-TP2, PCTP2, Pctpl, Sdccag28, SdccagG28, TISP-81 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016714	5601	MAPK9	http://www.ncbi.nlm.nih.gov/gene/?term=5601	"JNK-55, JNK2, JNK2A, JNK2ALPHA, JNK2B, JNK2BETA, PRKM9, SAPK, SAPK1a, p54a, p54aSAPK "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016715	5601	MAPK9	http://www.ncbi.nlm.nih.gov/gene/?term=5601	"JNK-55, JNK2, JNK2A, JNK2ALPHA, JNK2B, JNK2BETA, PRKM9, SAPK, SAPK1a, p54a, p54aSAPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016716	56034	PDGFC	http://www.ncbi.nlm.nih.gov/gene/?term=56034	"FALLOTEIN, SCDGF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016717	5603	MAPK13	http://www.ncbi.nlm.nih.gov/gene/?term=5603	"MAPK 13, MAPK-13, PRKM13, SAPK4, p38delta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016718	56040	Rplp1	http://www.ncbi.nlm.nih.gov/gene/?term=56040	"2410042H16Rik, Arpp1, C430017H15Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016719	56041	Uso1	http://www.ncbi.nlm.nih.gov/gene/?term=56041	"115kDa, TAP, Vdp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016720	56043	Akr1e1	http://www.ncbi.nlm.nih.gov/gene/?term=56043	"1810061I10Rik, Akr1e2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016721	56045	Samhd1	http://www.ncbi.nlm.nih.gov/gene/?term=56045	"E330031J07Rik, Mg11 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016722	56046	Uqcc1	http://www.ncbi.nlm.nih.gov/gene/?term=56046	"2310079L17Rik, 2410003P15Rik, 3110038N19Rik, Bfzb, Bfzp, Cbp3, Uqcc "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016723	56048	Lgals8	http://www.ncbi.nlm.nih.gov/gene/?term=56048	"1200015E08Rik, AI326142, D13Ertd524e, Lgals-8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016724	5604	MAP2K1	http://www.ncbi.nlm.nih.gov/gene/?term=5604	"CFC3, MAPKK1, MEK1, MKK1, PRKMK1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016725	5604	MAP2K1	http://www.ncbi.nlm.nih.gov/gene/?term=5604	"CFC3, MAPKK1, MEK1, MKK1, PRKMK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016726	56052	ALG1	http://www.ncbi.nlm.nih.gov/gene/?term=56052	"CDG1K, HMAT1, HMT-1, HMT1, MT-1, Mat-1, hMat-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016727	56057	Btg4	http://www.ncbi.nlm.nih.gov/gene/?term=56057	"C86116, PC3B "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016728	5605	MAP2K2	http://www.ncbi.nlm.nih.gov/gene/?term=5605	"CFC4, MAPKK2, MEK2, MKK2, PRKMK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016729	5605	MAP2K2	http://www.ncbi.nlm.nih.gov/gene/?term=5605	"CFC4, MAPKK2, MEK2, MKK2, PRKMK2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016730	5605	MAP2K2	http://www.ncbi.nlm.nih.gov/gene/?term=5605	"CFC4, MAPKK2, MEK2, MKK2, PRKMK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016731	56061	UBFD1	http://www.ncbi.nlm.nih.gov/gene/?term=56061	UBPH	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016732	56063	TMEM234	http://www.ncbi.nlm.nih.gov/gene/?term=56063	"AASL548, C1orf91, PRO1105, RP4-622L5, dJ622L5.7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016733	5606	MAP2K3	http://www.ncbi.nlm.nih.gov/gene/?term=5606	"MAPKK3, MEK3, MKK3, PRKMK3, SAPKK-2, SAPKK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016734	5606	MAP2K3	http://www.ncbi.nlm.nih.gov/gene/?term=5606	"MAPKK3, MEK3, MKK3, PRKMK3, SAPKK-2, SAPKK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016735	56075	Pdss1	http://www.ncbi.nlm.nih.gov/gene/?term=56075	"2610203G20Rik, 2700031G06Rik, TPT, TPT 1, Tprt, mDLP1, mSPS1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016736	56077	Dgke	http://www.ncbi.nlm.nih.gov/gene/?term=56077	"C87606, DAGK6, DGK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016737	56078	Car5b	http://www.ncbi.nlm.nih.gov/gene/?term=56078	"7330410H16Rik, CAVB, Ca5b, CarVb, D730005F19Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016738	56078	Car5b	http://www.ncbi.nlm.nih.gov/gene/?term=56078	"7330410H16Rik, CAVB, Ca5b, CarVb, D730005F19Rik "	mRNA	Mus musculus	20820888	Mitochondrion	Gland tissue	qRT-PCR	"In the present study, we examined the mRNA expression of all 13 enzymatically active CA isozymes by qRT-PCR in the mouse harderian gland. As shown in Fig. 1, nine of the 13 isozymes were detected in the harderian gland tissue at the mRNA level. Four isoforms were cytosolic (Car2, Car3, Car7, and Car13), three were membrane-associated (Car4, Car12, and Car15), one was mitochondrial (Car5b), and one was secreted (Car6). "
RLID00016739	5607	MAP2K5	http://www.ncbi.nlm.nih.gov/gene/?term=5607	"HsT17454, MAPKK5, MEK5, PRKMK5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016740	56086	Set	http://www.ncbi.nlm.nih.gov/gene/?term=56086	"2610030F17Rik, 5730420M11Rik, AA407739, I-2PP2A, StF-IT-1, TAF-I "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016741	56095	Ftsj3	http://www.ncbi.nlm.nih.gov/gene/?term=56095	"AA537063, AU045295, C79843, D11Ertd400e, Epcs3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016742	5609	MAP2K7	http://www.ncbi.nlm.nih.gov/gene/?term=5609	"JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7, SAPKK-4, SAPKK4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016743	5610	EIF2AK2	http://www.ncbi.nlm.nih.gov/gene/?term=5610	"EIF2AK1, PKR, PPP1R83, PRKR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016744	5611	DNAJC3	http://www.ncbi.nlm.nih.gov/gene/?term=5611	"ACPHD, ERdj6, HP58, P58, P58IPK, PRKRI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016745	5611	DNAJC3	http://www.ncbi.nlm.nih.gov/gene/?term=5611	"ACPHD, ERdj6, HP58, P58, P58IPK, PRKRI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016746	56125	PCDHB11	http://www.ncbi.nlm.nih.gov/gene/?term=56125	"ME2, PCDH-BETA11 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016747	56127	PCDHB9	http://www.ncbi.nlm.nih.gov/gene/?term=56127	"PCDH-BETA9, PCDH3H "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016748	56127	PCDHB9	http://www.ncbi.nlm.nih.gov/gene/?term=56127	"PCDH-BETA9, PCDH3H "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016749	5612	THAP12	http://www.ncbi.nlm.nih.gov/gene/?term=5612	"DAP4, P52rIPK, PRKRIR, THAP0 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016750	56149	Grasp	http://www.ncbi.nlm.nih.gov/gene/?term=56149	tamalin	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016751	56150	Mad2l1	http://www.ncbi.nlm.nih.gov/gene/?term=56150	"AA673185, MAD2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016752	56159	TEX11	http://www.ncbi.nlm.nih.gov/gene/?term=56159	"SPGFX2, TGC1, TSGA3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016753	56159	TEX11	http://www.ncbi.nlm.nih.gov/gene/?term=56159	"SPGFX2, TGC1, TSGA3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016754	56160	NSMCE3	http://www.ncbi.nlm.nih.gov/gene/?term=56160	"HCA4, MAGEG1, MAGEL3, NDNL2, NSE3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016755	56160	NSMCE3	http://www.ncbi.nlm.nih.gov/gene/?term=56160	"HCA4, MAGEG1, MAGEL3, NDNL2, NSE3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016756	56172	ANKH	http://www.ncbi.nlm.nih.gov/gene/?term=56172	"ANK, CCAL2, CMDJ, CPPDD, HANK, MANK "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016757	56172	ANKH	http://www.ncbi.nlm.nih.gov/gene/?term=56172	"ANK, CCAL2, CMDJ, CPPDD, HANK, MANK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016758	56172	ANKH	http://www.ncbi.nlm.nih.gov/gene/?term=56172	"ANK, CCAL2, CMDJ, CPPDD, HANK, MANK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016759	56174	Nagk	http://www.ncbi.nlm.nih.gov/gene/?term=56174	Gnk	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016760	56177	Olfm1	http://www.ncbi.nlm.nih.gov/gene/?term=56177	"AMY, AW742568, Noe1, OlfA, Pancortin, Pancortin3 "	mRNA	Mus musculus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00016761	5617	PRL	http://www.ncbi.nlm.nih.gov/gene/?term=5617	GHA1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016762	56180	MOSPD1	http://www.ncbi.nlm.nih.gov/gene/?term=56180	DJ473B4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016763	56181	MTFR1L	http://www.ncbi.nlm.nih.gov/gene/?term=56181	"FAM54B, HYST1888, MST116, MSTP116 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016764	5618	PRLR	http://www.ncbi.nlm.nih.gov/gene/?term=5618	"HPRL, MFAB, hPRLrI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016765	56190	Rbm38	http://www.ncbi.nlm.nih.gov/gene/?term=56190	"Rnpc1, Seb4, Seb4l "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016766	56191	Tro	http://www.ncbi.nlm.nih.gov/gene/?term=56191	"AA409408, Maged3, Maged3l, Tnnl, magphinin, Tro "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016767	56193	Plek	http://www.ncbi.nlm.nih.gov/gene/?term=56193	2010300B13Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016768	56194	Prpf40a	http://www.ncbi.nlm.nih.gov/gene/?term=56194	"2810012K09Rik, FBP11, Fnbp11, Fnbp3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016769	56195	Ptbp2	http://www.ncbi.nlm.nih.gov/gene/?term=56195	"Ptb2, brPTB, nPTB "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016770	56196	Tdp2	http://www.ncbi.nlm.nih.gov/gene/?term=56196	"D13Ertd656e, Ttrap "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016771	56200	Ddx21	http://www.ncbi.nlm.nih.gov/gene/?term=56200	"AI255159, AL022742, D10Ertd645e, D10Wsu42e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016772	56204	FAM214A	http://www.ncbi.nlm.nih.gov/gene/?term=56204	KIAA1370	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016773	56207	Uchl5	http://www.ncbi.nlm.nih.gov/gene/?term=56207	"5830413B11Rik, Uch37 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016774	56208	Becn1	http://www.ncbi.nlm.nih.gov/gene/?term=56208	"4921513J16Rik, 5430417M23Rik, Atg6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016775	56210	Rev1	http://www.ncbi.nlm.nih.gov/gene/?term=56210	"1110027I23Rik, AU022044l, Rev1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016776	5621	PRNP	http://www.ncbi.nlm.nih.gov/gene/?term=5621	"ASCR, AltPrP, CD230, CJD, GSS, KURU, PRIP, PrP, PrP27-30, PrP33-35C, PrPc, p27-30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016777	56241	SUSD2	http://www.ncbi.nlm.nih.gov/gene/?term=56241	BK65A6.2	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00016778	56248	Ak3	http://www.ncbi.nlm.nih.gov/gene/?term=56248	"AA407498, AI506714, AK-3l, Ak3l1, Akl3l, Ak3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016779	56252	YLPM1	http://www.ncbi.nlm.nih.gov/gene/?term=56252	"C14orf170, PPP1R169, ZAP113, ZAP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016780	56255	TMX4	http://www.ncbi.nlm.nih.gov/gene/?term=56255	"DJ971N18.2, PDIA14, TXNDC13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016781	56255	TMX4	http://www.ncbi.nlm.nih.gov/gene/?term=56255	"DJ971N18.2, PDIA14, TXNDC13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016782	56258	Hnrnph2	http://www.ncbi.nlm.nih.gov/gene/?term=56258	"DXHXS1271E, Ftp-3, Ftp3, H', HNRNP, Hnrph2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016783	56259	CTNNBL1	http://www.ncbi.nlm.nih.gov/gene/?term=56259	"C20orf33, NAP, P14L, PP8304, dJ633O20.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016784	56261	GPCPD1	http://www.ncbi.nlm.nih.gov/gene/?term=56261	"EDI3, GDE5, GDPD6, PREI4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016785	56262	LRRC8A	http://www.ncbi.nlm.nih.gov/gene/?term=56262	"AGM5, LRRC8, SWELL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016786	56264	Cpxm1	http://www.ncbi.nlm.nih.gov/gene/?term=56264	"AA986902, Cpx-1, Cpx1, Cpxm "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016787	56267	CCBL2	http://www.ncbi.nlm.nih.gov/gene/?term=56267	"KAT3, KATIII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016788	56267	KYAT3	http://www.ncbi.nlm.nih.gov/gene/?term=56267	"KAT3, KATIII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016789	56270	WDR45B	http://www.ncbi.nlm.nih.gov/gene/?term=56270	"WDR45L, WIPI-3, WIPI3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016790	56270	WDR45B	http://www.ncbi.nlm.nih.gov/gene/?term=56270	"WDR45L, WIPI-3, WIPI3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016791	56273	Pex14	http://www.ncbi.nlm.nih.gov/gene/?term=56273	"Pex14p, R75137 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016792	56274	Stk3	http://www.ncbi.nlm.nih.gov/gene/?term=56274	"0610042I06Rik, MST, Mst2, Mst3, Ste20, mess1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016793	56274	Stk3	http://www.ncbi.nlm.nih.gov/gene/?term=56274	"0610042I06Rik, MST, Mst2, Mst3, Ste20, mess1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016794	56278	Gkap1	http://www.ncbi.nlm.nih.gov/gene/?term=56278	"42kDa, 4933400B15Rik, D13Ertd340e, Gkap42 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016795	5627	PROS1	http://www.ncbi.nlm.nih.gov/gene/?term=5627	"PROS, PS21, PS22, PS23, PS24, PS25, PSA, THPH5, THPH6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016796	5627	PROS1	http://www.ncbi.nlm.nih.gov/gene/?term=5627	"PROS, PS21, PS22, PS23, PS24, PS25, PSA, THPH5, THPH6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016797	56280	Mrpl37	http://www.ncbi.nlm.nih.gov/gene/?term=56280	"2300004O14Rik, AI132596, MRP-L2, Rpml2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016798	56282	Mrpl12	http://www.ncbi.nlm.nih.gov/gene/?term=56282	"0610034O11Rik, 1500031N16Rik, MRP-L12, Rpml12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016799	56288	PARD3	http://www.ncbi.nlm.nih.gov/gene/?term=56288	"ASIP, Baz, PAR3, PAR3alpha, PARD-3A, PPP1R118, SE2-5L16, SE2-5LT1, SE2-5T2, PARD3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016800	56288	PARD3	http://www.ncbi.nlm.nih.gov/gene/?term=56288	"ASIP, Baz, PAR3, PAR3alpha, PARD-3, PARD3A, PPP1R118, SE2-5L16, SE2-5LT1, SE2-5T2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016801	56295	Higd1a	http://www.ncbi.nlm.nih.gov/gene/?term=56295	"2210020B17Rik, 7420700H20Rik, AI303276, AW049839, HIMP1, Hig1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00016802	56298	Atl2	http://www.ncbi.nlm.nih.gov/gene/?term=56298	"2010110I21Rik, AA407293, AV334690, Aip-2, Arl6ip2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016803	56306	Fam60a	http://www.ncbi.nlm.nih.gov/gene/?term=56306	"Ppcs1, Pptcs1, Tera "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016804	56307	Metap2	http://www.ncbi.nlm.nih.gov/gene/?term=56307	"4930584B20Rik, A930035J23Rik, AI047573, AL024412, AU014659, Amp2, Mnpep, p67, p67eIF2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016805	56314	Zfp113	http://www.ncbi.nlm.nih.gov/gene/?term=56314	"4732456B05Rik, mKIAA4229 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016806	56316	Ggcx	http://www.ncbi.nlm.nih.gov/gene/?term=56316		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016807	56317	Anapc7	http://www.ncbi.nlm.nih.gov/gene/?term=56317	"APC7, AW545589 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016808	5631	PRPS1	http://www.ncbi.nlm.nih.gov/gene/?term=5631	"ARTS, CMTX5, DFN2, DFNX1, PPRibP, PRS-I, PRSI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016809	56325	Abcb9	http://www.ncbi.nlm.nih.gov/gene/?term=56325	"TAPL, mKIAA1520 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016810	56327	Arl2	http://www.ncbi.nlm.nih.gov/gene/?term=56327	"2610009M23Rik, AI115441, AW553335 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016811	56327	Arl2	http://www.ncbi.nlm.nih.gov/gene/?term=56327	"2610009M23Rik, AI115441, AW553335 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016812	56334	Tmed2	http://www.ncbi.nlm.nih.gov/gene/?term=56334	"1110032D12Rik, 1810020N21Rik, Rnp24, Sid394, p24beta1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016813	56338	Txnip	http://www.ncbi.nlm.nih.gov/gene/?term=56338	"1200008J08Rik, AA682105, Hyplip1, THIF, Tbp-2, VDUP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016814	56339	METTL3	http://www.ncbi.nlm.nih.gov/gene/?term=56339	"IME4, M6A, MT-A70, Spo8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016815	56348	Hsd17b12	http://www.ncbi.nlm.nih.gov/gene/?term=56348	"2610510O05Rik, AI172963, KIK-I, Kik1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016816	5634	PRPS2	http://www.ncbi.nlm.nih.gov/gene/?term=5634	PRSII	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016817	5634	PRPS2	http://www.ncbi.nlm.nih.gov/gene/?term=5634	PRSII	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016818	56350	Arl3	http://www.ncbi.nlm.nih.gov/gene/?term=56350		mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00016819	56351	Ptges3	http://www.ncbi.nlm.nih.gov/gene/?term=56351	"5730442A20Rik, Ptges, Tebp, cPGES, p23, sid3177 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016820	56356	Gltp	http://www.ncbi.nlm.nih.gov/gene/?term=56356	"1110001F24Rik, C76925, C77564 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016821	56357	Ivd	http://www.ncbi.nlm.nih.gov/gene/?term=56357	"1300016K07Rik, 6720455E18Rik, AI463340 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016822	5635	PRPSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=5635	PAP39	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016823	5635	PRPSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=5635	PAP39	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016824	56362	Sult1b1	http://www.ncbi.nlm.nih.gov/gene/?term=56362	"ST1B1, St2b2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016825	56363	Tmeff2	http://www.ncbi.nlm.nih.gov/gene/?term=56363	"4832418D20Rik, 7630402F16Rik, TR-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016826	56363	Tmeff2	http://www.ncbi.nlm.nih.gov/gene/?term=56363	"4832418D20Rik, 7630402F16Rik, TR-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016827	5636	PRPSAP2	http://www.ncbi.nlm.nih.gov/gene/?term=5636	PAP41	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016828	56370	Tagln3	http://www.ncbi.nlm.nih.gov/gene/?term=56370	"2700038H05Rik, 2900005O10Rik, AI426007, Np25 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016829	56371	Fzr1	http://www.ncbi.nlm.nih.gov/gene/?term=56371	"AW108046, Cdh1, FZR, FZR2, Fyr, HCDH, HCDH1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016830	56374	Tmem59	http://www.ncbi.nlm.nih.gov/gene/?term=56374	"1110001M20Rik, 3110046P06Rik, AI256529, D4Ertd20e, MTDCF1, ORF18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016831	56375	B4galt4	http://www.ncbi.nlm.nih.gov/gene/?term=56375	"9130402O08Rik, B4galt-IV, b4Gal-T4, beta4Gal-T4, beta4GalT-IV "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016832	56376	Pdlim5	http://www.ncbi.nlm.nih.gov/gene/?term=56376	"1110001A05Rik, AI987914, C87059, Enh, Enh1, Enh2, Enh3, LIM "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016833	56381	Spen	http://www.ncbi.nlm.nih.gov/gene/?term=56381	"Mint, mKIAA0929 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016834	56381	Spen	http://www.ncbi.nlm.nih.gov/gene/?term=56381	"Mint, mKIAA0929 "	mRNA	Mus musculus	26190105	Nucleus	Embryotem cell	Microscopy	"Figure 6: 3DSIM Showing that Xist RNA, Rbm15, Wtap, and Spen Co-localize within Perichromatin Spaces. Data are collected from Figure 6. "
RLID00016835	5638	PRRG1	http://www.ncbi.nlm.nih.gov/gene/?term=5638	PRGP1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016836	5638	PRRG1	http://www.ncbi.nlm.nih.gov/gene/?term=5638	PRGP1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016837	56392	Shoc2	http://www.ncbi.nlm.nih.gov/gene/?term=56392	"AU017287, Sur8, mKIAA0862 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016838	56397	Morf4l2	http://www.ncbi.nlm.nih.gov/gene/?term=56397	"2410017O14Rik, Mrgx, Sid393p, mKIAA0026 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016839	56399	Akap8	http://www.ncbi.nlm.nih.gov/gene/?term=56399	"1200016A02Rik, AA673585, AKAP-8, AKAP95, AU015639 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016840	5639	PRRG2	http://www.ncbi.nlm.nih.gov/gene/?term=5639	PRGP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016841	5639	PRRG2	http://www.ncbi.nlm.nih.gov/gene/?term=5639	PRGP2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016842	56403	Syncrip	http://www.ncbi.nlm.nih.gov/gene/?term=56403	"2610109K23Rik, 4632417O19Rik, GRY-RBP, Nsap1, Nsap1l, pp68 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016843	56404	Trip4	http://www.ncbi.nlm.nih.gov/gene/?term=56404	"4930558E03Rik, ASC-1, Asc1, BB191711 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016844	56406	Ncoa6	http://www.ncbi.nlm.nih.gov/gene/?term=56406	"AIB3, ASC-2, ASC2, NRC, Ncoa7, PRIP, RAP250, mKIAA0181 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016845	56417	Adar	http://www.ncbi.nlm.nih.gov/gene/?term=56417	"AV2424511, Adar1p110, Adar1p150, mZaADAR, Adar "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016846	56419	Diaph3	http://www.ncbi.nlm.nih.gov/gene/?term=56419	"4930417P13Rik, Dia2, Diap3, Drf3, mDia2, mKIAA4117, p134MDia2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016847	5641	LGMN	http://www.ncbi.nlm.nih.gov/gene/?term=5641	"AEP1, PRSC1, LGMN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016848	5641	LGMN	http://www.ncbi.nlm.nih.gov/gene/?term=5641	"AEP1, PRSC1, LGMN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016849	5641	LGMN	http://www.ncbi.nlm.nih.gov/gene/?term=5641	"AEP1, PRSC1, LGMN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016850	5641	LGMN	http://www.ncbi.nlm.nih.gov/gene/?term=5641	"AEP, LGMN1, PRSC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016851	56420	Ppp4c	http://www.ncbi.nlm.nih.gov/gene/?term=56420	"1110002D08Rik, AU016079, Ppx "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016852	56421	Pfkp	http://www.ncbi.nlm.nih.gov/gene/?term=56421	"1200015H23Rik, 9330125N24Rik, ATP-PFK, PFK-C, PFK-P "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00016853	56422	Hbs1l	http://www.ncbi.nlm.nih.gov/gene/?term=56422	"2810035F15Rik, AI326327, eRFS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016854	56431	Dstn	http://www.ncbi.nlm.nih.gov/gene/?term=56431	"2610043P17Rik, ADF, AU042046, Dsn, corn1, sid23p "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016855	56434	Tspan3	http://www.ncbi.nlm.nih.gov/gene/?term=56434	"1700055K04Rik, TM4-A, Tm4sf8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016856	56434	Tspan3	http://www.ncbi.nlm.nih.gov/gene/?term=56434	"1700055K04Rik, TM4-A, Tm4sf8 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016857	56441	Nat6	http://www.ncbi.nlm.nih.gov/gene/?term=56441	"AI225910, Fus2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016858	56442	Serinc1	http://www.ncbi.nlm.nih.gov/gene/?term=56442	"1500011D18Rik, AI315070, AIGP-2, TMS-2, Tde1l, Tde2, Tms2, mKIAA1253 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016859	56445	Dnaja2	http://www.ncbi.nlm.nih.gov/gene/?term=56445	"1500017M13Rik, 2010206B19Rik, DNAJ, DNJ3, Dnaj3, HIRIP4, PRO3015, mDj3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016860	56447	Copz1	http://www.ncbi.nlm.nih.gov/gene/?term=56447	"5930435A22Rik, AA407760, D4Ertd360e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016861	5644	PRSS1	http://www.ncbi.nlm.nih.gov/gene/?term=5644	"TRP1, TRY1, TRY4, TRYP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016862	56453	Mbtps1	http://www.ncbi.nlm.nih.gov/gene/?term=56453	"0610038M03Rik, AV003995, S1P, SKI-1, Ski1, mKIAA0091 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016863	56455	Dynll1	http://www.ncbi.nlm.nih.gov/gene/?term=56455	"Dlc8, Dnclc1, Pin "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016864	56469	Pias1	http://www.ncbi.nlm.nih.gov/gene/?term=56469	"2900068C24Rik, Ddxbp1, GBP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016865	5646	PRSS3	http://www.ncbi.nlm.nih.gov/gene/?term=5646	"MTG, PRSS4, T9, TRY3, TRY4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016866	56490	Zbtb20	http://www.ncbi.nlm.nih.gov/gene/?term=56490	"1300017A20Rik, 7330412A13Rik, A930017C21Rik, D16Wsu73e, DPZF, HOF, ODA-8S, Oda8, Zfp288 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016867	56495	Asna1	http://www.ncbi.nlm.nih.gov/gene/?term=56495	"1810048H22Rik, ArsA "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016868	56496	Tspan6	http://www.ncbi.nlm.nih.gov/gene/?term=56496	"6720473L21Rik, AI316786, T245, TSPAN-6, Tm4sf, Tm4sf6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016869	5649	RELN	http://www.ncbi.nlm.nih.gov/gene/?term=5649	"ETL7, LIS2, PRO1598, RL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016870	56504	Srpk3	http://www.ncbi.nlm.nih.gov/gene/?term=56504	"Mssk1, Stk23 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016871	56513	Pard6a	http://www.ncbi.nlm.nih.gov/gene/?term=56513	"0710008C04Rik, 2610010A15Rik, PAR-6A, PAR6alpha, Par-6, Par6, Par6c, TAX40, Tip-40 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016872	56516	Rbms2	http://www.ncbi.nlm.nih.gov/gene/?term=56516	"2610315E04Rik, Scr3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016873	56520	Nme4	http://www.ncbi.nlm.nih.gov/gene/?term=56520	"2610027N22Rik, 2810024O08Rik, 5730493H09Rik, NM23-M4, Nm23M4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016874	56521	DNAJC12	http://www.ncbi.nlm.nih.gov/gene/?term=56521	JDP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016875	56529	Sec11a	http://www.ncbi.nlm.nih.gov/gene/?term=56529	"1810012E07Rik, 18kDa, Sec11l1, Sid2895p, Spc18, sid2895 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016876	5652	PRSS8	http://www.ncbi.nlm.nih.gov/gene/?term=5652	"CAP1, PROSTASIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016877	5652	PRSS8	http://www.ncbi.nlm.nih.gov/gene/?term=5652	"CAP1, PROSTASIN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016878	56530	Cnpy2	http://www.ncbi.nlm.nih.gov/gene/?term=56530	"5330432A10Rik, AW229003, D10Bwg1546e, Tmem4, Zsig9 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016879	56531	Ylpm1	http://www.ncbi.nlm.nih.gov/gene/?term=56531	"A930013E17Rik, ZAP, Zap3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016880	56535	Pex3	http://www.ncbi.nlm.nih.gov/gene/?term=56535	"1700014F15Rik, 2810027F19Rik, 2900010N04Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016881	56541	Habp4	http://www.ncbi.nlm.nih.gov/gene/?term=56541	"4933413D03Rik, 4933428J01Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016882	56548	CHST7	http://www.ncbi.nlm.nih.gov/gene/?term=56548	"C6ST-2, GST-5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016883	5654	HTRA1	http://www.ncbi.nlm.nih.gov/gene/?term=5654	"ARMD7, CADASIL2, CARASIL, HtrA, L56, ORF480, PRSS11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016884	5654	HTRA1	http://www.ncbi.nlm.nih.gov/gene/?term=5654	"ARMD7, CADASIL2, CARASIL, HtrA, L56, ORF480, PRSS11 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016885	5654	HTRA1	http://www.ncbi.nlm.nih.gov/gene/?term=5654	"ARMD7, CADASIL2, CARASIL, HtrA, L56, ORF480, PRSS11 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016886	56550	Ube2d2a	http://www.ncbi.nlm.nih.gov/gene/?term=56550	"1500034D03Rik, Ubc2e, Ube2d2, ubc4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016887	56552	Vmn2r26	http://www.ncbi.nlm.nih.gov/gene/?term=56552	"V2R1, V2r1b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016888	5655	KLK10	http://www.ncbi.nlm.nih.gov/gene/?term=5655	"NES1, PRSSL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016889	56605	ERO1B	http://www.ncbi.nlm.nih.gov/gene/?term=56605	"ERO1LB, Ero1beta "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016890	5660	PSAP	http://www.ncbi.nlm.nih.gov/gene/?term=5660	"GLBA, SAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016891	5660	PSAP	http://www.ncbi.nlm.nih.gov/gene/?term=5660	"GLBA, SAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016892	5660	PSAP	http://www.ncbi.nlm.nih.gov/gene/?term=5660	"GLBA, SAP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016893	56611	Anxa2	http://www.ncbi.nlm.nih.gov/gene/?term=56611	ANX2	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00016894	56622	Adam21	http://www.ncbi.nlm.nih.gov/gene/?term=56622	Adam31	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016895	56623	INPP5E	http://www.ncbi.nlm.nih.gov/gene/?term=56623	"CORS1, CPD4, JBTS1, MORMS, PPI5PIV "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016896	56626	Poll	http://www.ncbi.nlm.nih.gov/gene/?term=56626	"1110003P06Rik, AV007317 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016897	56632	Sphk2	http://www.ncbi.nlm.nih.gov/gene/?term=56632	C76851	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016898	56637	Gsk3b	http://www.ncbi.nlm.nih.gov/gene/?term=56637	"7330414F15Rik, 8430431H08Rik, C86142, GSK-3, GSK-3beta, GSK3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016899	5663	PSEN1	http://www.ncbi.nlm.nih.gov/gene/?term=5663	"AD3, FAD, PS-1, PS1, S182 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016900	5663	PSEN1	http://www.ncbi.nlm.nih.gov/gene/?term=5663	"AD3, FAD, PS-1, PS1, S182 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016901	5663	PSEN1	http://www.ncbi.nlm.nih.gov/gene/?term=5663	"AD3, FAD, PS-1, PS1, S182 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016902	56644	Clec7a	http://www.ncbi.nlm.nih.gov/gene/?term=56644	"BGR, Clecsf12, beta-GR "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016903	56647	BCCIP	http://www.ncbi.nlm.nih.gov/gene/?term=56647	"TOK-1, TOK1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016904	56647	BCCIP	http://www.ncbi.nlm.nih.gov/gene/?term=56647	"TOK-1, TOK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016905	56648	EIF5A2	http://www.ncbi.nlm.nih.gov/gene/?term=56648	"EIF-5A2, eIF5AII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016906	56648	EIF5A2	http://www.ncbi.nlm.nih.gov/gene/?term=56648	"EIF-5A2, eIF5AII "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016907	56648	EIF5A2	http://www.ncbi.nlm.nih.gov/gene/?term=56648	"EIF-5A2, eIF5AII "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016908	56649	TMPRSS4	http://www.ncbi.nlm.nih.gov/gene/?term=56649	"CAPH2, MT-SP2, TMPRSS3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016909	5664	PSEN2	http://www.ncbi.nlm.nih.gov/gene/?term=5664	"AD3L, AD4, CMD1V, PS2, STM2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016910	56650	CLDND1	http://www.ncbi.nlm.nih.gov/gene/?term=56650	"C3orf4, GENX-3745 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016911	56652	C10orf2	http://www.ncbi.nlm.nih.gov/gene/?term=56652	"ATXN8, IOSCA, MTDPS7, PEO, PEO1, PEOA3, PRLTS5, SANDO, SCA8, TWINL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016912	56654	NPDC1	http://www.ncbi.nlm.nih.gov/gene/?term=56654	"CAB, CAB-, CAB-1, CAB1, NPDC-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016913	56655	POLE4	http://www.ncbi.nlm.nih.gov/gene/?term=56655	"YHHQ1, p12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016914	56655	POLE4	http://www.ncbi.nlm.nih.gov/gene/?term=56655	"YHHQ1, p12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016915	56666	PANX2	http://www.ncbi.nlm.nih.gov/gene/?term=56666	"PX2, hPANX2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016916	56667	MUC13	http://www.ncbi.nlm.nih.gov/gene/?term=56667	"DRCC1, MUC-13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016917	56672	AKIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56672	"BCA3, C11orf17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016918	56672	AKIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56672	"BCA3, C11orf17 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016919	56672	AKIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56672	"BCA3, C11orf17 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016920	56674	TMEM9B	http://www.ncbi.nlm.nih.gov/gene/?term=56674	C11orf15	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016921	56675	NRIP3	http://www.ncbi.nlm.nih.gov/gene/?term=56675	"C11orf14, NY-SAR-105 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016922	56681	SAR1A	http://www.ncbi.nlm.nih.gov/gene/?term=56681	"SAR1, SARA1, Sara, masra2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016923	56690	Mlycd	http://www.ncbi.nlm.nih.gov/gene/?term=56690	"AI324784, Mcd "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016924	56703	Pigo	http://www.ncbi.nlm.nih.gov/gene/?term=56703	PIG-O	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016925	56704	JPH1	http://www.ncbi.nlm.nih.gov/gene/?term=56704	"CMT2K, JP-1, JP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016926	56704	JPH1	http://www.ncbi.nlm.nih.gov/gene/?term=56704	"CMT2K, JP-1, JP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016927	56706	Ccnl1	http://www.ncbi.nlm.nih.gov/gene/?term=56706	"2610030E23Rik, AU018493, Ccnl, ania-6a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016928	56717	Mtor	http://www.ncbi.nlm.nih.gov/gene/?term=56717	"2610315D21Rik, AI327068, FRAP, FRAP2, Frap1, RAFT1, RAPT1, flat "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016929	56717	Mtor	http://www.ncbi.nlm.nih.gov/gene/?term=56717	"2610315D21Rik, AI327068, FRAP, FRAP2, Frap1, RAFT1, RAPT1, flat "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016930	567234	lrmp	http://www.ncbi.nlm.nih.gov/gene/?term=567234	"si:dkey-172o10.2, si:dkey-172o10.4 "	mRNA	Danio rerio	22542100	Centrosome	Zygote	Whole mount in situ hybridization	"Both maternal lrmp messenger RNA (mRNA) and protein are highly localized in the zygote, in a largely overlapping pattern at nuclear membranes, centrosomes, and spindles. "
RLID00016931	567234	lrmp	http://www.ncbi.nlm.nih.gov/gene/?term=567234	"si:dkey-172o10.2, si:dkey-172o10.4 "	mRNA	Danio rerio	22542100	Nucleus	Zygote	Whole mount in situ hybridization	"Both maternal lrmp messenger RNA (mRNA) and protein are highly localized in the zygote, in a largely overlapping pattern at nuclear membranes, centrosomes, and spindles. "
RLID00016932	567234	lrmp	http://www.ncbi.nlm.nih.gov/gene/?term=567234	"si:dkey-172o10.2, si:dkey-172o10.4 "	mRNA	Danio rerio	22542100	Mitotic spindle	Zygote	Whole mount in situ hybridization	"Both maternal lrmp messenger RNA (mRNA) and protein are highly localized in the zygote, in a largely overlapping pattern at nuclear membranes, centrosomes, and spindles. "
RLID00016933	56726	Sh3bgrl	http://www.ncbi.nlm.nih.gov/gene/?term=56726	1190008F14Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016934	56731	SLC2A4RG	http://www.ncbi.nlm.nih.gov/gene/?term=56731	"GEF, HDBP-1, HDBP1, Si-1-2, Si-1-2-19 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016935	56736	Rnf14	http://www.ncbi.nlm.nih.gov/gene/?term=56736	"2310075C09Rik, 2610005D23Rik, AA986456, AU041447, D18Ertd188e, D7Bwg0165e, Triad2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016936	56737	Alg2	http://www.ncbi.nlm.nih.gov/gene/?term=56737	"1110018A23Rik, 1300013N08Rik, ALPG2, CDGIi, MNCb-5081 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016937	56749	Dhodh	http://www.ncbi.nlm.nih.gov/gene/?term=56749	"2810417D19Rik, AI834883 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016938	56760	Clec1b	http://www.ncbi.nlm.nih.gov/gene/?term=56760	"1810061I13Rik, Clec-2, Clec2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016939	56776	FMN2	http://www.ncbi.nlm.nih.gov/gene/?term=56776		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016940	56784	Ralgapa1	http://www.ncbi.nlm.nih.gov/gene/?term=56784	"2310003F20Rik, 4930400K19Rik, AI563624, GRIPE, Garnl1, Tulip1, mKIAA0884 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016941	56786	Tmem9b	http://www.ncbi.nlm.nih.gov/gene/?term=56786	"2310004K06Rik, AW539847, D7H11orf15, ICRFP703B1614Q5.3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016942	56790	Supt20	http://www.ncbi.nlm.nih.gov/gene/?term=56790	"AA667204, AI450544, D3Ertd300e, Fam48ah, p38IP, Supt20 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016943	56791	Ube2l6	http://www.ncbi.nlm.nih.gov/gene/?term=56791	"2810489I21Rik, RIG-B, UBCH8, Ubce8, Ubcm8 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016944	567	B2M	http://www.ncbi.nlm.nih.gov/gene/?term=567	IMD43	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016945	567	B2M	http://www.ncbi.nlm.nih.gov/gene/?term=567	IMD43	mRNA	Homo sapiens	25063809	Ribosome	HeLa cell	qRT-PCR	"Last, the B2M (350-bp) and GRP94 (2300-bp) mRNAs were enriched in the BrS and BrR polysome fractions in the absence but not the presence of EDTA (Fig. 1, F and G). "
RLID00016946	567	B2M	http://www.ncbi.nlm.nih.gov/gene/?term=567	IMD43	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016947	567	B2M	http://www.ncbi.nlm.nih.gov/gene/?term=567	IMD43	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016948	567	B2M	http://www.ncbi.nlm.nih.gov/gene/?term=567	IMD43	mRNA	Homo sapiens	25063809	Ribosome	HeLa cell	qRT-PCR	Figure 1: Endoplasmic reticulum-associated mRNAs are partitioned between detergent-resistant and detergent-sensitive membrane domains. Data are collected from Figure 1.
RLID00016949	567	B2M	http://www.ncbi.nlm.nih.gov/gene/?term=567	IMD43	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016950	56802	Nespas	http://www.ncbi.nlm.nih.gov/gene/?term=56802	"Gnas-as, Nespos "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016951	568084	grip2a	http://www.ncbi.nlm.nih.gov/gene/?term=568084	"grip2l, si:ch211-150e8.7, si:ch73-250d21.1, wu:fi03h07 "	mRNA	Danio rerio	24967891	Vegetal	Embryo	In situ hybridization	Grip2a mRNA is detected in the vegetal pole region of the yolk in early zygotes and cleavagestage embryos (Figure 3A-E)
RLID00016952	568084	grip2a	http://www.ncbi.nlm.nih.gov/gene/?term=568084	"grip2l, si:ch211-150e8.7, si:ch73-250d21.1, wu:fi03h07 "	mRNA	Danio rerio	26528729	Vegetal	Embryo	Whole mount in situ hybridization	Whole mount in situ hybridization shows that grip2a and wnt8a mRNA are localized at the base of the vegetal cortex and experience an off-cen-ter shift in control (DMSO-treated) embryos 
RLID00016953	568084	grip2a	http://www.ncbi.nlm.nih.gov/gene/?term=568084	"grip2l, si:ch211-150e8.7, si:ch73-250d21.1, wu:fi03h07 "	mRNA	Danio rerio	26528729	Vegetal	Embryo	Fluorescence in situ hybridization	"FIGURE 2. Dual label FISH of pairwise comparisons of wnt8a, grip2a and dazl mRNA localization at the vegetal cortex. (A-C) dazl (green) and wnt8a (red). (D-F) grip2a (green) and dazl (red). (G-I) grip2a (green) and wnt8a (red). In all cases mRNAs localize to discrete units, which do not overlap between different RNAs. Embryos are wild type fixed at 20mpf. Panels are 2-D projections of imaged vegetal cortex samples. Scale bar in (I) represents 5mm for all images. (Color figure available online.) "
RLID00016954	5681	PSKH1	http://www.ncbi.nlm.nih.gov/gene/?term=5681		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016955	5681	PSKH1	http://www.ncbi.nlm.nih.gov/gene/?term=5681		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016956	56829	ZC3HAV1	http://www.ncbi.nlm.nih.gov/gene/?term=56829	"ARTD13, FLB6421, PARP13, ZAP, ZC3H2, ZC3HDC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016957	56829	ZC3HAV1	http://www.ncbi.nlm.nih.gov/gene/?term=56829	"ARTD13, FLB6421, PARP13, ZAP, ZC3H2, ZC3HDC2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016958	56829	ZC3HAV1	http://www.ncbi.nlm.nih.gov/gene/?term=56829	"ARTD13, FLB6421, PARP13, ZAP, ZC3H2, ZC3HDC2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016959	56829	ZC3HAV1	http://www.ncbi.nlm.nih.gov/gene/?term=56829	"ARTD13, FLB6421, PARP13, ZAP, ZC3H2, ZC3HDC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016960	5682	PSMA1	http://www.ncbi.nlm.nih.gov/gene/?term=5682	"HC2, HEL-S-275, NU, PROS30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016961	5682	PSMA1	http://www.ncbi.nlm.nih.gov/gene/?term=5682	"HC2, HEL-S-275, NU, PROS30 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016962	5682	PSMA1	http://www.ncbi.nlm.nih.gov/gene/?term=5682	"HC2, HEL-S-275, NU, PROS30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016963	56832	IFNK	http://www.ncbi.nlm.nih.gov/gene/?term=56832	"IFNT1, INFE1 "	mRNA	Mus musculus	12391192	Dendrite	Monocytes	qRT-PCR	"Expression of the IFN-kappa mRNA was observed in resting dendritic cells and monocytes, and it was up-regulated by IFN-gamma stimulation in monocytes, while IFN-beta mRNA was minimally detectable under the same conditions. "
RLID00016964	56834	GPR137	http://www.ncbi.nlm.nih.gov/gene/?term=56834	"C11orf4, GPR137A, TM7SF1L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016965	5683	PSMA2	http://www.ncbi.nlm.nih.gov/gene/?term=5683	"HC3, MU, PMSA2, PSC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016966	5683	PSMA2	http://www.ncbi.nlm.nih.gov/gene/?term=5683	"HC3, MU, PMSA2, PSC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016967	56844	Tssc4	http://www.ncbi.nlm.nih.gov/gene/?term=56844	"AA241958, ESTM671070 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016968	5684	PSMA3	http://www.ncbi.nlm.nih.gov/gene/?term=5684	"HC8, PSC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016969	5684	PSMA3	http://www.ncbi.nlm.nih.gov/gene/?term=5684	"HC8, PSC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016970	5684	PSMA3	http://www.ncbi.nlm.nih.gov/gene/?term=5684	"HC8, PSC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016971	56851	EMC7	http://www.ncbi.nlm.nih.gov/gene/?term=56851	"C11orf3, C15orf24, HT022, ORF1-FL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016972	56852	RAD18	http://www.ncbi.nlm.nih.gov/gene/?term=56852	RNF73	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016973	56853	CELF4	http://www.ncbi.nlm.nih.gov/gene/?term=56853	"BRUNOL4, CELF-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016974	5685	PSMA4	http://www.ncbi.nlm.nih.gov/gene/?term=5685	"HC9, HsT17706, PSC9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016975	5685	PSMA4	http://www.ncbi.nlm.nih.gov/gene/?term=5685	"HC9, HsT17706, PSC9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016976	5685	PSMA4	http://www.ncbi.nlm.nih.gov/gene/?term=5685	"HC9, HsT17706, PSC9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016977	56868	Psg23	http://www.ncbi.nlm.nih.gov/gene/?term=56868	"1620401C02Rik, cea11 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00016978	5686	PSMA5	http://www.ncbi.nlm.nih.gov/gene/?term=5686	"PSC5, ZETA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016979	5686	PSMA5	http://www.ncbi.nlm.nih.gov/gene/?term=5686	"PSC5, ZETA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016980	5686	PSMA5	http://www.ncbi.nlm.nih.gov/gene/?term=5686	"PSC5, ZETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016981	56878	Rbms1	http://www.ncbi.nlm.nih.gov/gene/?term=56878	"2600014B10Rik, AI255215, MSSP-1, MSSP-2, MSSP-3, YC1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016982	56878	Rbms1	http://www.ncbi.nlm.nih.gov/gene/?term=56878	"2600014B10Rik, AI255215, MSSP-1, MSSP-2, MSSP-3, YC1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00016983	5687	PSMA6	http://www.ncbi.nlm.nih.gov/gene/?term=5687	"IOTA, PROS27, p27K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016984	5687	PSMA6	http://www.ncbi.nlm.nih.gov/gene/?term=5687	"IOTA, PROS27, p27K "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016985	5687	PSMA6	http://www.ncbi.nlm.nih.gov/gene/?term=5687	"IOTA, PROS27, p27K "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016986	56882	CDC42SE1	http://www.ncbi.nlm.nih.gov/gene/?term=56882	"SCIP1, SPEC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016987	56882	CDC42SE1	http://www.ncbi.nlm.nih.gov/gene/?term=56882	"SCIP1, SPEC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016988	56882	CDC42SE1	http://www.ncbi.nlm.nih.gov/gene/?term=56882	"SCIP1, SPEC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016989	56884	FSTL5	http://www.ncbi.nlm.nih.gov/gene/?term=56884		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016990	56886	UGGT1	http://www.ncbi.nlm.nih.gov/gene/?term=56886	"HUGT1, UGCGL1, UGT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016991	56886	UGGT1	http://www.ncbi.nlm.nih.gov/gene/?term=56886	"HUGT1, UGCGL1, UGT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016992	56888	KCMF1	http://www.ncbi.nlm.nih.gov/gene/?term=56888	"DEBT91, FIGC, PCMF, ZZZ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016993	56889	TM9SF3	http://www.ncbi.nlm.nih.gov/gene/?term=56889	"EP70-P-iso, SMBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016994	56889	TM9SF3	http://www.ncbi.nlm.nih.gov/gene/?term=56889	"EP70-P-iso, SMBP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016995	5688	PSMA7	http://www.ncbi.nlm.nih.gov/gene/?term=5688	"C6, HEL-S-276, HSPC, RC6-1, XAPC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00016996	5688	PSMA7	http://www.ncbi.nlm.nih.gov/gene/?term=5688	"C6, HEL-S-276, HSPC, RC6-1, XAPC7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00016997	5688	PSMA7	http://www.ncbi.nlm.nih.gov/gene/?term=5688	"C6, HEL-S-276, HSPC, RC6-1, XAPC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00016998	56890	MDM1	http://www.ncbi.nlm.nih.gov/gene/?term=56890		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00016999	56890	MDM1	http://www.ncbi.nlm.nih.gov/gene/?term=56890		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017000	56890	MDM1	http://www.ncbi.nlm.nih.gov/gene/?term=56890		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017001	56893	UBQLN4	http://www.ncbi.nlm.nih.gov/gene/?term=56893	"A1U, A1Up, C1orf6, CIP75, UBIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017002	56893	UBQLN4	http://www.ncbi.nlm.nih.gov/gene/?term=56893	"A1U, A1Up, C1orf6, CIP75, UBIN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017003	56893	UBQLN4	http://www.ncbi.nlm.nih.gov/gene/?term=56893	"A1U, A1Up, C1orf6, CIP75, UBIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017004	56894	AGPAT3	http://www.ncbi.nlm.nih.gov/gene/?term=56894	"LPAAT-GAMMA1, LPAAT3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017005	56895	AGPAT4	http://www.ncbi.nlm.nih.gov/gene/?term=56895	"1-AGPAT4, LPAAT-delta, dJ473J16.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017006	56896	DPYSL5	http://www.ncbi.nlm.nih.gov/gene/?term=56896	"CRAM, CRMP-5, CRMP5, Ulip6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017007	56896	DPYSL5	http://www.ncbi.nlm.nih.gov/gene/?term=56896	"CRAM, CRMP-5, CRMP5, Ulip6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017008	56896	DPYSL5	http://www.ncbi.nlm.nih.gov/gene/?term=56896	"CRAM, CRMP-5, CRMP5, Ulip6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017009	56897	WRNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56897	"WHIP, bA420G6.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017010	56897	WRNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56897	"WHIP, bA420G6.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017011	56898	BDH2	http://www.ncbi.nlm.nih.gov/gene/?term=56898	"DHRS6, EFA6R, PRO20933, SDR15C1, UCPA-OR, UNQ6308 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017012	56898	BDH2	http://www.ncbi.nlm.nih.gov/gene/?term=56898	"DHRS6, EFA6R, PRO20933, SDR15C1, UCPA-OR, UNQ6308 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017013	5689	PSMB1	http://www.ncbi.nlm.nih.gov/gene/?term=5689	"HC5, PMSB1, PSC5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017014	5689	PSMB1	http://www.ncbi.nlm.nih.gov/gene/?term=5689	"HC5, PMSB1, PSC5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017015	5689	PSMB1	http://www.ncbi.nlm.nih.gov/gene/?term=5689	"HC5, PMSB1, PSC5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017016	56900	TMEM167B	http://www.ncbi.nlm.nih.gov/gene/?term=56900	"AD-020, C1orf119 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017017	56900	TMEM167B	http://www.ncbi.nlm.nih.gov/gene/?term=56900	"AD-020, C1orf119 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017018	56901	NDUFA4L2	http://www.ncbi.nlm.nih.gov/gene/?term=56901	NUOMS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017019	56902	PNO1	http://www.ncbi.nlm.nih.gov/gene/?term=56902	"KHRBP1, RRP20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017020	56902	PNO1	http://www.ncbi.nlm.nih.gov/gene/?term=56902	"KHRBP1, RRP20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017021	56905	C15orf39	http://www.ncbi.nlm.nih.gov/gene/?term=56905		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017022	56907	SPIRE1	http://www.ncbi.nlm.nih.gov/gene/?term=56907	Spir-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017023	56907	SPIRE1	http://www.ncbi.nlm.nih.gov/gene/?term=56907	Spir-1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017024	56907	SPIRE1	http://www.ncbi.nlm.nih.gov/gene/?term=56907	Spir-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017025	5690	PSMB2	http://www.ncbi.nlm.nih.gov/gene/?term=5690	HC7-I	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017026	5690	PSMB2	http://www.ncbi.nlm.nih.gov/gene/?term=5690	HC7-I	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017027	5690	PSMB2	http://www.ncbi.nlm.nih.gov/gene/?term=5690	HC7-I	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017028	56910	STARD7	http://www.ncbi.nlm.nih.gov/gene/?term=56910	GTT1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017029	56912	IFT46	http://www.ncbi.nlm.nih.gov/gene/?term=56912	"C11orf2, C11orf60, CFAP32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017030	56912	IFT46	http://www.ncbi.nlm.nih.gov/gene/?term=56912	"C11orf2, C11orf60, CFAP32 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017031	56913	C1GALT1	http://www.ncbi.nlm.nih.gov/gene/?term=56913	"C1GALT, T-synthase "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017032	56915	EXOSC5	http://www.ncbi.nlm.nih.gov/gene/?term=56915	"RRP41B, RRP46, Rrp46p, hRrp46p, p12B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017033	56916	SMARCAD1	http://www.ncbi.nlm.nih.gov/gene/?term=56916	"ADERM, ETL1, HEL1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017034	56916	SMARCAD1	http://www.ncbi.nlm.nih.gov/gene/?term=56916	"ADERM, ETL1, HEL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017035	56918	C2orf83	http://www.ncbi.nlm.nih.gov/gene/?term=56918		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017036	56918	C2orf83	http://www.ncbi.nlm.nih.gov/gene/?term=56918		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017037	56919	DHX33	http://www.ncbi.nlm.nih.gov/gene/?term=56919	DDX33	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017038	5691	PSMB3	http://www.ncbi.nlm.nih.gov/gene/?term=5691	HC10-II	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017039	5691	PSMB3	http://www.ncbi.nlm.nih.gov/gene/?term=5691	HC10-II	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017040	56924	PAK6	http://www.ncbi.nlm.nih.gov/gene/?term=56924	PAK5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017041	56926	NCLN	http://www.ncbi.nlm.nih.gov/gene/?term=56926	NET59	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017042	56927	GPR108	http://www.ncbi.nlm.nih.gov/gene/?term=56927	LUSTR2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017043	56927	GPR108	http://www.ncbi.nlm.nih.gov/gene/?term=56927	LUSTR2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017044	56928	SPPL2B	http://www.ncbi.nlm.nih.gov/gene/?term=56928	"IMP-4, IMP4, PSH4, PSL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017045	56929	FEM1C	http://www.ncbi.nlm.nih.gov/gene/?term=56929	"EUROIMAGE686608, EUROIMAGE783647, FEM1A "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017046	5692	PSMB4	http://www.ncbi.nlm.nih.gov/gene/?term=5692	"HN3, HsN3, PROS-26, PROS26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017047	5692	PSMB4	http://www.ncbi.nlm.nih.gov/gene/?term=5692	"HN3, HsN3, PROS-26, PROS26 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017048	56931	DUS3L	http://www.ncbi.nlm.nih.gov/gene/?term=56931	DUS3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017049	56934	CA10	http://www.ncbi.nlm.nih.gov/gene/?term=56934	"CA-RPX, CARPX, HUCEP-15 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017050	56935	SMCO4	http://www.ncbi.nlm.nih.gov/gene/?term=56935	"C11orf75, FN5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017051	5693	PSMB5	http://www.ncbi.nlm.nih.gov/gene/?term=5693	"LMPX, MB1, X "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017052	5693	PSMB5	http://www.ncbi.nlm.nih.gov/gene/?term=5693	"LMPX, MB1, X "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017053	5693	PSMB5	http://www.ncbi.nlm.nih.gov/gene/?term=5693	"LMPX, MB1, X "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017054	56940	DUSP22	http://www.ncbi.nlm.nih.gov/gene/?term=56940	"JKAP, JSP-1, JSP1, LMW-DSP2, LMWDSP2, MKP-x, MKPX, VHX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017055	56940	DUSP22	http://www.ncbi.nlm.nih.gov/gene/?term=56940	"JKAP, JSP-1, JSP1, LMW-DSP2, LMWDSP2, MKP-x, MKPX, VHX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017056	56941	HMCES	http://www.ncbi.nlm.nih.gov/gene/?term=56941	"C3orf37, DC12, SRAPD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017057	56942	CMC2	http://www.ncbi.nlm.nih.gov/gene/?term=56942	"2310061C15Rik, C16orf61, DC13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017058	56942	CMC2	http://www.ncbi.nlm.nih.gov/gene/?term=56942	"2310061C15Rik, C16orf61, DC13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017059	56943	ENY2	http://www.ncbi.nlm.nih.gov/gene/?term=56943	"DC6, Sus1, e(y)2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017060	56943	ENY2	http://www.ncbi.nlm.nih.gov/gene/?term=56943	"DC6, Sus1, e(y)2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017061	56945	MRPS22	http://www.ncbi.nlm.nih.gov/gene/?term=56945	"C3orf5, COXPD5, GIBT, GK002, MRP-S22, RPMS22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017062	56946	EMSY	http://www.ncbi.nlm.nih.gov/gene/?term=56946	"C11orf30, GL002 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017063	56947	MFF	http://www.ncbi.nlm.nih.gov/gene/?term=56947	"C2orf33, GL004 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017064	5694	PSMB6	http://www.ncbi.nlm.nih.gov/gene/?term=5694	"DELTA, LMPY, Y "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017065	5694	PSMB6	http://www.ncbi.nlm.nih.gov/gene/?term=5694	"DELTA, LMPY, Y "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017066	5694	PSMB6	http://www.ncbi.nlm.nih.gov/gene/?term=5694	"DELTA, LMPY, Y "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017067	56950	SMYD2	http://www.ncbi.nlm.nih.gov/gene/?term=56950	"HSKM-B, KMT3C, ZMYND14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017068	56951	C5orf15	http://www.ncbi.nlm.nih.gov/gene/?term=56951	"HTGN29, KCT2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017069	56951	C5orf15	http://www.ncbi.nlm.nih.gov/gene/?term=56951	"HTGN29, KCT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017070	56952	PRTFDC1	http://www.ncbi.nlm.nih.gov/gene/?term=56952	HHGP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017071	56953	NT5M	http://www.ncbi.nlm.nih.gov/gene/?term=56953	"dNT-2, dNT2, mdN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017072	56954	NIT2	http://www.ncbi.nlm.nih.gov/gene/?term=56954	HEL-S-8a	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017073	56954	NIT2	http://www.ncbi.nlm.nih.gov/gene/?term=56954	HEL-S-8a	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017074	56954	NIT2	http://www.ncbi.nlm.nih.gov/gene/?term=56954	HEL-S-8a	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017075	5695	PSMB7	http://www.ncbi.nlm.nih.gov/gene/?term=5695	Z	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017076	5695	PSMB7	http://www.ncbi.nlm.nih.gov/gene/?term=5695	Z	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017077	5695	PSMB7	http://www.ncbi.nlm.nih.gov/gene/?term=5695	Z	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017078	56965	PARP6	http://www.ncbi.nlm.nih.gov/gene/?term=56965	"ARTD17, PARP-6-B1, PARP-6-C, pART17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017079	5696	PSMB8	http://www.ncbi.nlm.nih.gov/gene/?term=5696	"ALDD, D6S216, D6S216E, JMP, LMP7, NKJO, PSMB5i, RING10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017080	56971	CEACAM19	http://www.ncbi.nlm.nih.gov/gene/?term=56971	CEAL1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017081	56975	FAM20C	http://www.ncbi.nlm.nih.gov/gene/?term=56975	"DMP-4, DMP4, GEF-CK, RNS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017082	56983	POGLUT1	http://www.ncbi.nlm.nih.gov/gene/?term=56983	"C3orf9, CLP46, KDELCL1, KTELC1, MDS010, MDSRP, Rumi, hCLP46 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017083	56984	PSMG2	http://www.ncbi.nlm.nih.gov/gene/?term=56984	"CLAST3, HCCA3, HsT1707, MDS003, PAC2, TNFSF5IP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017084	56985	ADPRM	http://www.ncbi.nlm.nih.gov/gene/?term=56985	"C17orf48, MDS006, NBLA03831 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017085	56986	DTWD1	http://www.ncbi.nlm.nih.gov/gene/?term=56986	MDS009	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017086	56987	BBX	http://www.ncbi.nlm.nih.gov/gene/?term=56987	"ARTC1, HBP2, HSPC339, MDS001 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017087	56987	BBX	http://www.ncbi.nlm.nih.gov/gene/?term=56987	"ARTC1, HBP2, HSPC339, MDS001 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017088	5698	PSMB9	http://www.ncbi.nlm.nih.gov/gene/?term=5698	"LMP2, PSMB6i, RING12, beta1i "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017089	56990	CDC42SE2	http://www.ncbi.nlm.nih.gov/gene/?term=56990	SPEC2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017090	56990	CDC42SE2	http://www.ncbi.nlm.nih.gov/gene/?term=56990	SPEC2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017091	56992	KIF15	http://www.ncbi.nlm.nih.gov/gene/?term=56992	"HKLP2, KNSL7, NY-BR-62 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017092	56993	TOMM22	http://www.ncbi.nlm.nih.gov/gene/?term=56993	"1C9-2, MST065, MSTP065, TOM22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017093	56994	CHPT1	http://www.ncbi.nlm.nih.gov/gene/?term=56994	"CPT, CPT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017094	56994	CHPT1	http://www.ncbi.nlm.nih.gov/gene/?term=56994	"CPT, CPT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017095	56994	CHPT1	http://www.ncbi.nlm.nih.gov/gene/?term=56994	"CPT, CPT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017096	56995	TULP4	http://www.ncbi.nlm.nih.gov/gene/?term=56995	TUSP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017097	56995	TULP4	http://www.ncbi.nlm.nih.gov/gene/?term=56995	TUSP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017098	56996	SLC12A9	http://www.ncbi.nlm.nih.gov/gene/?term=56996	"CCC6, CIP1, WO3.3, hCCC6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017099	56997	ADCK3	http://www.ncbi.nlm.nih.gov/gene/?term=56997	"ARCA2, CABC1, COQ10D4, COQ8, SCAR9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017100	56997	ADCK3	http://www.ncbi.nlm.nih.gov/gene/?term=56997	"ARCA2, CABC1, COQ10D4, COQ8, SCAR9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017101	56998	CTNNBIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56998	ICAT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017102	56998	CTNNBIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56998	ICAT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017103	56998	CTNNBIP1	http://www.ncbi.nlm.nih.gov/gene/?term=56998	ICAT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017104	5699	PSMB10	http://www.ncbi.nlm.nih.gov/gene/?term=5699	"LMP10, MECL1, beta2i "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017105	57001	SDHAF3	http://www.ncbi.nlm.nih.gov/gene/?term=57001	"ACN9, DC11, Sdh7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017106	57002	YAE1D1	http://www.ncbi.nlm.nih.gov/gene/?term=57002	"C7orf36, GK003 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017107	57002	YAE1D1	http://www.ncbi.nlm.nih.gov/gene/?term=57002	"C7orf36, GK003 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017108	57003	CCDC47	http://www.ncbi.nlm.nih.gov/gene/?term=57003	"GK001, MSTP041 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017109	57003	CCDC47	http://www.ncbi.nlm.nih.gov/gene/?term=57003	"GK001, MSTP041 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017110	5700	PSMC1	http://www.ncbi.nlm.nih.gov/gene/?term=5700	"P26S4, S4, p56 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017111	57017	COQ9	http://www.ncbi.nlm.nih.gov/gene/?term=57017	"C16orf49, COQ10D5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017112	57017	COQ9	http://www.ncbi.nlm.nih.gov/gene/?term=57017	"C16orf49, COQ10D5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017113	57018	CCNL1	http://www.ncbi.nlm.nih.gov/gene/?term=57018	"ANIA6A, BM-001, PRO1073, ania-6a "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017114	57018	CCNL1	http://www.ncbi.nlm.nih.gov/gene/?term=57018	"ANIA6A, BM-001, PRO1073, ania-6a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017115	57019	CIAPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=57019	"Anamorsin, DRE2, PRO0915 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017116	57019	CIAPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=57019	"Anamorsin, DRE2, PRO0915 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017117	57019	CIAPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=57019	"Anamorsin, DRE2, PRO0915 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017118	5701	PSMC2	http://www.ncbi.nlm.nih.gov/gene/?term=5701	"MSS1, Nbla10058, S7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017119	5701	PSMC2	http://www.ncbi.nlm.nih.gov/gene/?term=5701	"MSS1, Nbla10058, S7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017120	5701	PSMC2	http://www.ncbi.nlm.nih.gov/gene/?term=5701	"MSS1, Nbla10058, S7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017121	57020	C16orf62	http://www.ncbi.nlm.nih.gov/gene/?term=57020		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017122	57026	PDXP	http://www.ncbi.nlm.nih.gov/gene/?term=57026	"CIN, PLP, dJ37E16.5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017123	57026	PDXP	http://www.ncbi.nlm.nih.gov/gene/?term=57026	"CIN, PLP, dJ37E16.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017124	57028	Pdxp	http://www.ncbi.nlm.nih.gov/gene/?term=57028	"1600027H05Rik, AB041662, PLPP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017125	5702	PSMC3	http://www.ncbi.nlm.nih.gov/gene/?term=5702	TBP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017126	57030	SLC17A7	http://www.ncbi.nlm.nih.gov/gene/?term=57030	"BNPI, VGLUT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017127	57035	RSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=57035	"C1orf63, DJ465N24.2.1, NPD014 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017128	57037	ANKMY2	http://www.ncbi.nlm.nih.gov/gene/?term=57037	ZMYND20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017129	57038	RARS2	http://www.ncbi.nlm.nih.gov/gene/?term=57038	"ArgRS, DALRD2, PCH6, PRO1992, RARSL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017130	57038	RARS2	http://www.ncbi.nlm.nih.gov/gene/?term=57038	"ArgRS, DALRD2, PCH6, PRO1992, RARSL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017131	57045	TWSG1	http://www.ncbi.nlm.nih.gov/gene/?term=57045	TSG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017132	57045	TWSG1	http://www.ncbi.nlm.nih.gov/gene/?term=57045	TSG	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017133	57045	TWSG1	http://www.ncbi.nlm.nih.gov/gene/?term=57045	TSG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017134	57047	PLSCR2	http://www.ncbi.nlm.nih.gov/gene/?term=57047		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017135	5704	PSMC4	http://www.ncbi.nlm.nih.gov/gene/?term=5704	"MIP224, RPT3, S6, TBP-7, TBP7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017136	5704	PSMC4	http://www.ncbi.nlm.nih.gov/gene/?term=5704	"MIP224, RPT3, S6, TBP-7, TBP7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017137	5704	PSMC4	http://www.ncbi.nlm.nih.gov/gene/?term=5704	"MIP224, RPT3, S6, TBP-7, TBP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017138	57050	UTP3	http://www.ncbi.nlm.nih.gov/gene/?term=57050	"CRL1, CRLZ1, SAS10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017139	5705	PSMC5	http://www.ncbi.nlm.nih.gov/gene/?term=5705	"S8, SUG-1, SUG1, TBP10, TRIP1, p45, p45/SUG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017140	57062	DDX24	http://www.ncbi.nlm.nih.gov/gene/?term=57062		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017141	57062	DDX24	http://www.ncbi.nlm.nih.gov/gene/?term=57062		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017142	57062	DDX24	http://www.ncbi.nlm.nih.gov/gene/?term=57062		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017143	5706	PSMC6	http://www.ncbi.nlm.nih.gov/gene/?term=5706	"CADP44, HEL-S-73, P44, SUG2, p42 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017144	5706	PSMC6	http://www.ncbi.nlm.nih.gov/gene/?term=5706	"CADP44, HEL-S-73, P44, SUG2, p42 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017145	5706	PSMC6	http://www.ncbi.nlm.nih.gov/gene/?term=5706	"CADP44, HEL-S-73, P44, SUG2, p42 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017146	5707	PSMD1	http://www.ncbi.nlm.nih.gov/gene/?term=5707	"P112, Rpn2, S1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017147	57082	CASC5	http://www.ncbi.nlm.nih.gov/gene/?term=57082	"AF15Q14, CT29, D40, KNL1, PPP1R55, Spc7, hKNL-1, hSpc105 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017148	57085	AGTRAP	http://www.ncbi.nlm.nih.gov/gene/?term=57085	ATRAP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017149	57085	AGTRAP	http://www.ncbi.nlm.nih.gov/gene/?term=57085	ATRAP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017150	57089	ENTPD7	http://www.ncbi.nlm.nih.gov/gene/?term=57089	LALP1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017151	5708	PSMD2	http://www.ncbi.nlm.nih.gov/gene/?term=5708	"P97, RPN1, S2, TRAP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017152	5708	PSMD2	http://www.ncbi.nlm.nih.gov/gene/?term=5708	"P97, RPN1, S2, TRAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017153	57095	PITHD1	http://www.ncbi.nlm.nih.gov/gene/?term=57095	"C1orf128, HT014, TXNL1CL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017154	57095	PITHD1	http://www.ncbi.nlm.nih.gov/gene/?term=57095	"C1orf128, HT014, TXNL1CL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017155	57099	AVEN	http://www.ncbi.nlm.nih.gov/gene/?term=57099	PDCD12	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017156	57099	AVEN	http://www.ncbi.nlm.nih.gov/gene/?term=57099	PDCD12	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017157	5709	PSMD3	http://www.ncbi.nlm.nih.gov/gene/?term=5709	"P58, RPN3, S3, TSTA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017158	5709	PSMD3	http://www.ncbi.nlm.nih.gov/gene/?term=5709	"P58, RPN3, S3, TSTA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017159	570	BAAT	http://www.ncbi.nlm.nih.gov/gene/?term=570	"BACAT, BAT "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017160	57103	TIGAR	http://www.ncbi.nlm.nih.gov/gene/?term=57103	"C12orf5, FR2BP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017161	57103	TIGAR	http://www.ncbi.nlm.nih.gov/gene/?term=57103	"C12orf5, FR2BP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017162	57104	PNPLA2	http://www.ncbi.nlm.nih.gov/gene/?term=57104	"1110001C14Rik, ATGL, FP17548, PEDF-R, TTS-2.2, TTS2, iPLA2zeta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017163	57104	PNPLA2	http://www.ncbi.nlm.nih.gov/gene/?term=57104	"1110001C14Rik, ATGL, FP17548, PEDF-R, TTS-2.2, TTS2, iPLA2zeta "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017164	57107	PDSS2	http://www.ncbi.nlm.nih.gov/gene/?term=57107	"C6orf210, COQ10D3, DLP1, bA59I9.3, hDLP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017165	57109	REXO4	http://www.ncbi.nlm.nih.gov/gene/?term=57109	"REX4, XPMC2, XPMC2H "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017166	5710	PSMD4	http://www.ncbi.nlm.nih.gov/gene/?term=5710	"AF, AF-1, ASF, MCB1, Rpn10, S5A, pUB-R5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017167	57110	HRASLS	http://www.ncbi.nlm.nih.gov/gene/?term=57110	"A-C1, H-REV107, HRASLS1, HRSL1, HSD28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017168	57111	RAB25	http://www.ncbi.nlm.nih.gov/gene/?term=57111	"CATX-8, RAB11C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017169	57118	CAMK1D	http://www.ncbi.nlm.nih.gov/gene/?term=57118	"CKLiK, CaM-K1, CaMKID "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017170	5711	PSMD5	http://www.ncbi.nlm.nih.gov/gene/?term=5711	S5B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017171	5711	PSMD5	http://www.ncbi.nlm.nih.gov/gene/?term=5711	S5B	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017172	5711	PSMD5	http://www.ncbi.nlm.nih.gov/gene/?term=5711	S5B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017173	57120	GOPC	http://www.ncbi.nlm.nih.gov/gene/?term=57120	"CAL, FIG1, PIST, dJ94G16.2, GOPC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017174	57127	RHBG	http://www.ncbi.nlm.nih.gov/gene/?term=57127	SLC42A2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017175	57128	LYRM4	http://www.ncbi.nlm.nih.gov/gene/?term=57128	"C6orf149, CGI-203, COXPD19, ISD11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017176	57128	LYRM4	http://www.ncbi.nlm.nih.gov/gene/?term=57128	"C6orf149, CGI-203, COXPD19, ISD11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017177	57129	MRPL47	http://www.ncbi.nlm.nih.gov/gene/?term=57129	"CGI-204, L47mt, MRP-L47, NCM1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017178	57130	ATP13A1	http://www.ncbi.nlm.nih.gov/gene/?term=57130	"ATP13A, CGI-152 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017179	57132	CHMP1B	http://www.ncbi.nlm.nih.gov/gene/?term=57132	"C10orf2, C18-ORF2, C18orf2, CHMP1.5, Vps46-2, Vps46B, hVps46-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017180	57132	CHMP1B	http://www.ncbi.nlm.nih.gov/gene/?term=57132	"C10orf2, C18-ORF2, C18orf2, CHMP1.5, Vps46-2, Vps46B, hVps46-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017181	57136	APMAP	http://www.ncbi.nlm.nih.gov/gene/?term=57136	"BSCv, C20orf3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017182	57136	APMAP	http://www.ncbi.nlm.nih.gov/gene/?term=57136	"BSCv, C20orf3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017183	5713	PSMD7	http://www.ncbi.nlm.nih.gov/gene/?term=5713	"MOV34, P40, Rpn8, S12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017184	57142	RTN4	http://www.ncbi.nlm.nih.gov/gene/?term=57142	"ASY, NI220/250, NOGO, NOGO-A, NOGOC, NSP, NSP-CL, Nbla00271, Nbla10545, Nogo-B, Nogo-C, RTN-X-A, RTN4-B1, RTN4-B2, RTN4-C, RTN4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017185	57142	RTN4	http://www.ncbi.nlm.nih.gov/gene/?term=57142	"ASY, NI220/250, NOGO, NOGO-A, NOGOC, NSP, NSP-CL, Nbla00271, Nbla10545, Nogo-B, Nogo-C, RTN-X-A, RTN4-B1, RTN4-B2, RTN4-C, RTN4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017186	57146	TMEM159	http://www.ncbi.nlm.nih.gov/gene/?term=57146		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017187	57146	TMEM159	http://www.ncbi.nlm.nih.gov/gene/?term=57146		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017188	57146	TMEM159	http://www.ncbi.nlm.nih.gov/gene/?term=57146		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017189	57146	TMEM159	http://www.ncbi.nlm.nih.gov/gene/?term=57146		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017190	57148	RALGAPB	http://www.ncbi.nlm.nih.gov/gene/?term=57148	"KIAA1219, RalGAPbeta "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017191	57148	RALGAPB	http://www.ncbi.nlm.nih.gov/gene/?term=57148	"KIAA1219, RalGAPbeta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017192	57149	LYRM1	http://www.ncbi.nlm.nih.gov/gene/?term=57149	A211C6.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017193	57149	LYRM1	http://www.ncbi.nlm.nih.gov/gene/?term=57149	A211C6.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017194	5714	PSMD8	http://www.ncbi.nlm.nih.gov/gene/?term=5714	"HEL-S-91n, HIP6, HYPF, Nin1p, Rpn12, S14, p31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017195	5714	PSMD8	http://www.ncbi.nlm.nih.gov/gene/?term=5714	"HEL-S-91n, HIP6, HYPF, Nin1p, Rpn12, S14, p31 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017196	5714	PSMD8	http://www.ncbi.nlm.nih.gov/gene/?term=5714	"HEL-S-91n, HIP6, HYPF, Nin1p, Rpn12, S14, p31 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017197	57150	SMIM8	http://www.ncbi.nlm.nih.gov/gene/?term=57150	"C6orf162, dJ102H19.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017198	57153	SLC44A2	http://www.ncbi.nlm.nih.gov/gene/?term=57153	"CTL2, PP1292 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017199	57153	SLC44A2	http://www.ncbi.nlm.nih.gov/gene/?term=57153	"CTL2, PP1292 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017200	57154	SMURF1	http://www.ncbi.nlm.nih.gov/gene/?term=57154		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017201	57154	SMURF1	http://www.ncbi.nlm.nih.gov/gene/?term=57154		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017202	57157	PHTF2	http://www.ncbi.nlm.nih.gov/gene/?term=57157		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017203	57157	PHTF2	http://www.ncbi.nlm.nih.gov/gene/?term=57157		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017204	57159	TRIM54	http://www.ncbi.nlm.nih.gov/gene/?term=57159	"MURF, MURF-3, RNF30, muRF3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017205	57159	TRIM54	http://www.ncbi.nlm.nih.gov/gene/?term=57159	"MURF, MURF-3, RNF30, muRF3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017206	57159	TRIM54	http://www.ncbi.nlm.nih.gov/gene/?term=57159	"MURF, MURF-3, RNF30, muRF3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017207	5715	PSMD9	http://www.ncbi.nlm.nih.gov/gene/?term=5715	"Rpn4, p27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017208	5715	PSMD9	http://www.ncbi.nlm.nih.gov/gene/?term=5715	"Rpn4, p27 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017209	5715	PSMD9	http://www.ncbi.nlm.nih.gov/gene/?term=5715	"Rpn4, p27 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017210	5715	PSMD9	http://www.ncbi.nlm.nih.gov/gene/?term=5715	"Rpn4, p27 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017211	57162	PELI1	http://www.ncbi.nlm.nih.gov/gene/?term=57162		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017212	57168	ASPHD2	http://www.ncbi.nlm.nih.gov/gene/?term=57168		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017213	57169	ZNFX1	http://www.ncbi.nlm.nih.gov/gene/?term=57169		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017214	57169	ZNFX1	http://www.ncbi.nlm.nih.gov/gene/?term=57169		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017215	5716	PSMD10	http://www.ncbi.nlm.nih.gov/gene/?term=5716	"dJ889N15.2, p28, p28(GANK) "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017216	5716	PSMD10	http://www.ncbi.nlm.nih.gov/gene/?term=5716	"dJ889N15.2, p28, p28(GANK) "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017217	5716	PSMD10	http://www.ncbi.nlm.nih.gov/gene/?term=5716	"dJ889N15.2, p28, p28(GANK) "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017218	57171	DOLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=57171	LSFR2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017219	57171	DOLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=57171	LSFR2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017220	57171	DOLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=57171	LSFR2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017221	57175	CORO1B	http://www.ncbi.nlm.nih.gov/gene/?term=57175	CORONIN-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017222	57175	CORO1B	http://www.ncbi.nlm.nih.gov/gene/?term=57175	CORONIN-2	mRNA	Homo sapiens	23667561	Cytosol	Endothelial cell	Immunocytochemistry	"Furthermore, a significant fraction of coronin is also diffusely distributed within the cell cytoplasm, but this population of coronin does not co-localize with F-actin or cortactin. Upon serum starvation, coronin redistributes from the cell periphery and is distributed only within the cell cytosol (Figure 3).Furthermore, a significant fraction of coronin is also diffusely distributed within the cell cytoplasm, but this population of coronin does not co-localize with F-actin or cortactin. Upon serum starvation, coronin redistributes from the cell periphery and is distributed only within the cell cytosol (Figure 3). "
RLID00017223	57175	CORO1B	http://www.ncbi.nlm.nih.gov/gene/?term=57175	CORONIN-2	mRNA	Homo sapiens	23667561	Lamellipodium	Endothelial cell	Immunocytochemistry	"Coronin 1B mRNA and protein are highly expressed in human pulmonary artery, umbilical vein, aortic and lung microvascular endothelial cells (Figure 1 A & B). Under normal growth conditions, as evidenced by immunocytochemistry, coronin 1B co-localizes with F-actin in a ?2 ?M thick region at the leading edge of the cell periphery (Figure 2). This is presumably the fast “tread-milling�region of F-actin polymerization that has been well-characterized for cell lamellipodia. Furthermore, a significant fraction of coronin is also diffusely distributed within the cell cytoplasm, but this population of coronin does not co-localize with F-actin or cortactin. Upon serum starvation, coronin redistributes from the cell periphery and is distributed only within the cell cytosol (Figure 3). "
RLID00017224	57176	VARS2	http://www.ncbi.nlm.nih.gov/gene/?term=57176	"COXPD20, VALRSL, VARSL, VARS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017225	57179	KIAA1191	http://www.ncbi.nlm.nih.gov/gene/?term=57179	"p33MONOX, p60MONOX "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017226	5717	PSMD11	http://www.ncbi.nlm.nih.gov/gene/?term=5717	"Rpn6, S9, p44.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017227	5717	PSMD11	http://www.ncbi.nlm.nih.gov/gene/?term=5717	"Rpn6, S9, p44.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017228	57180	ACTR3B	http://www.ncbi.nlm.nih.gov/gene/?term=57180	"ARP11, ARP3BETA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017229	57180	ACTR3B	http://www.ncbi.nlm.nih.gov/gene/?term=57180	"ARP11, ARP3BETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017230	57181	SLC39A10	http://www.ncbi.nlm.nih.gov/gene/?term=57181	LZT-Hs2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017231	57181	SLC39A10	http://www.ncbi.nlm.nih.gov/gene/?term=57181	LZT-Hs2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017232	57182	ANKRD50	http://www.ncbi.nlm.nih.gov/gene/?term=57182		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017233	57184	FAM219B	http://www.ncbi.nlm.nih.gov/gene/?term=57184	C15orf17	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017234	57184	FAM219B	http://www.ncbi.nlm.nih.gov/gene/?term=57184	C15orf17	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017235	57184	FAM219B	http://www.ncbi.nlm.nih.gov/gene/?term=57184	C15orf17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017236	57185	NIPAL3	http://www.ncbi.nlm.nih.gov/gene/?term=57185	"DJ462O23.2, NPAL3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017237	57187	THOC2	http://www.ncbi.nlm.nih.gov/gene/?term=57187	"CXorf3, MRX12, MRX35, THO2, dJ506G2.1, hTREX120 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017238	57187	THOC2	http://www.ncbi.nlm.nih.gov/gene/?term=57187	"CXorf3, MRX12, MRX35, THO2, dJ506G2.1, hTREX120 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017239	57189	KIAA1147	http://www.ncbi.nlm.nih.gov/gene/?term=57189	"LCHN, PRO2561 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017240	5718	PSMD12	http://www.ncbi.nlm.nih.gov/gene/?term=5718	"Rpn5, p55 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017241	5718	PSMD12	http://www.ncbi.nlm.nih.gov/gene/?term=5718	"Rpn5, p55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017242	57190	SEPN1	http://www.ncbi.nlm.nih.gov/gene/?term=57190	"CFTD, MDRS1, RSMD1, RSS, SELN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017243	57190	SEPN1	http://www.ncbi.nlm.nih.gov/gene/?term=57190	"CFTD, MDRS1, RSMD1, RSS, SELN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017244	57190	SEPN1	http://www.ncbi.nlm.nih.gov/gene/?term=57190	"CFTD, MDRS1, RSMD1, RSS, SELN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017245	57194	ATP10A	http://www.ncbi.nlm.nih.gov/gene/?term=57194	"ATP10C, ATPVA, ATPVC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017246	57194	ATP10A	http://www.ncbi.nlm.nih.gov/gene/?term=57194	"ATP10C, ATPVA, ATPVC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017247	5719	PSMD13	http://www.ncbi.nlm.nih.gov/gene/?term=5719	"HSPC027, Rpn9, S11, p40.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017248	571	BACH1	http://www.ncbi.nlm.nih.gov/gene/?term=571	"BACH-1, BTBD24 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017249	5720	PSME1	http://www.ncbi.nlm.nih.gov/gene/?term=5720	"HEL-S-129m, IFI5111, PA28A, PA28alpha, REGalpha "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017250	5720	PSME1	http://www.ncbi.nlm.nih.gov/gene/?term=5720	"HEL-S-129m, IFI5111, PA28A, PA28alpha, REGalpha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017251	5720	PSME1	http://www.ncbi.nlm.nih.gov/gene/?term=5720	"HEL-S-129m, IFI5111, PA28A, PA28alpha, REGalpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017252	57210	SLC45A4	http://www.ncbi.nlm.nih.gov/gene/?term=57210		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017253	57211	ADGRG6	http://www.ncbi.nlm.nih.gov/gene/?term=57211	"APG1, DREG, GPR126, LCCS9, PS1TP2, VIGR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017254	57212	TP73-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=57212	"KIAA0495, PDAM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017255	57212	TP73-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=57212	"KIAA0495, PDAM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017256	57213	SPRYD7	http://www.ncbi.nlm.nih.gov/gene/?term=57213	"C13orf1, CLLD6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017257	57213	SPRYD7	http://www.ncbi.nlm.nih.gov/gene/?term=57213	"C13orf1, CLLD6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017258	57213	SPRYD7	http://www.ncbi.nlm.nih.gov/gene/?term=57213	"C13orf1, CLLD6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017259	57213	SPRYD7	http://www.ncbi.nlm.nih.gov/gene/?term=57213	"C13orf1, CLLD6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017260	57214	CEMIP	http://www.ncbi.nlm.nih.gov/gene/?term=57214	"CCSP1, KIAA1199, TMEM2L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017261	57215	THAP11	http://www.ncbi.nlm.nih.gov/gene/?term=57215	"CTG-B43a, CTG-B45d, HRIHFB2206, RONIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017262	57215	THAP11	http://www.ncbi.nlm.nih.gov/gene/?term=57215	"CTG-B43a, CTG-B45d, HRIHFB2206, RONIN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017263	57215	THAP11	http://www.ncbi.nlm.nih.gov/gene/?term=57215	"CTG-B43a, CTG-B45d, HRIHFB2206, RONIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017264	5721	PSME2	http://www.ncbi.nlm.nih.gov/gene/?term=5721	"PA28B, PA28beta, REGbeta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017265	5721	PSME2	http://www.ncbi.nlm.nih.gov/gene/?term=5721	"PA28B, PA28beta, REGbeta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017266	57221	ARFGEF3	http://www.ncbi.nlm.nih.gov/gene/?term=57221	"A7322, BIG3, C6orf92, KIAA1244, PPP1R33, dJ171N11.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017267	57222	ERGIC1	http://www.ncbi.nlm.nih.gov/gene/?term=57222	"ERGIC-32, ERGIC32, NET24 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017268	57222	ERGIC1	http://www.ncbi.nlm.nih.gov/gene/?term=57222	"ERGIC-32, ERGIC32, NET24 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017269	57222	ERGIC1	http://www.ncbi.nlm.nih.gov/gene/?term=57222	"ERGIC-32, ERGIC32, NET24 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017270	57223	PPP4R3B	http://www.ncbi.nlm.nih.gov/gene/?term=57223	"FLFL2, PP4R3B, PSY2, SMEK2, smk1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017271	57223	PPP4R3B	http://www.ncbi.nlm.nih.gov/gene/?term=57223	"FLFL2, PP4R3B, PSY2, SMEK2, smk1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017272	57226	LYRM2	http://www.ncbi.nlm.nih.gov/gene/?term=57226	DJ122O8.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017273	57226	LYRM2	http://www.ncbi.nlm.nih.gov/gene/?term=57226	DJ122O8.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017274	57228	SMAGP	http://www.ncbi.nlm.nih.gov/gene/?term=57228	hSMAGP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017275	57228	SMAGP	http://www.ncbi.nlm.nih.gov/gene/?term=57228	hSMAGP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017276	57231	SNX14	http://www.ncbi.nlm.nih.gov/gene/?term=57231	"RGS-PX2, SCAR20 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017277	5723	PSPH	http://www.ncbi.nlm.nih.gov/gene/?term=5723	"PSPD, PSPH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017278	5723	PSPH	http://www.ncbi.nlm.nih.gov/gene/?term=5723	"PSPD, PSPH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017279	5723	PSPH	http://www.ncbi.nlm.nih.gov/gene/?term=5723	"PSP, PSPHD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017280	57246	Tbx20	http://www.ncbi.nlm.nih.gov/gene/?term=57246	"9430010M06Rik, AL022859, Tbx12 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017281	57247	Zfp276	http://www.ncbi.nlm.nih.gov/gene/?term=57247	"AW048709, D8Ertd370e, D8Ertd377e, Znf276 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017282	57258	Xpo4	http://www.ncbi.nlm.nih.gov/gene/?term=57258	"B430309A01Rik, mKIAA1721 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017283	57258	Xpo4	http://www.ncbi.nlm.nih.gov/gene/?term=57258	"B430309A01Rik, mKIAA1721 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017284	5725	PTBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5725	"HNRNP-I, HNRNPI, HNRPI, PTB, PTB-1, PTB-T, PTB2, PTB3, PTB4, pPTB "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017285	5725	PTBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5725	"HNRNP-I, HNRNPI, HNRPI, PTB, PTB-1, PTB-T, PTB2, PTB3, PTB4, pPTB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017286	57267	Apba3	http://www.ncbi.nlm.nih.gov/gene/?term=57267	"AW208791, Mint-3, X11gamma, lin-10, mint3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017287	57269	Olfr1507	http://www.ncbi.nlm.nih.gov/gene/?term=57269	"MOR244-1, Mor28, Or28 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017288	5727	PTCH1	http://www.ncbi.nlm.nih.gov/gene/?term=5727	"BCNS, HPE7, NBCCS, PTC, PTC1, PTCH, PTCH11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017289	5728	PTEN	http://www.ncbi.nlm.nih.gov/gene/?term=5728	"10q23del, BZS, CWS1, DEC, GLM2, MHAM, MMAC11, TEP1, PTEN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017290	5728	PTEN	http://www.ncbi.nlm.nih.gov/gene/?term=5728	"10q23del, BZS, CWS1, DEC, GLM2, MHAM, MMAC1, PTEN1, TEP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017291	57291	DANCR	http://www.ncbi.nlm.nih.gov/gene/?term=57291	"AGU2, ANCR, KIAA0114, SNHG13, lncRNA-ANCR "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017292	57291	DANCR	http://www.ncbi.nlm.nih.gov/gene/?term=57291	"AGU2, ANCR, KIAA0114, SNHG13, lncRNA-ANCR "	lncRNA	Homo sapiens	25690653	Cytoplasm	P493-6 cell	qRT-PCR	"To validate the isolation of nuclear and cytoplasmic fractions, the enrichment of 3 nuclear (ANRIL, MIAT, XIST) and 3 cytoplasmic (RPPH1, DANCR, tRNA-Lys) RNAs was analyzed by qRT-PCR. "
RLID00017293	57291	DANCR	http://www.ncbi.nlm.nih.gov/gene/?term=57291	"AGU2, ANCR, KIAA0114, SNHG13, lncRNA-ANCR "	lncRNA	Homo sapiens	25630241	Cytoplasm	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00017294	57291	DANCR	http://www.ncbi.nlm.nih.gov/gene/?term=57291	"AGU2, ANCR, KIAA0114, SNHG13, lncRNA-ANCR "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00017295	57294	Rps27	http://www.ncbi.nlm.nih.gov/gene/?term=57294	3200001M24Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017296	572	BAD	http://www.ncbi.nlm.nih.gov/gene/?term=572	"BBC2, BCL2L8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017297	572	BAD	http://www.ncbi.nlm.nih.gov/gene/?term=572	"BBC2, BCL2L8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017298	57316	C1d	http://www.ncbi.nlm.nih.gov/gene/?term=57316	"1110036E10Rik, AI875855, SUN-CoR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017299	57325	CSRP2BP	http://www.ncbi.nlm.nih.gov/gene/?term=57325	"ATAC2, CRP2BP, KAT14, PRO1194, dJ717M23.1 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00017300	57325	CSRP2BP	http://www.ncbi.nlm.nih.gov/gene/?term=57325	"ATAC2, CRP2BP, KAT14, PRO1194, dJ717M23.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017301	57325	CSRP2BP	http://www.ncbi.nlm.nih.gov/gene/?term=57325	"ATAC2, CRP2BP, KAT14, PRO1194, dJ717M23.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017302	57326	PBXIP1	http://www.ncbi.nlm.nih.gov/gene/?term=57326	HPIP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017303	57332	CBX8	http://www.ncbi.nlm.nih.gov/gene/?term=57332	"PC3, RC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017304	57335	ZNF286A	http://www.ncbi.nlm.nih.gov/gene/?term=57335	ZNF286	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017305	57335	ZNF286A	http://www.ncbi.nlm.nih.gov/gene/?term=57335	ZNF286	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017306	57335	ZNF286A	http://www.ncbi.nlm.nih.gov/gene/?term=57335	ZNF286	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017307	57337	SENP7	http://www.ncbi.nlm.nih.gov/gene/?term=57337		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017308	5733	PTGER3	http://www.ncbi.nlm.nih.gov/gene/?term=5733	"EP3, EP3-I, EP3-II, EP3-III, EP3-IV, EP3-VI, EP3e, PGE2-R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017309	57340	Jph3	http://www.ncbi.nlm.nih.gov/gene/?term=57340	"JP-3, Jp3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017310	5734	PTGER4	http://www.ncbi.nlm.nih.gov/gene/?term=5734	"EP4, EP4R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017311	57376	Smarce1	http://www.ncbi.nlm.nih.gov/gene/?term=57376	"2810417B20Rik, 5830412H02Rik, 9030408N19Rik, Baf27 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017312	57376	Smarce1	http://www.ncbi.nlm.nih.gov/gene/?term=57376	"2810417B20Rik, 5830412H02Rik, 9030408N19Rik, Baf27 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017313	57380	MRS2	http://www.ncbi.nlm.nih.gov/gene/?term=57380	"HPTL, MRS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017314	57380	MRS2	http://www.ncbi.nlm.nih.gov/gene/?term=57380	"HPT, MRS2L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017315	57381	RHOJ	http://www.ncbi.nlm.nih.gov/gene/?term=57381	"ARHJ, RASL7B, TC10B, TCL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017316	5738	PTGFRN	http://www.ncbi.nlm.nih.gov/gene/?term=5738	"CD315, CD9P-1, EWI-F, FPRP, SMAP-6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017317	5738	PTGFRN	http://www.ncbi.nlm.nih.gov/gene/?term=5738	"CD315, CD9P-1, EWI-F, FPRP, SMAP-6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017318	5738	PTGFRN	http://www.ncbi.nlm.nih.gov/gene/?term=5738	"CD315, CD9P-1, EWI-F, FPRP, SMAP-6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017319	573	BAG1	http://www.ncbi.nlm.nih.gov/gene/?term=573	"BAG-1, HAP, RAP46 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017320	5740235	RhoGAP1A	http://www.ncbi.nlm.nih.gov/gene/?term=5740235	"Dmel_CG40494, BCR, CG17617, CG17960, CG40453, CG40494, Dmel\CG40494, Dmel_CG00000, EG:23E12.2, EG:23E12.5, RhoGAP, rhoGAP1A "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00017321	57402	S100A14	http://www.ncbi.nlm.nih.gov/gene/?term=57402	"BCMP84, S100A15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017322	57403	RAB22A	http://www.ncbi.nlm.nih.gov/gene/?term=57403		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017323	57403	RAB22A	http://www.ncbi.nlm.nih.gov/gene/?term=57403		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017324	57403	RAB22A	http://www.ncbi.nlm.nih.gov/gene/?term=57403		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017325	57403	RAB22A	http://www.ncbi.nlm.nih.gov/gene/?term=57403		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017326	574042	SNORA10	http://www.ncbi.nlm.nih.gov/gene/?term=574042	"ACA10A, SNORA10 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00017327	574042	SNORA10	http://www.ncbi.nlm.nih.gov/gene/?term=574042	"ACA10A, SNORA10 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017328	574042	SNORA10	http://www.ncbi.nlm.nih.gov/gene/?term=574042	"ACA10A, SNORA10 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017329	57404	CYP20A1	http://www.ncbi.nlm.nih.gov/gene/?term=57404	CYP-M	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017330	57404	CYP20A1	http://www.ncbi.nlm.nih.gov/gene/?term=57404	CYP-M	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017331	57404	CYP20A1	http://www.ncbi.nlm.nih.gov/gene/?term=57404	CYP-M	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017332	5740599	pgc	http://www.ncbi.nlm.nih.gov/gene/?term=5740599	"Dmel_CG32885, CG11296, CG32885, CR32885, Dmel\CG32885, Pgc, Pgc1-1, pgr, pgc "	mRNA	Drosophila melanogaster	26242323	Germ plasm	Embryo	Fluorescence in situ hybridization	"Next we determined the distribution of the known germ plasm enriched mRNAs cycB, nos, pgc, gcl and oskar (osk) and one control mRNAccr4, which appears evenly distributed throughout the embryo4 (Fig. 2a,b,h). "
RLID00017333	5740599	pgc	http://www.ncbi.nlm.nih.gov/gene/?term=5740599	"Dmel_CG32885, CG11296, CG32885, CR32885, Dmel\CG32885, Pgc, Pgc1-1, pgr, pgc "	mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00017334	5740599	pgc	http://www.ncbi.nlm.nih.gov/gene/?term=5740599	"Dmel_CG32885, CG11296, CG32885, CR32885, Dmel\CG32885, Pgc, Pgc1-1, pgr, pgc "	mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00017335	57406	ABHD6	http://www.ncbi.nlm.nih.gov/gene/?term=57406		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017336	57407	NMRAL1	http://www.ncbi.nlm.nih.gov/gene/?term=57407	"HSCARG, SDR48A1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017337	5740	PTGIS	http://www.ncbi.nlm.nih.gov/gene/?term=5740	"CYP8, CYP8A1, PGIS, PTGI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017338	5740	PTGIS	http://www.ncbi.nlm.nih.gov/gene/?term=5740	"CYP8, CYP8A1, PGIS, PTGI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017339	5740	PTGIS	http://www.ncbi.nlm.nih.gov/gene/?term=5740	"CYP8, CYP8A1, PGIS, PTGI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017340	57410	SCYL1	http://www.ncbi.nlm.nih.gov/gene/?term=57410	"GKLP, HT019, NKTL, NTKL, P105, SCAR21, TAPK, TEIF, TRAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017341	57410	SCYL1	http://www.ncbi.nlm.nih.gov/gene/?term=57410	"GKLP, HT019, NKTL, NTKL, P105, SCAR21, TAPK, TEIF, TRAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017342	57412	AS3MT	http://www.ncbi.nlm.nih.gov/gene/?term=57412	CYT19	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017343	57412	AS3MT	http://www.ncbi.nlm.nih.gov/gene/?term=57412	CYT19	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017344	57414	RHBDD2	http://www.ncbi.nlm.nih.gov/gene/?term=57414	"NPD007, RHBDL7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017345	57418	WDR18	http://www.ncbi.nlm.nih.gov/gene/?term=57418	"Ipi3, R32184_1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017346	57429	Sult5a1	http://www.ncbi.nlm.nih.gov/gene/?term=57429	"Sult-x1, Sultx1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017347	57431	Dnajc4	http://www.ncbi.nlm.nih.gov/gene/?term=57431	"2010301J22Rik, Hspf2, Mcg18 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017348	57436	Gabarapl1	http://www.ncbi.nlm.nih.gov/gene/?term=57436	"3110025G09Rik, 9130422N19Rik, AI196471, Apg8l, Atg8l, GECI, MNCb-0091 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017349	57438	March7	http://www.ncbi.nlm.nih.gov/gene/?term=57438	"Axo, Axot, Gtrgeo17 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017350	57439	Tmem183a	http://www.ncbi.nlm.nih.gov/gene/?term=57439	"1300007B12Rik, 1700020N19Rik, Tmem183 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017351	5743	PTGS2	http://www.ncbi.nlm.nih.gov/gene/?term=5743	"COX-2, COX2, GRIPGHS, PGG/HS, PGHS-2, PHS-2, hCox-2 "	mRNA	Homo sapiens	26000482	Ribosome	HeLa cell	qRT-PCR	"Knockdown of Reg1 resulted in a large increase in IL6 and PTGS2 mRNA expression in the polysome fractions (fractions 7-12) compared with control cells, whereas the mRNA in non-polysome fractions (fractions 3-6) were comparable (Figure 3 H). "
RLID00017352	57440	Ehd3	http://www.ncbi.nlm.nih.gov/gene/?term=57440	Ehd2	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017353	57441	Gmnn	http://www.ncbi.nlm.nih.gov/gene/?term=57441	"AW546347, Gem "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017354	574437	Xlr3b	http://www.ncbi.nlm.nih.gov/gene/?term=574437	"EG574437, Xlr3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017355	57443	Fbxo3	http://www.ncbi.nlm.nih.gov/gene/?term=57443	"1200002G09Rik, 1700026K02Rik, AI046358, Fba "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017356	57446	NDRG3	http://www.ncbi.nlm.nih.gov/gene/?term=57446		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017357	57446	NDRG3	http://www.ncbi.nlm.nih.gov/gene/?term=57446		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017358	57446	NDRG3	http://www.ncbi.nlm.nih.gov/gene/?term=57446		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017359	57448	BIRC6	http://www.ncbi.nlm.nih.gov/gene/?term=57448	"APOLLON, BRUCE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017360	57449	PLEKHG5	http://www.ncbi.nlm.nih.gov/gene/?term=57449	"CMTRIC, DSMA4, GEF720, Syx, Tech "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017361	5744	PTHLH	http://www.ncbi.nlm.nih.gov/gene/?term=5744	"BDE2, HHM, PLP, PTHR, PTHRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017362	57456	KIAA1143	http://www.ncbi.nlm.nih.gov/gene/?term=57456		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017363	57456	KIAA1143	http://www.ncbi.nlm.nih.gov/gene/?term=57456		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017364	57460	PPM1H	http://www.ncbi.nlm.nih.gov/gene/?term=57460	"ARHCL1, NERPP-2C, URCC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017365	57460	PPM1H	http://www.ncbi.nlm.nih.gov/gene/?term=57460	"ARHCL1, NERPP-2C, URCC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017366	57462	KIAA1161	http://www.ncbi.nlm.nih.gov/gene/?term=57462	NET37	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017367	57462	KIAA1161	http://www.ncbi.nlm.nih.gov/gene/?term=57462	NET37	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017368	57462	KIAA1161	http://www.ncbi.nlm.nih.gov/gene/?term=57462	NET37	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017369	57464	STRIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57464	"FAM40B, FAR11B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017370	57464	STRIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57464	"FAM40B, FAR11B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017371	57464	STRIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57464	"FAM40B, FAR11B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017372	57465	TBC1D24	http://www.ncbi.nlm.nih.gov/gene/?term=57465	"DFNA65, DFNB86, DOORS, EIEE16, FIME, TLDC6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017373	57470	LRRC47	http://www.ncbi.nlm.nih.gov/gene/?term=57470		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017374	57470	LRRC47	http://www.ncbi.nlm.nih.gov/gene/?term=57470		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017375	57470	LRRC47	http://www.ncbi.nlm.nih.gov/gene/?term=57470		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017376	57474	ZNF490	http://www.ncbi.nlm.nih.gov/gene/?term=57474		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017377	57474	ZNF490	http://www.ncbi.nlm.nih.gov/gene/?term=57474		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017378	57475	PLEKHH1	http://www.ncbi.nlm.nih.gov/gene/?term=57475		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017379	57476	GRAMD1B	http://www.ncbi.nlm.nih.gov/gene/?term=57476		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017380	57478	USP31	http://www.ncbi.nlm.nih.gov/gene/?term=57478		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017381	57478	USP31	http://www.ncbi.nlm.nih.gov/gene/?term=57478		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017382	57478	USP31	http://www.ncbi.nlm.nih.gov/gene/?term=57478		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017383	57479	PRR12	http://www.ncbi.nlm.nih.gov/gene/?term=57479	KIAA1205	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00017384	5747	PTK2	http://www.ncbi.nlm.nih.gov/gene/?term=5747	"FADK, FAK, FAK1, FRNK, PPP1R71, p125FAK, pp125FAK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017385	5747	PTK2	http://www.ncbi.nlm.nih.gov/gene/?term=5747	"FADK, FAK, FAK1, FRNK, PPP1R71, p125FAK, pp125FAK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017386	57481	KIAA1210	http://www.ncbi.nlm.nih.gov/gene/?term=57481		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017387	57481	KIAA1210	http://www.ncbi.nlm.nih.gov/gene/?term=57481		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017388	57486	NLN	http://www.ncbi.nlm.nih.gov/gene/?term=57486	"AGTBP, EP24.16, MEP, MOP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017389	57486	NLN	http://www.ncbi.nlm.nih.gov/gene/?term=57486	"AGTBP, EP24.16, MEP, MOP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017390	57486	NLN	http://www.ncbi.nlm.nih.gov/gene/?term=57486	"AGTBP, EP24.16, MEP, MOP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017391	57488	ESYT2	http://www.ncbi.nlm.nih.gov/gene/?term=57488	"CHR2SYT, E-Syt2, FAM62B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017392	57488	ESYT2	http://www.ncbi.nlm.nih.gov/gene/?term=57488	"CHR2SYT, E-Syt2, FAM62B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017393	57492	ARID1B	http://www.ncbi.nlm.nih.gov/gene/?term=57492	"6A3-5, BAF250B, BRIGHT, DAN15, ELD/OSA1, MRD12, OSA2, P250R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017394	57493	HEG1	http://www.ncbi.nlm.nih.gov/gene/?term=57493	"HEG, MST112, MSTP112 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017395	57496	MKL2	http://www.ncbi.nlm.nih.gov/gene/?term=57496	"MRTF-B, MRTFB, NPD001 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017396	57496	MKL2	http://www.ncbi.nlm.nih.gov/gene/?term=57496	"MRTF-B, MRTFB, NPD001 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017397	57498	KIDINS220	http://www.ncbi.nlm.nih.gov/gene/?term=57498	ARMS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017398	57498	KIDINS220	http://www.ncbi.nlm.nih.gov/gene/?term=57498	ARMS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017399	57502	NLGN4X	http://www.ncbi.nlm.nih.gov/gene/?term=57502	"ASPGX2, AUTSX2, HLNX, HNL4X, NLGN4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017400	57504	MTA3	http://www.ncbi.nlm.nih.gov/gene/?term=57504		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017401	57505	AARS2	http://www.ncbi.nlm.nih.gov/gene/?term=57505	"AARSL, COXPD8, LKENP, MT-ALARS, MTALARS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017402	57506	MAVS	http://www.ncbi.nlm.nih.gov/gene/?term=57506	"CARDIF, IPS-1, IPS1, VISA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017403	57506	MAVS	http://www.ncbi.nlm.nih.gov/gene/?term=57506	"CARDIF, IPS-1, IPS1, VISA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017404	57507	ZNF608	http://www.ncbi.nlm.nih.gov/gene/?term=57507	NY-REN-36	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017405	57507	ZNF608	http://www.ncbi.nlm.nih.gov/gene/?term=57507	NY-REN-36	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017406	57508	INTS2	http://www.ncbi.nlm.nih.gov/gene/?term=57508	"INT2, KIAA1287 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017407	57508	INTS2	http://www.ncbi.nlm.nih.gov/gene/?term=57508	"INT2, KIAA1287 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017408	57508	INTS2	http://www.ncbi.nlm.nih.gov/gene/?term=57508	"INT2, KIAA1287 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017409	57509	MTUS1	http://www.ncbi.nlm.nih.gov/gene/?term=57509	"ATBP, ATIP, ICIS, MP44, MTSG1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017410	57510	XPO5	http://www.ncbi.nlm.nih.gov/gene/?term=57510	exp5	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017411	57510	XPO5	http://www.ncbi.nlm.nih.gov/gene/?term=57510	exp5	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017412	57510	XPO5	http://www.ncbi.nlm.nih.gov/gene/?term=57510	exp5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017413	57512	GPR158	http://www.ncbi.nlm.nih.gov/gene/?term=57512		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017414	57513	CASKIN2	http://www.ncbi.nlm.nih.gov/gene/?term=57513	ANKS5B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017415	57515	SERINC1	http://www.ncbi.nlm.nih.gov/gene/?term=57515	"TDE1L, TDE2, TMS-2, TMS2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017416	57515	SERINC1	http://www.ncbi.nlm.nih.gov/gene/?term=57515	"TDE1L, TDE2, TMS-2, TMS2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017417	57515	SERINC1	http://www.ncbi.nlm.nih.gov/gene/?term=57515	"TDE1L, TDE2, TMS-2, TMS2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017418	57519	STARD9	http://www.ncbi.nlm.nih.gov/gene/?term=57519	KIF16A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017419	57521	RPTOR	http://www.ncbi.nlm.nih.gov/gene/?term=57521	"KOG1, Mip1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017420	57521	RPTOR	http://www.ncbi.nlm.nih.gov/gene/?term=57521	"KOG1, Mip1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017421	57523	NYNRIN	http://www.ncbi.nlm.nih.gov/gene/?term=57523	"CGIN1, KIAA1305 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00017422	57523	NYNRIN	http://www.ncbi.nlm.nih.gov/gene/?term=57523	"CGIN1, KIAA1305 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017423	57531	HACE1	http://www.ncbi.nlm.nih.gov/gene/?term=57531	SPPRS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017424	57531	HACE1	http://www.ncbi.nlm.nih.gov/gene/?term=57531	SPPRS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017425	57532	NUFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57532	"182-FIP, 82-FIP, FIP-82, PIG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017426	57532	NUFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57532	"182-FIP, 82-FIP, FIP-82, PIG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017427	57532	NUFIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57532	"182-FIP, 82-FIP, FIP-82, PIG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017428	57533	TBC1D14	http://www.ncbi.nlm.nih.gov/gene/?term=57533		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017429	57534	MIB1	http://www.ncbi.nlm.nih.gov/gene/?term=57534	"DIP-1, DIP1, LVNC7, MIB, ZZANK2, ZZZ6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017430	57534	MIB1	http://www.ncbi.nlm.nih.gov/gene/?term=57534	"DIP-1, DIP1, LVNC7, MIB, ZZANK2, ZZZ6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017431	57534	MIB1	http://www.ncbi.nlm.nih.gov/gene/?term=57534	"DIP-1, DIP1, LVNC7, MIB, ZZANK2, ZZZ6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017432	5753	PTK6	http://www.ncbi.nlm.nih.gov/gene/?term=5753	BRK	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017433	57542	KLHL42	http://www.ncbi.nlm.nih.gov/gene/?term=57542	"Ctb9, KLHDC5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017434	57542	KLHL42	http://www.ncbi.nlm.nih.gov/gene/?term=57542	"Ctb9, KLHDC5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017435	57544	TXNDC16	http://www.ncbi.nlm.nih.gov/gene/?term=57544	"ERp90, KIAA1344 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017436	57545	CC2D2A	http://www.ncbi.nlm.nih.gov/gene/?term=57545	"JBTS9, MKS6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017437	57545	CC2D2A	http://www.ncbi.nlm.nih.gov/gene/?term=57545	"JBTS9, MKS6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017438	57545	CC2D2A	http://www.ncbi.nlm.nih.gov/gene/?term=57545	"JBTS9, MKS6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017439	5754	PTK7	http://www.ncbi.nlm.nih.gov/gene/?term=5754	"CCK-4, CCK4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017440	57551	TAOK1	http://www.ncbi.nlm.nih.gov/gene/?term=57551	"KFC-B, MAP3K16, MARKK, PSK-2, PSK2, TAO1, hKFC-B, hTAOK1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017441	57551	TAOK1	http://www.ncbi.nlm.nih.gov/gene/?term=57551	"KFC-B, MAP3K16, MARKK, PSK-2, PSK2, TAO1, hKFC-B, hTAOK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017442	57552	NCEH1	http://www.ncbi.nlm.nih.gov/gene/?term=57552	"AADACL1, NCEH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017443	57553	MICAL3	http://www.ncbi.nlm.nih.gov/gene/?term=57553	MICAL-3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017444	57556	SEMA6A	http://www.ncbi.nlm.nih.gov/gene/?term=57556	"HT018, SEMA1, SEMAQ, VIA, SEMA6A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017445	57556	SEMA6A	http://www.ncbi.nlm.nih.gov/gene/?term=57556	"HT018, SEMA, SEMA6A1, SEMAQ, VIA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017446	57560	IFT80	http://www.ncbi.nlm.nih.gov/gene/?term=57560	"ATD2, SRTD2, WDR56 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017447	57560	IFT80	http://www.ncbi.nlm.nih.gov/gene/?term=57560	"ATD2, SRTD2, WDR56 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017448	57561	ARRDC3	http://www.ncbi.nlm.nih.gov/gene/?term=57561	TLIMP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017449	57561	ARRDC3	http://www.ncbi.nlm.nih.gov/gene/?term=57561	TLIMP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017450	57563	KLHL8	http://www.ncbi.nlm.nih.gov/gene/?term=57563		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017451	57563	KLHL8	http://www.ncbi.nlm.nih.gov/gene/?term=57563		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017452	57568	SIPA1L2	http://www.ncbi.nlm.nih.gov/gene/?term=57568	SPAL2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017453	5756	TWF1	http://www.ncbi.nlm.nih.gov/gene/?term=5756	"A6, PTK9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017454	57572	DOCK6	http://www.ncbi.nlm.nih.gov/gene/?term=57572	"AOS2, ZIR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017455	57579	FAM135A	http://www.ncbi.nlm.nih.gov/gene/?term=57579	KIAA1411	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017456	5757	PTMA	http://www.ncbi.nlm.nih.gov/gene/?term=5757	TMSA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017457	57580	PREX1	http://www.ncbi.nlm.nih.gov/gene/?term=57580	P-REX1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017458	57583	TMEM181	http://www.ncbi.nlm.nih.gov/gene/?term=57583	"GPR178, KIAA1423 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017459	57584	ARHGAP21	http://www.ncbi.nlm.nih.gov/gene/?term=57584	ARHGAP10	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017460	57584	ARHGAP21	http://www.ncbi.nlm.nih.gov/gene/?term=57584	ARHGAP10	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017461	57586	SYT13	http://www.ncbi.nlm.nih.gov/gene/?term=57586		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017462	57586	SYT13	http://www.ncbi.nlm.nih.gov/gene/?term=57586		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017463	57587	CFAP97	http://www.ncbi.nlm.nih.gov/gene/?term=57587	"KIAA1430, hmw "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017464	57589	RIC1	http://www.ncbi.nlm.nih.gov/gene/?term=57589	"CIP150, KIAA1432, bA207C16.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017465	57590	WDFY1	http://www.ncbi.nlm.nih.gov/gene/?term=57590	"FENS-1, WDF1, ZFYVE17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017466	57590	WDFY1	http://www.ncbi.nlm.nih.gov/gene/?term=57590	"FENS-1, WDF1, ZFYVE17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017467	57591	MKL1	http://www.ncbi.nlm.nih.gov/gene/?term=57591	"BSAC, MAL, MRTF-A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017468	57594	HOMEZ	http://www.ncbi.nlm.nih.gov/gene/?term=57594	KIAA1443	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017469	57594	HOMEZ	http://www.ncbi.nlm.nih.gov/gene/?term=57594	KIAA1443	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017470	57599	WDR48	http://www.ncbi.nlm.nih.gov/gene/?term=57599	"P80, SPG60, UAF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017471	57599	WDR48	http://www.ncbi.nlm.nih.gov/gene/?term=57599	"P80, SPG60, UAF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017472	575	ADGRB1	http://www.ncbi.nlm.nih.gov/gene/?term=575	"BAI1, GDAIF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017473	57600	FNIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57600	"FNIPL, MAPO1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017474	57600	FNIP2	http://www.ncbi.nlm.nih.gov/gene/?term=57600	"FNIPL, MAPO1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017475	57604	KIAA1456	http://www.ncbi.nlm.nih.gov/gene/?term=57604	"C8orf79, TRM9L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017476	57604	KIAA1456	http://www.ncbi.nlm.nih.gov/gene/?term=57604	"C8orf79, TRM9L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017477	57606	SLAIN2	http://www.ncbi.nlm.nih.gov/gene/?term=57606	KIAA1458	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017478	57609	DIP2B	http://www.ncbi.nlm.nih.gov/gene/?term=57609		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017479	57610	RANBP10	http://www.ncbi.nlm.nih.gov/gene/?term=57610		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017480	57610	RANBP10	http://www.ncbi.nlm.nih.gov/gene/?term=57610		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017481	57611	ISLR2	http://www.ncbi.nlm.nih.gov/gene/?term=57611	LINX	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017482	57611	ISLR2	http://www.ncbi.nlm.nih.gov/gene/?term=57611	LINX	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017483	57613	FAM234B	http://www.ncbi.nlm.nih.gov/gene/?term=57613	KIAA1467	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017484	57613	FAM234B	http://www.ncbi.nlm.nih.gov/gene/?term=57613	KIAA1467	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017485	57614	KIAA1468	http://www.ncbi.nlm.nih.gov/gene/?term=57614	"HsT3308, HsT885 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017486	57619	SHROOM3	http://www.ncbi.nlm.nih.gov/gene/?term=57619	"APXL3, MSTP013, SHRM, ShrmL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017487	57620	STIM2	http://www.ncbi.nlm.nih.gov/gene/?term=57620		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017488	57620	STIM2	http://www.ncbi.nlm.nih.gov/gene/?term=57620		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017489	57621	ZBTB2	http://www.ncbi.nlm.nih.gov/gene/?term=57621	ZNF437	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017490	57622	LRFN1	http://www.ncbi.nlm.nih.gov/gene/?term=57622	SALM2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017491	57626	KLHL1	http://www.ncbi.nlm.nih.gov/gene/?term=57626	MRP2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017492	57626	KLHL1	http://www.ncbi.nlm.nih.gov/gene/?term=57626	MRP2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017493	57628	DPP10	http://www.ncbi.nlm.nih.gov/gene/?term=57628	"DPL2, DPPY, DPRP-3, DPRP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017494	57630	SH3RF1	http://www.ncbi.nlm.nih.gov/gene/?term=57630	"POSH, RNF142, SH3MD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017495	57633	LRRN1	http://www.ncbi.nlm.nih.gov/gene/?term=57633	"FIGLER3, NLRR-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017496	57634	EP400	http://www.ncbi.nlm.nih.gov/gene/?term=57634	"CAGH32, P400, TNRC12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017497	5763	PTMS	http://www.ncbi.nlm.nih.gov/gene/?term=5763	ParaT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017498	5763	PTMS	http://www.ncbi.nlm.nih.gov/gene/?term=5763	ParaT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017499	57648	KIAA1522	http://www.ncbi.nlm.nih.gov/gene/?term=57648		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017500	57648	KIAA1522	http://www.ncbi.nlm.nih.gov/gene/?term=57648		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017501	57649	PHF12	http://www.ncbi.nlm.nih.gov/gene/?term=57649	PF1	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017502	5764	PTN	http://www.ncbi.nlm.nih.gov/gene/?term=5764	"HARP, HB-GAM, HBBM, HBGF-8, HBGF8, HBNF, HBNF-1, NEGF1, OSF-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017503	5764	PTN	http://www.ncbi.nlm.nih.gov/gene/?term=5764	"HARP, HBGF8, HBNF, NEGF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017504	57650	KIAA1524	http://www.ncbi.nlm.nih.gov/gene/?term=57650	"CIP2A, p90 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017505	57654	UVSSA	http://www.ncbi.nlm.nih.gov/gene/?term=57654	"KIAA1530, UVSS3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017506	57654	UVSSA	http://www.ncbi.nlm.nih.gov/gene/?term=57654	"KIAA1530, UVSS3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017507	57655	GRAMD1A	http://www.ncbi.nlm.nih.gov/gene/?term=57655	KIAA1533	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017508	57659	ZBTB4	http://www.ncbi.nlm.nih.gov/gene/?term=57659	"KAISO-L1, ZNF903 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017509	57661	PHRF1	http://www.ncbi.nlm.nih.gov/gene/?term=57661	"PPP1R125, RNF221 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017510	57661	PHRF1	http://www.ncbi.nlm.nih.gov/gene/?term=57661	"PPP1R125, RNF221 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017511	57665	RDH14	http://www.ncbi.nlm.nih.gov/gene/?term=57665	"PAN2, SDR7C4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017512	57669	EPB41L5	http://www.ncbi.nlm.nih.gov/gene/?term=57669	"BE37, YMO1, YRT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017513	57669	EPB41L5	http://www.ncbi.nlm.nih.gov/gene/?term=57669	"BE37, YMO1, YRT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017514	57669	EPB41L5	http://www.ncbi.nlm.nih.gov/gene/?term=57669	"BE37, YMO1, YRT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017515	57673	BEND3	http://www.ncbi.nlm.nih.gov/gene/?term=57673	KIAA1553	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017516	57674	RNF213	http://www.ncbi.nlm.nih.gov/gene/?term=57674	"ALO17, C17orf27, KIAA1618, MYMY2, MYSTR, NET57 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017517	57674	RNF213	http://www.ncbi.nlm.nih.gov/gene/?term=57674	"ALO17, C17orf27, KIAA1618, MYMY2, MYSTR, NET57 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017518	57677	ZFP14	http://www.ncbi.nlm.nih.gov/gene/?term=57677	ZNF531	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017519	57677	ZFP14	http://www.ncbi.nlm.nih.gov/gene/?term=57677	ZNF531	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017520	57678	GPAM	http://www.ncbi.nlm.nih.gov/gene/?term=57678	"GPAT, GPAT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017521	57679	ALS2	http://www.ncbi.nlm.nih.gov/gene/?term=57679	"ALS2CR6, ALSJ, IAHSP, PLSJ "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017522	57680	CHD8	http://www.ncbi.nlm.nih.gov/gene/?term=57680	"AUTS18, HELSNF1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017523	57680	CHD8	http://www.ncbi.nlm.nih.gov/gene/?term=57680	"AUTS18, HELSNF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017524	57683	ZDBF2	http://www.ncbi.nlm.nih.gov/gene/?term=57683		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017525	57683	ZDBF2	http://www.ncbi.nlm.nih.gov/gene/?term=57683		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017526	57687	VAT1L	http://www.ncbi.nlm.nih.gov/gene/?term=57687		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017527	5768	QSOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5768	"Q6, QSCN6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017528	5768	QSOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5768	"Q6, QSCN6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017529	57695	USP37	http://www.ncbi.nlm.nih.gov/gene/?term=57695		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017530	57696	DDX55	http://www.ncbi.nlm.nih.gov/gene/?term=57696		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017531	57696	DDX55	http://www.ncbi.nlm.nih.gov/gene/?term=57696		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017532	57698	SHTN1	http://www.ncbi.nlm.nih.gov/gene/?term=57698	KIAA1598	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017533	57704	GBA2	http://www.ncbi.nlm.nih.gov/gene/?term=57704	"AD035, NLGase, SPG46 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017534	57707	TLDC1	http://www.ncbi.nlm.nih.gov/gene/?term=57707	KIAA1609	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017535	57708	MIER1	http://www.ncbi.nlm.nih.gov/gene/?term=57708	"ER1, MI-ER1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017536	57708	MIER1	http://www.ncbi.nlm.nih.gov/gene/?term=57708	"ER1, MI-ER1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017537	57709	SLC7A14	http://www.ncbi.nlm.nih.gov/gene/?term=57709	PPP1R142	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017538	57709	SLC7A14	http://www.ncbi.nlm.nih.gov/gene/?term=57709	PPP1R142	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017539	5770	PTPN1	http://www.ncbi.nlm.nih.gov/gene/?term=5770	PTP1B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017540	5770	PTPN1	http://www.ncbi.nlm.nih.gov/gene/?term=5770	PTP1B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017541	57711	ZNF529	http://www.ncbi.nlm.nih.gov/gene/?term=57711		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017542	57711	ZNF529	http://www.ncbi.nlm.nih.gov/gene/?term=57711		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017543	57713	SFMBT2	http://www.ncbi.nlm.nih.gov/gene/?term=57713		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017544	57717	PCDHB16	http://www.ncbi.nlm.nih.gov/gene/?term=57717	"ME1, PCDH-BETA16, PCDH3X, PCDHB8a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017545	57717	PCDHB16	http://www.ncbi.nlm.nih.gov/gene/?term=57717	"ME1, PCDH-BETA16, PCDH3X, PCDHB8a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017546	5771	PTPN2	http://www.ncbi.nlm.nih.gov/gene/?term=5771	"PTN2, PTPT, TC-PTP, TCELLPTP, TCPTP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017547	57720	GPR107	http://www.ncbi.nlm.nih.gov/gene/?term=57720	"GCDRP, LUSTR1, bA138E2.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017548	57720	GPR107	http://www.ncbi.nlm.nih.gov/gene/?term=57720	"GCDRP, LUSTR1, bA138E2.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017549	57722	IGDCC4	http://www.ncbi.nlm.nih.gov/gene/?term=57722	"DDM36, NOPE "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017550	57722	IGDCC4	http://www.ncbi.nlm.nih.gov/gene/?term=57722	"DDM36, NOPE "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017551	57722	IGDCC4	http://www.ncbi.nlm.nih.gov/gene/?term=57722	"DDM36, NOPE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017552	57724	EPG5	http://www.ncbi.nlm.nih.gov/gene/?term=57724	"HEEW1, KIAA1632, VICIS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017553	57728	WDR19	http://www.ncbi.nlm.nih.gov/gene/?term=57728	"ATD5, CED4, DYF-2, IFT144, NPHP13, ORF26, Oseg6, PWDMP, SRTD5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017554	57743	Sec61a2	http://www.ncbi.nlm.nih.gov/gene/?term=57743		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017555	57746	Piwil2	http://www.ncbi.nlm.nih.gov/gene/?term=57746	"Piwil1l, mili "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017556	57748	Jmy	http://www.ncbi.nlm.nih.gov/gene/?term=57748		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017557	57750	Wdr12	http://www.ncbi.nlm.nih.gov/gene/?term=57750	"4933402C23Rik, Ytm1, Ytm1p "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017558	57753	Noc3l	http://www.ncbi.nlm.nih.gov/gene/?term=57753	"AF233884, Fad24 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017559	57758	SCUBE2	http://www.ncbi.nlm.nih.gov/gene/?term=57758	"CEGB1, CEGF1, CEGP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017560	57761	TRIB3	http://www.ncbi.nlm.nih.gov/gene/?term=57761	"C20orf97, NIPK, SINK, SKIP3, TRB3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017561	57763	ANKRA2	http://www.ncbi.nlm.nih.gov/gene/?term=57763	ANKRA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017562	57763	ANKRA2	http://www.ncbi.nlm.nih.gov/gene/?term=57763	ANKRA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017563	57776	Ttyh1	http://www.ncbi.nlm.nih.gov/gene/?term=57776	"4930459B04Rik, 6330408P11Rik, TTY1, mTTY1, tty "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017564	57782	Rbak	http://www.ncbi.nlm.nih.gov/gene/?term=57782		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017565	57783	Tnip1	http://www.ncbi.nlm.nih.gov/gene/?term=57783	"ABIN, ABIN-1, ABIN1, AU018810, Naf1, Nef, VAN "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017566	57786	RBAK	http://www.ncbi.nlm.nih.gov/gene/?term=57786	ZNF769	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017567	5778	PTPN7	http://www.ncbi.nlm.nih.gov/gene/?term=5778	"BPTP-4, HEPTP, LC-PTP, LPTP, PTPNI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017568	57794	SUGP1	http://www.ncbi.nlm.nih.gov/gene/?term=57794	"F23858, RBP, SF4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017569	57798	GATAD1	http://www.ncbi.nlm.nih.gov/gene/?term=57798	"CMD2B, ODAG, RG083M05.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017570	57799	RAB40C	http://www.ncbi.nlm.nih.gov/gene/?term=57799	"RARL, RASL8C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017571	57799	RAB40C	http://www.ncbi.nlm.nih.gov/gene/?term=57799	"RARL, RASL8C "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017572	577	ADGRB3	http://www.ncbi.nlm.nih.gov/gene/?term=577	BAI3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017573	57801	HES4	http://www.ncbi.nlm.nih.gov/gene/?term=57801	bHLHb42	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017574	57804	POLD4	http://www.ncbi.nlm.nih.gov/gene/?term=57804	"POLDS, p12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017575	57805	CCAR2	http://www.ncbi.nlm.nih.gov/gene/?term=57805	"DBC-1, DBC1, KIAA1967, NET35, p30 DBC, p30DBC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017576	57805	CCAR2	http://www.ncbi.nlm.nih.gov/gene/?term=57805	"DBC-1, DBC1, KIAA1967, NET35, p30 DBC, p30DBC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017577	57808	Rpl35a	http://www.ncbi.nlm.nih.gov/gene/?term=57808	"2810431L15Rik, Rpl35 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017578	57808	Rpl35a	http://www.ncbi.nlm.nih.gov/gene/?term=57808	"2810431L15Rik, Rpl35 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00017579	5780	PTPN9	http://www.ncbi.nlm.nih.gov/gene/?term=5780	"MEG2, PTPMEG2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017580	5780	PTPN9	http://www.ncbi.nlm.nih.gov/gene/?term=5780	"MEG2, PTPMEG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017581	57815	Spata5	http://www.ncbi.nlm.nih.gov/gene/?term=57815	"2510048F20Rik, C78064, Spaf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017582	57815	Spata5	http://www.ncbi.nlm.nih.gov/gene/?term=57815	"2510048F20Rik, C78064, Spaf "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017583	57817	HAMP	http://www.ncbi.nlm.nih.gov/gene/?term=57817	"HEPC, HFE2B, LEAP1, PLTR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017584	57818	G6PC2	http://www.ncbi.nlm.nih.gov/gene/?term=57818	IGRP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017585	57818	G6PC2	http://www.ncbi.nlm.nih.gov/gene/?term=57818	IGRP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017586	57819	LSM2	http://www.ncbi.nlm.nih.gov/gene/?term=57819	"C6orf28, G7B, YBL026W, snRNP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017587	5781	PTPN11	http://www.ncbi.nlm.nih.gov/gene/?term=5781	"BPTP3, CFC, JMML, METCDS, NS1, PTP-1D, PTP2C, SH-PTP2, SH-PTP3, SHP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017588	5781	PTPN11	http://www.ncbi.nlm.nih.gov/gene/?term=5781	"BPTP3, CFC, JMML, METCDS, NS1, PTP-1D, PTP2C, SH-PTP2, SH-PTP3, SHP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017589	5781	PTPN11	http://www.ncbi.nlm.nih.gov/gene/?term=5781	"BPTP3, CFC, JMML, METCDS, NS1, PTP-1D, PTP2C, SH-PTP2, SH-PTP3, SHP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017590	57820	CCNB1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=57820	"C14orf18, HEI10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017591	57820	CCNB1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=57820	"C14orf18, HEI10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017592	57820	CCNB1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=57820	"C14orf18, HEI10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017593	57826	RAP2C	http://www.ncbi.nlm.nih.gov/gene/?term=57826		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017594	57827	C6orf47	http://www.ncbi.nlm.nih.gov/gene/?term=57827	"D6S53E, G4, NG34 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017595	5782	PTPN12	http://www.ncbi.nlm.nih.gov/gene/?term=5782	"PTP-PEST, PTPG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017596	5782	PTPN12	http://www.ncbi.nlm.nih.gov/gene/?term=5782	"PTP-PEST, PTPG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017597	57835	SLC4A5	http://www.ncbi.nlm.nih.gov/gene/?term=57835	NBC4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017598	5783	PTPN13	http://www.ncbi.nlm.nih.gov/gene/?term=5783	"FAP-1, PNP1, PTP-BAS, PTP-BL, PTP1E, PTPL1, PTPLE, hPTP1E "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017599	5783	PTPN13	http://www.ncbi.nlm.nih.gov/gene/?term=5783	"FAP-1, PNP1, PTP-BAS, PTP-BL, PTP1E, PTPL1, PTPLE, hPTP1E "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017600	57862	ZNF410	http://www.ncbi.nlm.nih.gov/gene/?term=57862	"APA-1, APA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017601	57869	Adck2	http://www.ncbi.nlm.nih.gov/gene/?term=57869	"AA408112, BB006057 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017602	5786	PTPRA	http://www.ncbi.nlm.nih.gov/gene/?term=5786	"HEPTP, HLPR, HPTPA, HPTPalpha, LRP, PTPA, PTPRL2, R-PTP-alpha, RPTPA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017603	57874	Hacd3	http://www.ncbi.nlm.nih.gov/gene/?term=57874	"4930523M17Rik, AW742319, B-ind1, Hcad3, Hspc121, Ptplad1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017604	5787	PTPRB	http://www.ncbi.nlm.nih.gov/gene/?term=5787	"HPTP-BETA, HPTPB, PTPB, R-PTP-BETA, VEPTP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017605	5787	PTPRB	http://www.ncbi.nlm.nih.gov/gene/?term=5787	"HPTP-BETA, HPTPB, PTPB, R-PTP-BETA, VEPTP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017606	5787	PTPRB	http://www.ncbi.nlm.nih.gov/gene/?term=5787	"HPTP-BETA, HPTPB, PTPB, R-PTP-BETA, VEPTP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017607	5788	PTPRC	http://www.ncbi.nlm.nih.gov/gene/?term=5788	"B220, CD45, CD45R, GP180, L-CA, LCA, LY5, T200 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00017608	5788	PTPRC	http://www.ncbi.nlm.nih.gov/gene/?term=5788	"B220, CD45, CD45R, GP180, L-CA, LCA, LY5, T200 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017609	5788	PTPRC	http://www.ncbi.nlm.nih.gov/gene/5788	"LCA, LY5, B220, CD45, L-CA, T200, CD45R, GP180 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00017610	5789	PTPRD	http://www.ncbi.nlm.nih.gov/gene/?term=5789	"HPTP, HPTPD, HPTPDELTA, PTPD, RPTPDELTA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017611	578	BAK1	http://www.ncbi.nlm.nih.gov/gene/?term=578	"BAK, BAK-LIKE, BCL2L7, CDN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017612	578	BAK1	http://www.ncbi.nlm.nih.gov/gene/?term=578	"BAK, BAK-LIKE, BCL2L7, CDN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017613	57905	Isy1	http://www.ncbi.nlm.nih.gov/gene/?term=57905	"5830446M03Rik, AI181014, AU020769 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017614	57908	Zfp318	http://www.ncbi.nlm.nih.gov/gene/?term=57908	"2610034E08Rik, D530032D06Rik, TZF, Znf318 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017615	57912	Cdc42se1	http://www.ncbi.nlm.nih.gov/gene/?term=57912	"1300002M12Rik, AW558204, Cdcse1, SCIP1, Spec1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017616	5791	PTPRE	http://www.ncbi.nlm.nih.gov/gene/?term=5791	"HPTPE, PTPE, R-PTP-EPSILON "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017617	5791	PTPRE	http://www.ncbi.nlm.nih.gov/gene/?term=5791	"HPTPE, PTPE, R-PTP-EPSILON "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017618	5792	PTPRF	http://www.ncbi.nlm.nih.gov/gene/?term=5792	"BNAH2, LAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017619	5792	PTPRF	http://www.ncbi.nlm.nih.gov/gene/?term=5792	"BNAH2, LAR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017620	5793	PTPRG	http://www.ncbi.nlm.nih.gov/gene/?term=5793	"HPTPG, PTPG, R-PTP-GAMMA, RPTPG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017621	5793	PTPRG	http://www.ncbi.nlm.nih.gov/gene/?term=5793	"HPTPG, PTPG, R-PTP-GAMMA, RPTPG "	mRNA	Homo sapiens	19662205	Dendrite	Monocytes	Northern blot	"We have recently demonstrated that PTPgamma mRNA is expressed in monocytes, tissue-localized myeloid dendritic cells and in both myeloid and plasmacytoid dendritic cells in peripheral blood. "
RLID00017622	5793	PTPRG	http://www.ncbi.nlm.nih.gov/gene/?term=5793	"HPTPG, PTPG, R-PTP-GAMMA, RPTPG "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017623	5795	PTPRJ	http://www.ncbi.nlm.nih.gov/gene/?term=5795	"CD148, DEP1, HPTPeta, R-PTP-ETA, SCC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017624	5796	PTPRK	http://www.ncbi.nlm.nih.gov/gene/?term=5796	R-PTP-kappa	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017625	5796	PTPRK	http://www.ncbi.nlm.nih.gov/gene/?term=5796	R-PTP-kappa	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017626	5798	PTPRN	http://www.ncbi.nlm.nih.gov/gene/?term=5798	"IA-2, IA-2/PTP, IA2, ICA512, R-PTP-N "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017627	5799	PTPRN2	http://www.ncbi.nlm.nih.gov/gene/?term=5799	"IA-2beta, IAR, ICAAR, PTPRP, R-PTP-N2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017628	5801	PTPRR	http://www.ncbi.nlm.nih.gov/gene/?term=5801	"EC-PTP, PCPTP1, PTP-SL, PTPBR7, PTPRQ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017629	5802754	SPRRNA.31	http://www.ncbi.nlm.nih.gov/gene/?term=5802754	SPRRNA.31	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.31
RLID00017630	5802769	SPRRNA.32	http://www.ncbi.nlm.nih.gov/gene/?term=5802769	SPRRNA.32	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.32
RLID00017631	5802772	SPRRNA.33	http://www.ncbi.nlm.nih.gov/gene/?term=5802772	SPRRNA.33	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.33
RLID00017632	5802814	SPRRNA.41	http://www.ncbi.nlm.nih.gov/gene/?term=5802814	SPRRNA.41	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.41
RLID00017633	5802824	SPRRNA.36	http://www.ncbi.nlm.nih.gov/gene/?term=5802824	SPRRNA.36	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.36
RLID00017634	5802825	snu32	http://www.ncbi.nlm.nih.gov/gene/?term=5802825	SPSNRNA.07	snoRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNRNA.07
RLID00017635	5802833	SPRRNA.38	http://www.ncbi.nlm.nih.gov/gene/?term=5802833	SPRRNA.38	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.38
RLID00017636	5802949	snoR54b	http://www.ncbi.nlm.nih.gov/gene/?term=5802949	SPSNORNA.14	snoRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPSNORNA.14
RLID00017637	5802	PTPRS	http://www.ncbi.nlm.nih.gov/gene/?term=5802	PTPSIGMA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017638	5802	PTPRS	http://www.ncbi.nlm.nih.gov/gene/?term=5802	PTPSIGMA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017639	58039	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=58039		mRNA	Danio rerio	10330505	Vegetal	Embryo	In situ hybridization	"In ovary, it was localized in the cortex of oocytes. At the onset of embryogenesis, maternal zDazl mRNA was detected at the vegetal pole. It migrated toward blastomeres through cytoplasmic streams as early embryogenesis proceeded. This is the first report showing maternal mRNA localization at the vegetal pole in fish and the existence of mRNA streams in the yolk cytoplasm. "
RLID00017640	58039	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=58039		mRNA	Danio rerio	10781958	Vegetal	Oocyte	In situ hybridization	"Both brul and dazl mRNAs were localized at the vegetal cortex in the stage III-oocyte (Fig. 5C,F). "
RLID00017641	58039	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=58039		mRNA	Danio rerio	17293094	Germ plasm	Oocyte	In situ hybridization	"Here we report that the germ plasm RNAs vasa, nanos1, and dazl co-localize with the mitochondrial cloud (MC) and are transported to the vegetal cortex during early oogenesis. "
RLID00017642	58039	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=58039		mRNA	Danio rerio	17293094	Mitochondrion	Oocyte	In situ hybridization	"Here we report that the germ plasm RNAs vasa, nanos1, and dazl co-localize with the mitochondrial cloud (MC) and are transported to the vegetal cortex during early oogenesis. "
RLID00017643	58039	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=58039		mRNA	Danio rerio	24967891	Vegetal	Embryo	In situ hybridization	"The localization patterns of dazl mRNA, a germ plasm component initially localized to the vegetal pole of the egg ([36,46,47]; Figure 8A), is not affected in these mutants (Figure 8D). "
RLID00017644	58039	dazl	http://www.ncbi.nlm.nih.gov/gene/?term=58039		mRNA	Danio rerio	26528729	Vegetal	Embryo	Fluorescence in situ hybridization	"FIGURE 2. Dual label FISH of pairwise comparisons of wnt8a, grip2a and dazl mRNA localization at the vegetal cortex. (A-C) dazl (green) and wnt8a (red). (D-F) grip2a (green) and dazl (red). (G-I) grip2a (green) and wnt8a (red). In all cases mRNAs localize to discrete units, which do not overlap between different RNAs. Embryos are wild type fixed at 20mpf. Panels are 2-D projections of imaged vegetal cortex samples. Scale bar in (I) represents 5mm for all images. (Color figure available online.) "
RLID00017645	5805	PTS	http://www.ncbi.nlm.nih.gov/gene/?term=5805	PTPS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017646	5805	PTS	http://www.ncbi.nlm.nih.gov/gene/?term=5805	PTPS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017647	5805	PTS	http://www.ncbi.nlm.nih.gov/gene/?term=5805	PTPS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017648	580	BARD1	http://www.ncbi.nlm.nih.gov/gene/?term=580		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017649	580	BARD1	http://www.ncbi.nlm.nih.gov/gene/?term=580		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017650	580	BARD1	http://www.ncbi.nlm.nih.gov/gene/?term=580		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017651	5810	RAD1	http://www.ncbi.nlm.nih.gov/gene/?term=5810	"HRAD1, REC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017652	58137	celf1	http://www.ncbi.nlm.nih.gov/gene/?term=58137	"Bruno-like, brul, cb920, cugbp1 "	mRNA	Danio rerio	10781958	Vegetal	Oocyte	In situ hybridization	"At the onset of embryogenesis, brulmRNA was localized at the vegetal pole, and it then migrated toward the blastoderm (Fig. 3A±C).Fig. 3. brul mRNA localization during early embryogenesis. (A) Five minutes after fertilization, brulmRNA is localized at the vegetal pole. (B) Thirty minutes after fertilization, the mRNA streams toward the blastodisc of the zygote "
RLID00017653	58137	celf1	http://www.ncbi.nlm.nih.gov/gene/?term=58137	"Bruno-like, brul, cb920, cugbp1 "	mRNA	Danio rerio	10781958	Vegetal	Oocyte	In situ hybridization	"In the same oocyte, brul mRNA was accumulated at the vegetal cortex, although it was also detectable around the germinal vesicle (Fig. 4A). "
RLID00017654	5813	PURA	http://www.ncbi.nlm.nih.gov/gene/?term=5813	"MRD31, PUR-ALPHA, PUR1LPHA, PURA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017655	5813	PURA	http://www.ncbi.nlm.nih.gov/gene/?term=5813	"MRD31, PUR-ALPHA, PUR1, PURALPHA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017656	5814	PURB	http://www.ncbi.nlm.nih.gov/gene/?term=5814	PURBETA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017657	5814	PURB	http://www.ncbi.nlm.nih.gov/gene/?term=5814	PURBETA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017658	58155	PTBP2	http://www.ncbi.nlm.nih.gov/gene/?term=58155	"PTBLP, brPTB, nPTB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017659	58158	NEUROD4	http://www.ncbi.nlm.nih.gov/gene/?term=58158	"ATH-3, ATH3, Atoh3, MATH-3, MATH3, bHLHa4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017660	58172	Sertad2	http://www.ncbi.nlm.nih.gov/gene/?term=58172	"AB041541, AU021878, Kiaa0127, MNCb-1504, SEI-2, Sei2, TRIP-Br2, mKIAA0127 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017661	58175	Rgs20	http://www.ncbi.nlm.nih.gov/gene/?term=58175	"2900073E09Rik, Rgsz1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017662	58175	Rgs20	http://www.ncbi.nlm.nih.gov/gene/?term=58175	"2900073E09Rik, Rgsz1 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00017663	5817	PVR	http://www.ncbi.nlm.nih.gov/gene/?term=5817	"CD155, HVED, NECL5, Necl-5, PVS, TAGE4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017664	5817	PVR	http://www.ncbi.nlm.nih.gov/gene/?term=5817	"CD155, HVED, NECL5, Necl-5, PVS, TAGE4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017665	58180	Hic2	http://www.ncbi.nlm.nih.gov/gene/?term=58180	"AA409108, HRG22, mKIAA1020 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017666	58186	Rad18	http://www.ncbi.nlm.nih.gov/gene/?term=58186	"2810024C04Riksc, Rad18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017667	58186	Rad18	http://www.ncbi.nlm.nih.gov/gene/?term=58186	"2810024C04Riksc, Rad18 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017668	5818	NECTIN1	http://www.ncbi.nlm.nih.gov/gene/?term=5818	"CD111, CLPED1, ED4, HIgR, HV1S, HVEC, OFC7, PRR, PRR1, PVRL1, PVRR, PVRR1, SK-12, nectin-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017669	58190	CTDSP1	http://www.ncbi.nlm.nih.gov/gene/?term=58190	"NIF3, NLI-IF, NLIIF, SCP1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017670	58191	CXCL16	http://www.ncbi.nlm.nih.gov/gene/?term=58191	"CXCLG16, SR-PSOX, SRPSOX "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017671	58191	CXCL16	http://www.ncbi.nlm.nih.gov/gene/?term=58191	"CXCLG16, SR-PSOX, SRPSOX "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017672	58191	CXCL16	http://www.ncbi.nlm.nih.gov/gene/?term=58191	"CXCLG16, SR-PSOX, SRPSOX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017673	58193	Extl2	http://www.ncbi.nlm.nih.gov/gene/?term=58193	"3000001D04Rik, AW146439 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017674	58194	Sh3kbp1	http://www.ncbi.nlm.nih.gov/gene/?term=58194	"1200007H22Rik, 1700125L08Rik, 5830464D22Rik, AI447724, IN85, Ruk, Seta "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017675	5819	NECTIN2	http://www.ncbi.nlm.nih.gov/gene/?term=5819	"CD112, HVEB, PRR2, PVRL2, PVRR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017676	581	BAX	http://www.ncbi.nlm.nih.gov/gene/?term=581	BCL2L4	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017677	58202	Nelfb	http://www.ncbi.nlm.nih.gov/gene/?term=58202	"A730008L03Rik, AB041607, AI663983, Cobra1, Nelf-b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017678	5820	PVT1	http://www.ncbi.nlm.nih.gov/gene/?term=5820	"LINC00079, NCRNA00079, onco-lncRNA-100 "	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017679	58212	Srrm3	http://www.ncbi.nlm.nih.gov/gene/?term=58212	"2900083I11Rik, AB041661, SRm300-like, Srrm2l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017680	5822	PWP2	http://www.ncbi.nlm.nih.gov/gene/?term=5822	"EHOC-17H, UTP1, PWP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017681	5822	PWP2	http://www.ncbi.nlm.nih.gov/gene/?term=5822	"EHOC-17, PWP2H, UTP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017682	58231	Stk4	http://www.ncbi.nlm.nih.gov/gene/?term=58231	"AI447339, AU020804, Kas-2, Mst1, Ysk3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017683	58237	Nkain4	http://www.ncbi.nlm.nih.gov/gene/?term=58237	"AB030182, C030019F02Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017684	58239	Dexi	http://www.ncbi.nlm.nih.gov/gene/?term=58239	"1810029J14Rik, AI836170, AW413143, D16Bwg0586e, Myle "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017685	58240	Hs1bp3	http://www.ncbi.nlm.nih.gov/gene/?term=58240		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017686	58243	Nap1l5	http://www.ncbi.nlm.nih.gov/gene/?term=58243	1110020M21Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017687	58245	Gpr180	http://www.ncbi.nlm.nih.gov/gene/?term=58245	"AB041545, E130016I23Rik, Itr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017688	58249	Fibp	http://www.ncbi.nlm.nih.gov/gene/?term=58249	"2010004G08Rik, 2010005N21Rik, 3010027N18Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017689	5824	PEX19	http://www.ncbi.nlm.nih.gov/gene/?term=5824	"D1S2223E, HK33, PBD12A, PMP1, PMPI, PXF, PXMP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017690	58250	Chst11	http://www.ncbi.nlm.nih.gov/gene/?term=58250	"1110020P09Rik, C4ST, C4ST-1, C4ST1, C4s "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017691	5825	ABCD3	http://www.ncbi.nlm.nih.gov/gene/?term=5825	"ABC43, CBAS5, PMP70, PXMP1, ZWS2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017692	5825	ABCD3	http://www.ncbi.nlm.nih.gov/gene/?term=5825	"ABC43, CBAS5, PMP70, PXMP1, ZWS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017693	5826	ABCD4	http://www.ncbi.nlm.nih.gov/gene/?term=5826	"ABC41, EST352188, MAHCJ, P70R, P79R, PMP69, PXMP1L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017694	5827	PXMP2	http://www.ncbi.nlm.nih.gov/gene/?term=5827	PMP22	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017695	5827	PXMP2	http://www.ncbi.nlm.nih.gov/gene/?term=5827	PMP22	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017696	5828	PEX2	http://www.ncbi.nlm.nih.gov/gene/?term=5828	"PAF1, PBD5A, PBD5B, PMP3, PMP35, PXMP3, RNF72, ZWS3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017697	5828	PEX2	http://www.ncbi.nlm.nih.gov/gene/?term=5828	"PAF1, PBD5A, PBD5B, PMP3, PMP35, PXMP3, RNF72, ZWS3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017698	5828	PEX2	http://www.ncbi.nlm.nih.gov/gene/?term=5828	"PAF1, PBD5A, PBD5B, PMP3, PMP35, PXMP3, RNF72, ZWS3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017699	5828	PEX2	http://www.ncbi.nlm.nih.gov/gene/?term=5828	"PAF1, PBD5A, PBD5B, PMP3, PMP35, PXMP3, RNF72, ZWS3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017700	5829	PXN	http://www.ncbi.nlm.nih.gov/gene/?term=5829		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017701	5830	PEX5	http://www.ncbi.nlm.nih.gov/gene/?term=5830	"PBD2A, PBD2B, PTS1-BP, PTS1R, PXR1, RCDP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017702	5831	PYCR1	http://www.ncbi.nlm.nih.gov/gene/?term=5831	"ARCL2B, ARCL3B, P5C, P5CR, PIG45, PP222, PRO3, PYCR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017703	5832	ALDH18A1	http://www.ncbi.nlm.nih.gov/gene/?term=5832	"ADCL3, ARCL3A, GSAS, P5CS, PYCS, SPG9A, SPG9B "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017704	5832	ALDH18A1	http://www.ncbi.nlm.nih.gov/gene/?term=5832	"ADCL3, ARCL3A, GSAS, P5CS, PYCS, SPG9A, SPG9B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017705	5833	PCYT2	http://www.ncbi.nlm.nih.gov/gene/?term=5833	ET	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017706	5833	PCYT2	http://www.ncbi.nlm.nih.gov/gene/?term=5833	ET	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017707	5834	PYGB	http://www.ncbi.nlm.nih.gov/gene/?term=5834	GPBB	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017708	5834	PYGB	http://www.ncbi.nlm.nih.gov/gene/?term=5834	GPBB	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017709	5834	PYGB	http://www.ncbi.nlm.nih.gov/gene/?term=5834	GPBB	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017710	5836	PYGL	http://www.ncbi.nlm.nih.gov/gene/?term=5836	GSD6	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017711	5836	PYGL	http://www.ncbi.nlm.nih.gov/gene/?term=5836	GSD6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017712	5837	PYGM	http://www.ncbi.nlm.nih.gov/gene/?term=5837		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017713	583	BBS2	http://www.ncbi.nlm.nih.gov/gene/?term=583	"BBS, RP74 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017714	583	BBS2	http://www.ncbi.nlm.nih.gov/gene/?term=583	"BBS, RP74 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017715	583	BBS2	http://www.ncbi.nlm.nih.gov/gene/?term=583	"BBS, RP74 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017716	58475	MS4A7	http://www.ncbi.nlm.nih.gov/gene/?term=58475	"4SPAN2, CD20L4, CFFM4, MS4A8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017717	58477	SRPRB	http://www.ncbi.nlm.nih.gov/gene/?term=58477	APMCF1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017718	58477	SRPRB	http://www.ncbi.nlm.nih.gov/gene/?term=58477	APMCF1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017719	58477	SRPRB	http://www.ncbi.nlm.nih.gov/gene/?term=58477	APMCF1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017720	58478	ENOPH1	http://www.ncbi.nlm.nih.gov/gene/?term=58478	"E1, MASA, MST145, mtnC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017721	58478	ENOPH1	http://www.ncbi.nlm.nih.gov/gene/?term=58478	"E1, MASA, MST145, mtnC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017722	58478	ENOPH1	http://www.ncbi.nlm.nih.gov/gene/?term=58478	"E1, MASA, MST145, mtnC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017723	58478	ENOPH1	http://www.ncbi.nlm.nih.gov/gene/?term=58478	"E1, MASA, MST145, mtnC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017724	58480	RHOU	http://www.ncbi.nlm.nih.gov/gene/?term=58480	"ARHU, CDC42L1, G28K, WRCH1, hG28K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017725	58485	TRAPPC1	http://www.ncbi.nlm.nih.gov/gene/?term=58485	"BET5, MUM2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017726	58485	TRAPPC1	http://www.ncbi.nlm.nih.gov/gene/?term=58485	"BET5, MUM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017727	58486	ZBED5	http://www.ncbi.nlm.nih.gov/gene/?term=58486	Buster1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017728	58486	ZBED5	http://www.ncbi.nlm.nih.gov/gene/?term=58486	Buster1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017729	58487	CREBZF	http://www.ncbi.nlm.nih.gov/gene/?term=58487	"SMILE, ZF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017730	58487	CREBZF	http://www.ncbi.nlm.nih.gov/gene/?term=58487	"SMILE, ZF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017731	58488	PCTP	http://www.ncbi.nlm.nih.gov/gene/?term=58488	"PC-TP, STARD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017732	58488	PCTP	http://www.ncbi.nlm.nih.gov/gene/?term=58488	"PC-TP, STARD2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017733	58488	PCTP	http://www.ncbi.nlm.nih.gov/gene/?term=58488	"PC-TP, STARD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017734	58490	RPRD1B	http://www.ncbi.nlm.nih.gov/gene/?term=58490	"C20orf77, CREPT, NET60, dJ1057B20.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017735	58490	RPRD1B	http://www.ncbi.nlm.nih.gov/gene/?term=58490	"C20orf77, CREPT, NET60, dJ1057B20.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017736	58493	INIP	http://www.ncbi.nlm.nih.gov/gene/?term=58493	"C9orf80, HSPC043, MISE, SOSSC, SSBIP1, hSSBIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017737	58497	PRUNE	http://www.ncbi.nlm.nih.gov/gene/?term=58497	"DRES-17, DRES17, HTCD37 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017738	58497	PRUNE	http://www.ncbi.nlm.nih.gov/gene/?term=58497	"DRES-17, DRES17, HTCD37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017739	58498	MYL7	http://www.ncbi.nlm.nih.gov/gene/?term=58498	"MYL2A, MYLC2A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017740	58500	ZNF250	http://www.ncbi.nlm.nih.gov/gene/?term=58500	"ZFP647, ZNF647 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017741	58500	ZNF250	http://www.ncbi.nlm.nih.gov/gene/?term=58500	"ZFP647, ZNF647 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017742	58505	OSTC	http://www.ncbi.nlm.nih.gov/gene/?term=58505	DC2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017743	58506	SCAF1	http://www.ncbi.nlm.nih.gov/gene/?term=58506	SRA1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017744	58508	KMT2C	http://www.ncbi.nlm.nih.gov/gene/?term=58508	"HALR, MLL3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017745	58508	KMT2C	http://www.ncbi.nlm.nih.gov/gene/?term=58508	"HALR, MLL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017746	58509	CACTIN	http://www.ncbi.nlm.nih.gov/gene/?term=58509	"C19orf29, NY-REN-24, fSAPc "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017747	58509	CACTIN	http://www.ncbi.nlm.nih.gov/gene/?term=58509	"C19orf29, NY-REN-24, fSAPc "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017748	58515	SELK	http://www.ncbi.nlm.nih.gov/gene/?term=58515	"HSPC030, HSPC297, SelK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017749	58515	SELK	http://www.ncbi.nlm.nih.gov/gene/?term=58515	"HSPC030, HSPC297, SelK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017750	58516	FAM60A	http://www.ncbi.nlm.nih.gov/gene/?term=58516	"C12orf14, L4, TERA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017751	58516	FAM60A	http://www.ncbi.nlm.nih.gov/gene/?term=58516	"C12orf14, L4, TERA "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017752	58516	FAM60A	http://www.ncbi.nlm.nih.gov/gene/?term=58516	"C12orf14, L4, TERA "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017753	58517	RBM25	http://www.ncbi.nlm.nih.gov/gene/?term=58517	"NET52, RED120, RNPC7, S164, Snu71, fSAP94 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017754	58517	RBM25	http://www.ncbi.nlm.nih.gov/gene/?term=58517	"NET52, RED120, RNPC7, S164, Snu71, fSAP94 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017755	58517	RBM25	http://www.ncbi.nlm.nih.gov/gene/?term=58517	"NET52, RED120, RNPC7, S164, Snu71, fSAP94 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017756	58525	WIZ	http://www.ncbi.nlm.nih.gov/gene/?term=58525	ZNF803	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017757	58527	ABRACL	http://www.ncbi.nlm.nih.gov/gene/?term=58527	"C6orf115, Costars, HSPC280, PRO2013 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017758	58533	SNX6	http://www.ncbi.nlm.nih.gov/gene/?term=58533	"MSTP010, TFAF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017759	58533	SNX6	http://www.ncbi.nlm.nih.gov/gene/?term=58533	"MSTP010, TFAF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017760	58533	SNX6	http://www.ncbi.nlm.nih.gov/gene/?term=58533	"MSTP010, TFAF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017761	5859	QARS	http://www.ncbi.nlm.nih.gov/gene/?term=5859	"GLNRS, MSCCA, PRO2195 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017762	5859	QARS	http://www.ncbi.nlm.nih.gov/gene/?term=5859	"GLNRS, MSCCA, PRO2195 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017763	5859	QARS	http://www.ncbi.nlm.nih.gov/gene/?term=5859	"GLNRS, MSCCA, PRO2195 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017764	585	BBS4	http://www.ncbi.nlm.nih.gov/gene/?term=585		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017765	585	BBS4	http://www.ncbi.nlm.nih.gov/gene/?term=585		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017766	5860	QDPR	http://www.ncbi.nlm.nih.gov/gene/?term=5860	"DHPR, PKU2, SDR33C1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017767	5860	QDPR	http://www.ncbi.nlm.nih.gov/gene/?term=5860	"DHPR, PKU2, SDR33C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017768	5861	RAB1A	http://www.ncbi.nlm.nih.gov/gene/?term=5861	"RAB1, YPT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017769	5861	RAB1A	http://www.ncbi.nlm.nih.gov/gene/?term=5861	"RAB1, YPT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017770	5862	RAB2A	http://www.ncbi.nlm.nih.gov/gene/?term=5862	"LHX, RAB2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017771	5862	RAB2A	http://www.ncbi.nlm.nih.gov/gene/?term=5862	"LHX, RAB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017772	5863	RGL2	http://www.ncbi.nlm.nih.gov/gene/?term=5863	"HKE1.5, KE1.5, RAB2L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017773	5863	RGL2	http://www.ncbi.nlm.nih.gov/gene/?term=5863	"HKE1.5, KE1.5, RAB2L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017774	5864	RAB3A	http://www.ncbi.nlm.nih.gov/gene/?term=5864		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017775	5865	RAB3B	http://www.ncbi.nlm.nih.gov/gene/?term=5865		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017776	5865	RAB3B	http://www.ncbi.nlm.nih.gov/gene/?term=5865		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017777	5866	RAB3IL1	http://www.ncbi.nlm.nih.gov/gene/?term=5866	GRAB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017778	5867	RAB4A	http://www.ncbi.nlm.nih.gov/gene/?term=5867	"HRES-1, HRES-1/RAB4, HRES1, RAB4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017779	5867	RAB4A	http://www.ncbi.nlm.nih.gov/gene/?term=5867	"HRES-1, HRES-1/RAB4, HRES1, RAB4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017780	5867	RAB4A	http://www.ncbi.nlm.nih.gov/gene/?term=5867	"HRES-1, HRES-1/RAB4, HRES1, RAB4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017781	5868	RAB5A	http://www.ncbi.nlm.nih.gov/gene/?term=5868	RAB5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017782	5868	RAB5A	http://www.ncbi.nlm.nih.gov/gene/?term=5868	RAB5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017783	5869	RAB5B	http://www.ncbi.nlm.nih.gov/gene/?term=5869		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017784	586	BCAT1	http://www.ncbi.nlm.nih.gov/gene/?term=586	"BCATC, BCT1, ECA39, MECA39, PNAS121, PP18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017785	5870	RAB6A	http://www.ncbi.nlm.nih.gov/gene/?term=5870	RAB6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017786	5870	RAB6A	http://www.ncbi.nlm.nih.gov/gene/?term=5870	RAB6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017787	5871	MAP4K2	http://www.ncbi.nlm.nih.gov/gene/?term=5871	"BL44, GCK, RAB8IP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017788	5873	RAB27A	http://www.ncbi.nlm.nih.gov/gene/?term=5873	"GS2, HsT18676, RAB27, RAM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017789	5873	RAB27A	http://www.ncbi.nlm.nih.gov/gene/?term=5873	"GS2, HsT18676, RAB27, RAM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017790	5873	RAB27A	http://www.ncbi.nlm.nih.gov/gene/?term=5873	"GS2, HsT18676, RAB27, RAM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017791	5875	RABGGTA	http://www.ncbi.nlm.nih.gov/gene/?term=5875	PTAR3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017792	5876	RABGGTB	http://www.ncbi.nlm.nih.gov/gene/?term=5876	GGTB	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017793	5876	RABGGTB	http://www.ncbi.nlm.nih.gov/gene/?term=5876	GGTB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017794	5877	RABIF	http://www.ncbi.nlm.nih.gov/gene/?term=5877	"MSS4, RASGFR3, RASGRF3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017795	5877	RABIF	http://www.ncbi.nlm.nih.gov/gene/?term=5877	"MSS4, RASGFR3, RASGRF3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017796	5878	RAB5C	http://www.ncbi.nlm.nih.gov/gene/?term=5878	"L1880L, RAB5L, RABL, RAB5C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017797	5878	RAB5C	http://www.ncbi.nlm.nih.gov/gene/?term=5878	"L1880L, RAB5L, RABL, RAB5C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017798	5878	RAB5C	http://www.ncbi.nlm.nih.gov/gene/?term=5878	"L1880, RAB5CL, RAB5L, RABL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017799	58799	Crbn	http://www.ncbi.nlm.nih.gov/gene/?term=58799	"2610203G15Rik, 2900045O07Rik, AF229032, AW108261, piL "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017800	5879	RAC1	http://www.ncbi.nlm.nih.gov/gene/?term=5879	"MIG5, Rac-1, TC-25, p21-Rac1 "	mRNA	Homo sapiens	23452202	Lamellipodium	Lung fibroblast	Fluorescence in situ hybridization	"Rac1, ArpC2 and β-actin mRNAs co-localize with actively translating ribosomes on lamellipodia. "
RLID00017801	5879	RAC1	http://www.ncbi.nlm.nih.gov/gene/?term=5879	"MIG5, Rac-1, TC-25, p21-Rac1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017802	5879	RAC1	http://www.ncbi.nlm.nih.gov/gene/?term=5879	"MIG5, Rac-1, TC-25, p21-Rac1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017803	587	BCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=587	"BCAM, BCATM, BCT2, PP18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017804	587	BCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=587	"BCAM, BCATM, BCT2, PP18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017805	58800	Trpm7	http://www.ncbi.nlm.nih.gov/gene/?term=58800	"2310022G15Rik, 4833414K03Rik, 5033407O22Rik, CHAK, CHAK1, LTrpC-7, Ltpr7, Ltrpc7, TRPPLIK "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017806	58800	Trpm7	http://www.ncbi.nlm.nih.gov/gene/?term=58800	"2310022G15Rik, 4833414K03Rik, 5033407O22Rik, CHAK, CHAK1, LTrpC-7, Ltpr7, Ltrpc7, TRPPLIK "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017807	58804	Cdc42ep5	http://www.ncbi.nlm.nih.gov/gene/?term=58804	"1700027J19Rik, 2010007O02Rik, Borg3, C85526, CEP5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017808	5880	RAC2	http://www.ncbi.nlm.nih.gov/gene/?term=5880	"EN-7, Gx, HSPC022, p21-Rac2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017809	58810	Akr1a1	http://www.ncbi.nlm.nih.gov/gene/?term=58810	"2610201A18Rik, Akr1a4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017810	5881	RAC3	http://www.ncbi.nlm.nih.gov/gene/?term=5881		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017811	5884	RAD17	http://www.ncbi.nlm.nih.gov/gene/?term=5884	"CCYC, HRAD17, R24L, RAD17SP, RAD24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017812	5885	RAD21	http://www.ncbi.nlm.nih.gov/gene/?term=5885	"CDLS4, HR21, HRAD21, MCD1, NXP1, SCC1, hHR21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017813	5885	RAD21	http://www.ncbi.nlm.nih.gov/gene/?term=5885	"CDLS4, HR21, HRAD21, MCD1, NXP1, SCC1, hHR21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017814	5886	RAD23A	http://www.ncbi.nlm.nih.gov/gene/?term=5886	"HHR23A, HR23A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017815	5886	RAD23A	http://www.ncbi.nlm.nih.gov/gene/?term=5886	"HHR23A, HR23A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017816	5887	RAD23B	http://www.ncbi.nlm.nih.gov/gene/?term=5887	"HHR23B, HR23B, P58 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017817	5887	RAD23B	http://www.ncbi.nlm.nih.gov/gene/?term=5887	"HHR23B, HR23B, P58 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017818	5887	RAD23B	http://www.ncbi.nlm.nih.gov/gene/?term=5887	"HHR23B, HR23B, P58 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017819	58887	Repin1	http://www.ncbi.nlm.nih.gov/gene/?term=58887	"AI425994, Ap4, E430037F08Rik, Zfp-464, Zfp464 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017820	5888	RAD51	http://www.ncbi.nlm.nih.gov/gene/?term=5888	"BRCC5, FANCR, HRAD51, HsRad51, HsT16930, MRMV2, RAD51A, RECA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017821	5889	RAD51C	http://www.ncbi.nlm.nih.gov/gene/?term=5889	"BROVCA3, FANCO, R51H3, RAD51L2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017822	58911	Sumf1	http://www.ncbi.nlm.nih.gov/gene/?term=58911	"AA543204, AI463102, AI851573, FGE "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017823	5892	RAD51D	http://www.ncbi.nlm.nih.gov/gene/?term=5892	"BROVCA4, R51H3, RAD51L3, TRAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017824	58940	H2afz	http://www.ncbi.nlm.nih.gov/gene/?term=58940	H2A.Z-1	mRNA	Rattus norvegicus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00017825	5894	RAF1	http://www.ncbi.nlm.nih.gov/gene/?term=5894	"CMD1NN, CRAF, NS5, Raf-1, c-Raf "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017826	58985	IL22RA1	http://www.ncbi.nlm.nih.gov/gene/?term=58985	"CRF2-9, IL22R, IL22R1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017827	5898	RALA	http://www.ncbi.nlm.nih.gov/gene/?term=5898	RAL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017828	5898	RALA	http://www.ncbi.nlm.nih.gov/gene/?term=5898	RAL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017829	58994	Smpd3	http://www.ncbi.nlm.nih.gov/gene/?term=58994	"4631433G07Rik, AI427456, AW537966, fro, nSMase2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017830	5899	RALB	http://www.ncbi.nlm.nih.gov/gene/?term=5899		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017831	5899	RALB	http://www.ncbi.nlm.nih.gov/gene/?term=5899		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017832	59002	Wrap73	http://www.ncbi.nlm.nih.gov/gene/?term=59002	"2610044M17Rik, 5330425N03Rik, Dd57, Wdr8 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017833	59004	Pias4	http://www.ncbi.nlm.nih.gov/gene/?term=59004	"PIASY, Pias-gamma, Piasg "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017834	59007	Ngly1	http://www.ncbi.nlm.nih.gov/gene/?term=59007	"1110002C09Rik, PNGase, Png1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017835	59007	Ngly1	http://www.ncbi.nlm.nih.gov/gene/?term=59007	"1110002C09Rik, PNGase, Png1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017836	59008	Anapc5	http://www.ncbi.nlm.nih.gov/gene/?term=59008	"2510006G12Rik, AA408751, AA536819, AA986414, APC5, Anpc5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017837	5900	RALGDS	http://www.ncbi.nlm.nih.gov/gene/?term=5900	"RGDS, RGF, RalGEF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017838	5900	RALGDS	http://www.ncbi.nlm.nih.gov/gene/?term=5900	"RGDS, RGF, RalGEF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017839	59013	Hnrnph1	http://www.ncbi.nlm.nih.gov/gene/?term=59013	"AI642080, E430005G16Rik, Hnrnph, Hnrph1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017840	59014	Rrs1	http://www.ncbi.nlm.nih.gov/gene/?term=59014	"5730466A07Rik, AA415037, D1Ertd701e, Rrr "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017841	59015	Nup160	http://www.ncbi.nlm.nih.gov/gene/?term=59015	"160kDa, 2810011M03Rik, AA414952, AU020188, Gtl-13, Gtl1-13, Gtl13, mKIAA0197 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017842	5901	RAN	http://www.ncbi.nlm.nih.gov/gene/?term=5901	"ARA24, Gsp1, TC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017843	5901	RAN	http://www.ncbi.nlm.nih.gov/gene/?term=5901	"ARA24, Gsp1, TC4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017844	5901	RAN	http://www.ncbi.nlm.nih.gov/gene/?term=5901	"ARA24, Gsp1, TC4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017845	59022	Edf1	http://www.ncbi.nlm.nih.gov/gene/?term=59022	"0610008L11Rik, AA409425 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017846	59025	Usp14	http://www.ncbi.nlm.nih.gov/gene/?term=59025	"2610005K12Rik, 2610037B11Rik, AW107924, C78769, ax, nmf375 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017847	59025	Usp14	http://www.ncbi.nlm.nih.gov/gene/?term=59025	"2610005K12Rik, 2610037B11Rik, AW107924, C78769, ax, nmf375 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017848	59026	Huwe1	http://www.ncbi.nlm.nih.gov/gene/?term=59026	"5430439H10Rik, AU041296, Arf-bp1, C430014N20Rik, C80292, Gm1718, Ib772, LASU1, Mule, Ureb1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017849	59027	Nampt	http://www.ncbi.nlm.nih.gov/gene/?term=59027	"1110035O14Rik, AI314458, AI480535, NAmPRTase, Pbef, Pbef1, Visfatin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017850	59029	Psmd14	http://www.ncbi.nlm.nih.gov/gene/?term=59029	"2610312C03Rik, 3200001M20Rik, AA986732, Pad1, Poh1, rpm11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017851	59029	Psmd14	http://www.ncbi.nlm.nih.gov/gene/?term=59029	"2610312C03Rik, 3200001M20Rik, AA986732, Pad1, Poh1, rpm11 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017852	5902	RANBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5902	HTF9A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017853	5902	RANBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5902	HTF9A	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017854	5902	RANBP1	http://www.ncbi.nlm.nih.gov/gene/?term=5902	HTF9A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017855	59030	Mkks	http://www.ncbi.nlm.nih.gov/gene/?term=59030	"1300013E18Rik, AI463362, AI957237, Bbs6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017856	59036	Dact1	http://www.ncbi.nlm.nih.gov/gene/?term=59036	"4921528D17Rik, AI115603, DAPPER, DAPPER1, FRODO, Frd1, Frodo1, MDpr1, MTNG3, THYEX3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017857	59038	Pxmp4	http://www.ncbi.nlm.nih.gov/gene/?term=59038	"3010018P03Rik, Pmp24 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017858	5903	RANBP2	http://www.ncbi.nlm.nih.gov/gene/?term=5903	"ADANE, ANE1, IIAE3, NUP358, TRP1, TRP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017859	5903	RANBP2	http://www.ncbi.nlm.nih.gov/gene/?term=5903	"ADANE, ANE1, IIAE3, NUP358, TRP1, TRP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017860	59040	Rhot1	http://www.ncbi.nlm.nih.gov/gene/?term=59040	"2210403N23Rik, AA415293, AF244542, AI834919, Arht1, C430039G08Rik, Miro1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017861	59044	Rnf130	http://www.ncbi.nlm.nih.gov/gene/?term=59044	"2510042A13Rik, G1RZFP, G1rp, GOLIATH, GP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017862	59050	Nsa2	http://www.ncbi.nlm.nih.gov/gene/?term=59050	"5730427N09Rik, LNR42p, Tinp1, Yr29, Nsa2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017863	59052	Mettl9	http://www.ncbi.nlm.nih.gov/gene/?term=59052	"0610012D09Rik, AA517660, Drev, MNCb-5680 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017864	59053	Hgh1	http://www.ncbi.nlm.nih.gov/gene/?term=59053	"Brp16, D15Ertd741e, Fam203a, MNCb-5873 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017865	59058	Bhlhe22	http://www.ncbi.nlm.nih.gov/gene/?term=59058	"Beta3, Bhlhb5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017866	5905	RANGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=5905	"Fug1, RANGAP, SD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017867	5905	RANGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=5905	"Fug1, RANGAP, SD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017868	5905	RANGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=5905	"Fug1, RANGAP, SD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017869	59069	Tpm3	http://www.ncbi.nlm.nih.gov/gene/?term=59069	"TM30nm, TMnm, Tm5NM, Tpm-5, Tpm5, Trop-5, gamma-TM, hTM30nm, hTMnm "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00017870	5906	RAP1A	http://www.ncbi.nlm.nih.gov/gene/?term=5906	"C21KG, G-22K, KREV-1, KREV1, RAP1, SMGP21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017871	59079	Erbb2ip	http://www.ncbi.nlm.nih.gov/gene/?term=59079	"1700028E05Rik, Erbin, mKIAA1225 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017872	59082	CARD18	http://www.ncbi.nlm.nih.gov/gene/?term=59082	"ICEBERG, UNQ5804, pseudo-ICE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017873	59085	Asl	http://www.ncbi.nlm.nih.gov/gene/?term=59085		mRNA	Rattus norvegicus	8726358	Mitochondrion	Liver	In situ hybridization	"These ratios showed that the mRNAs for argininosuccinate synthetase and argininosuccinate lyase were located next to the cytoplasmic side of the mitochondrial membrane and in the nearby endoplasmic reticulum. These data show that ASL mRNA is preferentially located at the mitochondrial outer membrane and in the ER. Thus,ASS mRNA, likeASL mRNA, is preferentially located at the mitochondrial outer membrane and in the ER. This suggests that COIII mRNA is actually predominantly associated with those portions of the inner membrane which lie at the mitochondrial perimeter rather than along the cristae. "
RLID00017874	59085	Asl	http://www.ncbi.nlm.nih.gov/gene/?term=59085		mRNA	Rattus norvegicus	8726358	Endoplasmic reticulum	Liver	In situ hybridization	"These ratios showed that the mRNAs for argininosuccinate synthetase and argininosuccinate lyase were located next to the cytoplasmic side of the mitochondrial membrane and in the nearby endoplasmic reticulum. These data show that ASL mRNA is preferentially located at the mitochondrial outer membrane and in the ER. Thus,ASS mRNA, likeASL mRNA, is preferentially located at the mitochondrial outer membrane and in the ER. This suggests that COIII mRNA is actually predominantly associated with those portions of the inner membrane which lie at the mitochondrial perimeter rather than along the cristae. "
RLID00017875	5908	RAP1B	http://www.ncbi.nlm.nih.gov/gene/?term=5908	"K-REV, RAL1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017876	5908	RAP1B	http://www.ncbi.nlm.nih.gov/gene/?term=5908	"K-REV, RAL1B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017877	5908	RAP1B	http://www.ncbi.nlm.nih.gov/gene/?term=5908	"K-REV, RAL1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017878	5909	RAP1GAP	http://www.ncbi.nlm.nih.gov/gene/?term=5909	"RAP1GA1, RAP1GAP1, RAP1GAPII, RAPGAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017879	590	BCHE	http://www.ncbi.nlm.nih.gov/gene/?term=590	"CHE1, CHE2, E1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017880	5910	RAP1GDS1	http://www.ncbi.nlm.nih.gov/gene/?term=5910	"GDS1, SmgGDS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017881	5910	RAP1GDS1	http://www.ncbi.nlm.nih.gov/gene/?term=5910	"GDS1, SmgGDS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017882	5911	RAP2A	http://www.ncbi.nlm.nih.gov/gene/?term=5911	"K-REV, KREV, RAP2, RbBP-30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017883	5911	RAP2A	http://www.ncbi.nlm.nih.gov/gene/?term=5911	"K-REV, KREV, RAP2, RbBP-30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017884	59126	Nek6	http://www.ncbi.nlm.nih.gov/gene/?term=59126	1300007C09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00017885	5912	RAP2B	http://www.ncbi.nlm.nih.gov/gene/?term=5912		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017886	59170	CG18809	http://www.ncbi.nlm.nih.gov/gene/?term=59170	"Dmel_ CG1809, Dmel\CG18809 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00017887	5917	RARS	http://www.ncbi.nlm.nih.gov/gene/?term=5917	"ArgRS, DALRD1, HLD9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017888	5917	RARS	http://www.ncbi.nlm.nih.gov/gene/?term=5917	"ArgRS, DALRD1, HLD9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017889	5917	RARS	http://www.ncbi.nlm.nih.gov/gene/?term=5917	"ArgRS, DALRD1, HLD9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017890	5924	RASGRF2	http://www.ncbi.nlm.nih.gov/gene/?term=5924	"GRF2, RAS-GRF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017891	59253	CG18508	http://www.ncbi.nlm.nih.gov/gene/?term=59253	"Dmel_ CG4015, Dmel\CG18508, EG:140G11.3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00017892	59253	CG18508	http://www.ncbi.nlm.nih.gov/gene/?term=59253	"Dmel_ CG4015, Dmel\CG18508, EG:140G11.3 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00017893	5925	RB1	http://www.ncbi.nlm.nih.gov/gene/?term=5925	"OSRC, PPP1R130, RB, p105-Rb, pRb, pp110 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017894	59266	Hcn4	http://www.ncbi.nlm.nih.gov/gene/?term=59266		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00017895	59271	EVA1C	http://www.ncbi.nlm.nih.gov/gene/?term=59271	"B18, B19, C21orf63, C21orf64, FAM176C, PRED34, SUE21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017896	59274	MESDC1	http://www.ncbi.nlm.nih.gov/gene/?term=59274		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017897	59274	MESDC1	http://www.ncbi.nlm.nih.gov/gene/?term=59274		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017898	59277	NTN4	http://www.ncbi.nlm.nih.gov/gene/?term=59277	PRO3091	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017899	5927	KDM5A	http://www.ncbi.nlm.nih.gov/gene/?term=5927	"RBBP-2, RBBP2, RBP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017900	5927	KDM5A	http://www.ncbi.nlm.nih.gov/gene/?term=5927	"RBBP-2, RBBP2, RBP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017901	59286	UBL5	http://www.ncbi.nlm.nih.gov/gene/?term=59286	HUB1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017902	59286	UBL5	http://www.ncbi.nlm.nih.gov/gene/?term=59286	HUB1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017903	59286	UBL5	http://www.ncbi.nlm.nih.gov/gene/?term=59286	HUB1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017904	5928	RBBP4	http://www.ncbi.nlm.nih.gov/gene/?term=5928	"NURF55, RBAP48, lin-53 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017905	5928	RBBP4	http://www.ncbi.nlm.nih.gov/gene/?term=5928	"NURF55, RBAP48, lin-53 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017906	5928	RBBP4	http://www.ncbi.nlm.nih.gov/gene/?term=5928	"NURF55, RBAP48, lin-53 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017907	5928	RBBP4	http://www.ncbi.nlm.nih.gov/gene/?term=5928	"NURF55, RBAP48, lin-53 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017908	59307	SIGIRR	http://www.ncbi.nlm.nih.gov/gene/?term=59307	TIR8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017909	5930	RBBP6	http://www.ncbi.nlm.nih.gov/gene/?term=5930	"MY038, P2P-R, PACT, RBQ-1, SNAMA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017910	5931	RBBP7	http://www.ncbi.nlm.nih.gov/gene/?term=5931	RbAp46	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017911	59338	PLEKHA1	http://www.ncbi.nlm.nih.gov/gene/?term=59338	TAPP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017912	59338	PLEKHA1	http://www.ncbi.nlm.nih.gov/gene/?term=59338	TAPP1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017913	59338	PLEKHA1	http://www.ncbi.nlm.nih.gov/gene/?term=59338	TAPP1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017914	59339	PLEKHA2	http://www.ncbi.nlm.nih.gov/gene/?term=59339	TAPP2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017915	59339	PLEKHA2	http://www.ncbi.nlm.nih.gov/gene/?term=59339	TAPP2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017916	59339	PLEKHA2	http://www.ncbi.nlm.nih.gov/gene/?term=59339	TAPP2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017917	59339	PLEKHA2	http://www.ncbi.nlm.nih.gov/gene/?term=59339	TAPP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017918	5933	RBL1	http://www.ncbi.nlm.nih.gov/gene/?term=5933	"CP107, PRB1, p107 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017919	59342	SCPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=59342	"HSCP1, RISC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017920	59342	SCPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=59342	"HSCP1, RISC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017921	59343	SENP2	http://www.ncbi.nlm.nih.gov/gene/?term=59343	"AXAM2, SMT3IP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017922	59343	SENP2	http://www.ncbi.nlm.nih.gov/gene/?term=59343	"AXAM2, SMT3IP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017923	59345	GNB4	http://www.ncbi.nlm.nih.gov/gene/?term=59345	CMTD1F	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017924	59348	ZNF350	http://www.ncbi.nlm.nih.gov/gene/?term=59348	"ZBRK1, ZFQR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017925	59348	ZNF350	http://www.ncbi.nlm.nih.gov/gene/?term=59348	"ZBRK1, ZFQR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017926	59349	KLHL12	http://www.ncbi.nlm.nih.gov/gene/?term=59349	"C3IP1, DKIR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017927	5934	RBL2	http://www.ncbi.nlm.nih.gov/gene/?term=5934	"P130, Rb2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017928	5935	RBM3	http://www.ncbi.nlm.nih.gov/gene/?term=5935	"IS1-RNPL, RNPL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017929	5935	RBM3	http://www.ncbi.nlm.nih.gov/gene/?term=5935	"IS1-RNPL, RNPL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017930	5936	RBM4	http://www.ncbi.nlm.nih.gov/gene/?term=5936	"LARKA, ZCCHC21, ZCRB3A, RBM4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017931	5936	RBM4	http://www.ncbi.nlm.nih.gov/gene/?term=5936	"LARK, RBM4A, ZCCHC21, ZCRB3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017932	5939	RBMS2	http://www.ncbi.nlm.nih.gov/gene/?term=5939	SCR3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017933	593	BCKDHA	http://www.ncbi.nlm.nih.gov/gene/?term=593	"BCKDE1A, MSU, MSUD1, OVD1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017934	594837	SNORD101	http://www.ncbi.nlm.nih.gov/gene/?term=594837	U101	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017935	594837	SNORD101	http://www.ncbi.nlm.nih.gov/gene/?term=594837	U101	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017936	594837	SNORD101	http://www.ncbi.nlm.nih.gov/gene/?term=594837	U101	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017937	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00017938	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"The most abundant snoRNA found in the serum exosomes were SNORD100, SNORD27 and SNORD31 (Supplementary file). The functions of these snoRNA species are largely unknown; however, they have been detected in myeloma. "
RLID00017939	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017940	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00017941	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00017942	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017943	594838	SNORD100	http://www.ncbi.nlm.nih.gov/gene/?term=594838	HBII-429	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017944	594839	SNORA33	http://www.ncbi.nlm.nih.gov/gene/?term=594839	ACA33	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017945	594839	SNORA33	http://www.ncbi.nlm.nih.gov/gene/?term=594839	ACA33	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017946	5949	RBP3	http://www.ncbi.nlm.nih.gov/gene/?term=5949	"D10S64, D10S65, D10S66, IRBP, RBPI, RP66 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017947	594	BCKDHB	http://www.ncbi.nlm.nih.gov/gene/?term=594	"BCKDE1B, BCKDH E1-beta, E1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017948	594	BCKDHB	http://www.ncbi.nlm.nih.gov/gene/?term=594	"BCKDE1B, BCKDH E1-beta, E1B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017949	594	BCKDHB	http://www.ncbi.nlm.nih.gov/gene/?term=594	"BCKDE1B, BCKDH E1-beta, E1B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017950	595097	SNORD16	http://www.ncbi.nlm.nih.gov/gene/?term=595097	U16	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017951	595097	SNORD16	http://www.ncbi.nlm.nih.gov/gene/?term=595097	U16	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017952	595098	SNORD18A	http://www.ncbi.nlm.nih.gov/gene/?term=595098	U18A	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00017953	5954	RCN1	http://www.ncbi.nlm.nih.gov/gene/?term=5954	"HEL-S-84, PIG20, RCAL, RCN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017954	5954	RCN1	http://www.ncbi.nlm.nih.gov/gene/?term=5954	"HEL-S-84, PIG20, RCAL, RCN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017955	5955	RCN2	http://www.ncbi.nlm.nih.gov/gene/?term=5955	"E6BP, ERC-55, ERC55, TCBP49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017956	5955	RCN2	http://www.ncbi.nlm.nih.gov/gene/?term=5955	"E6BP, ERC-55, ERC55, TCBP49 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017957	5959	RDH5	http://www.ncbi.nlm.nih.gov/gene/?term=5959	"9cRDH, HSD17B9, RDH1, SDR9C5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017958	595	CCND1	http://www.ncbi.nlm.nih.gov/gene/?term=595	"BCL1, D11S287E, PRAD1, U21B31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017959	595	CCND1	http://www.ncbi.nlm.nih.gov/gene/?term=595	"BCL1, D11S287E, PRAD1, U21B31 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017960	5962	RDX	http://www.ncbi.nlm.nih.gov/gene/?term=5962	DFNB24	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017961	5962	RDX	http://www.ncbi.nlm.nih.gov/gene/?term=5962	DFNB24	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017962	5965	RECQL	http://www.ncbi.nlm.nih.gov/gene/?term=5965	"RECQL1, RecQ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017963	5966	REL	http://www.ncbi.nlm.nih.gov/gene/?term=5966	C-Rel	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017964	5967	REG1A	http://www.ncbi.nlm.nih.gov/gene/?term=5967	"ICRF, P19, PSP, PSPS, PSPS1, PTP, REG "	mRNA	Homo sapiens	26000482	Ribosome	HeLa cell	qRT-PCR	"To further investigate whether Reg1 localizes to translationally active polysomes, HeLa cell lysates were subjected to polysome fractionations ( Figure 3 E). Immunoblot analysis revealed that endogenous Reg1 localized in polysomal fractions in addition to non-polysome (non-ribosome and 40S-80S) fractions ( Fig- ure 3 E), though Roquin-1 and -2 were localized in the non-poly- some fractions. "
RLID00017965	596	BCL2	http://www.ncbi.nlm.nih.gov/gene/?term=596	"Bcl-2, PPP1R50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017966	5970	RELA	http://www.ncbi.nlm.nih.gov/gene/?term=5970	"NFKB3, p65 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017967	5970	RELA	http://www.ncbi.nlm.nih.gov/gene/?term=5970	"NFKB3, p65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017968	5971	RELB	http://www.ncbi.nlm.nih.gov/gene/?term=5971	"I-REL, IREL, REL-B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017969	5972	REN	http://www.ncbi.nlm.nih.gov/gene/?term=5972	HNFJ2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017970	5976	UPF1	http://www.ncbi.nlm.nih.gov/gene/?term=5976	"HUPF1, NORF1, RENT1, pNORF1, smg-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017971	5976	UPF1	http://www.ncbi.nlm.nih.gov/gene/?term=5976	"HUPF1, NORF1, RENT1, pNORF1, smg-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017972	5976	UPF1	http://www.ncbi.nlm.nih.gov/gene/?term=5976	"HUPF1, NORF1, RENT1, pNORF1, smg-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017973	5977	DPF2	http://www.ncbi.nlm.nih.gov/gene/?term=5977	"REQ, UBID4, ubi-d4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017974	5977	DPF2	http://www.ncbi.nlm.nih.gov/gene/?term=5977	"REQ, UBID4, ubi-d4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017975	5977	DPF2	http://www.ncbi.nlm.nih.gov/gene/?term=5977	"REQ, UBID4, ubi-d4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017976	5978	REST	http://www.ncbi.nlm.nih.gov/gene/?term=5978	"NRSF, WT6, XBR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017977	5978	REST	http://www.ncbi.nlm.nih.gov/gene/?term=5978	"NRSF, WT6, XBR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017978	5978	REST	http://www.ncbi.nlm.nih.gov/gene/?term=5978	"NRSF, WT6, XBR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017979	5979	RET	http://www.ncbi.nlm.nih.gov/gene/?term=5979	"CDHF12, CDHR16, HSCR1, MEN2A, MEN2B, MTC1, PTC, RET-ELE1, RET51 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017980	5980	REV3L	http://www.ncbi.nlm.nih.gov/gene/?term=5980	"POLZ, REV3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017981	5981	RFC1	http://www.ncbi.nlm.nih.gov/gene/?term=5981	"A1, MHCBFB, PO-GA, RECC1, RFC40, RFC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017982	5981	RFC1	http://www.ncbi.nlm.nih.gov/gene/?term=5981	"A1, MHCBFB, PO-GA, RECC1, RFC, RFC140 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017983	5982	RFC2	http://www.ncbi.nlm.nih.gov/gene/?term=5982	RFC40	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017984	5983	RFC3	http://www.ncbi.nlm.nih.gov/gene/?term=5983	RFC38	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017985	5983	RFC3	http://www.ncbi.nlm.nih.gov/gene/?term=5983	RFC38	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017986	5984	RFC4	http://www.ncbi.nlm.nih.gov/gene/?term=5984	"A1, RFC37 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017987	5984	RFC4	http://www.ncbi.nlm.nih.gov/gene/?term=5984	"A1, RFC37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017988	5985	RFC5	http://www.ncbi.nlm.nih.gov/gene/?term=5985	RFC36	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017989	5986	RFNG	http://www.ncbi.nlm.nih.gov/gene/?term=5986		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017990	5987	TRIM27	http://www.ncbi.nlm.nih.gov/gene/?term=5987	"RFP, RNF76 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017991	5987	TRIM27	http://www.ncbi.nlm.nih.gov/gene/?term=5987	"RFP, RNF76 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00017992	5987	TRIM27	http://www.ncbi.nlm.nih.gov/gene/?term=5987	"RFP, RNF76 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017993	5989	RFX1	http://www.ncbi.nlm.nih.gov/gene/?term=5989	"EFC, RFX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017994	5990	RFX2	http://www.ncbi.nlm.nih.gov/gene/?term=5990		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017995	5993	RFX5	http://www.ncbi.nlm.nih.gov/gene/?term=5993		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017996	5994	RFXAP	http://www.ncbi.nlm.nih.gov/gene/?term=5994		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00017997	5997	RGS2	http://www.ncbi.nlm.nih.gov/gene/?term=5997	G0S8	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00017998	5998	RGS3	http://www.ncbi.nlm.nih.gov/gene/?term=5998	"C2PA, RGP3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00017999	5998	RGS3	http://www.ncbi.nlm.nih.gov/gene/?term=5998	"C2PA, RGP3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018000	5998	RGS3	http://www.ncbi.nlm.nih.gov/gene/?term=5998	"C2PA, RGP3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018001	599	BCL2L2	http://www.ncbi.nlm.nih.gov/gene/?term=599	"BCL-W, BCL2-L-2, BCLW, PPP1R51 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018002	59	ACTA2	http://www.ncbi.nlm.nih.gov/gene/?term=59	"AAT6, ACTSA, MYMY5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018003	59	ACTA2	http://www.ncbi.nlm.nih.gov/gene/?term=59	"AAT6, ACTSA, MYMY5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018004	6001	RGS10	http://www.ncbi.nlm.nih.gov/gene/?term=6001		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018005	6001	RGS10	http://www.ncbi.nlm.nih.gov/gene/?term=6001		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018006	6002	RGS12	http://www.ncbi.nlm.nih.gov/gene/?term=6002		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018007	6002	RGS12	http://www.ncbi.nlm.nih.gov/gene/?term=6002		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018008	6002	RGS12	http://www.ncbi.nlm.nih.gov/gene/?term=6002		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018009	6004	RGS16	http://www.ncbi.nlm.nih.gov/gene/?term=6004	"A28-RGS14, A28-RGS14P, RGS-R "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018010	6005	RHAG	http://www.ncbi.nlm.nih.gov/gene/?term=6005	"CD241, OHS, RH2, RH50A, Rh50, Rh50GP, SLC42A1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018011	6006	RHCE	http://www.ncbi.nlm.nih.gov/gene/?term=6006	"CD240CE, RH, RH30A, RHC, RHE, RHIXB, RHPI, Rh4, RhIVb(J), RhVI, RhVIII "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018012	6007	RHD	http://www.ncbi.nlm.nih.gov/gene/?term=6007	"CD240D, DIIIc, RH, RH30, RHCEDVA(TT), RHDel, RHPII, RHXIII, Rh4, RhDCw, RhII, RhK562-II, RhPI, RHD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018013	6007	RHD	http://www.ncbi.nlm.nih.gov/gene/?term=6007	"CD240D, DIIIc, RH, RH30, RHCEDVA(TT), RHDel, RHPII, RHXIII, Rh4, RhDCw, RhII, RhK562-II, RhPI, RHD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018014	6007	RHD	http://www.ncbi.nlm.nih.gov/gene/?term=6007	"CD240D, DIIIc, RH, RH30, RHCED, RHDVA(TT), RHDel, RHPII, RHXIII, Rh4, RhDCw, RhII, RhK562-II, RhPI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018015	6009	RHEB	http://www.ncbi.nlm.nih.gov/gene/?term=6009	RHEB2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018016	6009	RHEB	http://www.ncbi.nlm.nih.gov/gene/?term=6009	RHEB2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018017	6010	RHO	http://www.ncbi.nlm.nih.gov/gene/?term=6010	"CSNBAD1, OPN2, RP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018018	6015	RING1	http://www.ncbi.nlm.nih.gov/gene/?term=6015	"RING1A, RNF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018019	6015	RING1	http://www.ncbi.nlm.nih.gov/gene/?term=6015	"RING1A, RNF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018020	6016	RIT1	http://www.ncbi.nlm.nih.gov/gene/?term=6016	"NS8, RIBB, RIT, ROC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018021	6018	RLF	http://www.ncbi.nlm.nih.gov/gene/?term=6018	"ZN-15L, ZNF292L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018022	6018	RLF	http://www.ncbi.nlm.nih.gov/gene/?term=6018	"ZN-15L, ZNF292L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018023	6023	RMRP	http://www.ncbi.nlm.nih.gov/gene/?term=6023	"CHH, NME1R, RRP2, RMRP "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018024	6023	RMRP	http://www.ncbi.nlm.nih.gov/gene/?term=6023	"CHH, NME1R, RRP2, RMRP "	lncRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00018025	6029	RN7SL1	http://www.ncbi.nlm.nih.gov/gene/?term=6029	"7L1a, 7SL, RN7SL, RNSRP1 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018026	6029	RN7SL1	http://www.ncbi.nlm.nih.gov/gene/?term=6029	"7L1a, 7SL, RN7SL, RNSRP1 "	lncRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00018027	60312	AFAP1	http://www.ncbi.nlm.nih.gov/gene/?term=60312	"AFAP, AFAP-11010, AFAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018028	60313	GPBP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=60313	SP192	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018029	60343	FAM3A	http://www.ncbi.nlm.nih.gov/gene/?term=60343	"2.19, DLD, DXS560S, XAP-7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018030	60343	FAM3A	http://www.ncbi.nlm.nih.gov/gene/?term=60343	"2.19, DLD, DXS560S, XAP-7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018031	60344	Fign	http://www.ncbi.nlm.nih.gov/gene/?term=60344	"fi, fidget "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018032	6035	RNASE1	http://www.ncbi.nlm.nih.gov/gene/?term=6035	"RAC1, RIB1, RNS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018033	60364	Donson	http://www.ncbi.nlm.nih.gov/gene/?term=60364	"1110025J21Rik, AI845729, ORF60 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018034	60370	AVPI1	http://www.ncbi.nlm.nih.gov/gene/?term=60370	"PP5395, VIP32, VIT32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018035	60386	SLC25A19	http://www.ncbi.nlm.nih.gov/gene/?term=60386	"DNC, MCPHA, MUP1, THMD3, THMD4, TPC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018036	6039	RNASE6	http://www.ncbi.nlm.nih.gov/gene/?term=6039	"RAD1, RNS6, RNasek6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018037	60412	EXOC4	http://www.ncbi.nlm.nih.gov/gene/?term=60412	"SEC8, SEC8L1, Sec8p "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018038	60425	Doc2g	http://www.ncbi.nlm.nih.gov/gene/?term=60425	D830013O18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018039	60436	TGIF2	http://www.ncbi.nlm.nih.gov/gene/?term=60436		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018040	60436	TGIF2	http://www.ncbi.nlm.nih.gov/gene/?term=60436		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018041	6043	SNORA63	http://www.ncbi.nlm.nih.gov/gene/?term=6043	"E3, E3-2, RNE3, RNU107A, elF-4AII, SNORA63 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018042	6043	SNORA63	http://www.ncbi.nlm.nih.gov/gene/?term=6043	"E3, E3-2, RNE3, RNU107A, elF-4AII, SNORA63 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018043	60440	Iigp1	http://www.ncbi.nlm.nih.gov/gene/?term=60440	"2900074L10Rik, AI046432, AW111922, Ifgga1, Iigp, Irga6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018044	6045	RNF2	http://www.ncbi.nlm.nih.gov/gene/?term=6045	"BAP-1, BAP1, DING, HIPI3, RING1B, RING2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018045	6046	BRD2	http://www.ncbi.nlm.nih.gov/gene/?term=6046	"D6S113E, FSH, FSRG1, NAT, O27.1.1, RING3, RNF3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018046	6046	BRD2	http://www.ncbi.nlm.nih.gov/gene/?term=6046	"D6S113E, FSH, FSRG1, NAT, O27.1.1, RING3, RNF3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018047	6046	BRD2	http://www.ncbi.nlm.nih.gov/gene/?term=6046	"D6S113E, FSH, FSRG1, NAT, O27.1.1, RING3, RNF3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018048	6046	BRD2	http://www.ncbi.nlm.nih.gov/gene/?term=6046	"D6S113E, FSH, FSRG1, NAT, O27.1.1, RING3, RNF3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018049	6046	BRD2	http://www.ncbi.nlm.nih.gov/gene/?term=6046	"D6S113E, FSH, FSRG1, NAT, O27.1.1, RING3, RNF3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018050	6047	RNF4	http://www.ncbi.nlm.nih.gov/gene/?term=6047	"RES4-26, SLX5, SNURF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018051	6047	RNF4	http://www.ncbi.nlm.nih.gov/gene/?term=6047	"RES4-26, SLX5, SNURF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018052	6047	RNF4	http://www.ncbi.nlm.nih.gov/gene/?term=6047	"RES4-26, SLX5, SNURF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018053	60481	ELOVL5	http://www.ncbi.nlm.nih.gov/gene/?term=60481	"HELO1, SCA38, dJ483K16.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018054	60481	ELOVL5	http://www.ncbi.nlm.nih.gov/gene/?term=60481	"HELO1, SCA38, dJ483K16.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018055	60481	ELOVL5	http://www.ncbi.nlm.nih.gov/gene/?term=60481	"HELO1, SCA38, dJ483K16.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018056	60485	SAV1	http://www.ncbi.nlm.nih.gov/gene/?term=60485	"SAV, WW45, WWP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018057	60487	TRMT11	http://www.ncbi.nlm.nih.gov/gene/?term=60487	"C6orf75, MDS024, TRM11, TRMT11-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018058	60488	MRPS35	http://www.ncbi.nlm.nih.gov/gene/?term=60488	"HDCMD11P, MDS023, MRP-S28, MRPS28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018059	60488	MRPS35	http://www.ncbi.nlm.nih.gov/gene/?term=60488	"HDCMD11P, MDS023, MRP-S28, MRPS28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018060	60489	APOBEC3G	http://www.ncbi.nlm.nih.gov/gene/?term=60489	"A3G, ARCD, ARP-9, ARP9, CEM-15, CEM15, MDS019, bK150C2.7, dJ494G10.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018061	6048	RNF5	http://www.ncbi.nlm.nih.gov/gene/?term=6048	"RING5, RMA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018062	60490	PPCDC	http://www.ncbi.nlm.nih.gov/gene/?term=60490	"MDS018, PPC-DC, coaC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018063	60491	NIF3L1	http://www.ncbi.nlm.nih.gov/gene/?term=60491	"ALS2CR1, CALS-7, MDS015 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018064	60492	CCDC90B	http://www.ncbi.nlm.nih.gov/gene/?term=60492	"MDS011, MDS025 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018065	60496	AASDHPPT	http://www.ncbi.nlm.nih.gov/gene/?term=60496	"AASD-PPT, ACPS, CGI-80, LYS2, LYS5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018066	6049	RNF6	http://www.ncbi.nlm.nih.gov/gene/?term=6049		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018067	604	BCL6	http://www.ncbi.nlm.nih.gov/gene/?term=604	"BCL5, BCL6A, LAZ3, ZBTB27, ZNF51 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018068	60509	AGBL5	http://www.ncbi.nlm.nih.gov/gene/?term=60509	CCP5	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018069	6050	RNH1	http://www.ncbi.nlm.nih.gov/gene/?term=6050	"RAI, RNH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018070	6050	RNH1	http://www.ncbi.nlm.nih.gov/gene/?term=6050	"RAI, RNH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018071	6051	RNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=6051	AP-B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018072	6051	RNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=6051	AP-B	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018073	6051	RNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=6051	AP-B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018074	60526	LDAH	http://www.ncbi.nlm.nih.gov/gene/?term=60526	"C2orf43, hLDAH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018075	60526	LDAH	http://www.ncbi.nlm.nih.gov/gene/?term=60526	"C2orf43, hLDAH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018076	60528	ELAC2	http://www.ncbi.nlm.nih.gov/gene/?term=60528	"COXPD17, ELC2, HPC2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018077	60532	Wtap	http://www.ncbi.nlm.nih.gov/gene/?term=60532	"2810408K05Rik, 9430038B09Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018078	60532	Wtap	http://www.ncbi.nlm.nih.gov/gene/?term=60532	"2810408K05Rik, 9430038B09Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018079	60532	Wtap	http://www.ncbi.nlm.nih.gov/gene/?term=60532	"2810408K05Rik, 9430038B09Rik "	mRNA	Mus musculus	26190105	Nucleus	Embryotem cell	Microscopy	"Figure 6: 3DSIM Showing that Xist RNA, Rbm15, Wtap, and Spen Co-localize within Perichromatin Spaces. Data are collected from Figure 6. "
RLID00018080	60558	GUF1	http://www.ncbi.nlm.nih.gov/gene/?term=60558	EF-4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018081	60559	SPCS3	http://www.ncbi.nlm.nih.gov/gene/?term=60559	"PRO3567, SPC22/23, SPC3, YLR066W "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018082	60559	SPCS3	http://www.ncbi.nlm.nih.gov/gene/?term=60559	"PRO3567, SPC22/23, SPC3, YLR066W "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018083	60560	NAA35	http://www.ncbi.nlm.nih.gov/gene/?term=60560	"EGAP, MAK10, MAK10P, bA379P1.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018084	60592	SCOC	http://www.ncbi.nlm.nih.gov/gene/?term=60592	"HRIHFB2072O, UNC-69, SCOC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018085	60597	Mapk8ip2	http://www.ncbi.nlm.nih.gov/gene/?term=60597	"3230402N03Rik, AI847694, AW049958, IB2, Jip2, R75148 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018086	60599	Trp53inp1	http://www.ncbi.nlm.nih.gov/gene/?term=60599	"2700057G22Rik, SIP, SIP18, SIP27, Stinp, Teap "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018087	6059	ABCE1	http://www.ncbi.nlm.nih.gov/gene/?term=6059	"ABC38, OABP, RLI, RNASEL1, RNASELI, RNS4I "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018088	6059	ABCE1	http://www.ncbi.nlm.nih.gov/gene/?term=6059	"ABC38, OABP, RLI, RNASEL1, RNASELI, RNS4I "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018089	6059	ABCE1	http://www.ncbi.nlm.nih.gov/gene/?term=6059	"ABC38, OABP, RLI, RNASEL1, RNASELI, RNS4I "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018090	6060	RNU1-4	http://www.ncbi.nlm.nih.gov/gene/?term=6060	"HSD2, HSD5, HSD6, HSD7, RNU1, RNU1D2, RNU1E2, RNU1F1, RNU1G1, RNU1G2, U1B2, U1D2, U1E2, U1F "	snRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018091	6060	RNU1-4	http://www.ncbi.nlm.nih.gov/gene/?term=6060	"HSD2, HSD5, HSD6, HSD7, RNU1, RNU1D2, RNU1E2, RNU1F1, RNU1G1, RNU1G2, U1B2, U1D2, U1E2, U1F "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018092	60625	DHX35	http://www.ncbi.nlm.nih.gov/gene/?term=60625	"C20orf15, DDX35, KAIA0875 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018093	60626	RIC8A	http://www.ncbi.nlm.nih.gov/gene/?term=60626	RIC8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018094	606495	CYB5RL	http://www.ncbi.nlm.nih.gov/gene/?term=606495		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018095	606496	Gsk3a	http://www.ncbi.nlm.nih.gov/gene/?term=606496	2700086H06Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018096	606497	Otx2os1	http://www.ncbi.nlm.nih.gov/gene/?term=606497		lncRNA	Mus musculus	15703187	Nucleus	Embryonic tissue	In situ hybridization|RT-PCR	"We detected the expression in adult retina (postnatal day 30, P30) of Six3OS, Six6OS, Otx2OS, CrxOS and RaxOS (Fig. 3 and data not shown). In general, these transcripts were all expressed at higher levels in the inner nuclear layer (INL) and in the ganglion cell layer (GCL).  "
RLID00018097	606497	Otx2os1	http://www.ncbi.nlm.nih.gov/gene/?term=606497		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018098	606500	SNORD68	http://www.ncbi.nlm.nih.gov/gene/?term=606500	HBII-202	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018099	606500	SNORD68	http://www.ncbi.nlm.nih.gov/gene/?term=606500	HBII-202	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018100	606500	SNORD68	http://www.ncbi.nlm.nih.gov/gene/?term=606500	HBII-202	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018101	60658	nos1	http://www.ncbi.nlm.nih.gov/gene/?term=60658	"nNOS, nos "	mRNA	Danio rerio	16457796	Germ plasm	Embryo	Fluorescence in situ hybridization	"Fig. 1. Endogenous patterns of RNA localization of dnd, nos1, vas, and dazl RNAs during the first cell cycle. Animal views of embryos fixed at progressively older stages of development (A-D: 15 min p.f.; E-H: 30 min. p.f.; I-L: 45 min p.f.) and labeled using FISH to detect germ plasm RNAs (dnd (A, E, I); nos1 (B, F, J); vas(C,G, K); dazl (D, H, L). (A-D) Immediately after fertilization, dnd, nos1, and vas RNA aggregates can be observed as a band at the animal pole, while dazl RNA aggregates are not initially present in the animal pole. (E-H) During the initiation of furrow formation, RNA aggregates fordnd, nos1, and vas begin to be recruited as a rod at the forming furrow (arrows in E-G). At this stage, dazl RNA is not yet detectable at the furrows (H). (I-L) As the furrow matures, there is an increase in the amount of dnd, nos1, and vasRNAs recruited at the furrow, and dazlRNA becomes detectable at the furrow (arrows in I-L). Scale bar in panel (L) represents 100 μmThus, although all four RNAs are recruited to the forming furrow, RNAs for dnd, nos1, and vas are already present in the animal pole in the freshly laid egg, while dazlRNA arrives to the animal pole from the vegetal region at a later stage. Based on their different times of appearance at the animal region, we refer to the dnd, nos1, and vas RNAs as the early animal germ plasm RNAs, while dazl is also referred to as a vegetally localized germ plasm RNA. "
RLID00018102	6066	RNU2-1	http://www.ncbi.nlm.nih.gov/gene/?term=6066	"RNU2, U2 "	snRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00018103	6066	RNU2-1	http://www.ncbi.nlm.nih.gov/gene/?term=6066	"RNU2, U2 "	snRNA	Homo sapiens	1530887	Nucleus	HeLa cell	In situ hybridization	"The localization of U1 and U2 small nuclear RNAs (snRNAs) has been examined by in situ hybridization using 2'-O-alkyl oligonucleotide probes. We have found that these snRNAs, which are essential for pre-mRNA splicing, localize in a speckled distribution, in addition to being present in three of four foci, in HeLa cell nuclei. However, in cells of defined passage, such as Detroit 551 and WI-38 fibroblasts, these snRNAs are concentrated in nuclear speckles, and foci are not observed. "
RLID00018104	6066	RNU2-1	http://www.ncbi.nlm.nih.gov/gene/?term=6066	"RNU2, U2 "	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018105	6066	RNU2-1	http://www.ncbi.nlm.nih.gov/gene/?term=6066	"RNU2, U2 "	snRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018106	60673	ATG101	http://www.ncbi.nlm.nih.gov/gene/?term=60673	C12orf44	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018107	60673	ATG101	http://www.ncbi.nlm.nih.gov/gene/?term=60673	C12orf44	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018108	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	20124551	Nucleus	HeLa cell 	Fluorescence in situ hybridization	"We examined the subcellular localization of Gas5 in HeLa cells with RNA fluorescent in situ hybridization. Gas5 was localized both in the cytoplasm and the nucleus, but its presence was more prominent in the former compartment in agreement with a previous report (Fig. 3A, top panels).  "
RLID00018109	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018110	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	20124551	Cytoplasm	HeLa cell 	Fluorescence in situ hybridization	"We examined the subcellular localization of Gas5 in HeLa cells with RNA fluorescent in situ hybridization. Gas5 was localized both in the cytoplasm and the nucleus, but its presence was more prominent in the former compartment in agreement with a previous report (Fig. 3A, top panels).  "
RLID00018111	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	26446789	Cytoplasm	Hepatic stellate cell	qRT-PCR	"In addition, GAS5 was mainly localized in the cytoplasm. "
RLID00018112	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	22955988	Nucleus	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00018113	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	mRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00018114	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	mRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00018115	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00018116	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2 "	lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00018117	60676	PAPPA2	http://www.ncbi.nlm.nih.gov/gene/?term=60676	"PAPP-A2, PAPP-E, PAPPE, PLAC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018118	60678	EEFSEC	http://www.ncbi.nlm.nih.gov/gene/?term=60678	"EFSEC, SELB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018119	60681	FKBP10	http://www.ncbi.nlm.nih.gov/gene/?term=60681	"BRKS1, FKBP65, OI11, OI6, PPIASE, hFKBP65 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018120	60681	FKBP10	http://www.ncbi.nlm.nih.gov/gene/?term=60681	"BRKS1, FKBP65, OI11, OI6, PPIASE, hFKBP65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018121	60684	TRAPPC11	http://www.ncbi.nlm.nih.gov/gene/?term=60684	"C4orf41, FOIGR, GRY, LGMD2S "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018122	60685	ZFAND3	http://www.ncbi.nlm.nih.gov/gene/?term=60685	TEX27	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018123	6069	RNU4-7P	http://www.ncbi.nlm.nih.gov/gene/?term=6069	"RNU4P1, U4, U4/7 "	snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018124	607000	MED31	http://www.ncbi.nlm.nih.gov/gene/?term=607000		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018125	607044	RNF41	http://www.ncbi.nlm.nih.gov/gene/?term=607044		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018126	6071	RNU6V	http://www.ncbi.nlm.nih.gov/gene/?term=6071	"87U6, LH87 "	snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018127	607260	PFDN5	http://www.ncbi.nlm.nih.gov/gene/?term=607260		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018128	607367	RFXAP	http://www.ncbi.nlm.nih.gov/gene/?term=607367		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018129	607383	RASSF4	http://www.ncbi.nlm.nih.gov/gene/?term=607383		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018130	607430	PPIL3	http://www.ncbi.nlm.nih.gov/gene/?term=607430		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018131	607633	RPL21	http://www.ncbi.nlm.nih.gov/gene/?term=607633		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018132	607652	WDR37	http://www.ncbi.nlm.nih.gov/gene/?term=607652		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018133	607878	PIN4	http://www.ncbi.nlm.nih.gov/gene/?term=607878		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018134	6079	SNORD15A	http://www.ncbi.nlm.nih.gov/gene/?term=6079	"RNU15A, SNORNA, U15A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018135	6079	SNORD15A	http://www.ncbi.nlm.nih.gov/gene/?term=6079	"RNU15A, SNORNA, U15A "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00018136	6079	SNORD15A	http://www.ncbi.nlm.nih.gov/gene/?term=6079	"RNU15A, SNORNA, U15A "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018137	6079	SNORD15A	http://www.ncbi.nlm.nih.gov/gene/?term=6079	"RNU15A, SNORNA, U15A "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018138	6080	SNORA73A	http://www.ncbi.nlm.nih.gov/gene/?term=6080	"E1, E1-7, E1b, RNE1, RNU17A, U17A "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018139	6080	SNORA73A	http://www.ncbi.nlm.nih.gov/gene/?term=6080	"E1, E1-7, E1b, RNE1, RNU17A, U17A "	snoRNA	Homo sapiens	9671460	Nucleus	HeLa cell	Northern blot	"We investigated the cellular localization of the U17HG RNA. Cell fractionation experiments indicated that U17HG RNA is enriched in the cytoplasm (Fig.5A), similar to UHG RNA, another noncoding snoRNA host having no protein-coding potential (Fig.5B). As expected, U17 snoRNA, used as a control, was found mainly in the nuclear fraction (Fig.5C). "
RLID00018140	6080	SNORA73A	http://www.ncbi.nlm.nih.gov/gene/?term=6080	"E1, E1-7, E1b, RNE1, RNU17A, U17A "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018141	6080	SNORA73A	http://www.ncbi.nlm.nih.gov/gene/?term=6080	"E1, E1-7, E1b, RNE1, RNU17A, U17A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018142	6082	SNORD20	http://www.ncbi.nlm.nih.gov/gene/?term=6082	"RNU20, U20 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018143	6082	SNORD20	http://www.ncbi.nlm.nih.gov/gene/?term=6082	"RNU20, U20 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018144	6082	SNORD20	http://www.ncbi.nlm.nih.gov/gene/?term=6082	"RNU20, U20 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018145	6082	SNORD20	http://www.ncbi.nlm.nih.gov/gene/?term=6082	"RNU20, U20 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018146	6083	SNORD21	http://www.ncbi.nlm.nih.gov/gene/?term=6083	"RNU21, U21 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018147	6083	SNORD21	http://www.ncbi.nlm.nih.gov/gene/?term=6083	"RNU21, U21 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00018148	6083	SNORD21	http://www.ncbi.nlm.nih.gov/gene/?term=6083	"RNU21, U21 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018149	6083	SNORD21	http://www.ncbi.nlm.nih.gov/gene/?term=6083	"RNU21, U21 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018150	608666	SNX24	http://www.ncbi.nlm.nih.gov/gene/?term=608666		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018151	608922	PPP6C	http://www.ncbi.nlm.nih.gov/gene/?term=608922		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018152	609036	DSCC1	http://www.ncbi.nlm.nih.gov/gene/?term=609036		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018153	609164	GTF2F2	http://www.ncbi.nlm.nih.gov/gene/?term=609164		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018154	6091	ROBO1	http://www.ncbi.nlm.nih.gov/gene/?term=6091	"DUTT1, SAX3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018155	6091	ROBO1	http://www.ncbi.nlm.nih.gov/gene/?term=6091	"DUTT1, SAX3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018156	6092	ROBO2	http://www.ncbi.nlm.nih.gov/gene/?term=6092	SAX3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018157	609356	MPC1	http://www.ncbi.nlm.nih.gov/gene/?term=609356	BRP44L	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018158	6093	ROCK1	http://www.ncbi.nlm.nih.gov/gene/?term=6093	"P160ROCK, ROCK-I "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018159	6093	ROCK1	http://www.ncbi.nlm.nih.gov/gene/?term=6093	"P160ROCK, ROCK-I "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018160	6094	ROM1	http://www.ncbi.nlm.nih.gov/gene/?term=6094	"ROM, ROSP1, RP7, TSPAN23 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018161	609530	RPL31	http://www.ncbi.nlm.nih.gov/gene/?term=609530		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018162	609743	WWTR1	http://www.ncbi.nlm.nih.gov/gene/?term=609743		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018163	609840	AP1M1	http://www.ncbi.nlm.nih.gov/gene/?term=609840		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018164	6098	ROS1	http://www.ncbi.nlm.nih.gov/gene/?term=6098	"MCF3, ROS, c-ros-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018165	609906	MRPS16	http://www.ncbi.nlm.nih.gov/gene/?term=609906		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018166	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018167	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	22895844	Exosome	Colon|Liver|Lung	qRT-PCR	"When the RNA species within exosomes derived from the three CRC cell lines were examined, the mRNAs of housekeeping genes such as ACTB and GAPDH, the microRNAs such as miR-21, miR-192 and miR-221, and the natural antisense RNAs of LRRC24, MDM2 and CDKN1A genes, were detected. "
RLID00018168	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	12923260	Cell leading edge	Jurkat cell	In situ hybridization	"As well, beta-actin mRNA is known to undergo cytoskeleton-dependent transport to the leading edge of cells and, as demonstrated by in situ hybridization studies, displays both a leading edge and a distinct, perinuclear localization, similar to that depicted in Figures 6 and 7. "
RLID00018169	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	15081402	Nucleus	HeLa cell	In situ hybridization	"Distributions of mature mRNA and pre-mRNA for b-actin transcripts were determined by RT-PCR using total RNA from each subnuclear fraction. PCR products in panels 1-3 indicate a band derived from mature mRNA of β-actin, and those in lanes 4-6 are from pre-mRNA. "
RLID00018170	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	18535985	Cell leading edge	SW480 CRC cell	Fluorescence in situ hybridization|qRT-PCR	"In culture, VICKZ proteins rapidly accumulate in processes at the leading edge of PMA-stimulated SW480 CRC cells, where they co-localize with beta-actin mRNA.  "
RLID00018171	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	20453113	Cytosol	NCI/ADR-RES cell	qRT-PCR	"The relative partitioning of both cytosolic (ACTB, H3.3) and ER-bound (MDR1, CANX) transcripts between both fractions was marked, despite the small carryover of cytosol in the ER fraction (Fig. 2B). Polysome profile analyses from the isolated fractions indicated that these transcripts migrated in polyribosome-containing fractions (Fig. 2C). Notably, the distribution of ER-bound transcripts between the ER and cytosol did not change on arsenite treatment of NCI/ADR-RES cells (Fig. 2D). Data are collected from Figure 2. "
RLID00018172	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	23452202	Lamellipodium	Lung fibroblast	Fluorescence in situ hybridization	"Rac1, ArpC2 and β-actin mRNAs co-localize with actively translating ribosomes on lamellipodia. "
RLID00018173	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	23452202	Cell leading edge	Lung fibroblast	qRT-PCR	"In the present study with MRC5 cells, we show that β-actin mRNA is similarly localized to active foci on the leading edge of the cell and is furthermore recruited to polysomes.  "
RLID00018174	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	26195734	Mitochondrion	HeLa cell	Sticky-Flare Synthesis	"In this case, β-actin Sticky-flares exhibited a starkly different intracellular distribution, showing a high degree of colocalization with mitochondria (Fig. 5). This colocalization of β-actin mRNA and mitochondria in HeLa cells has not been demonstrated before, and the reason behind such highly spatially restricted expression is not known. "
RLID00018175	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	26239904	Ribosome	Kidney	RT-PCR	"Although the underlying mechanisms were not known, this increased association might be attributed to the diffused localization of the 32-447aa mutant, thereby allowing the mutant to associate not only with ATF4 mRNAs on the ER but also with the mRNAs in cytoplasm. (D-F) The abundance of ATF4 or β-actin mRNA in the subpolysome or polysome pool. "
RLID00018176	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018177	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018178	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018179	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	22193719	Cytoplasm	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00018180	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	22679391	Cytoplasm	U2OS cell	RT-PCR	"Figure 3A: The levels of Sec61α and βactin transcripts isolated from unbound (i.e., non-ER) cytoplasmic and ER fractions from either cycloheximide treated (“Control� or puromycin treated EDTA extracted (“Puromycin+EDTA� U2OS cells were assessed by quantitative RT-PCR analysis. "
RLID00018181	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	25753659	Cytosol	HT1080 cell	Fluorescence in situ hybridization|qRT-PCR	"Figure S2: Expression of mRNA candidates in ribosomes-containing sub-compartments. A: Representative Western blot analyses of markers in the sub-compartments. S10 supernatants as used in Figure 1 for polysomal gradient analysis represent a cytoplasmic fraction as demonstrated by cytosolic markers (GAPDH, beta-Actin). Both, cytoplasmic and sediment fractions contain polysomes as shown by ribosomal markers (28S and 18S rRNA, ribosomal protein RPL7A). Sediments, however, contain ER as indicated by the presence of the ER marker proteins (PDI and aromatase). "
RLID00018182	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	25753659	Ribosome	HT1080 cell	qRT-PCR	Figure S1: Polysomal gradient analysis. HT1080 cells were incubated under control (21% oxygen) or hypoxic (1% oxygen) conditions for up to 36 h as described in Figure 1. Shown are representative original RT-PCR data (30 cycles for beta-Actin and the external standard [extSt]; 35 cycles for the other genes) from pooled samples to visualize mRNA distribution following fractionation of sucrose gradients at control conditions (C) and 36 h of hypoxia (Hy). The external standard (a synthetic in vitro transcript) was diluted to appropriate concentration for qPCR and added directly after gradient fractionation and prior to RNA isolation as a technical control. The external standard served for fraction dependent normalization.
RLID00018183	60	ACTB	http://www.ncbi.nlm.nih.gov/gene/?term=60	"BRWS1, PS1TP5BP1 "	mRNA	Homo sapiens	23452202	Ribosome	Lung fibroblast	qRT-PCR	"In the present study with MRC5 cells, we show that β-actin mRNA is similarly localized to active foci on the leading edge of the cell and is furthermore recruited to polysomes.  "
RLID00018184	6100	RP9	http://www.ncbi.nlm.nih.gov/gene/?term=6100	"PAP-1, PAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018185	610267	ALDH16A1	http://www.ncbi.nlm.nih.gov/gene/?term=610267		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018186	6102	RP2	http://www.ncbi.nlm.nih.gov/gene/?term=6102	"DELXp11.3, NM23-H10, NME10, TBCCD2, XRP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018187	6102	RP2	http://www.ncbi.nlm.nih.gov/gene/?term=6102	"DELXp11.3, NM23-H10, NME10, TBCCD2, XRP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018188	610533	DPH3	http://www.ncbi.nlm.nih.gov/gene/?term=610533		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018189	610538	DEK	http://www.ncbi.nlm.nih.gov/gene/?term=610538		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018190	610596	RPS29	http://www.ncbi.nlm.nih.gov/gene/?term=610596		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018191	610883	ACOT13	http://www.ncbi.nlm.nih.gov/gene/?term=610883	THEM2	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018192	610925	PKIG	http://www.ncbi.nlm.nih.gov/gene/?term=610925		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018193	610942	CYB5B	http://www.ncbi.nlm.nih.gov/gene/?term=610942		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018194	611248	ARL2BP	http://www.ncbi.nlm.nih.gov/gene/?term=611248		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018195	611783	EFCAB2	http://www.ncbi.nlm.nih.gov/gene/?term=611783		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018196	6118	RPA2	http://www.ncbi.nlm.nih.gov/gene/?term=6118	"REPA2, RP-A p32, RP-A p34, RPA32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018197	6118	RPA2	http://www.ncbi.nlm.nih.gov/gene/?term=6118	"REPA2, RP-A p32, RP-A p34, RPA32 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018198	611923	SRP9	http://www.ncbi.nlm.nih.gov/gene/?term=611923		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018199	6119	RPA3	http://www.ncbi.nlm.nih.gov/gene/?term=6119	"REPA3, RP-A p14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018200	6119	RPA3	http://www.ncbi.nlm.nih.gov/gene/?term=6119	"REPA3, RP-A p14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018201	6119	RPA3	http://www.ncbi.nlm.nih.gov/gene/?term=6119	"REPA3, RP-A p14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018202	6120	RPE	http://www.ncbi.nlm.nih.gov/gene/?term=6120	RPE2-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018203	6120	RPE	http://www.ncbi.nlm.nih.gov/gene/?term=6120	RPE2-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018204	612309	ABLIM3	http://www.ncbi.nlm.nih.gov/gene/?term=612309		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018205	612448	RPS6KA2	http://www.ncbi.nlm.nih.gov/gene/?term=612448		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018206	6124	RPL4	http://www.ncbi.nlm.nih.gov/gene/?term=6124	L4	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018207	6125	RPL5	http://www.ncbi.nlm.nih.gov/gene/?term=6125	"DBA6, L5, MSTP030, PPP1R135 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018208	6125	RPL5	http://www.ncbi.nlm.nih.gov/gene/?term=6125	"DBA6, L5, MSTP030, PPP1R135 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018209	6125	RPL5	http://www.ncbi.nlm.nih.gov/gene/?term=6125	"DBA6, L5, MSTP030, PPP1R135 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018210	612796	ARL6	http://www.ncbi.nlm.nih.gov/gene/?term=612796		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018211	6128	RPL6	http://www.ncbi.nlm.nih.gov/gene/?term=6128	"L6, SHUJUN-2, TAXREB107, TXREB1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018212	6128	RPL6	http://www.ncbi.nlm.nih.gov/gene/?term=6128	"L6, SHUJUN-2, TAXREB107, TXREB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018213	612924	MOB1A	http://www.ncbi.nlm.nih.gov/gene/?term=612924	"MOBK1B, MOBKL1B "	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018214	612942	LOC612942	http://www.ncbi.nlm.nih.gov/gene/?term=612942	"MSANTD3, TMEFF1 "	mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018215	612965	FKBP1B	http://www.ncbi.nlm.nih.gov/gene/?term=612965		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00018216	6129	RPL7	http://www.ncbi.nlm.nih.gov/gene/?term=6129	"L7, humL7-1 "	mRNA	Homo sapiens	12399102	Cell body	Purkinje cell	In situ hybridization	In addition we performed in situ hybridization on a developmental series of human cerebellar sections and demonstrate that the L7/Pcp-2 mRNA is also localized in dendrites of humans.  
RLID00018217	6129	RPL7	http://www.ncbi.nlm.nih.gov/gene/?term=6129	"L7, humL7-1 "	mRNA	Homo sapiens	12399102	Dendrite	Purkinje cell	In situ hybridization	In addition we performed in situ hybridization on a developmental series of human cerebellar sections and demonstrate that the L7/Pcp-2 mRNA is also localized in dendrites of humans.  
RLID00018218	613037	LOC613037	http://www.ncbi.nlm.nih.gov/gene/?term=613037		lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00018219	6130	RPL7A	http://www.ncbi.nlm.nih.gov/gene/?term=6130	"L7A, SURF3, TRUP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018220	613117	4930571B16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=613117		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018221	6132	RPL8	http://www.ncbi.nlm.nih.gov/gene/?term=6132	L8	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018222	6133	RPL9	http://www.ncbi.nlm.nih.gov/gene/?term=6133	"L9, NPC-A-16 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018223	6133	RPL9	http://www.ncbi.nlm.nih.gov/gene/?term=6133	"L9, NPC-A-16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018224	6133	RPL9	http://www.ncbi.nlm.nih.gov/gene/?term=6133	"L9, NPC-A-16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018225	6134	RPL10	http://www.ncbi.nlm.nih.gov/gene/?term=6134	"AUTSX5, DXS648, DXS648E, L10, NOV, QM "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018226	6134	RPL10	http://www.ncbi.nlm.nih.gov/gene/?term=6134	"AUTSX5, DXS648, DXS648E, L10, NOV, QM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018227	6135	RPL11	http://www.ncbi.nlm.nih.gov/gene/?term=6135	"DBA7, GIG34, L11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018228	6136	RPL12	http://www.ncbi.nlm.nih.gov/gene/?term=6136	L12	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018229	6136	RPL12	http://www.ncbi.nlm.nih.gov/gene/?term=6136	L12	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018230	6137	RPL13	http://www.ncbi.nlm.nih.gov/gene/?term=6137	"BBC1, D16S444E, D16S44E, L13 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018231	6137	RPL13	http://www.ncbi.nlm.nih.gov/gene/?term=6137	"BBC1, D16S444E, D16S44E, L13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018232	6138	RPL15	http://www.ncbi.nlm.nih.gov/gene/?term=6138	"DBA12, EC45, L15, RPL10, RPLY10, RPYL10 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018233	6138	RPL15	http://www.ncbi.nlm.nih.gov/gene/?term=6138	"DBA12, EC45, L15, RPL10, RPLY10, RPYL10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018234	6139	RPL17	http://www.ncbi.nlm.nih.gov/gene/?term=6139	"L17, PD-1, RPL23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018235	6139	RPL17	http://www.ncbi.nlm.nih.gov/gene/?term=6139	"L17, PD-1, RPL23 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018236	6139	RPL17	http://www.ncbi.nlm.nih.gov/gene/?term=6139	"L17, PD-1, RPL23 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018237	613	BCR	http://www.ncbi.nlm.nih.gov/gene/?term=613	"ALL1, CML, D22S11, D22S662, PHL, BCR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018238	613	BCR	http://www.ncbi.nlm.nih.gov/gene/?term=613	"ALL, BCR1, CML, D22S11, D22S662, PHL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018239	6141	RPL18	http://www.ncbi.nlm.nih.gov/gene/?term=6141	L18	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018240	6141	RPL18	http://www.ncbi.nlm.nih.gov/gene/?term=6141	L18	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018241	6142	RPL18A	http://www.ncbi.nlm.nih.gov/gene/?term=6142	L18A	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018242	6142	RPL18A	http://www.ncbi.nlm.nih.gov/gene/?term=6142	L18A	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018243	6144	RPL21	http://www.ncbi.nlm.nih.gov/gene/?term=6144	"HYPT12, L21 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018244	6144	RPL21	http://www.ncbi.nlm.nih.gov/gene/?term=6144	"HYPT12, L21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018245	6146	RPL22	http://www.ncbi.nlm.nih.gov/gene/?term=6146	"EAP, HBP15, HBP15/L22, L22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018246	6147	RPL23A	http://www.ncbi.nlm.nih.gov/gene/?term=6147	"L23A, MDA20 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018247	6150	MRPL23	http://www.ncbi.nlm.nih.gov/gene/?term=6150	"L23MRP, RPL23, RPL23L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018248	6152	RPL24	http://www.ncbi.nlm.nih.gov/gene/?term=6152	"HEL-S-310, L24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018249	6154	RPL26	http://www.ncbi.nlm.nih.gov/gene/?term=6154	"DBA11, L26 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018250	6154	RPL26	http://www.ncbi.nlm.nih.gov/gene/?term=6154	"DBA11, L26 "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00018251	6155	RPL27	http://www.ncbi.nlm.nih.gov/gene/?term=6155	L27	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018252	6156	RPL30	http://www.ncbi.nlm.nih.gov/gene/?term=6156	L30	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018253	6156	RPL30	http://www.ncbi.nlm.nih.gov/gene/?term=6156	L30	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018254	6156	RPL30	http://www.ncbi.nlm.nih.gov/gene/?term=6156	L30	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018255	6157	RPL27A	http://www.ncbi.nlm.nih.gov/gene/?term=6157	L27A	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018256	6157	RPL27A	http://www.ncbi.nlm.nih.gov/gene/?term=6157	L27A	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018257	6157	RPL27A	http://www.ncbi.nlm.nih.gov/gene/?term=6157	L27A	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018258	6157	RPL27A	http://www.ncbi.nlm.nih.gov/gene/?term=6157	L27A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018259	6158	RPL28	http://www.ncbi.nlm.nih.gov/gene/?term=6158	L28	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018260	6158	RPL28	http://www.ncbi.nlm.nih.gov/gene/?term=6158	L28	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018261	6159	RPL29	http://www.ncbi.nlm.nih.gov/gene/?term=6159	"HIP, HUMRPL29, L29P10, RPL29_3_370, RPL29 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018262	6159	RPL29	http://www.ncbi.nlm.nih.gov/gene/?term=6159	"HIP, HUMRPL29, L29, RPL29P10, RPL29_3_370 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018263	6160	RPL31	http://www.ncbi.nlm.nih.gov/gene/?term=6160	L31	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018264	6160	RPL31	http://www.ncbi.nlm.nih.gov/gene/?term=6160	L31	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018265	6161	RPL32	http://www.ncbi.nlm.nih.gov/gene/?term=6161	"L32, PP9932 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018266	6165	RPL35A	http://www.ncbi.nlm.nih.gov/gene/?term=6165	"DBA5, L35A "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018267	6165	RPL35A	http://www.ncbi.nlm.nih.gov/gene/?term=6165	"DBA5, L35A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018268	6166	RPL36AL	http://www.ncbi.nlm.nih.gov/gene/?term=6166	RPL36A	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018269	6166	RPL36AL	http://www.ncbi.nlm.nih.gov/gene/?term=6166	RPL36A	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018270	6166	RPL36AL	http://www.ncbi.nlm.nih.gov/gene/?term=6166	RPL36A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018271	6167	RPL37	http://www.ncbi.nlm.nih.gov/gene/?term=6167	L37	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018272	6167	RPL37	http://www.ncbi.nlm.nih.gov/gene/?term=6167	L37	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018273	6168	RPL37A	http://www.ncbi.nlm.nih.gov/gene/?term=6168	L37A	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018274	6169	RPL38	http://www.ncbi.nlm.nih.gov/gene/?term=6169	L38	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018275	6170	RPL39	http://www.ncbi.nlm.nih.gov/gene/?term=6170	"L39P42, RPL39_23_1806, RPL39 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018276	6170	RPL39	http://www.ncbi.nlm.nih.gov/gene/?term=6170	"L39P42, RPL39_23_1806, RPL39 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018277	6170	RPL39	http://www.ncbi.nlm.nih.gov/gene/?term=6170	"L39P42, RPL39_23_1806, RPL39 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018278	6170	RPL39	http://www.ncbi.nlm.nih.gov/gene/?term=6170	"L39, RPL39P42, RPL39_23_1806 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018279	6171	RPL41	http://www.ncbi.nlm.nih.gov/gene/?term=6171	L41	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018280	6175	RPLP0	http://www.ncbi.nlm.nih.gov/gene/?term=6175	"L10E, LP0, P0, PRLP0, RPP0 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018281	6176	RPLP1	http://www.ncbi.nlm.nih.gov/gene/?term=6176	"LP1, P1, RPP1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018282	6181	RPLP2	http://www.ncbi.nlm.nih.gov/gene/?term=6181	"D11S2243E, LP2, P2, RPP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018283	6182	MRPL12	http://www.ncbi.nlm.nih.gov/gene/?term=6182	"5c5-2, L12mt, MRP-L31/34, MRPL7, MRPL7/L12, RPML12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018284	6183	MRPS12	http://www.ncbi.nlm.nih.gov/gene/?term=6183	"MPR-S12, MT-RPS12, RPMS12, RPS12, RPSM12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018285	6183	MRPS12	http://www.ncbi.nlm.nih.gov/gene/?term=6183	"MPR-S12, MT-RPS12, RPMS12, RPS12, RPSM12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018286	6184	RPN1	http://www.ncbi.nlm.nih.gov/gene/?term=6184	"OST1, RBPH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018287	6184	RPN1	http://www.ncbi.nlm.nih.gov/gene/?term=6184	"OST1, RBPH1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018288	6184	RPN1	http://www.ncbi.nlm.nih.gov/gene/?term=6184	"OST1, RBPH1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018289	6185	RPN2	http://www.ncbi.nlm.nih.gov/gene/?term=6185	"RIBIIR, RPN-II, RPNII, SWP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018290	6187	RPS2	http://www.ncbi.nlm.nih.gov/gene/?term=6187	"LLREP3, S2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018291	6187	RPS2	http://www.ncbi.nlm.nih.gov/gene/?term=6187	"LLREP3, S2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018292	6187	RPS2	http://www.ncbi.nlm.nih.gov/gene/?term=6187	"LLREP3, S2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018293	6188	RPS3	http://www.ncbi.nlm.nih.gov/gene/?term=6188	S3	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018294	6188	RPS3	http://www.ncbi.nlm.nih.gov/gene/?term=6188	S3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018295	6188	RPS3	http://www.ncbi.nlm.nih.gov/gene/?term=6188	S3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018296	6189	RPS3A	http://www.ncbi.nlm.nih.gov/gene/?term=6189	"FTE1, MFTL, S3A "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018297	6189	RPS3A	http://www.ncbi.nlm.nih.gov/gene/?term=6189	"FTE1, MFTL, S3A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018298	6189	RPS3A	http://www.ncbi.nlm.nih.gov/gene/?term=6189	"FTE1, MFTL, S3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018299	6191	RPS4X	http://www.ncbi.nlm.nih.gov/gene/?term=6191	"CCG2, DXS306, RPS4, S4, SCAR, SCR10 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018300	6191	RPS4X	http://www.ncbi.nlm.nih.gov/gene/?term=6191	"CCG2, DXS306, RPS4, S4, SCAR, SCR10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018301	619207	SCART1	http://www.ncbi.nlm.nih.gov/gene/?term=619207		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018302	619208	FAM229B	http://www.ncbi.nlm.nih.gov/gene/?term=619208	C6orf225	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018303	619292	G430095P16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=619292		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018304	619295	Lrp8os2	http://www.ncbi.nlm.nih.gov/gene/?term=619295	B230314M03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018305	6192	RPS4Y1	http://www.ncbi.nlm.nih.gov/gene/?term=6192	"RPS4Y, S4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018306	619383	SCARNA9	http://www.ncbi.nlm.nih.gov/gene/?term=619383	"Z32, mgU2-19/30 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018307	619383	SCARNA9	http://www.ncbi.nlm.nih.gov/gene/?term=619383	"Z32, mgU2-19/30 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018308	6193	RPS5	http://www.ncbi.nlm.nih.gov/gene/?term=6193	S5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018309	6193	RPS5	http://www.ncbi.nlm.nih.gov/gene/?term=6193	S5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018310	619498	SNORD74	http://www.ncbi.nlm.nih.gov/gene/?term=619498	"SNORD74A, U74, Z18 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018311	619498	SNORD74	http://www.ncbi.nlm.nih.gov/gene/?term=619498	"SNORD74A, U74, Z18 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018312	619498	SNORD74	http://www.ncbi.nlm.nih.gov/gene/?term=619498	"SNORD74A, U74, Z18 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00018313	619498	SNORD74	http://www.ncbi.nlm.nih.gov/gene/?term=619498	"SNORD74A, U74, Z18 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018314	619498	SNORD74	http://www.ncbi.nlm.nih.gov/gene/?term=619498	"SNORD74A, U74, Z18 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018315	6194	RPS6	http://www.ncbi.nlm.nih.gov/gene/?term=6194	S6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018316	619562	SNORA3A	http://www.ncbi.nlm.nih.gov/gene/?term=619562	"ACA3, SNORA3, SNORA45A "	snoRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018317	619564	SNORD72	http://www.ncbi.nlm.nih.gov/gene/?term=619564	HBII-240	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018318	619564	SNORD72	http://www.ncbi.nlm.nih.gov/gene/?term=619564	HBII-240	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018319	619565	SNORA52	http://www.ncbi.nlm.nih.gov/gene/?term=619565	ACA52	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00018320	619567	SNORD2	http://www.ncbi.nlm.nih.gov/gene/?term=619567	"R39B, SNR39B "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00018321	619567	SNORD2	http://www.ncbi.nlm.nih.gov/gene/?term=619567	"R39B, SNR39B "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018322	619567	SNORD2	http://www.ncbi.nlm.nih.gov/gene/?term=619567	"R39B, SNR39B "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018323	619567	SNORD2	http://www.ncbi.nlm.nih.gov/gene/?term=619567	"R39B, SNR39B "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00018324	619567	SNORD2	http://www.ncbi.nlm.nih.gov/gene/?term=619567	"R39B, SNR39B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018325	619567	SNORD2	http://www.ncbi.nlm.nih.gov/gene/?term=619567	"R39B, SNR39B "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018326	619570	SNORD95	http://www.ncbi.nlm.nih.gov/gene/?term=619570	U95	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00018327	619570	SNORD95	http://www.ncbi.nlm.nih.gov/gene/?term=619570	U95	snoRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018328	619571	SNORD96A	http://www.ncbi.nlm.nih.gov/gene/?term=619571	U96A	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00018329	619571	SNORD96A	http://www.ncbi.nlm.nih.gov/gene/?term=619571	U96A	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00018330	6195	RPS6KA1	http://www.ncbi.nlm.nih.gov/gene/?term=6195	"HU-1, MAPKAPK1A, RSK, RSK1, p90Rsk "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018331	6195	RPS6KA1	http://www.ncbi.nlm.nih.gov/gene/?term=6195	"HU-1, MAPKAPK1A, RSK, RSK1, p90Rsk "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018332	6196	RPS6KA2	http://www.ncbi.nlm.nih.gov/gene/?term=6196	"HU-2, MAPKAPK1C, RSK, RSK3, S6K-alpha, S6K-alpha2, p90-RSK3, p90RSK2, pp90RSK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018333	619719	6430590A07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=619719	EG619719	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018334	6197	RPS6KA3	http://www.ncbi.nlm.nih.gov/gene/?term=6197	"CLS, HU-3, ISPK-1, MAPKAPK1B, MRX19, RSK, RSK2, S6K-alpha3, p90-RSK2, pp90RSK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018335	6197	RPS6KA3	http://www.ncbi.nlm.nih.gov/gene/?term=6197	"CLS, HU-3, ISPK-1, MAPKAPK1B, MRX19, RSK, RSK2, S6K-alpha3, p90-RSK2, pp90RSK2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018336	6197	RPS6KA3	http://www.ncbi.nlm.nih.gov/gene/?term=6197	"CLS, HU-3, ISPK-1, MAPKAPK1B, MRX19, RSK, RSK2, S6K-alpha3, p90-RSK2, pp90RSK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018337	6198	RPS6KB1	http://www.ncbi.nlm.nih.gov/gene/?term=6198	"PS6K, S6K, S6K-beta-1, S6K1, STK14A, p70 S6KA, p70(S6K)-alpha, p70-S6K, p70-alpha "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018338	6198	RPS6KB1	http://www.ncbi.nlm.nih.gov/gene/?term=6198	"PS6K, S6K, S6K-beta-1, S6K1, STK14A, p70 S6KA, p70(S6K)-alpha, p70-S6K, p70-alpha "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018339	6198	RPS6KB1	http://www.ncbi.nlm.nih.gov/gene/?term=6198	"PS6K, S6K, S6K-beta-1, S6K1, STK14A, p70 S6KA, p70(S6K)-alpha, p70-S6K, p70-alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018340	6199	RPS6KB2	http://www.ncbi.nlm.nih.gov/gene/?term=6199	"KLS, P70-beta, P70-beta-1, P70-beta-2, S6K-beta2, S6K2, SRK, STK14B, p70(S6K)-beta, p70S6Kb "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018341	6199	RPS6KB2	http://www.ncbi.nlm.nih.gov/gene/?term=6199	"KLS, P70-beta, P70-beta-1, P70-beta-2, S6K-beta2, S6K2, SRK, STK14B, p70(S6K)-beta, p70S6Kb "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018342	6201	RPS7	http://www.ncbi.nlm.nih.gov/gene/?term=6201	"DBA8, S7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018343	6201	RPS7	http://www.ncbi.nlm.nih.gov/gene/?term=6201	"DBA8, S7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018344	6202	RPS8	http://www.ncbi.nlm.nih.gov/gene/?term=6202	S8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018345	6203	RPS9	http://www.ncbi.nlm.nih.gov/gene/?term=6203	S9	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018346	6203	RPS9	http://www.ncbi.nlm.nih.gov/gene/?term=6203	S9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018347	6204	RPS10	http://www.ncbi.nlm.nih.gov/gene/?term=6204	"DBA9, S10 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018348	6206	RPS12	http://www.ncbi.nlm.nih.gov/gene/?term=6206	S12	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018349	6206	RPS12	http://www.ncbi.nlm.nih.gov/gene/?term=6206	S12	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018350	6206	RPS12	http://www.ncbi.nlm.nih.gov/gene/?term=6206	S12	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018351	6207	RPS13	http://www.ncbi.nlm.nih.gov/gene/?term=6207	S13	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018352	6207	RPS13	http://www.ncbi.nlm.nih.gov/gene/?term=6207	S13	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018353	6208	RPS14	http://www.ncbi.nlm.nih.gov/gene/?term=6208	"EMTB, S14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018354	6208	RPS14	http://www.ncbi.nlm.nih.gov/gene/?term=6208	"EMTB, S14 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018355	6208	RPS14	http://www.ncbi.nlm.nih.gov/gene/?term=6208	"EMTB, S14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018356	6209	RPS15	http://www.ncbi.nlm.nih.gov/gene/?term=6209	"RIG, S15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018357	6210	RPS15A	http://www.ncbi.nlm.nih.gov/gene/?term=6210	S15a	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018358	6210	RPS15A	http://www.ncbi.nlm.nih.gov/gene/?term=6210	S15a	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018359	6210	RPS15A	http://www.ncbi.nlm.nih.gov/gene/?term=6210	S15a	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018360	6217	RPS16	http://www.ncbi.nlm.nih.gov/gene/?term=6217	S16	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018361	6217	RPS16	http://www.ncbi.nlm.nih.gov/gene/?term=6217	S16	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018362	6218	RPS17	http://www.ncbi.nlm.nih.gov/gene/?term=6218	"DBA4L, RPS17L1, RPS17L2, S17, RPS17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018363	622124	Gm20750	http://www.ncbi.nlm.nih.gov/gene/?term=622124		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018364	622129	Gm6288	http://www.ncbi.nlm.nih.gov/gene/?term=622129	EG622129	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018365	622208	Gm6297	http://www.ncbi.nlm.nih.gov/gene/?term=622208		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018366	6222	RPS18	http://www.ncbi.nlm.nih.gov/gene/?term=6222	"D6S218E, HKE3, KE-3, KE3, S18 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018367	6223	RPS19	http://www.ncbi.nlm.nih.gov/gene/?term=6223	"DBA, DBA1, S19 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018368	6223	RPS19	http://www.ncbi.nlm.nih.gov/gene/?term=6223	"DBA, DBA1, S19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018369	6224	RPS20	http://www.ncbi.nlm.nih.gov/gene/?term=6224	S20	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018370	6224	RPS20	http://www.ncbi.nlm.nih.gov/gene/?term=6224	S20	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018371	6224	RPS20	http://www.ncbi.nlm.nih.gov/gene/?term=6224	S20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018372	622675	Zfp827	http://www.ncbi.nlm.nih.gov/gene/?term=622675	"2810449M09Rik, D630040G17Rik, Znf827 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018373	6227	RPS21	http://www.ncbi.nlm.nih.gov/gene/?term=6227	"HLDF, S21 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018374	6228	RPS23	http://www.ncbi.nlm.nih.gov/gene/?term=6228	S23	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018375	622	BDH1	http://www.ncbi.nlm.nih.gov/gene/?term=622	"BDH, SDR9C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018376	622	BDH1	http://www.ncbi.nlm.nih.gov/gene/?term=622	"BDH, SDR9C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018377	6230	RPS25	http://www.ncbi.nlm.nih.gov/gene/?term=6230	S25	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018378	6231	RPS26	http://www.ncbi.nlm.nih.gov/gene/?term=6231	"DBA10, S26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018379	6232	RPS27	http://www.ncbi.nlm.nih.gov/gene/?term=6232	"MPS-1, MPS1, S27 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018380	6233	RPS27A	http://www.ncbi.nlm.nih.gov/gene/?term=6233	"CEP80, HEL112, S27A, UBA80, UBC, UBCEP1, UBCEP80 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018381	6233	RPS27A	http://www.ncbi.nlm.nih.gov/gene/?term=6233	"CEP80, HEL112, S27A, UBA80, UBC, UBCEP1, UBCEP80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018382	6234	RPS28	http://www.ncbi.nlm.nih.gov/gene/?term=6234	"DBA15, S28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018383	6234	RPS28	http://www.ncbi.nlm.nih.gov/gene/?term=6234	"DBA15, S28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018384	6235	RPS29	http://www.ncbi.nlm.nih.gov/gene/?term=6235	"DBA13, S29 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018385	6238	RRBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6238	"ES/130, ES130, RRp, hES "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018386	6239	RREB1	http://www.ncbi.nlm.nih.gov/gene/?term=6239	"FINB, HNT, LZ321, RREB-1, Zep-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018387	6239	RREB1	http://www.ncbi.nlm.nih.gov/gene/?term=6239	"FINB, HNT, LZ321, RREB-1, Zep-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018388	624086	A230045G11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=624086	EG624086	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018389	6240	RRM1	http://www.ncbi.nlm.nih.gov/gene/?term=6240	"R1, RIR1, RR1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018390	6240	RRM1	http://www.ncbi.nlm.nih.gov/gene/?term=6240	"R1, RIR1, RR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018391	6240	RRM1	http://www.ncbi.nlm.nih.gov/gene/?term=6240	"R1, RIR1, RR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018392	6241	RRM2	http://www.ncbi.nlm.nih.gov/gene/?term=6241	"R2, RR2, RR2M "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018393	6241	RRM2	http://www.ncbi.nlm.nih.gov/gene/?term=6241	"R2, RR2, RR2M "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018394	6241	RRM2	http://www.ncbi.nlm.nih.gov/gene/?term=6241	"R2, RR2, RR2M "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018395	624295	LOC624295	http://www.ncbi.nlm.nih.gov/gene/?term=624295		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018396	6242	RTKN	http://www.ncbi.nlm.nih.gov/gene/?term=6242		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018397	6249	CLIP1	http://www.ncbi.nlm.nih.gov/gene/?term=6249	"CLIP, CLIP-17070, CYLN1, RSN, CLIP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018398	6249	CLIP1	http://www.ncbi.nlm.nih.gov/gene/?term=6249	"CLIP, CLIP-17070, CYLN1, RSN, CLIP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018399	6249	CLIP1	http://www.ncbi.nlm.nih.gov/gene/?term=6249	"CLIP, CLIP-170, CLIP170, CYLN1, RSN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018400	625175	1700028E10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=625175	"A630054D14, Gm6561 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018401	6251	RSU1	http://www.ncbi.nlm.nih.gov/gene/?term=6251	RSP-1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018402	6252	RTN1	http://www.ncbi.nlm.nih.gov/gene/?term=6252	NSP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018403	6253	RTN2	http://www.ncbi.nlm.nih.gov/gene/?term=6253	"NSP2, NSPL1, NSPLI, SPG12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018404	625424	Gm6583	http://www.ncbi.nlm.nih.gov/gene/?term=625424	EG625424	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018405	6256	RXRA	http://www.ncbi.nlm.nih.gov/gene/?term=6256	NR2B1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018406	6257	RXRB	http://www.ncbi.nlm.nih.gov/gene/?term=6257	"DAUDI6, H-2RIIBP, NR2B2, RCoR-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018407	6257	RXRB	http://www.ncbi.nlm.nih.gov/gene/?term=6257	"DAUDI6, H-2RIIBP, NR2B2, RCoR-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018408	6259	RYK	http://www.ncbi.nlm.nih.gov/gene/?term=6259	"D3S3195, JTK5, JTK5A1, RYK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018409	6259	RYK	http://www.ncbi.nlm.nih.gov/gene/?term=6259	"D3S3195, JTK5, JTK5A1, RYK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018410	6259	RYK	http://www.ncbi.nlm.nih.gov/gene/?term=6259	"D3S3195, JTK5, JTK5A, RYK1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018411	626000	Ccnd3-ps	http://www.ncbi.nlm.nih.gov/gene/?term=626000		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018412	626832	Gm6710	http://www.ncbi.nlm.nih.gov/gene/?term=626832	"1600017I02Rik, 2310011F05Rik, 2900089K14Rik, 3100002L24Rik, WF-4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018413	6271	S100A1	http://www.ncbi.nlm.nih.gov/gene/?term=6271	"S100, S100-alpha, S100A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018414	6272	SORT1	http://www.ncbi.nlm.nih.gov/gene/?term=6272	"Gp95, LDLCQ6, NT3, NTR3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018415	627488	Gm6763	http://www.ncbi.nlm.nih.gov/gene/?term=627488	"EG627488, Gm21293 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018416	6275	S100A4	http://www.ncbi.nlm.nih.gov/gene/?term=6275	"18A2, 42A, CAPL, FSP1, MTS1, P9KA, PEL98 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018417	6277	S100A6	http://www.ncbi.nlm.nih.gov/gene/?term=6277	"2A9, 5B10, CABP, CACY, PRA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018418	6281	S100A10	http://www.ncbi.nlm.nih.gov/gene/?term=6281	"42C, ANX2L, ANX2LG, CAL1L, CLP11, Ca[1], GP11, P11, p10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018419	6281	S100A10	http://www.ncbi.nlm.nih.gov/gene/?term=6281	"42C, ANX2L, ANX2LG, CAL1L, CLP11, Ca[1], GP11, P11, p10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018420	6282	S100A11	http://www.ncbi.nlm.nih.gov/gene/?term=6282	"HEL-S-43, MLN70, S100C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018421	6282	S100A11	http://www.ncbi.nlm.nih.gov/gene/?term=6282	"HEL-S-43, MLN70, S100C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018422	6282	S100A11	http://www.ncbi.nlm.nih.gov/gene/?term=6282	"HEL-S-43, MLN70, S100C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018423	6284	S100A13	http://www.ncbi.nlm.nih.gov/gene/?term=6284		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018424	6284	S100A13	http://www.ncbi.nlm.nih.gov/gene/?term=6284		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018425	6285	S100B	http://www.ncbi.nlm.nih.gov/gene/?term=6285	"NEF, S100, S100-B, S100beta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018426	6286	S100P	http://www.ncbi.nlm.nih.gov/gene/?term=6286	MIG9	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018427	6286	S100P	http://www.ncbi.nlm.nih.gov/gene/?term=6286	MIG9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018428	6293	VPS52	http://www.ncbi.nlm.nih.gov/gene/?term=6293	"ARE1, SAC2, SACM2L, dJ1033B10.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018429	6293	VPS52	http://www.ncbi.nlm.nih.gov/gene/?term=6293	"ARE1, SAC2, SACM2L, dJ1033B10.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018430	629481	Gm29687	http://www.ncbi.nlm.nih.gov/gene/?term=629481		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018431	6294	SAFB	http://www.ncbi.nlm.nih.gov/gene/?term=6294	"HAP, HET, SAB-B1, SAF-B, SAF-B11, SAFB "	lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018432	6295	SAG	http://www.ncbi.nlm.nih.gov/gene/?term=6295	"RP47, S-AG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018433	6296	ACSM3	http://www.ncbi.nlm.nih.gov/gene/?term=6296	"SA, SAH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018434	6297	SALL2	http://www.ncbi.nlm.nih.gov/gene/?term=6297	"COLB, HSAL2, Sal-2, ZNF795, p150(Sal2) "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018435	6301	SARS	http://www.ncbi.nlm.nih.gov/gene/?term=6301	"SERRS, SERS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018436	6301	SARS	http://www.ncbi.nlm.nih.gov/gene/?term=6301	"SERRS, SERS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018437	63027	SLC22A23	http://www.ncbi.nlm.nih.gov/gene/?term=63027	C6orf85	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018438	6302	TSPAN31	http://www.ncbi.nlm.nih.gov/gene/?term=6302	SAS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018439	6302	TSPAN31	http://www.ncbi.nlm.nih.gov/gene/?term=6302	SAS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018440	63035	BCORL1	http://www.ncbi.nlm.nih.gov/gene/?term=63035	"BCoR-L1, CXorf10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018441	6303	SAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6303	"DC21, KFSD, KFSDX, SAT, SSAT, SSAT-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018442	6303	SAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6303	"DC21, KFSD, KFSDX, SAT, SSAT, SSAT-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018443	6303	SAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6303	"DC21, KFSD, KFSDX, SAT, SSAT, SSAT-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018444	6303	SAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6303	"DC21, KFSD, KFSDX, SAT, SSAT, SSAT-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018445	6304	SATB1	http://www.ncbi.nlm.nih.gov/gene/?term=6304		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018446	6305	SBF1	http://www.ncbi.nlm.nih.gov/gene/?term=6305	"CMT4B3, DENND7A, MTMR5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018447	6305	SBF1	http://www.ncbi.nlm.nih.gov/gene/?term=6305	"CMT4B3, DENND7A, MTMR5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018448	6307	MSMO1	http://www.ncbi.nlm.nih.gov/gene/?term=6307	"DESP4, ERG25, MCCPD, SC4MOL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018449	6307	MSMO1	http://www.ncbi.nlm.nih.gov/gene/?term=6307	"DESP4, ERG25, MCCPD, SC4MOL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018450	6307	MSMO1	http://www.ncbi.nlm.nih.gov/gene/?term=6307	"DESP4, ERG25, MCCPD, SC4MOL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018451	6307	MSMO1	http://www.ncbi.nlm.nih.gov/gene/?term=6307	"DESP4, ERG25, MCCPD, SC4MOL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018452	6307	MSMO1	http://www.ncbi.nlm.nih.gov/gene/?term=6307	"DESP4, ERG25, SC4MOL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018453	6309	SC5D	http://www.ncbi.nlm.nih.gov/gene/?term=6309	"ERG3, S5DESL, SC5D "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018454	6309	SC5D	http://www.ncbi.nlm.nih.gov/gene/?term=6309	"ERG3, S5DESL, SC5D "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018455	6309	SC5D	http://www.ncbi.nlm.nih.gov/gene/?term=6309	"ERG3, S5DESL, SC5D "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018456	6309	SC5D	http://www.ncbi.nlm.nih.gov/gene/?term=6309	"ERG3, S5DES, SC5DL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018457	631145	Fam90a1b	http://www.ncbi.nlm.nih.gov/gene/?term=631145	4932442L08Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018458	6311	ATXN2	http://www.ncbi.nlm.nih.gov/gene/?term=6311	"ASL13, ATX2, SCA2, TNRC13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018459	6311	ATXN2	http://www.ncbi.nlm.nih.gov/gene/?term=6311	"ASL13, ATX2, SCA2, TNRC13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018460	6314	ATXN7	http://www.ncbi.nlm.nih.gov/gene/?term=6314	"ADCAII, OPCA3, SCA7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018461	6319	SCD	http://www.ncbi.nlm.nih.gov/gene/?term=6319	"FADS5, MSTP0081, SCDOS, hSCD1, SCD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018462	6319	SCD	http://www.ncbi.nlm.nih.gov/gene/?term=6319	"FADS5, MSTP0081, SCDOS, hSCD1, SCD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018463	6319	SCD	http://www.ncbi.nlm.nih.gov/gene/?term=6319	"FADS5, MSTP008, SCD1, SCDOS, hSCD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018464	6320	CLEC11A	http://www.ncbi.nlm.nih.gov/gene/?term=6320	"CLECSF3, LSLCL, P47, SCGF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018465	632687	March10	http://www.ncbi.nlm.nih.gov/gene/?term=632687	"4933417C16Rik, AV039223, OTTMUSG00000002847, Rnf190 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018466	6335	SCN9A	http://www.ncbi.nlm.nih.gov/gene/?term=6335	"ETHA, FEB3B, GEFSP7, HSAN2D, NE-NA, NENA, Nav1.7, PN1, SFNP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018467	6337	SCNN1A	http://www.ncbi.nlm.nih.gov/gene/?term=6337	"BESC2, ENaCa, ENaCalpha, SCNEA, SCNN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018468	633	BGN	http://www.ncbi.nlm.nih.gov/gene/?term=633	"DSPG1, PG-S1, PGI, SLRR1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018469	6341	SCO1	http://www.ncbi.nlm.nih.gov/gene/?term=6341	SCOD1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018470	6342	SCP2	http://www.ncbi.nlm.nih.gov/gene/?term=6342	"NLTP, NSL-TP, SCP-2, SCP-CHI, SCP-X, SCPX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018471	6342	SCP2	http://www.ncbi.nlm.nih.gov/gene/?term=6342	"NLTP, NSL-TP, SCP-2, SCP-CHI, SCP-X, SCPX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018472	6342	SCP2	http://www.ncbi.nlm.nih.gov/gene/?term=6342	"NLTP, NSL-TP, SCP-2, SCP-CHI, SCP-X, SCPX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018473	634	CEACAM1	http://www.ncbi.nlm.nih.gov/gene/?term=634	"BGP, BGP1, BGPI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018474	635253	Usp51	http://www.ncbi.nlm.nih.gov/gene/?term=635253	AV136873	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018475	6359	CCL15	http://www.ncbi.nlm.nih.gov/gene/?term=6359	"HCC-2, HMRP-2B, LKN-1, LKN1, MIP-1 delta, MIP-1D, MIP-5, MRP-2B, NCC-3, NCC3, SCYA15, SCYL3, SY15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018476	6360	CCL16	http://www.ncbi.nlm.nih.gov/gene/?term=6360	"CKb12, HCC-4, ILINCK, LCC-1, LEC, LMC, Mtn-1, NCC-4, NCC4, SCYA16, SCYL4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018477	6360	CCL16	http://www.ncbi.nlm.nih.gov/gene/?term=6360	"CKb12, HCC-4, ILINCK, LCC-1, LEC, LMC, Mtn-1, NCC-4, NCC4, SCYA16, SCYL4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018478	6360	CCL16	http://www.ncbi.nlm.nih.gov/gene/?term=6360	"CKb12, HCC-4, ILINCK, LCC-1, LEC, LMC, Mtn-1, NCC-4, NCC4, SCYA16, SCYL4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018479	6363	CCL19	http://www.ncbi.nlm.nih.gov/gene/?term=6363	"CKb11, ELC, MIP-3b, MIP3B, SCYA19 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018480	6367	CCL22	http://www.ncbi.nlm.nih.gov/gene/?term=6367	"A-152E5.1, ABCD-1, DC/B-CK, MDC, SCYA22, STCP-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018481	6367	CCL22	http://www.ncbi.nlm.nih.gov/gene/?term=6367	"A-152E5.1, ABCD-1, DC/B-CK, MDC, SCYA22, STCP-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018482	636931	Trim71	http://www.ncbi.nlm.nih.gov/gene/?term=636931	"2610206G21Rik, AL022943, Gm1127, Lin41, lin-41, mLin41, mlin-41 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018483	637008	Gm11793	http://www.ncbi.nlm.nih.gov/gene/?term=637008	OTTMUSG00000004294	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018484	6370	CCL25	http://www.ncbi.nlm.nih.gov/gene/?term=6370	"Ckb15, SCYA25, TECK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018485	6375	XCL1	http://www.ncbi.nlm.nih.gov/gene/?term=6375	"ATAC, LPTN, LTN, SCM-1, SCM-1a, SCM1, SCM1A, SCYC1 "	mRNA	Homo sapiens	11696436	Dendrite	Monocyte	qRT-PCR	Lptn mRNA expression was investigated at different stages of dendritic cell differentiation and maturation. RT-PCR analysis of freshly isolated monocytes and day 3-harvested immature dendritic cells showed no expression of Lptn mRNA.
RLID00018486	637	BID	http://www.ncbi.nlm.nih.gov/gene/?term=637	FP497	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018487	637	BID	http://www.ncbi.nlm.nih.gov/gene/?term=637	FP497	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018488	637	BID	http://www.ncbi.nlm.nih.gov/gene/?term=637	FP497	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018489	63826	SRR	http://www.ncbi.nlm.nih.gov/gene/?term=63826	"ILV1, ISO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018490	6382	SDC1	http://www.ncbi.nlm.nih.gov/gene/?term=6382	"CD138, SDC, SYND1, syndecan "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018491	6382	SDC1	http://www.ncbi.nlm.nih.gov/gene/?term=6382	"CD138, SDC, SYND1, syndecan "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018492	63830	Kcnq1ot1	http://www.ncbi.nlm.nih.gov/gene/?term=63830	"Kvlqt1-as, Lit1, Tssc8 "	lncRNA	Mus musculus	18951091	Nucleus	Placenta|Liver	In situ hybridization|qRT-PCR	"To address this, we have analyzed the nuclear and cytoplasmic levels of Kcnq1ot1 in MEFs using RPA and found that it is exclusively localized in the nuclear compartment, consistent with its role in transcriptional silencing ( Figure 1D).  "
RLID00018493	63830	Kcnq1ot1	http://www.ncbi.nlm.nih.gov/gene/?term=63830	"Kvlqt1-as, Lit1, Tssc8 "	lncRNA	Mus musculus	19144718	Nucleus	Fibroblasts	In situ hybridization|qRT-PCR	"Here, we show that Kcnq1ot1 is transcribed by RNA polymerase II, is unspliced, is relatively stable and is localised in the nucleus. "
RLID00018494	63830	Kcnq1ot1	http://www.ncbi.nlm.nih.gov/gene/?term=63830	"Kvlqt1-as, Lit1, Tssc8 "	lncRNA	Mus musculus	21775415	Nucleus	Embryonic stem cell	In situ hybridization|qRT-PCR	"Short hairpin RNA (shRNA)-mediated Kcnq1ot1 RNA depletion in embryonic stem (ES), trophoblast stem (TS) and extra-embryonic endoderm stem (XEN) cells had no observable effect on imprinted gene expression, nor on ICR DNA methylation, although a significant decrease in Kcnq1ot1 nuclear volume was observed. "
RLID00018495	63830	Kcnq1ot1	http://www.ncbi.nlm.nih.gov/gene/?term=63830	"Kvlqt1-as, Lit1, Tssc8 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018496	63830	Kcnq1ot1	http://www.ncbi.nlm.nih.gov/gene/?term=63830	"Kvlqt1-as, Lit1, Tssc8 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018497	6383	SDC2	http://www.ncbi.nlm.nih.gov/gene/?term=6383	"CD362, HSPG, HSPG1, SYND2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018498	6383	SDC2	http://www.ncbi.nlm.nih.gov/gene/?term=6383	"CD362, HSPG, HSPG1, SYND2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018499	6385	SDC4	http://www.ncbi.nlm.nih.gov/gene/?term=6385	SYND4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018500	6385	SDC4	http://www.ncbi.nlm.nih.gov/gene/?term=6385	SYND4	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018501	6385	SDC4	http://www.ncbi.nlm.nih.gov/gene/?term=6385	SYND4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018502	63868	Hspd1	http://www.ncbi.nlm.nih.gov/gene/?term=63868	"Hsp60-30p, Hspd1 "	mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00018503	63868	Hspd1	http://www.ncbi.nlm.nih.gov/gene/?term=63868	"Hsp60-30p, Hspd1 "	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00018504	6386	SDCBP	http://www.ncbi.nlm.nih.gov/gene/?term=6386	"MDA-9, MDA9, ST1, SYCL, TACIP18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018505	6386	SDCBP	http://www.ncbi.nlm.nih.gov/gene/?term=6386	"MDA-9, MDA9, ST1, SYCL, TACIP18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018506	63872	Zfp296	http://www.ncbi.nlm.nih.gov/gene/?term=63872	2210018A16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018507	63875	MRPL17	http://www.ncbi.nlm.nih.gov/gene/?term=63875	"L17mt, LIP2, MRP-L17, MRP-L26, RPL17L, RPML26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018508	63877	FAM204A	http://www.ncbi.nlm.nih.gov/gene/?term=63877	"C10orf84, bA319I23.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018509	63877	FAM204A	http://www.ncbi.nlm.nih.gov/gene/?term=63877	"C10orf84, bA319I23.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018510	63877	FAM204A	http://www.ncbi.nlm.nih.gov/gene/?term=63877	"C10orf84, bA319I23.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018511	6387	CXCL12	http://www.ncbi.nlm.nih.gov/gene/?term=6387	"IRH, PBSF, SCYB12, SDF1, TLSF, TPAR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018512	6388	SDF2	http://www.ncbi.nlm.nih.gov/gene/?term=6388		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018513	6388	SDF2	http://www.ncbi.nlm.nih.gov/gene/?term=6388		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018514	6388	SDF2	http://www.ncbi.nlm.nih.gov/gene/?term=6388		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018515	63891	RNF123	http://www.ncbi.nlm.nih.gov/gene/?term=63891	"FP1477, KPC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018516	63892	THADA	http://www.ncbi.nlm.nih.gov/gene/?term=63892	GITA	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018517	63892	THADA	http://www.ncbi.nlm.nih.gov/gene/?term=63892	GITA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018518	63894	VIPAS39	http://www.ncbi.nlm.nih.gov/gene/?term=63894	"C14orf133, SPE-39, SPE39, VIPAR, VPS16B, hSPE-39 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018519	63897	HEATR6	http://www.ncbi.nlm.nih.gov/gene/?term=63897	ABC1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018520	6389	SDHA	http://www.ncbi.nlm.nih.gov/gene/?term=6389	"CMD1GG, FP, PGL5, SDH1, SDH2, SDHF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018521	6389	SDHA	http://www.ncbi.nlm.nih.gov/gene/?term=6389	"CMD1GG, FP, PGL5, SDH1, SDH2, SDHF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018522	638	BIK	http://www.ncbi.nlm.nih.gov/gene/?term=638	"BIP1, BP4, NBK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018523	63901	FAM111A	http://www.ncbi.nlm.nih.gov/gene/?term=63901	"GCLEB, KCS2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018524	63905	MANBAL	http://www.ncbi.nlm.nih.gov/gene/?term=63905		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018525	63905	MANBAL	http://www.ncbi.nlm.nih.gov/gene/?term=63905		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018526	63906	GPATCH3	http://www.ncbi.nlm.nih.gov/gene/?term=63906	GPATC3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018527	6390	SDHB	http://www.ncbi.nlm.nih.gov/gene/?term=6390	"CWS2, IP, PGL4, SDH, SDH1, SDH2, SDHIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018528	6390	SDHB	http://www.ncbi.nlm.nih.gov/gene/?term=6390	"CWS2, IP, PGL4, SDH, SDH1, SDH2, SDHIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018529	63910	SLC17A9	http://www.ncbi.nlm.nih.gov/gene/?term=63910	"C20orf59, POROK8, VNUT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018530	63913	Fam129a	http://www.ncbi.nlm.nih.gov/gene/?term=63913	"AI256368, AU019833, Niban "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018531	63915	BLOC1S5	http://www.ncbi.nlm.nih.gov/gene/?term=63915	"BLOS5, MU, MUTED "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018532	6391	SDHC	http://www.ncbi.nlm.nih.gov/gene/?term=6391	"CYB560, CYBL, PGL3, QPS1, SDH3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018533	6391	SDHC	http://www.ncbi.nlm.nih.gov/gene/?term=6391	"CYB560, CYBL, PGL3, QPS1, SDH3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018534	63920	ZBED8	http://www.ncbi.nlm.nih.gov/gene/?term=63920	"Buster3, C5orf54 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018535	63922	CHTF18	http://www.ncbi.nlm.nih.gov/gene/?term=63922	"C16orf41, C321D2.2, C321D2.3, C321D2.4, CHL12, Ctf18, RUVBL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018536	63924	CIDEC	http://www.ncbi.nlm.nih.gov/gene/?term=63924	"CIDE-3, CIDE3, FPLD5, FSP27 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018537	63925	ZNF335	http://www.ncbi.nlm.nih.gov/gene/?term=63925	"MCPH10, NIF-1, NIF1, NIF2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018538	63929	XPNPEP3	http://www.ncbi.nlm.nih.gov/gene/?term=63929	"APP3, ICP55, NPHPL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018539	63929	XPNPEP3	http://www.ncbi.nlm.nih.gov/gene/?term=63929	"APP3, ICP55, NPHPL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018540	6392	SDHD	http://www.ncbi.nlm.nih.gov/gene/?term=6392	"CBT1, CII-4, CWS3, PGL, PGL1, QPs3, SDH4, cybS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018541	6392	SDHD	http://www.ncbi.nlm.nih.gov/gene/?term=6392	"CBT1, CII-4, CWS3, PGL, PGL1, QPs3, SDH4, cybS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018542	63931	MRPS14	http://www.ncbi.nlm.nih.gov/gene/?term=63931	"DJ262D12.2, HSMRPS14, MRP-S14, S14mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018543	63932	CXorf56	http://www.ncbi.nlm.nih.gov/gene/?term=63932		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018544	63933	MCUR1	http://www.ncbi.nlm.nih.gov/gene/?term=63933	"C6orf79, CCDC90A "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018545	63933	MCUR1	http://www.ncbi.nlm.nih.gov/gene/?term=63933	"C6orf79, CCDC90A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018546	639396	Gm7265	http://www.ncbi.nlm.nih.gov/gene/?term=639396	EG639396	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018547	63939	FAM217B	http://www.ncbi.nlm.nih.gov/gene/?term=63939	"C20orf177, dJ551D2.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018548	63940	GPSM3	http://www.ncbi.nlm.nih.gov/gene/?term=63940	"AGS4, C6orf9, G18, G18.1a, G18.1b, G18.2, NG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018549	63943	FKBPL	http://www.ncbi.nlm.nih.gov/gene/?term=63943	"DIR1, FKBP4, NG7, WISP39 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018550	63943	FKBPL	http://www.ncbi.nlm.nih.gov/gene/?term=63943	"DIR1, FKBP4, NG7, WISP39 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018551	6396	SEC13	http://www.ncbi.nlm.nih.gov/gene/?term=6396	"D3S1231EL1, SEC13R, npp-20, SEC13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018552	6396	SEC13	http://www.ncbi.nlm.nih.gov/gene/?term=6396	"D3S1231E, SEC13L1, SEC13R, npp-20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018553	63971	KIF13A	http://www.ncbi.nlm.nih.gov/gene/?term=63971	"RBKIN, bA500C11.2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018554	63977	PRDM15	http://www.ncbi.nlm.nih.gov/gene/?term=63977	"C21orf83, PFM15, ZNF298 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018555	63979	FIGNL1	http://www.ncbi.nlm.nih.gov/gene/?term=63979		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018556	6397	SEC14L1	http://www.ncbi.nlm.nih.gov/gene/?term=6397	"PRELID4A, SEC14L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018557	63982	ANO3	http://www.ncbi.nlm.nih.gov/gene/?term=63982	"C11orf25, DYT23, DYT24, GENX-3947, TMEM16C "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018558	63993	Slc5a7	http://www.ncbi.nlm.nih.gov/gene/?term=63993	CHT1	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018559	6399	TRAPPC2	http://www.ncbi.nlm.nih.gov/gene/?term=6399	"MIP2A, SEDL, SEDTP1, TRS20, ZNF547L, hYP38334, TRAPPC2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018560	6399	TRAPPC2	http://www.ncbi.nlm.nih.gov/gene/?term=6399	"MIP2A, SEDL, SEDTP1, TRS20, ZNF547L, hYP38334, TRAPPC2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018561	6399	TRAPPC2	http://www.ncbi.nlm.nih.gov/gene/?term=6399	"MIP2A, SEDL, SEDTP1, TRS20, ZNF547L, hYP38334, TRAPPC2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018562	6399	TRAPPC2	http://www.ncbi.nlm.nih.gov/gene/?term=6399	"MIP2A, SEDL, SEDT, TRAPPC2P1, TRS20, ZNF547L, hYP38334 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018563	64008	Aqp9	http://www.ncbi.nlm.nih.gov/gene/?term=64008	"1700020I22Rik, AI266899, AQP-9 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018564	64009	Syne1	http://www.ncbi.nlm.nih.gov/gene/?term=64009	"8B, A330049M09Rik, BE692247, C130039F11Rik, CPG2, Myne1, mKIAA1756 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018565	6400	SEL1L	http://www.ncbi.nlm.nih.gov/gene/?term=6400	"PRO1063, SEL1-LIKE1, SEL1L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018566	6400	SEL1L	http://www.ncbi.nlm.nih.gov/gene/?term=6400	"PRO1063, SEL1-LIKE, SEL1L1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018567	6405	SEMA3F	http://www.ncbi.nlm.nih.gov/gene/?term=6405	"SEMA-IV, SEMA4, SEMAK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018568	64062	RBM26	http://www.ncbi.nlm.nih.gov/gene/?term=64062	"ARRS2, C13orf10, PPP1R132, PRO1777, SE70-2, ZC3H17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018569	64065	PERP	http://www.ncbi.nlm.nih.gov/gene/?term=64065	"KCP1, KRTCAP1, PIGPC1, THW, dJ496H19.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018570	64065	PERP	http://www.ncbi.nlm.nih.gov/gene/?term=64065	"KCP1, KRTCAP1, PIGPC1, THW, dJ496H19.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018571	64073	C19orf33	http://www.ncbi.nlm.nih.gov/gene/?term=64073	"H2RSP, IMUP, IMUP-1, IMUP-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018572	64077	LHPP	http://www.ncbi.nlm.nih.gov/gene/?term=64077	HDHD2B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018573	64077	LHPP	http://www.ncbi.nlm.nih.gov/gene/?term=64077	HDHD2B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018574	6407	SEMG2	http://www.ncbi.nlm.nih.gov/gene/?term=6407	SGII	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018575	64081	PBLD	http://www.ncbi.nlm.nih.gov/gene/?term=64081	"HEL-S-306, MAWBP, MAWDBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018576	64083	GOLPH3	http://www.ncbi.nlm.nih.gov/gene/?term=64083	"GOPP1, GPP34, MIDAS, Vps74 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018577	64083	GOLPH3	http://www.ncbi.nlm.nih.gov/gene/?term=64083	"GOPP1, GPP34, MIDAS, Vps74 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018578	64083	GOLPH3	http://www.ncbi.nlm.nih.gov/gene/?term=64083	"GOPP1, GPP34, MIDAS, Vps74 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018579	64087	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=64087	MCCB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018580	64087	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=64087	MCCB	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018581	64087	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=64087	MCCB	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018582	64087	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=64087	MCCB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018583	64092	SAMSN1	http://www.ncbi.nlm.nih.gov/gene/?term=64092	"HACS1, NASH1, SASH2, SH3D6B, SLy2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018584	64094	SMOC2	http://www.ncbi.nlm.nih.gov/gene/?term=64094	"DTDP1, MST117, MSTP117, MSTP140, SMAP2, bA270C4A.1, bA37D8.1, dJ421D16.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018585	64110	MAGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=64110		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018586	64110	MAGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=64110		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018587	64112	MOAP1	http://www.ncbi.nlm.nih.gov/gene/?term=64112	"MAP-1, PNMA4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018588	64112	MOAP1	http://www.ncbi.nlm.nih.gov/gene/?term=64112	"MAP-1, PNMA4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018589	64113	Moap1	http://www.ncbi.nlm.nih.gov/gene/?term=64113	"AA987038, Map-1, Pnma4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018590	64114	TMBIM1	http://www.ncbi.nlm.nih.gov/gene/?term=64114	"LFG3, MST100, MSTP100, PP1201, RECS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018591	64115	C10orf54	http://www.ncbi.nlm.nih.gov/gene/?term=64115	"B7-H5, B7H5, DD1alpha, GI24, PP2135, SISP1, VISTA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018592	64116	SLC39A8	http://www.ncbi.nlm.nih.gov/gene/?term=64116	"BIGM103, CDG2N, LZT-Hs6, PP3105, ZIP8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018593	64118	DUS1L	http://www.ncbi.nlm.nih.gov/gene/?term=64118	"DUS1, PP3111 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018594	64118	DUS1L	http://www.ncbi.nlm.nih.gov/gene/?term=64118	"DUS1, PP3111 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018595	64121	RRAGC	http://www.ncbi.nlm.nih.gov/gene/?term=64121	"GTR2, RAGC, TIB929 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018596	64129	TINAGL1	http://www.ncbi.nlm.nih.gov/gene/?term=64129	"ARG1, LCN7, LIECG3, TINAGRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018597	64131	XYLT1	http://www.ncbi.nlm.nih.gov/gene/?term=64131	"DBQD2, PXYLT1, XT-I, XT1, XTI, XYLTI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018598	641368	Spint5	http://www.ncbi.nlm.nih.gov/gene/?term=641368	"Gm14316, OTTMUSG00000016293 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018599	64144	Mllt1	http://www.ncbi.nlm.nih.gov/gene/?term=64144	"AA407901, BAM11, ENL, LTG19 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018600	641451	SNORA19	http://www.ncbi.nlm.nih.gov/gene/?term=641451	ACA19	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018601	64145	RBSN	http://www.ncbi.nlm.nih.gov/gene/?term=64145	"Rabenosyn-5, ZFYVE20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018602	64145	RBSN	http://www.ncbi.nlm.nih.gov/gene/?term=64145	"Rabenosyn-5, ZFYVE20 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018603	64146	PDF	http://www.ncbi.nlm.nih.gov/gene/?term=64146		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018604	64147	KIF9	http://www.ncbi.nlm.nih.gov/gene/?term=64147		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018605	64147	KIF9	http://www.ncbi.nlm.nih.gov/gene/?term=64147		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018606	64149	C17orf75	http://www.ncbi.nlm.nih.gov/gene/?term=64149	NJMU-R1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018607	64149	C17orf75	http://www.ncbi.nlm.nih.gov/gene/?term=64149	NJMU-R1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018608	6414	SEPP1	http://www.ncbi.nlm.nih.gov/gene/?term=6414	"SELP, SEPP, SeP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018609	6414	SEPP1	http://www.ncbi.nlm.nih.gov/gene/?term=6414	"SELP, SEPP, SeP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018610	6414	SEPP1	http://www.ncbi.nlm.nih.gov/gene/?term=6414	"SELP, SEPP, SeP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018611	64151	NCAPG	http://www.ncbi.nlm.nih.gov/gene/?term=64151	"CAPG, CHCG, NY-MEL-3, YCG1 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018612	64151	NCAPG	http://www.ncbi.nlm.nih.gov/gene/?term=64151	"CAPG, CHCG, NY-MEL-3, YCG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018613	64156	Uba52	http://www.ncbi.nlm.nih.gov/gene/?term=64156	"Rps27a, Ubb "	mRNA	Rattus norvegicus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00018614	64158	Tuba1a	http://www.ncbi.nlm.nih.gov/gene/?term=64158	Tuba1	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00018615	64158	Tuba1a	http://www.ncbi.nlm.nih.gov/gene/?term=64158	Tuba1	mRNA	Rattus norvegicus	2148487	Cell body	Neuron	In situ hybridization	"In contrast, mRNAs encoding GAP-43 and alpha-tubulin were restricted to the cell body and largely excluded from dendrites as well as axons. "
RLID00018616	6415	SEPW1	http://www.ncbi.nlm.nih.gov/gene/?term=6415	selW	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018617	6415	SEPW1	http://www.ncbi.nlm.nih.gov/gene/?term=6415	selW	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018618	6415	SEPW1	http://www.ncbi.nlm.nih.gov/gene/?term=6415	selW	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018619	641638	SNHG6	http://www.ncbi.nlm.nih.gov/gene/?term=641638	"HBII-276HG, NCRNA00058, U87HG "	lncRNA	Homo sapiens	16226852	Cytoplasm	HeLa cell	Northern blot	We investigated the cellular localization of the U87HG RNA. Human HeLa cells were fractionated into nuclear and cytoplasmic fractions. U87HG RNA was detected mainly in the cytoplasm (Fig. 4).
RLID00018620	641638	SNHG6	http://www.ncbi.nlm.nih.gov/gene/?term=641638	"HBII-276HG, NCRNA00058, U87HG "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018621	64168	NECAB1	http://www.ncbi.nlm.nih.gov/gene/?term=64168	"EFCBP1, STIP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018622	641700	ECSCR	http://www.ncbi.nlm.nih.gov/gene/?term=641700	"ARIA, ECSM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018623	64172	OSGEPL1	http://www.ncbi.nlm.nih.gov/gene/?term=64172	Qri7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018624	64174	DPEP2	http://www.ncbi.nlm.nih.gov/gene/?term=64174	MBD2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018625	64175	P3H1	http://www.ncbi.nlm.nih.gov/gene/?term=64175	"GROS1, LEPRE1, OI8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018626	6418	SET	http://www.ncbi.nlm.nih.gov/gene/?term=6418	"2PP2A, I2PP2A, IGAAD, IPP2A2, PHAPII, TAF-I, TAF-IBETA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018627	6418	SET	http://www.ncbi.nlm.nih.gov/gene/?term=6418	"2PP2A, I2PP2A, IGAAD, IPP2A2, PHAPII, TAF-I, TAF-IBETA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018628	6418	SET	http://www.ncbi.nlm.nih.gov/gene/?term=6418	"2PP2A, I2PP2A, IGAAD, IPP2A2, PHAPII, TAF-I, TAF-IBETA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018629	6419	SETMAR	http://www.ncbi.nlm.nih.gov/gene/?term=6419	"HsMar1, METNASE, Mar1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018630	641	BLM	http://www.ncbi.nlm.nih.gov/gene/?term=641	"BS, RECQ2, RECQL2, RECQL3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018631	64202	Calr	http://www.ncbi.nlm.nih.gov/gene/?term=64202		mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00018632	64202	Calr	http://www.ncbi.nlm.nih.gov/gene/?term=64202		mRNA	Rattus norvegicus	20308067	Axon	Neuron	Fluorescence in situ hybridization	"MRNAs encoding the endoplasmic reticulum chaperone proteins calreticulin and Grp78/BiP were previously detected in sensory axons by RT-PCR and array hybridization (7, 30). Because these analyses used lysed axons that could contain proximal axonal segments, we used FISH to directly visualize the mRNAs in dissociated cultures of DRG neurons. DRG neurons showed punctate FISH signals for beta-actin, calreticulin, and Grp78/BiP mRNAs that extended into growth cones (Fig. 1A). This granular distribution is similar to other mRNAs localizing to dendrites and axons (21).mRNAs encoding the endoplasmic reticulum chaperone proteins calreticulin and Grp78/BiP were previously detected in sensory axons by RT-PCR and array hybridization (7, 30). Because these analyses used lysed axons that could contain proximal axonal segments, we used FISH to directly visualize the mRNAs in dissociated cultures of DRG neurons. DRG neurons showed punctate FISH signals for beta-actin, calreticulin, and Grp78/BiP mRNAs that extended into growth cones (Fig. 1A). This granular distribution is similar to other mRNAs localizing to dendrites and axons (21). "
RLID00018633	64202	Calr	http://www.ncbi.nlm.nih.gov/gene/?term=64202		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00018634	64207	IRF2BPL	http://www.ncbi.nlm.nih.gov/gene/?term=64207	"C14orf4, EAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018635	64208	POPDC3	http://www.ncbi.nlm.nih.gov/gene/?term=64208	"POP3, bA355M14.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018636	64210	MMS19	http://www.ncbi.nlm.nih.gov/gene/?term=64210	"MET18L, hMMS19, MMS19 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018637	64210	MMS19	http://www.ncbi.nlm.nih.gov/gene/?term=64210	"MET18, MMS19L, hMMS19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018638	64213	St7	http://www.ncbi.nlm.nih.gov/gene/?term=64213	"9430001H04Rik, Fam4a2, HELG, RAY1, SEN4, TSG7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018639	64215	DNAJC1	http://www.ncbi.nlm.nih.gov/gene/?term=64215	"DNAJL1, ERdj1, HTJ1, MTJ1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018640	64215	DNAJC1	http://www.ncbi.nlm.nih.gov/gene/?term=64215	"DNAJL1, ERdj1, HTJ1, MTJ1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018641	64216	TFB2M	http://www.ncbi.nlm.nih.gov/gene/?term=64216	"Hkp1, mtTFB2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018642	64216	TFB2M	http://www.ncbi.nlm.nih.gov/gene/?term=64216	"Hkp1, mtTFB2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018643	6421	SFPQ	http://www.ncbi.nlm.nih.gov/gene/?term=6421	"POMP100, PPP1R140, PSF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018644	64222	TOR3A	http://www.ncbi.nlm.nih.gov/gene/?term=64222	"ADIR, ADIR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018645	64224	HERPUD2	http://www.ncbi.nlm.nih.gov/gene/?term=64224		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018646	64224	HERPUD2	http://www.ncbi.nlm.nih.gov/gene/?term=64224		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018647	64225	ATL2	http://www.ncbi.nlm.nih.gov/gene/?term=64225	"ARL3IP2, ARL6IP2, atlastin2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018648	64225	ATL2	http://www.ncbi.nlm.nih.gov/gene/?term=64225	"ARL3IP2, ARL6IP2, atlastin2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018649	642273	FAM110C	http://www.ncbi.nlm.nih.gov/gene/?term=642273		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018650	6422	SFRP1	http://www.ncbi.nlm.nih.gov/gene/?term=6422	"FRP, FRP-1, FRP1, FrzA, SARP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018651	64231	MS4A6A	http://www.ncbi.nlm.nih.gov/gene/?term=64231	"4SPAN3, 4SPAN3.2, CD20L3, CDA01, MS4A6, MST090, MSTP090 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018652	64236	PDLIM2	http://www.ncbi.nlm.nih.gov/gene/?term=64236	"MYSTIQUE, SLIM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018653	64236	PDLIM2	http://www.ncbi.nlm.nih.gov/gene/?term=64236	"MYSTIQUE, SLIM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018654	6423	SFRP2	http://www.ncbi.nlm.nih.gov/gene/?term=6423	"FRP-2, SARP1, SDF-5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018655	642475	MROH6	http://www.ncbi.nlm.nih.gov/gene/?term=642475	C8orf73	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018656	6426	SRSF1	http://www.ncbi.nlm.nih.gov/gene/?term=6426	"ASF, SF2, SF2p33, SFRS1, SRp30a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018657	6426	SRSF1	http://www.ncbi.nlm.nih.gov/gene/?term=6426	"ASF, SF2, SF2p33, SFRS1, SRp30a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018658	6427	SRSF2	http://www.ncbi.nlm.nih.gov/gene/?term=6427	"PR264, SC-35, SC35, SFRS2, SFRS2A, SRp30b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018659	64282	PAPD5	http://www.ncbi.nlm.nih.gov/gene/?term=64282	TRF4-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018660	64282	PAPD5	http://www.ncbi.nlm.nih.gov/gene/?term=64282	TRF4-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018661	64284	RAB17	http://www.ncbi.nlm.nih.gov/gene/?term=64284		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018662	64285	RHBDF1	http://www.ncbi.nlm.nih.gov/gene/?term=64285	"C16orf8, Dist1, EGFR-RS, gene-89, gene-90, hDist1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018663	64285	RHBDF1	http://www.ncbi.nlm.nih.gov/gene/?term=64285	"C16orf8, Dist1, EGFR-RS, gene-89, gene-90, hDist1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018664	64288	ZSCAN31	http://www.ncbi.nlm.nih.gov/gene/?term=64288	"ZNF20-Lp, ZNF310P, ZNF323 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018665	64288	ZSCAN31	http://www.ncbi.nlm.nih.gov/gene/?term=64288	"ZNF20-Lp, ZNF310P, ZNF323 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018666	64288	ZSCAN31	http://www.ncbi.nlm.nih.gov/gene/?term=64288	"ZNF20-Lp, ZNF310P, ZNF323 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018667	6428	SRSF3	http://www.ncbi.nlm.nih.gov/gene/?term=6428	"SFRS3, SRp20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018668	64291	Osbpl1a	http://www.ncbi.nlm.nih.gov/gene/?term=64291	"G430090F17Rik, Gm753, ORP-1, Osbpl1b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018669	642946	FLVCR1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=642946	"LQK1, NCRNA00292 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018670	642968	FAM163B	http://www.ncbi.nlm.nih.gov/gene/?term=642968	C9orf166	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018671	642987	TMEM232	http://www.ncbi.nlm.nih.gov/gene/?term=642987		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018672	6429	SRSF4	http://www.ncbi.nlm.nih.gov/gene/?term=6429	"SFRS4, SRP75 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018673	6429	SRSF4	http://www.ncbi.nlm.nih.gov/gene/?term=6429	"SFRS4, SRP75 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018674	642	BLMH	http://www.ncbi.nlm.nih.gov/gene/?term=642	"BH, BMH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018675	642	BLMH	http://www.ncbi.nlm.nih.gov/gene/?term=642	"BH, BMH "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018676	642	BLMH	http://www.ncbi.nlm.nih.gov/gene/?term=642	"BH, BMH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018677	64307	Rpl24	http://www.ncbi.nlm.nih.gov/gene/?term=64307		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00018678	6430	SRSF5	http://www.ncbi.nlm.nih.gov/gene/?term=6430	"HRS, SFRS5, SRP40 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018679	6430	SRSF5	http://www.ncbi.nlm.nih.gov/gene/?term=6430	"HRS, SFRS5, SRP40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018680	643155	SMIM15	http://www.ncbi.nlm.nih.gov/gene/?term=643155	C5orf43	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018681	64318	NOC3L	http://www.ncbi.nlm.nih.gov/gene/?term=64318	"AD24, C10orf117, FAD24 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018682	6431	SRSF6	http://www.ncbi.nlm.nih.gov/gene/?term=6431	"B52, HEL-S-91, SFRS6, SRP55 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018683	6431	SRSF6	http://www.ncbi.nlm.nih.gov/gene/?term=6431	"B52, HEL-S-91, SFRS6, SRP55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018684	643201	LOC643201	http://www.ncbi.nlm.nih.gov/gene/?term=643201		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018685	64320	RNF25	http://www.ncbi.nlm.nih.gov/gene/?term=64320	AO7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018686	64320	RNF25	http://www.ncbi.nlm.nih.gov/gene/?term=64320	AO7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018687	64321	SOX17	http://www.ncbi.nlm.nih.gov/gene/?term=64321	VUR3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018688	643246	MAP1LC3B2	http://www.ncbi.nlm.nih.gov/gene/?term=643246	ATG8G	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018689	64324	NSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64324	"ARA267, KMT3B, SOTOS, SOTOS1, STO "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018690	64324	NSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64324	"ARA267, KMT3B, SOTOS, SOTOS1, STO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018691	643253	CCT6P1	http://www.ncbi.nlm.nih.gov/gene/?term=643253	"CCT6-5P, CCT6AP1 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018692	64326	RFWD2	http://www.ncbi.nlm.nih.gov/gene/?term=64326	"COP1, RNF200 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018693	64326	RFWD2	http://www.ncbi.nlm.nih.gov/gene/?term=64326	"COP1, RNF200 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018694	64326	RFWD2	http://www.ncbi.nlm.nih.gov/gene/?term=64326	"COP1, RNF200 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018695	64327	LMBR1	http://www.ncbi.nlm.nih.gov/gene/?term=64327	"ACHP, C7orf2, DIF14, LSS, PPD2, THYP, TPT, ZRS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018696	64328	XPO4	http://www.ncbi.nlm.nih.gov/gene/?term=64328	exp4	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018697	64328	XPO4	http://www.ncbi.nlm.nih.gov/gene/?term=64328	exp4	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018698	64328	XPO4	http://www.ncbi.nlm.nih.gov/gene/?term=64328	exp4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018699	6432	SRSF7	http://www.ncbi.nlm.nih.gov/gene/?term=6432	"9G8, AAG3, SFRS7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018700	6432	SRSF7	http://www.ncbi.nlm.nih.gov/gene/?term=6432	"9G8, AAG3, SFRS7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018701	643314	KIAA0754	http://www.ncbi.nlm.nih.gov/gene/?term=643314		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018702	643314	KIAA0754	http://www.ncbi.nlm.nih.gov/gene/?term=643314		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018703	64332	NFKBIZ	http://www.ncbi.nlm.nih.gov/gene/?term=64332	"IKBZ, INAP, MAIL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018704	64339	Fndc4	http://www.ncbi.nlm.nih.gov/gene/?term=64339	"2810430J06Rik, 6330410H20Rik, AB030187, AI838506, AW487863, FRCP1, Fnmp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018705	6433	SFSWAP	http://www.ncbi.nlm.nih.gov/gene/?term=6433	"SFRS8, SWAP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018706	6433	SFSWAP	http://www.ncbi.nlm.nih.gov/gene/?term=6433	"SFRS8, SWAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018707	64342	HS1BP3	http://www.ncbi.nlm.nih.gov/gene/?term=64342	"ETM2, HS1-BP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018708	64343	AZI2	http://www.ncbi.nlm.nih.gov/gene/?term=64343	"AZ2, NAP1, TILP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018709	64343	AZI2	http://www.ncbi.nlm.nih.gov/gene/?term=64343	"AZ2, NAP1, TILP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018710	64344	HIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=64344	"HIF-3A, HIF3-alpha-1, IPAS, MOP7, PASD7, bHLHe17 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018711	64344	HIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=64344	"HIF-3A, HIF3-alpha-1, IPAS, MOP7, PASD7, bHLHe17 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018712	64347	Sncg	http://www.ncbi.nlm.nih.gov/gene/?term=64347		mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00018713	64347	Sncg	http://www.ncbi.nlm.nih.gov/gene/?term=64347		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00018714	6434	TRA2B	http://www.ncbi.nlm.nih.gov/gene/?term=6434	"Htra2-beta, PPP1R156, SFRS10, SRFS10, TRA2-BETA, TRAN2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018715	6434	TRA2B	http://www.ncbi.nlm.nih.gov/gene/?term=6434	"Htra2-beta, PPP1R156, SFRS10, SRFS10, TRA2-BETA, TRAN2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018716	64356	Nrgn	http://www.ncbi.nlm.nih.gov/gene/?term=64356	"BICKS, RC3 "	mRNA	Rattus norvegicus	7773006	Dendrite	Neuron	In situ hybridization	"Table 1. As of 1994, mRNAs that have been localized within dendrites by in situ hybridization.  Data are collected from Table 1. "
RLID00018717	64356	Nrgn	http://www.ncbi.nlm.nih.gov/gene/?term=64356	"BICKS, RC3 "	mRNA	Rattus norvegicus	7877439	Dendrite	Neuron	In situ hybridization	"In addition, stain was also found within the proximal portion of apical dendrites of specific cortical neurons, primarily those within layers 5 and 6 of neocortex(Fig. 2A). Labeling was found to extend as far as six cell widths into the apical dendrite (inset in Fig. 2A) suggesting that RC3 mRNA may be translocated into the dendrites of specific cortical neurons.  "
RLID00018718	64359	NXN	http://www.ncbi.nlm.nih.gov/gene/?term=64359	"NRX, TRG-4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018719	64359	NXN	http://www.ncbi.nlm.nih.gov/gene/?term=64359	"NRX, TRG-4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018720	64359	NXN	http://www.ncbi.nlm.nih.gov/gene/?term=64359	"NRX, TRG-4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018721	643749	TRAF3IP2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=643749	"C6UAS, C6orf3, NCRNA00248, TRAF3IP2-AS2 "	lncRNA	Homo sapiens	26222413	Nucleus	Neuron	In situ hybridization|qRT-PCR	"In contrast to LINC00162, TRAF3IP2-AS1 transcript showed a surprisingly strong nuclear localization in DA cells (Fig. 2g and h). "
RLID00018722	643749	TRAF3IP2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=643749	"C6UAS, C6orf3, NCRNA00248, TRAF3IP2-AS2 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018723	64374	SIL1	http://www.ncbi.nlm.nih.gov/gene/?term=64374	"BAP, MSS, ULG5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018724	64375	IKZF4	http://www.ncbi.nlm.nih.gov/gene/?term=64375	"EOS, ZNFN1A4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018725	64376	IKZF5	http://www.ncbi.nlm.nih.gov/gene/?term=64376	"PEGASUS, ZNFN1A5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018726	643834	PGA3	http://www.ncbi.nlm.nih.gov/gene/?term=643834		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018727	643836	ZFP62	http://www.ncbi.nlm.nih.gov/gene/?term=643836	"ZET, ZNF755 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018728	643836	ZFP62	http://www.ncbi.nlm.nih.gov/gene/?term=643836	"ZET, ZNF755 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018729	64383	Sirt2	http://www.ncbi.nlm.nih.gov/gene/?term=64383	"5730427M03Rik, SIR2L2, Sir2l "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018730	643866	CBLN3	http://www.ncbi.nlm.nih.gov/gene/?term=643866	PRO1486	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018731	64393	ZMAT3	http://www.ncbi.nlm.nih.gov/gene/?term=64393	"PAG608, WIG-1, WIG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018732	64395	GMCL1	http://www.ncbi.nlm.nih.gov/gene/?term=64395	"BTBD13, GCL, GCL1, SPATA29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018733	64397	ZNF106	http://www.ncbi.nlm.nih.gov/gene/?term=64397	"SH3BP3, ZFP106, ZNF474 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018734	643988	C1orf233	http://www.ncbi.nlm.nih.gov/gene/?term=643988		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018735	64398	MPP5	http://www.ncbi.nlm.nih.gov/gene/?term=64398	PALS1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018736	64398	MPP5	http://www.ncbi.nlm.nih.gov/gene/?term=64398	PALS1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018737	64400	AKTIP	http://www.ncbi.nlm.nih.gov/gene/?term=64400	"FT1, FTS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018738	64400	AKTIP	http://www.ncbi.nlm.nih.gov/gene/?term=64400	"FT1, FTS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018739	644019	CBWD6	http://www.ncbi.nlm.nih.gov/gene/?term=644019		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018740	64403	CDH24	http://www.ncbi.nlm.nih.gov/gene/?term=64403	CDH11L	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018741	644096	SDHAF1	http://www.ncbi.nlm.nih.gov/gene/?term=644096	LYRM8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018742	6440	SFTPC	http://www.ncbi.nlm.nih.gov/gene/?term=6440	"BRICD6, PSP-C, SFTP2, SMDP2, SP-C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018743	64411	ARAP3	http://www.ncbi.nlm.nih.gov/gene/?term=64411	"CENTD3, DRAG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018744	64412	GZF1	http://www.ncbi.nlm.nih.gov/gene/?term=64412	"ZBTB23, ZNF336 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018745	64418	TMEM168	http://www.ncbi.nlm.nih.gov/gene/?term=64418		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018746	64419	MTMR14	http://www.ncbi.nlm.nih.gov/gene/?term=64419	C3orf29	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018747	6441	SFTPD	http://www.ncbi.nlm.nih.gov/gene/?term=6441	"COLEC7, PSP-D, SFTP4, SP-D "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018748	64420	SUSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64420		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018749	64422	ATG3	http://www.ncbi.nlm.nih.gov/gene/?term=64422	"APG3, APG3-LIKE, APG3L, PC3-96 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018750	64422	ATG3	http://www.ncbi.nlm.nih.gov/gene/?term=64422	"APG3, APG3-LIKE, APG3L, PC3-96 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018751	64422	ATG3	http://www.ncbi.nlm.nih.gov/gene/?term=64422	"APG3, APG3-LIKE, APG3L, PC3-96 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018752	64423	INF2	http://www.ncbi.nlm.nih.gov/gene/?term=64423	"C14orf151, C14orf173, CMTDIE, FSGS5, pp9484 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018753	64425	POLR1E	http://www.ncbi.nlm.nih.gov/gene/?term=64425	"PAF53, PRAF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018754	64425	POLR1E	http://www.ncbi.nlm.nih.gov/gene/?term=64425	"PAF53, PRAF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018755	64426	SUDS3	http://www.ncbi.nlm.nih.gov/gene/?term=64426	"SAP45, SDS3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018756	64427	TTC31	http://www.ncbi.nlm.nih.gov/gene/?term=64427		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018757	64428	NARFL	http://www.ncbi.nlm.nih.gov/gene/?term=64428	"HPRN, IOP1, LET1L, PRN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018758	6442	SGCA	http://www.ncbi.nlm.nih.gov/gene/?term=6442	"50-DAG, A2, ADL, DAG2, DMDA2, LGMD2D, SCARMD1, adhalin "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018759	64430	PCNX4	http://www.ncbi.nlm.nih.gov/gene/?term=64430	"C14orf135, FBP2, PCNXL4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018760	64431	ACTR6	http://www.ncbi.nlm.nih.gov/gene/?term=64431	"ARP6, CDA12, HSPC281, MSTP136, hARP6, hARPX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018761	64431	ACTR6	http://www.ncbi.nlm.nih.gov/gene/?term=64431	"ARP6, CDA12, HSPC281, MSTP136, hARP6, hARPX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018762	64432	MRPS25	http://www.ncbi.nlm.nih.gov/gene/?term=64432	"MRP-S25, RPMS25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018763	64432	MRPS25	http://www.ncbi.nlm.nih.gov/gene/?term=64432	"MRP-S25, RPMS25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018764	64434	NOM1	http://www.ncbi.nlm.nih.gov/gene/?term=64434	"C7orf3, PPP1R113, SGD1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018765	64434	NOM1	http://www.ncbi.nlm.nih.gov/gene/?term=64434	"C7orf3, PPP1R113, SGD1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018766	6443	SGCB	http://www.ncbi.nlm.nih.gov/gene/?term=6443	"A3b, LGMD2E, SGC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018767	6443	SGCB	http://www.ncbi.nlm.nih.gov/gene/?term=6443	"A3b, LGMD2E, SGC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018768	6443	SGCB	http://www.ncbi.nlm.nih.gov/gene/?term=6443	"A3b, LGMD2E, SGC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018769	6443	SGCB	http://www.ncbi.nlm.nih.gov/gene/?term=6443	"A3b, LGMD2E, SGC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018770	6443	SGCB	http://www.ncbi.nlm.nih.gov/gene/?term=6443	"A3b, LGMD2E, SGC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018771	64450	Gpr85	http://www.ncbi.nlm.nih.gov/gene/?term=64450	2900026B03Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018772	644591	PPIAL4G	http://www.ncbi.nlm.nih.gov/gene/?term=644591	COAS-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018773	6446	SGK1	http://www.ncbi.nlm.nih.gov/gene/?term=6446	SGK	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018774	6446	SGK1	http://www.ncbi.nlm.nih.gov/gene/?term=6446	SGK	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018775	644714	LIMD1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=644714		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018776	64478	CSMD1	http://www.ncbi.nlm.nih.gov/gene/?term=64478	PPP1R24	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018777	644844	PHGR1	http://www.ncbi.nlm.nih.gov/gene/?term=644844		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018778	644873	LINC01184	http://www.ncbi.nlm.nih.gov/gene/?term=644873		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018779	644961	ACTG1P20	http://www.ncbi.nlm.nih.gov/gene/?term=644961		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018780	644	BLVRA	http://www.ncbi.nlm.nih.gov/gene/?term=644	"BLVR, BVR, BVRA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018781	644	BLVRA	http://www.ncbi.nlm.nih.gov/gene/?term=644	"BLVR, BVR, BVRA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018782	645073	GAGE12G	http://www.ncbi.nlm.nih.gov/gene/?term=645073	"AL4, CT4.7, GAGE-12G "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018783	6450	SH3BGR	http://www.ncbi.nlm.nih.gov/gene/?term=6450	21-GARP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018784	6451	SH3BGRL	http://www.ncbi.nlm.nih.gov/gene/?term=6451	"HEL-S-115, SH3BGR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018785	645249	MNX1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=645249		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018786	645296	RPL17P39	http://www.ncbi.nlm.nih.gov/gene/?term=645296	"RPL17_14_1450, hCG2004593 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018787	645296	RPL17P39	http://www.ncbi.nlm.nih.gov/gene/?term=645296	"RPL17_14_1450, hCG2004593 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018788	64529	Ctsb	http://www.ncbi.nlm.nih.gov/gene/?term=64529		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00018789	6452	SH3BP2	http://www.ncbi.nlm.nih.gov/gene/?term=6452	"3BP-2, 3BP2, CRBM, CRPM, RES4-23 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018790	6452	SH3BP2	http://www.ncbi.nlm.nih.gov/gene/?term=6452	"3BP-2, 3BP2, CRBM, CRPM, RES4-23 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018791	6452	SH3BP2	http://www.ncbi.nlm.nih.gov/gene/?term=6452	"3BP-2, 3BP2, CRBM, CRPM, RES4-23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018792	645441	RPL17P6	http://www.ncbi.nlm.nih.gov/gene/?term=645441	RPL17_1_64	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018793	645441	RPL17P6	http://www.ncbi.nlm.nih.gov/gene/?term=645441	RPL17_1_64	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018794	645553	LOC645553	http://www.ncbi.nlm.nih.gov/gene/?term=645553		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018795	6455	SH3GL1	http://www.ncbi.nlm.nih.gov/gene/?term=6455	"CNSA1, EEN, SH3D2B, SH3P8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018796	6455	SH3GL1	http://www.ncbi.nlm.nih.gov/gene/?term=6455	"CNSA1, EEN, SH3D2B, SH3P8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018797	6455	SH3GL1	http://www.ncbi.nlm.nih.gov/gene/?term=6455	"CNSA1, EEN, SH3D2B, SH3P8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018798	64577	ALDH8A1	http://www.ncbi.nlm.nih.gov/gene/?term=64577	"ALDH12, DJ352A20.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018799	6457	SH3GL3	http://www.ncbi.nlm.nih.gov/gene/?term=6457	"CNSA3, EEN-B2, HsT19371, SH3D2C, SH3P13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018800	6457	SH3GL3	http://www.ncbi.nlm.nih.gov/gene/?term=6457	"CNSA3, EEN-B2, HsT19371, SH3D2C, SH3P13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018801	64581	CLEC7A	http://www.ncbi.nlm.nih.gov/gene/?term=64581	"BGR, CANDF4, CD369, CLECSF12, DECTIN1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018802	64581	CLEC7A	http://www.ncbi.nlm.nih.gov/gene/?term=64581	"BGR, CANDF4, CD369, CLECSF12, DECTIN1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018803	64593	RBMY3AP	http://www.ncbi.nlm.nih.gov/gene/?term=64593	"RBMY3P, RBMY4P, SPATA14 "	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00018804	64598	MOSPD3	http://www.ncbi.nlm.nih.gov/gene/?term=64598	"CDS3, NET30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018805	64599	GIGYF1	http://www.ncbi.nlm.nih.gov/gene/?term=64599	"GYF1, PERQ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018806	645	BLVRB	http://www.ncbi.nlm.nih.gov/gene/?term=645	"BVRB, FLR, HEL-S-10, SDR43U1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018807	645	BLVRB	http://www.ncbi.nlm.nih.gov/gene/?term=645	"BVRB, FLR, HEL-S-10, SDR43U1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018808	645	BLVRB	http://www.ncbi.nlm.nih.gov/gene/?term=645	"BVRB, FLR, HEL-S-10, SDR43U1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018809	64602	Ireb2	http://www.ncbi.nlm.nih.gov/gene/?term=64602	"D9Ertd85e, Irp2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018810	6461	SHB	http://www.ncbi.nlm.nih.gov/gene/?term=6461	bA3J10.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018811	6461	SHB	http://www.ncbi.nlm.nih.gov/gene/?term=6461	bA3J10.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018812	646450	ARIH2OS	http://www.ncbi.nlm.nih.gov/gene/?term=646450	C3orf71	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018813	646450	ARIH2OS	http://www.ncbi.nlm.nih.gov/gene/?term=646450	C3orf71	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018814	64645	MFSD14A	http://www.ncbi.nlm.nih.gov/gene/?term=64645	HIAT1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018815	6464	SHC1	http://www.ncbi.nlm.nih.gov/gene/?term=6464	"SHC, SHCA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018816	6464	SHC1	http://www.ncbi.nlm.nih.gov/gene/?term=6464	"SHC, SHCA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018817	64654	Fgf23	http://www.ncbi.nlm.nih.gov/gene/?term=64654		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018818	64654	Fgf23	http://www.ncbi.nlm.nih.gov/gene/?term=64654		mRNA	Mus musculus	16012775	Dendrite	-	Next generation sequencing	"Because mouse Fgf23 mRNA was expressed in dendritic cells and activated spleen, tumor infiltrating dendritic cells are candidate sources of FGF23 secretion in TIO patients. "
RLID00018819	64655	Mrps22	http://www.ncbi.nlm.nih.gov/gene/?term=64655	"3100002P07Rik, Rpms22 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018820	64656	Mrps23	http://www.ncbi.nlm.nih.gov/gene/?term=64656	"D11Bwg1153e, MRP-S23, Rpms23, S23mt "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018821	646588	LOC646588	http://www.ncbi.nlm.nih.gov/gene/?term=646588		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018822	64682	ANAPC1	http://www.ncbi.nlm.nih.gov/gene/?term=64682	"APC1, MCPR, TSG24 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018823	64682	ANAPC1	http://www.ncbi.nlm.nih.gov/gene/?term=64682	"APC1, MCPR, TSG24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018824	64689	GORASP1	http://www.ncbi.nlm.nih.gov/gene/?term=64689	"GOLPH5, GRASP65, P65 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018825	64689	GORASP1	http://www.ncbi.nlm.nih.gov/gene/?term=64689	"GOLPH5, GRASP65, P65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018826	646962	HRCT1	http://www.ncbi.nlm.nih.gov/gene/?term=646962	"LGLL338, PRO537, UNQ338 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018827	64697	Keg1	http://www.ncbi.nlm.nih.gov/gene/?term=64697	"0610008P16Rik, AI316519, GS4059 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018828	64697	Keg1	http://www.ncbi.nlm.nih.gov/gene/?term=64697	"0610008P16Rik, AI316519, GS4059 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018829	64699	TMPRSS3	http://www.ncbi.nlm.nih.gov/gene/?term=64699	"DFNB10, DFNB8, ECHOS1, TADG12 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018830	64699	TMPRSS3	http://www.ncbi.nlm.nih.gov/gene/?term=64699	"DFNB10, DFNB8, ECHOS1, TADG12 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018831	6469	SHH	http://www.ncbi.nlm.nih.gov/gene/?term=6469	"HHG1, HLP3, HPE3, MCOPCB5, SMMCI, TPT, TPTPS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018832	646	BNC1	http://www.ncbi.nlm.nih.gov/gene/?term=646	"BNC, BSN1, HsT19447 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018833	647087	C7orf73	http://www.ncbi.nlm.nih.gov/gene/?term=647087	PL-5283	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018834	647087	C7orf73	http://www.ncbi.nlm.nih.gov/gene/?term=647087	PL-5283	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018835	647087	C7orf73	http://www.ncbi.nlm.nih.gov/gene/?term=647087	PL-5283	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018836	647087	C7orf73	http://www.ncbi.nlm.nih.gov/gene/?term=647087	PL-5283	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018837	64708	COPS7B	http://www.ncbi.nlm.nih.gov/gene/?term=64708	"CSN7B, SGN7b "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018838	64708	COPS7B	http://www.ncbi.nlm.nih.gov/gene/?term=64708	"CSN7B, SGN7b "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018839	6470	SHMT1	http://www.ncbi.nlm.nih.gov/gene/?term=6470	"CSHMT, SHMT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018840	6470	SHMT1	http://www.ncbi.nlm.nih.gov/gene/?term=6470	"CSHMT, SHMT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018841	6470	SHMT1	http://www.ncbi.nlm.nih.gov/gene/?term=6470	"CSHMT, SHMT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018842	64710	NUCKS1	http://www.ncbi.nlm.nih.gov/gene/?term=64710	"JC7, NUCKS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018843	64710	NUCKS1	http://www.ncbi.nlm.nih.gov/gene/?term=64710	"JC7, NUCKS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018844	64717	TRG-CCC2-2	http://www.ncbi.nlm.nih.gov/gene/?term=64717	"TRG-CCC2-1, TRG4, TRNAG4 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018845	6472	SHMT2	http://www.ncbi.nlm.nih.gov/gene/?term=6472	"GLYA, HEL-S-51e, SHMT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018846	6473	SHOX	http://www.ncbi.nlm.nih.gov/gene/?term=6473	"GCFX, PHOGY, SS, SHOX "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018847	6473	SHOX	http://www.ncbi.nlm.nih.gov/gene/?term=6473	"GCFX, PHOGY, SS, SHOX "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018848	64743	WDR13	http://www.ncbi.nlm.nih.gov/gene/?term=64743	MG21	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018849	64743	WDR13	http://www.ncbi.nlm.nih.gov/gene/?term=64743	MG21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018850	64744	SMAP2	http://www.ncbi.nlm.nih.gov/gene/?term=64744	SMAP1L	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018851	64745	METTL17	http://www.ncbi.nlm.nih.gov/gene/?term=64745	METT11D1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018852	64746	ACBD3	http://www.ncbi.nlm.nih.gov/gene/?term=64746	"GCP60, GOCAP1, GOLPH1, PAP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018853	64747	MFSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64747	SMAP4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018854	64747	MFSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64747	SMAP4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018855	6474	SHOX2	http://www.ncbi.nlm.nih.gov/gene/?term=6474	"OG12, OG12X, SHOT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018856	64750	SMURF2	http://www.ncbi.nlm.nih.gov/gene/?term=64750		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018857	64750	SMURF2	http://www.ncbi.nlm.nih.gov/gene/?term=64750		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018858	64755	C16orf58	http://www.ncbi.nlm.nih.gov/gene/?term=64755	RUS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018859	64756	ATPAF1	http://www.ncbi.nlm.nih.gov/gene/?term=64756	"ATP11, ATP11p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018860	64756	ATPAF1	http://www.ncbi.nlm.nih.gov/gene/?term=64756	"ATP11, ATP11p "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018861	64756	ATPAF1	http://www.ncbi.nlm.nih.gov/gene/?term=64756	"ATP11, ATP11p "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018862	64756	ATPAF1	http://www.ncbi.nlm.nih.gov/gene/?term=64756	"ATP11, ATP11p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018863	64757	MARC1	http://www.ncbi.nlm.nih.gov/gene/?term=64757	MOSC1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018864	64759	TNS3	http://www.ncbi.nlm.nih.gov/gene/?term=64759	"TEM6, TENS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018865	64761	PARP12	http://www.ncbi.nlm.nih.gov/gene/?term=64761	"ARTD12, MST109, MSTP109, ZC3H1, ZC3HDC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018866	64761	PARP12	http://www.ncbi.nlm.nih.gov/gene/?term=64761	"ARTD12, MST109, MSTP109, ZC3H1, ZC3HDC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018867	64762	GAREM1	http://www.ncbi.nlm.nih.gov/gene/?term=64762	"C18orf11, FAM59A, GAREM, Gm944 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018868	64763	ZNF574	http://www.ncbi.nlm.nih.gov/gene/?term=64763	FP972	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018869	64764	CREB3L2	http://www.ncbi.nlm.nih.gov/gene/?term=64764	BBF2H7	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018870	64768	IPPK	http://www.ncbi.nlm.nih.gov/gene/?term=64768	"C9orf12, INSP5K2, IP5K, IPK1, bA476B13.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018871	64768	IPPK	http://www.ncbi.nlm.nih.gov/gene/?term=64768	"C9orf12, INSP5K2, IP5K, IPK1, bA476B13.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018872	64768	IPPK	http://www.ncbi.nlm.nih.gov/gene/?term=64768	"C9orf12, INSP5K2, IP5K, IPK1, bA476B13.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018873	64769	MEAF6	http://www.ncbi.nlm.nih.gov/gene/?term=64769	"C1orf149, CENP-28, EAF6, NY-SAR-91 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018874	64769	MEAF6	http://www.ncbi.nlm.nih.gov/gene/?term=64769	"C1orf149, CENP-28, EAF6, NY-SAR-91 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018875	64770	CCDC14	http://www.ncbi.nlm.nih.gov/gene/?term=64770		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018876	64773	PCED1A	http://www.ncbi.nlm.nih.gov/gene/?term=64773	"C20orf81, FAM113A, bA12M19.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018877	64776	C11orf1	http://www.ncbi.nlm.nih.gov/gene/?term=64776		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018878	64777	RMND5B	http://www.ncbi.nlm.nih.gov/gene/?term=64777	"GID2, GID2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018879	64778	FNDC3B	http://www.ncbi.nlm.nih.gov/gene/?term=64778	"FAD104, PRO4979, YVTM2421 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018880	64778	FNDC3B	http://www.ncbi.nlm.nih.gov/gene/?term=64778	"FAD104, PRO4979, YVTM2421 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018881	64780	MICAL1	http://www.ncbi.nlm.nih.gov/gene/?term=64780	"MICAL, MICAL-1, NICAL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018882	64782	AEN	http://www.ncbi.nlm.nih.gov/gene/?term=64782	"ISG20L1, pp12744 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018883	64783	RBM15	http://www.ncbi.nlm.nih.gov/gene/?term=64783	"OTT, OTT1, SPEN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018884	64784	CRTC3	http://www.ncbi.nlm.nih.gov/gene/?term=64784	"TORC-3, TORC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018885	64785	GINS3	http://www.ncbi.nlm.nih.gov/gene/?term=64785	PSF3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018886	64785	GINS3	http://www.ncbi.nlm.nih.gov/gene/?term=64785	PSF3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018887	64785	GINS3	http://www.ncbi.nlm.nih.gov/gene/?term=64785	PSF3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018888	64785	GINS3	http://www.ncbi.nlm.nih.gov/gene/?term=64785	PSF3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018889	64786	TBC1D15	http://www.ncbi.nlm.nih.gov/gene/?term=64786	RAB7-GAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018890	64787	EPS8L2	http://www.ncbi.nlm.nih.gov/gene/?term=64787	EPS8R2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018891	6478	SIAH2	http://www.ncbi.nlm.nih.gov/gene/?term=6478	hSiah2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018892	6478	SIAH2	http://www.ncbi.nlm.nih.gov/gene/?term=6478	hSiah2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018893	64792	IFT22	http://www.ncbi.nlm.nih.gov/gene/?term=64792	RABL5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018894	64793	CEP85	http://www.ncbi.nlm.nih.gov/gene/?term=64793	CCDC21	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018895	64793	CEP85	http://www.ncbi.nlm.nih.gov/gene/?term=64793	CCDC21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018896	64794	DDX31	http://www.ncbi.nlm.nih.gov/gene/?term=64794	PPP1R25	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018897	64795	RMND5A	http://www.ncbi.nlm.nih.gov/gene/?term=64795	"CTLH, GID2, GID2A, RMD5, p44CTLH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018898	64795	RMND5A	http://www.ncbi.nlm.nih.gov/gene/?term=64795	"CTLH, GID2, GID2A, RMD5, p44CTLH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018899	64801	ARV1	http://www.ncbi.nlm.nih.gov/gene/?term=64801		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018900	64802	NMNAT1	http://www.ncbi.nlm.nih.gov/gene/?term=64802	"LCA9, NMNAT, PNAT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018901	64802	NMNAT1	http://www.ncbi.nlm.nih.gov/gene/?term=64802	"LCA9, NMNAT, PNAT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018902	6480	ST6GAL1	http://www.ncbi.nlm.nih.gov/gene/?term=6480	"SIAT1, ST6GalI, ST6N "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018903	6480	ST6GAL1	http://www.ncbi.nlm.nih.gov/gene/?term=6480	"SIAT1, ST6GalI, ST6N "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018904	64817	Svep1	http://www.ncbi.nlm.nih.gov/gene/?term=64817	"1110021D17Rik, 4833413O10Rik, AA387071, D430029O09Rik, Polydom "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018905	64818	Krt81	http://www.ncbi.nlm.nih.gov/gene/?term=64818	"AA589625, Krt2-19 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018906	6482	ST3GAL1	http://www.ncbi.nlm.nih.gov/gene/?term=6482	"Gal-NAc6S, SIAT4A, SIATFL, ST3GalA, ST3GalA.1, ST3GalIA, ST3GalIA, 1, ST3O "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018907	64834	ELOVL1	http://www.ncbi.nlm.nih.gov/gene/?term=64834	"CGI-88, Ssc1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018908	64837	KLC2	http://www.ncbi.nlm.nih.gov/gene/?term=64837		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018909	64839	FBXL17	http://www.ncbi.nlm.nih.gov/gene/?term=64839	"FBXO13, Fbl17, Fbx13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018910	64839	FBXL17	http://www.ncbi.nlm.nih.gov/gene/?term=64839	"FBXO13, Fbl17, Fbx13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018911	6483	ST3GAL2	http://www.ncbi.nlm.nih.gov/gene/?term=6483	"Gal-NAc6S, SIAT4B, ST3GALII, ST3GalA.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018912	64841	GNPNAT1	http://www.ncbi.nlm.nih.gov/gene/?term=64841	"GNA1, GNPNAT, Gpnat1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018913	64843	ISL2	http://www.ncbi.nlm.nih.gov/gene/?term=64843		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018914	64844	MARCH7	http://www.ncbi.nlm.nih.gov/gene/?term=64844	"AXO, AXOT, MARCH-VII, RNF177 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018915	64848	YTHDC2	http://www.ncbi.nlm.nih.gov/gene/?term=64848	CAHL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018916	64849	SLC13A3	http://www.ncbi.nlm.nih.gov/gene/?term=64849	"NADC3, SDCT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018917	6484	ST3GAL4	http://www.ncbi.nlm.nih.gov/gene/?term=6484	"CGS23, NANTA3, SAT3, SIAT4, SIAT4C, ST3GalIV, STZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018918	6484	ST3GAL4	http://www.ncbi.nlm.nih.gov/gene/?term=6484	"CGS23, NANTA3, SAT3, SIAT4, SIAT4C, ST3GalIV, STZ "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018919	64852	TUT1	http://www.ncbi.nlm.nih.gov/gene/?term=64852	"PAPD2, RBM21, STARPAP, TUTase, URLC6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018920	64853	AIDA	http://www.ncbi.nlm.nih.gov/gene/?term=64853	C1orf80	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018921	64853	AIDA	http://www.ncbi.nlm.nih.gov/gene/?term=64853	C1orf80	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018922	64854	USP46	http://www.ncbi.nlm.nih.gov/gene/?term=64854		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018923	64854	USP46	http://www.ncbi.nlm.nih.gov/gene/?term=64854		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018924	64854	USP46	http://www.ncbi.nlm.nih.gov/gene/?term=64854		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018925	64855	FAM129B	http://www.ncbi.nlm.nih.gov/gene/?term=64855	"C9orf88, MEG-3, MINERVA, OC58, bA356B19.6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018926	64856	VWA1	http://www.ncbi.nlm.nih.gov/gene/?term=64856	WARP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018927	64857	PLEKHG2	http://www.ncbi.nlm.nih.gov/gene/?term=64857	"ARHGEF42, CLG, LDAMD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018928	64857	PLEKHG2	http://www.ncbi.nlm.nih.gov/gene/?term=64857	"ARHGEF42, CLG, LDAMD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018929	64863	METTL4	http://www.ncbi.nlm.nih.gov/gene/?term=64863	HsT661	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018930	64866	CDCP1	http://www.ncbi.nlm.nih.gov/gene/?term=64866	"CD318, SIMA135, TRASK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018931	64866	CDCP1	http://www.ncbi.nlm.nih.gov/gene/?term=64866	"CD318, SIMA135, TRASK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018932	64866	CDCP1	http://www.ncbi.nlm.nih.gov/gene/?term=64866	"CD318, SIMA135, TRASK "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018933	6487	ST3GAL3	http://www.ncbi.nlm.nih.gov/gene/?term=6487	"EIEE15, MRT12, SIAT6, ST3GALII, ST3GalIII, ST3N "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018934	64897	C12orf43	http://www.ncbi.nlm.nih.gov/gene/?term=64897		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018935	648	BMI1	http://www.ncbi.nlm.nih.gov/gene/?term=648	"FLVI2/BMI1, PCGF4, RNF51, flvi-2/bmi-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018936	648	BMI1	http://www.ncbi.nlm.nih.gov/gene/?term=648	"FLVI2/BMI1, PCGF4, RNF51, flvi-2/bmi-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018937	64900	LPIN3	http://www.ncbi.nlm.nih.gov/gene/?term=64900	"LIPN3L, SMP2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018938	64900	LPIN3	http://www.ncbi.nlm.nih.gov/gene/?term=64900	"LIPN3L, SMP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018939	64900	LPIN3	http://www.ncbi.nlm.nih.gov/gene/?term=64900	"LIPN3L, SMP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018940	6490	PMEL	http://www.ncbi.nlm.nih.gov/gene/?term=6490	"D12S53E, ME20, ME20-M, ME20M, P1, P100, PMEL17, SI, SIL, SILV, gp100 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018941	6491	STIL	http://www.ncbi.nlm.nih.gov/gene/?term=6491	"MCPH7, SIL "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018942	6491	STIL	http://www.ncbi.nlm.nih.gov/gene/?term=6491	"MCPH7, SIL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018943	6491	STIL	http://www.ncbi.nlm.nih.gov/gene/?term=6491	"MCPH7, SIL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018944	64921	CASD1	http://www.ncbi.nlm.nih.gov/gene/?term=64921	"C7orf12, NBLA04196 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018945	64924	SLC30A5	http://www.ncbi.nlm.nih.gov/gene/?term=64924	"ZNT5, ZNTL1, ZTL1, ZnT-5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018946	64924	SLC30A5	http://www.ncbi.nlm.nih.gov/gene/?term=64924	"ZNT5, ZNTL1, ZTL1, ZnT-5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018947	64924	SLC30A5	http://www.ncbi.nlm.nih.gov/gene/?term=64924	"ZNT5, ZNTL1, ZTL1, ZnT-5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018948	64924	SLC30A5	http://www.ncbi.nlm.nih.gov/gene/?term=64924	"ZNT5, ZNTL1, ZTL1, ZnT-5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018949	64927	TTC23	http://www.ncbi.nlm.nih.gov/gene/?term=64927	HCC-8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018950	64928	MRPL14	http://www.ncbi.nlm.nih.gov/gene/?term=64928	"L14mt, L32mt, MRP-L14, MRP-L32, MRPL32, RMPL32, RPML32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018951	64930	Tsc1	http://www.ncbi.nlm.nih.gov/gene/?term=64930		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018952	64943	NT5DC2	http://www.ncbi.nlm.nih.gov/gene/?term=64943		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018953	64945	Cldn12	http://www.ncbi.nlm.nih.gov/gene/?term=64945		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018954	64946	CENPH	http://www.ncbi.nlm.nih.gov/gene/?term=64946		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018955	64946	CENPH	http://www.ncbi.nlm.nih.gov/gene/?term=64946		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018956	64946	CENPH	http://www.ncbi.nlm.nih.gov/gene/?term=64946		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00018957	64949	MRPS26	http://www.ncbi.nlm.nih.gov/gene/?term=64949	"C20orf193, GI008, MRP-S13, MRP-S26, MRPS13, NY-BR-87, RPMS13, dJ534B8.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018958	64949	MRPS26	http://www.ncbi.nlm.nih.gov/gene/?term=64949	"C20orf193, GI008, MRP-S13, MRP-S26, MRPS13, NY-BR-87, RPMS13, dJ534B8.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018959	6494	SIPA1	http://www.ncbi.nlm.nih.gov/gene/?term=6494	SPA1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018960	64951	MRPS24	http://www.ncbi.nlm.nih.gov/gene/?term=64951	"HSPC335, MRP-S24, S24mt, bMRP-47, bMRP47 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018961	64960	MRPS15	http://www.ncbi.nlm.nih.gov/gene/?term=64960	"DC37, MPR-S15, RPMS15, S15mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018962	64963	MRPS11	http://www.ncbi.nlm.nih.gov/gene/?term=64963	"HCC-2, MRP-S11, S11mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018963	64965	MRPS9	http://www.ncbi.nlm.nih.gov/gene/?term=64965	"MRP-S9, RPMS9, S9mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018964	64965	MRPS9	http://www.ncbi.nlm.nih.gov/gene/?term=64965	"MRP-S9, RPMS9, S9mt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018965	64968	MRPS6	http://www.ncbi.nlm.nih.gov/gene/?term=64968	"C21orf101, MRP-S6, RPMS6, S6mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018966	64968	MRPS6	http://www.ncbi.nlm.nih.gov/gene/?term=64968	"C21orf101, MRP-S6, RPMS6, S6mt "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018967	64969	MRPS5	http://www.ncbi.nlm.nih.gov/gene/?term=64969	"MRP-S5, S5mt "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018968	64969	MRPS5	http://www.ncbi.nlm.nih.gov/gene/?term=64969	"MRP-S5, S5mt "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018969	64975	MRPL41	http://www.ncbi.nlm.nih.gov/gene/?term=64975	"BMRP, MRP-L27, MRPL27, PIG3, RPML27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018970	64976	MRPL40	http://www.ncbi.nlm.nih.gov/gene/?term=64976	"L40mt, MRP-L22, MRP-L40, MRPL22, NLVCF, URIM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018971	64978	MRPL38	http://www.ncbi.nlm.nih.gov/gene/?term=64978	"HSPC262, L38MT, MRP-L3, MRP-L38, RPML3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018972	64979	MRPL36	http://www.ncbi.nlm.nih.gov/gene/?term=64979	"BRIP1, L36mt, MRP-L36, PRPL36, RPMJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018973	64979	MRPL36	http://www.ncbi.nlm.nih.gov/gene/?term=64979	"BRIP1, L36mt, MRP-L36, PRPL36, RPMJ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018974	6497	SKI	http://www.ncbi.nlm.nih.gov/gene/?term=6497	"SGS, SKV "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018975	64981	MRPL34	http://www.ncbi.nlm.nih.gov/gene/?term=64981	L34mt	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018976	64983	MRPL32	http://www.ncbi.nlm.nih.gov/gene/?term=64983	"HSPC283, L32mt, MRP-L32, bMRP-59b "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018977	64983	MRPL32	http://www.ncbi.nlm.nih.gov/gene/?term=64983	"HSPC283, L32mt, MRP-L32, bMRP-59b "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018978	649	BMP1	http://www.ncbi.nlm.nih.gov/gene/?term=649	"OI13, PCOLC, PCP, PCP2, TLD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018979	65003	MRPL11	http://www.ncbi.nlm.nih.gov/gene/?term=65003	"CGI-113, L11MT, MRP-L11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018980	65005	MRPL9	http://www.ncbi.nlm.nih.gov/gene/?term=65005	L9mt	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018981	65008	MRPL1	http://www.ncbi.nlm.nih.gov/gene/?term=65008	"BM022, L1MT, MRP-L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018982	65008	MRPL1	http://www.ncbi.nlm.nih.gov/gene/?term=65008	"BM022, L1MT, MRP-L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018983	65009	NDRG4	http://www.ncbi.nlm.nih.gov/gene/?term=65009	"BDM1, SMAP-8, SMAP8 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00018984	6500	SKP1	http://www.ncbi.nlm.nih.gov/gene/?term=6500	"EMC19, OCP-II, OCP2A, TCEB1L, p19A, SKP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018985	6500	SKP1	http://www.ncbi.nlm.nih.gov/gene/?term=6500	"EMC19, OCP-II, OCP2, SKP1A, TCEB1L, p19A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018986	65010	SLC26A6	http://www.ncbi.nlm.nih.gov/gene/?term=65010		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018987	65010	SLC26A6	http://www.ncbi.nlm.nih.gov/gene/?term=65010		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018988	65018	PINK1	http://www.ncbi.nlm.nih.gov/gene/?term=65018	"BRPK, PARK6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018989	65018	PINK1	http://www.ncbi.nlm.nih.gov/gene/?term=65018	"BRPK, PARK6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018990	65019	Rpl23	http://www.ncbi.nlm.nih.gov/gene/?term=65019	2810009A01Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00018991	65020	Zfp110	http://www.ncbi.nlm.nih.gov/gene/?term=65020	"2900024E01Rik, N28112, NRIF, Nrif1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00018992	6502	SKP2	http://www.ncbi.nlm.nih.gov/gene/?term=6502	"FBL1, FBXL1, FLB1, p45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018993	65055	REEP1	http://www.ncbi.nlm.nih.gov/gene/?term=65055	"C2orf23, HMN5B, SPG31, Yip2a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018994	65056	GPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=65056	"GPBP, SSH6, VASCULIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018995	65056	GPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=65056	"GPBP, SSH6, VASCULIN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00018996	65056	GPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=65056	"GPBP, SSH6, VASCULIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018997	65057	ACD	http://www.ncbi.nlm.nih.gov/gene/?term=65057	"PIP1, PTOP, TINT1, TPP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00018998	65057	ACD	http://www.ncbi.nlm.nih.gov/gene/?term=65057	"PIP1, PTOP, TINT1, TPP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00018999	65062	TMEM237	http://www.ncbi.nlm.nih.gov/gene/?term=65062	"ALS2CR4, JBTS14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019000	65062	TMEM237	http://www.ncbi.nlm.nih.gov/gene/?term=65062	"ALS2CR4, JBTS14 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019001	6506	SLC1A2	http://www.ncbi.nlm.nih.gov/gene/?term=6506	"EAAT2, GLT-1, HBGT "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019002	6506	SLC1A2	http://www.ncbi.nlm.nih.gov/gene/?term=6506	"EAAT2, GLT-1, HBGT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019003	65078	RTN4R	http://www.ncbi.nlm.nih.gov/gene/?term=65078	"NGR, NOGOR "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019004	65078	RTN4R	http://www.ncbi.nlm.nih.gov/gene/?term=65078	"NGR, NOGOR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019005	6507	SLC1A3	http://www.ncbi.nlm.nih.gov/gene/?term=6507	"EA6, EAAT1, GLAST, GLAST1 "	mRNA	Homo sapiens	16042756	Endoplasmic reticulum	HEK293 cell	RT-PCR	"When expressed in HEK293 cells, EAAT1ex9skip mRNA is translated into a truncated protein localized in the endoplasmic reticulum. "
RLID00019006	65080	MRPL44	http://www.ncbi.nlm.nih.gov/gene/?term=65080	"COXPD16, L44MT, MRP-L44 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019007	65080	MRPL44	http://www.ncbi.nlm.nih.gov/gene/?term=65080	"COXPD16, L44MT, MRP-L44 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019008	65080	MRPL44	http://www.ncbi.nlm.nih.gov/gene/?term=65080	"COXPD16, L44MT, MRP-L44 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019009	65082	VPS33A	http://www.ncbi.nlm.nih.gov/gene/?term=65082		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019010	65082	VPS33A	http://www.ncbi.nlm.nih.gov/gene/?term=65082		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019011	65082	VPS33A	http://www.ncbi.nlm.nih.gov/gene/?term=65082		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019012	65083	NOL6	http://www.ncbi.nlm.nih.gov/gene/?term=65083	"NRAP, UTP22, bA311H10.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019013	65083	NOL6	http://www.ncbi.nlm.nih.gov/gene/?term=65083	"NRAP, UTP22, bA311H10.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019014	65084	TMEM135	http://www.ncbi.nlm.nih.gov/gene/?term=65084	PMP52	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019015	6508	SLC4A3	http://www.ncbi.nlm.nih.gov/gene/?term=6508	"AE3, SLC2C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019016	65094	JMJD4	http://www.ncbi.nlm.nih.gov/gene/?term=65094		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019017	65094	JMJD4	http://www.ncbi.nlm.nih.gov/gene/?term=65094		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019018	65098	Zfand6	http://www.ncbi.nlm.nih.gov/gene/?term=65098	"3110005P07Rik, Awp1, Za20d3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019019	65098	Zfand6	http://www.ncbi.nlm.nih.gov/gene/?term=65098	"3110005P07Rik, Awp1, Za20d3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019020	6509	SLC1A4	http://www.ncbi.nlm.nih.gov/gene/?term=6509	"ASCT1, SATT, SPATCCM "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019021	650	BMP2	http://www.ncbi.nlm.nih.gov/gene/?term=650	"BDA2A, BMP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019022	650	BMP2	http://www.ncbi.nlm.nih.gov/gene/?term=650	"BDA2, BMP2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019023	65103	Arl6ip6	http://www.ncbi.nlm.nih.gov/gene/?term=65103	"2310057C01Rik, 2610529A11Rik, Aip-6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019024	65108	MARCKSL1	http://www.ncbi.nlm.nih.gov/gene/?term=65108	"F52, MACMARCKS, MLP, MLP1, MRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019025	6510	SLC1A5	http://www.ncbi.nlm.nih.gov/gene/?term=6510	"AAAT, ASCT2, ATBO, M7V1, M7VS1, R16, RDRC "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019026	6510	SLC1A5	http://www.ncbi.nlm.nih.gov/gene/?term=6510	"AAAT, ASCT2, ATBO, M7V1, M7VS1, R16, RDRC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019027	6510	SLC1A5	http://www.ncbi.nlm.nih.gov/gene/?term=6510	"AAAT, ASCT2, ATBO, M7V1, M7VS1, R16, RDRC "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019028	65114	Vps35	http://www.ncbi.nlm.nih.gov/gene/?term=65114	"AI647796, Mem3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019029	65117	RSRC2	http://www.ncbi.nlm.nih.gov/gene/?term=65117		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019030	65124	SOWAHC	http://www.ncbi.nlm.nih.gov/gene/?term=65124	"ANKRD57, C2orf26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019031	65125	WNK1	http://www.ncbi.nlm.nih.gov/gene/?term=65125	"HSAN2, HSN2, KDP, PPP1R167, PRKWNK1, PSK, p65 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019032	65125	WNK1	http://www.ncbi.nlm.nih.gov/gene/?term=65125	"HSAN2, HSN2, KDP, PPP1R167, PRKWNK1, PSK, p65 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019033	65125	WNK1	http://www.ncbi.nlm.nih.gov/gene/?term=65125	"HSAN2, HSN2, KDP, PPP1R167, PRKWNK1, PSK, p65 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019034	6512	SLC1A7	http://www.ncbi.nlm.nih.gov/gene/?term=6512	"AAAT, EAAT5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019035	6513	SLC2A1	http://www.ncbi.nlm.nih.gov/gene/?term=6513	"CSE, DYT17, DYT18, DYT9, EIG12, GLUT, GLUT-1, GLUT1, GLUT1DS, HTLVR, PED, SDCHCN "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019036	6513	SLC2A1	http://www.ncbi.nlm.nih.gov/gene/?term=6513	"CSE, DYT17, DYT18, DYT9, EIG12, GLUT, GLUT-1, GLUT1, GLUT1DS, HTLVR, PED, SDCHCN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019037	6515	SLC2A3	http://www.ncbi.nlm.nih.gov/gene/?term=6515	GLUT3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019038	651746	ANKRD33B	http://www.ncbi.nlm.nih.gov/gene/?term=651746		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019039	6517	SLC2A4	http://www.ncbi.nlm.nih.gov/gene/?term=6517	GLUT4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019040	6517	SLC2A4	http://www.ncbi.nlm.nih.gov/gene/?term=6517	GLUT4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019041	65180	Kcnd2	http://www.ncbi.nlm.nih.gov/gene/?term=65180	"Kv4.2, RK5, Shal1 "	mRNA	Rattus norvegicus	21034530	Dendrite	Hippocampus	In situ hybridization	"In this study, Kv4.2 mRNAs were shown to be localized in the dendrites near postsynaptic regions. "
RLID00019042	6518	SLC2A5	http://www.ncbi.nlm.nih.gov/gene/?term=6518	"GLUT-5, GLUT5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019043	651	BMP3	http://www.ncbi.nlm.nih.gov/gene/?term=651	BMP-3A	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019044	651	BMP3	http://www.ncbi.nlm.nih.gov/gene/?term=651	BMP-3A	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019045	6520	SLC3A2	http://www.ncbi.nlm.nih.gov/gene/?term=6520	"4F2, 4F2HC, 4T2HC, CD98, CD98HC, MDU1, NACAE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019046	6520	SLC3A2	http://www.ncbi.nlm.nih.gov/gene/?term=6520	"4F2, 4F2HC, 4T2HC, CD98, CD98HC, MDU1, NACAE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019047	65220	NADK	http://www.ncbi.nlm.nih.gov/gene/?term=65220	dJ283E3.1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019048	65220	NADK	http://www.ncbi.nlm.nih.gov/gene/?term=65220	dJ283E3.1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019049	6522	SLC4A2	http://www.ncbi.nlm.nih.gov/gene/?term=6522	"AE2, BND3L, EPB3L1, HKB3, NBND3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019050	6522	SLC4A2	http://www.ncbi.nlm.nih.gov/gene/?term=6522	"AE2, BND3L, EPB3L1, HKB3, NBND3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019051	6523	SLC5A1	http://www.ncbi.nlm.nih.gov/gene/?term=6523	"D22S675, NAGT, SGLT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019052	65243	ZFP69B	http://www.ncbi.nlm.nih.gov/gene/?term=65243	"ZKSCAN23B, ZNF643, ZSCAN54B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019053	65243	ZFP69B	http://www.ncbi.nlm.nih.gov/gene/?term=65243	"ZKSCAN23B, ZNF643, ZSCAN54B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019054	65246	Xpo7	http://www.ncbi.nlm.nih.gov/gene/?term=65246	"4930506C02Rik, BB164534, Ranbp16, mKIAA0745 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019055	65254	Dpysl5	http://www.ncbi.nlm.nih.gov/gene/?term=65254	"CRAM, CRMP-5, Crmp5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019056	65258	MPPE1	http://www.ncbi.nlm.nih.gov/gene/?term=65258	PGAP5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019057	6525	SMTN	http://www.ncbi.nlm.nih.gov/gene/?term=6525		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019058	65260	COA7	http://www.ncbi.nlm.nih.gov/gene/?term=65260	"C1orf163, RESA1, SELRC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019059	65263	PYCRL	http://www.ncbi.nlm.nih.gov/gene/?term=65263	PYCR3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019060	65264	UBE2Z	http://www.ncbi.nlm.nih.gov/gene/?term=65264	"HOYS7, USE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019061	65264	UBE2Z	http://www.ncbi.nlm.nih.gov/gene/?term=65264	"HOYS7, USE1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019062	65264	UBE2Z	http://www.ncbi.nlm.nih.gov/gene/?term=65264	"HOYS7, USE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019063	65265	C8orf33	http://www.ncbi.nlm.nih.gov/gene/?term=65265		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019064	65267	WNK3	http://www.ncbi.nlm.nih.gov/gene/?term=65267	PRKWNK3	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00019065	65267	WNK3	http://www.ncbi.nlm.nih.gov/gene/?term=65267	PRKWNK3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019066	65267	WNK3	http://www.ncbi.nlm.nih.gov/gene/?term=65267	PRKWNK3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019067	65267	WNK3	http://www.ncbi.nlm.nih.gov/gene/?term=65267	PRKWNK3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019068	6526	SLC5A3	http://www.ncbi.nlm.nih.gov/gene/?term=6526	"BCW2, SMIT, SMIT1, SMIT2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019069	6528	SLC5A5	http://www.ncbi.nlm.nih.gov/gene/?term=6528	"NIS, TDH1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019070	6528	SLC5A5	http://www.ncbi.nlm.nih.gov/gene/?term=6528	"NIS, TDH1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019071	652965	SNORA48	http://www.ncbi.nlm.nih.gov/gene/?term=652965	"ACA48A, SNORA48 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019072	652965	SNORA48	http://www.ncbi.nlm.nih.gov/gene/?term=652965	"ACA48A, SNORA48 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019073	652966	SNORD10	http://www.ncbi.nlm.nih.gov/gene/?term=652966	mgU6-77	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019074	652995	UCA1	http://www.ncbi.nlm.nih.gov/gene/?term=652995	"CUDR, LINC00178, NCRNA00178, UCAT1, onco-lncRNA-36 "	lncRNA	Homo sapiens	20117985	Cytoplasm	Bladder cancer cell	In situ hybridization|RT-PCR	"UCA1 gene locates in the cytoplasm, and its mRNA expression level is closely correlated to the progression of bladder cancer, indication its potential as a specific molecular marker of bladder cancer. "
RLID00019075	652995	UCA1	http://www.ncbi.nlm.nih.gov/gene/?term=652995	"CUDR, LINC00178, NCRNA00178, UCAT1, onco-lncRNA-36 "	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019076	6529	SLC6A1	http://www.ncbi.nlm.nih.gov/gene/?term=6529	"GABATHG, GABATR, GAT1, MAE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019077	652	BMP4	http://www.ncbi.nlm.nih.gov/gene/?term=652	"BMP2B, BMP2B1, MCOPS6, OFC11, ZYME "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019078	653121	ZBTB8A	http://www.ncbi.nlm.nih.gov/gene/?term=653121	"BOZF1, ZBTB8, ZNF916A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019079	653121	ZBTB8A	http://www.ncbi.nlm.nih.gov/gene/?term=653121	"BOZF1, ZBTB8, ZNF916A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019080	653220	XAGE1B	http://www.ncbi.nlm.nih.gov/gene/?term=653220	"CT12.1, CT12.1A, CT12.1B, CTP9, GAGED2, XAGE-1, XAGE1, XAGE1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019081	653226	SRP9P1	http://www.ncbi.nlm.nih.gov/gene/?term=653226	SRP9L1	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019082	6533	SLC6A6	http://www.ncbi.nlm.nih.gov/gene/?term=6533	TAUT	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019083	653423	SPAG11A	http://www.ncbi.nlm.nih.gov/gene/?term=653423	"EDDM2A, HE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019084	653464	SRGAP2C	http://www.ncbi.nlm.nih.gov/gene/?term=653464	SRGAP2P1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019085	653567	TMEM236	http://www.ncbi.nlm.nih.gov/gene/?term=653567	"FAM23A, FAM23B, bA162I21.2, bA16O1.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019086	653567	TMEM236	http://www.ncbi.nlm.nih.gov/gene/?term=653567	"FAM23A, FAM23B, bA162I21.2, bA16O1.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019087	653567	TMEM236	http://www.ncbi.nlm.nih.gov/gene/?term=653567	"FAM23A, FAM23B, bA162I21.2, bA16O1.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019088	6535	SLC6A8	http://www.ncbi.nlm.nih.gov/gene/?term=6535	"CCDS1, CRT, CRTR, CT1, CTR5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019089	6535	SLC6A8	http://www.ncbi.nlm.nih.gov/gene/?term=6535	"CCDS1, CRT, CRTR, CT1, CTR5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019090	653604	HIST2H3D	http://www.ncbi.nlm.nih.gov/gene/?term=653604		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019091	653604	HIST2H3D	http://www.ncbi.nlm.nih.gov/gene/?term=653604		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019092	653784	MZT2A	http://www.ncbi.nlm.nih.gov/gene/?term=653784	"FAM128A, MOZART2A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019093	653784	MZT2A	http://www.ncbi.nlm.nih.gov/gene/?term=653784	"FAM128A, MOZART2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019094	653820	FAM72B	http://www.ncbi.nlm.nih.gov/gene/?term=653820	p17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019095	653	BMP5	http://www.ncbi.nlm.nih.gov/gene/?term=653		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019096	6541	SLC7A1	http://www.ncbi.nlm.nih.gov/gene/?term=6541	"ATRC1, CAT-1, ERR, HCAT1, REC1L "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019097	6541	SLC7A1	http://www.ncbi.nlm.nih.gov/gene/?term=6541	"ATRC1, CAT-1, ERR, HCAT1, REC1L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019098	6542	SLC7A2	http://www.ncbi.nlm.nih.gov/gene/?term=6542	"ATRC2, CAT2, HCAT2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019099	6542	SLC7A2	http://www.ncbi.nlm.nih.gov/gene/?term=6542	"ATRC2, CAT2, HCAT2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019100	654319	SNORA5A	http://www.ncbi.nlm.nih.gov/gene/?term=654319	"ACA5, ACA5A/B/C "	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019101	654320	SNORA8	http://www.ncbi.nlm.nih.gov/gene/?term=654320	ACA8	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019102	654320	SNORA8	http://www.ncbi.nlm.nih.gov/gene/?term=654320	ACA8	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019103	654320	SNORA8	http://www.ncbi.nlm.nih.gov/gene/?term=654320	ACA8	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019104	654321	SNORA75	http://www.ncbi.nlm.nih.gov/gene/?term=654321	"SNORA75A, U23 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019105	654322	SNORA13	http://www.ncbi.nlm.nih.gov/gene/?term=654322	ACA13	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019106	654322	SNORA13	http://www.ncbi.nlm.nih.gov/gene/?term=654322	ACA13	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019107	6543	SLC8A2	http://www.ncbi.nlm.nih.gov/gene/?term=6543	NCX2	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00019108	654412	FAM138B	http://www.ncbi.nlm.nih.gov/gene/?term=654412	"F379, bA395L14.6 "	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00019109	654412	FAM138B	http://www.ncbi.nlm.nih.gov/gene/?term=654412	"F379, bA395L14.6 "	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00019110	654433	PAX8-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=654433		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019111	654434	SNHG20	http://www.ncbi.nlm.nih.gov/gene/?term=654434	"C17orf86, LINC00338, NCRNA00338, SCARNA16HG "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019112	654462	Kncn	http://www.ncbi.nlm.nih.gov/gene/?term=654462	"Kino, L5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019113	654483	BOLA2B	http://www.ncbi.nlm.nih.gov/gene/?term=654483	BOLA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019114	654493	8030494B02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=654493		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019115	654494	Gm7337	http://www.ncbi.nlm.nih.gov/gene/?term=654494	EG654494	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019116	6546	SLC8A1	http://www.ncbi.nlm.nih.gov/gene/?term=6546	NCX1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019117	654795	Sdr39u1	http://www.ncbi.nlm.nih.gov/gene/?term=654795	2310014G06Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019118	654796	9530036O11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=654796		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019119	654809	4930428O21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=654809		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019120	6549	SLC9A2	http://www.ncbi.nlm.nih.gov/gene/?term=6549	NHE2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019121	654	BMP6	http://www.ncbi.nlm.nih.gov/gene/?term=654	"VGR, VGR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019122	654	BMP6	http://www.ncbi.nlm.nih.gov/gene/?term=654	"VGR, VGR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019123	6550	SLC9A3	http://www.ncbi.nlm.nih.gov/gene/?term=6550	"DIAR8, NHE-3, NHE3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019124	6553	SLC9A5	http://www.ncbi.nlm.nih.gov/gene/?term=6553	NHE5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019125	6556	SLC11A1	http://www.ncbi.nlm.nih.gov/gene/?term=6556	"LSH, NRAMP, NRAMP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019126	6556	SLC11A1	http://www.ncbi.nlm.nih.gov/gene/?term=6556	"LSH, NRAMP, NRAMP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019127	6558	SLC12A2	http://www.ncbi.nlm.nih.gov/gene/?term=6558	"BSC, BSC2, NKCC1, PPP1R141 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019128	6558	SLC12A2	http://www.ncbi.nlm.nih.gov/gene/?term=6558	"BSC, BSC2, NKCC1, PPP1R141 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019129	6558	SLC12A2	http://www.ncbi.nlm.nih.gov/gene/?term=6558	"BSC, BSC2, NKCC1, PPP1R141 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019130	655	BMP7	http://www.ncbi.nlm.nih.gov/gene/?term=655	OP-1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019131	6560	SLC12A4	http://www.ncbi.nlm.nih.gov/gene/?term=6560	KCC1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019132	6561	SLC13A1	http://www.ncbi.nlm.nih.gov/gene/?term=6561	"NAS1, NaSi-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019133	6561	SLC13A1	http://www.ncbi.nlm.nih.gov/gene/?term=6561	"NAS1, NaSi-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019134	6561	SLC13A1	http://www.ncbi.nlm.nih.gov/gene/?term=6561	"NAS1, NaSi-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019135	6566	SLC16A1	http://www.ncbi.nlm.nih.gov/gene/?term=6566	"HHF7, MCT, MCT1, MCT1D "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019136	6566	SLC16A1	http://www.ncbi.nlm.nih.gov/gene/?term=6566	"HHF7, MCT, MCT1, MCT1D "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019137	6567	SLC16A2	http://www.ncbi.nlm.nih.gov/gene/?term=6567	"AHDS, DXS128, DXS128E, MCT 7, MCT 8, MCT7, MCT8, MRX22, XPCT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019138	656	BMP8B	http://www.ncbi.nlm.nih.gov/gene/?term=656	"BMP8, OP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019139	6573	SLC19A1	http://www.ncbi.nlm.nih.gov/gene/?term=6573	"CHMD, FOLT, IFC1, REFC, RFC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019140	6573	SLC19A1	http://www.ncbi.nlm.nih.gov/gene/?term=6573	"CHMD, FOLT, IFC1, REFC, RFC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019141	6574	SLC20A1	http://www.ncbi.nlm.nih.gov/gene/?term=6574	"GLVR1, Glvr-1, PIT1, PiT-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019142	6574	SLC20A1	http://www.ncbi.nlm.nih.gov/gene/?term=6574	"GLVR1, Glvr-1, PIT1, PiT-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019143	6574	SLC20A1	http://www.ncbi.nlm.nih.gov/gene/?term=6574	"GLVR1, Glvr-1, PIT1, PiT-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019144	6575	SLC20A2	http://www.ncbi.nlm.nih.gov/gene/?term=6575	"GLVR-2, GLVR2, IBGC1, IBGC3, MLVAR, PIT-2, PIT2, RAM1, Ram-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019145	6576	SLC25A1	http://www.ncbi.nlm.nih.gov/gene/?term=6576	"CTP, D2L2AD, SEA, SLC20A3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019146	6576	SLC25A1	http://www.ncbi.nlm.nih.gov/gene/?term=6576	"CTP, D2L2AD, SEA, SLC20A3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019147	6578	SLCO2A1	http://www.ncbi.nlm.nih.gov/gene/?term=6578	"MATR1, OATP2A1, PGT, PHOAR2, SLC21A2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019148	6579	SLCO1A2	http://www.ncbi.nlm.nih.gov/gene/?term=6579	"OATP, OATP-A, OATP1A2, SLC21A3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019149	6581	SLC22A3	http://www.ncbi.nlm.nih.gov/gene/?term=6581	"EMT, EMTH, OCT3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019150	6583	SLC22A4	http://www.ncbi.nlm.nih.gov/gene/?term=6583	OCTN1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019151	658	BMPR1B	http://www.ncbi.nlm.nih.gov/gene/?term=658	"ALK-6, ALK6, AMDD, BDA1D, BDA2, CDw293 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019152	658	BMPR1B	http://www.ncbi.nlm.nih.gov/gene/?term=658	"ALK-6, ALK6, AMDD, BDA1D, BDA2, CDw293 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019153	6590	SLPI	http://www.ncbi.nlm.nih.gov/gene/?term=6590	"ALK1, ALP, BLPI, HUSI, HUSI-I, MPI, WAP4, WFDC4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019154	6590	SLPI	http://www.ncbi.nlm.nih.gov/gene/?term=6590	"ALK1, ALP, BLPI, HUSI, HUSI-I, MPI, WAP4, WFDC4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019155	6595	SMARCA2	http://www.ncbi.nlm.nih.gov/gene/?term=6595	"BAF190, BRM, NCBRS, SNF2, SNF2L2, SNF2LA, SWI2, Sth1p, hBRM, hSNF2a "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019156	6595	SMARCA2	http://www.ncbi.nlm.nih.gov/gene/?term=6595	"BAF190, BRM, NCBRS, SNF2, SNF2L2, SNF2LA, SWI2, Sth1p, hBRM, hSNF2a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019157	65960	Twsg1	http://www.ncbi.nlm.nih.gov/gene/?term=65960	"1810013J15Rik, 9030422N06Rik, AW552143, D17Ertd403e, Tsg, Twg "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019158	65961	Utp3	http://www.ncbi.nlm.nih.gov/gene/?term=65961	"2400011K09Rik, AW557551, C87704, Crl1, Crlz1, Sas10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019159	65962	Slc9a3r2	http://www.ncbi.nlm.nih.gov/gene/?term=65962	"0610011L07Rik, 1200011K07Rik, 2010007A20Rik, E3karp, NHERF-2, Nherf2, Octs2, Sip-1, Sip1, Sryip1, Tka-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019160	65967	Eefsec	http://www.ncbi.nlm.nih.gov/gene/?term=65967	"Selb, sec "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019161	65971	Tbata	http://www.ncbi.nlm.nih.gov/gene/?term=65971	"1700021K02Rik, AI428928, Spatial, Titest "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019162	65973	Asph	http://www.ncbi.nlm.nih.gov/gene/?term=65973	"2310005F16Rik, 3110001L23Rik, AI848629, AW261690, AW561901, BAH, C79816, cI-37 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019163	65977	PLEKHA3	http://www.ncbi.nlm.nih.gov/gene/?term=65977	FAPP1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019164	65977	PLEKHA3	http://www.ncbi.nlm.nih.gov/gene/?term=65977	FAPP1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019165	65979	PHACTR4	http://www.ncbi.nlm.nih.gov/gene/?term=65979	PPP1R124	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019166	65979	PHACTR4	http://www.ncbi.nlm.nih.gov/gene/?term=65979	PPP1R124	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019167	6597	SMARCA4	http://www.ncbi.nlm.nih.gov/gene/?term=6597	"BAF190, BAF190A, BRG1, MRD16, RTPS2, SNF2, SNF2L4, SNF2LB, SWI2, hSNF2b "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019168	65980	BRD9	http://www.ncbi.nlm.nih.gov/gene/?term=65980	"LAVS3040, PRO9856 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019169	65985	AACS	http://www.ncbi.nlm.nih.gov/gene/?term=65985	"ACSF1, SUR-5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019170	65985	AACS	http://www.ncbi.nlm.nih.gov/gene/?term=65985	"ACSF1, SUR-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019171	65986	ZBTB10	http://www.ncbi.nlm.nih.gov/gene/?term=65986	RINZF	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019172	65987	KCTD14	http://www.ncbi.nlm.nih.gov/gene/?term=65987		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019173	65988	ZNF747	http://www.ncbi.nlm.nih.gov/gene/?term=65988		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019174	65988	ZNF747	http://www.ncbi.nlm.nih.gov/gene/?term=65988		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019175	65989	DLK2	http://www.ncbi.nlm.nih.gov/gene/?term=65989	"DLK-2, EGFL9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019176	6598	SMARCB1	http://www.ncbi.nlm.nih.gov/gene/?term=6598	"BAF47, INI1, MRD15, PPP1R144, RDT, RTPS1, SNF5, SNF5L1, SWNTS1, Sfh1p, Snr1, hSNFS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019177	6598	SMARCB1	http://www.ncbi.nlm.nih.gov/gene/?term=6598	"BAF47, INI1, MRD15, PPP1R144, RDT, RTPS1, SNF5, SNF5L1, SWNTS1, Sfh1p, Snr1, hSNFS "	mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00019178	6598	SMARCB1	http://www.ncbi.nlm.nih.gov/gene/?term=6598	"BAF47, INI1, MRD15, PPP1R144, RDT, RTPS1, SNF5, SNF5L1, SWNTS1, Sfh1p, Snr1, hSNFS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019179	65990	FAM173A	http://www.ncbi.nlm.nih.gov/gene/?term=65990	C16orf24	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019180	65991	FUNDC2	http://www.ncbi.nlm.nih.gov/gene/?term=65991	"DC44, HCBP6, HCC3, PD03104 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019181	65991	FUNDC2	http://www.ncbi.nlm.nih.gov/gene/?term=65991	"DC44, HCBP6, HCC3, PD03104 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019182	65992	DDRGK1	http://www.ncbi.nlm.nih.gov/gene/?term=65992	"C20orf116, UFBP1, dJ1187M17.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019183	65992	DDRGK1	http://www.ncbi.nlm.nih.gov/gene/?term=65992	"C20orf116, UFBP1, dJ1187M17.3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019184	65993	MRPS34	http://www.ncbi.nlm.nih.gov/gene/?term=65993	"MRP-S12, MRP-S34, MRPS12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019185	65998	C11orf95	http://www.ncbi.nlm.nih.gov/gene/?term=65998		lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019186	65998	C11orf95	http://www.ncbi.nlm.nih.gov/gene/?term=65998		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019187	65999	LRRC61	http://www.ncbi.nlm.nih.gov/gene/?term=65999	HSPC295	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019188	6599	SMARCC1	http://www.ncbi.nlm.nih.gov/gene/?term=6599	"BAF155, CRACC1, Rsc8, SRG3, SWI3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019189	6599	SMARCC1	http://www.ncbi.nlm.nih.gov/gene/?term=6599	"BAF155, CRACC1, Rsc8, SRG3, SWI3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019190	659	BMPR2	http://www.ncbi.nlm.nih.gov/gene/?term=659	"BMPR-II, BMPR3, BMR2, BRK-3, POVD1, PPH1, T-ALK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019191	659	BMPR2	http://www.ncbi.nlm.nih.gov/gene/?term=659	"BMPR-II, BMPR3, BMR2, BRK-3, POVD1, PPH1, T-ALK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019192	66000	TMEM108	http://www.ncbi.nlm.nih.gov/gene/?term=66000	CT124	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019193	66005	CHID1	http://www.ncbi.nlm.nih.gov/gene/?term=66005	"GL008, SI-CLP, SICLP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019194	66005	CHID1	http://www.ncbi.nlm.nih.gov/gene/?term=66005	"GL008, SI-CLP, SICLP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019195	66008	TRAK2	http://www.ncbi.nlm.nih.gov/gene/?term=66008	"ALS2CR3, CALS-C, GRIF-1, GRIF1, MILT2, OIP98 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019196	66008	TRAK2	http://www.ncbi.nlm.nih.gov/gene/?term=66008	"ALS2CR3, CALS-C, GRIF-1, GRIF1, MILT2, OIP98 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019197	6601	SMARCC2	http://www.ncbi.nlm.nih.gov/gene/?term=6601	"BAF170, CRACC2, Rsc8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019198	6602	SMARCD1	http://www.ncbi.nlm.nih.gov/gene/?term=6602	"BAF60A, CRACD1, Rsc6p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019199	66036	MTMR9	http://www.ncbi.nlm.nih.gov/gene/?term=66036	"C8orf9, LIP-STYX, MTMR8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019200	66036	MTMR9	http://www.ncbi.nlm.nih.gov/gene/?term=66036	"C8orf9, LIP-STYX, MTMR8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019201	66036	MTMR9	http://www.ncbi.nlm.nih.gov/gene/?term=66036	"C8orf9, LIP-STYX, MTMR8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019202	66036	MTMR9	http://www.ncbi.nlm.nih.gov/gene/?term=66036	"C8orf9, LIP-STYX, MTMR8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019203	66036	MTMR9	http://www.ncbi.nlm.nih.gov/gene/?term=66036	"C8orf9, LIP-STYX, MTMR8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019204	6603	SMARCD2	http://www.ncbi.nlm.nih.gov/gene/?term=6603	"BAF60B, CRACD2, PRO2451, Rsc6p "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019205	66049	Rogdi	http://www.ncbi.nlm.nih.gov/gene/?term=66049	"0610011C19Rik, AU020118, C76152, Lzf "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019206	6604	SMARCD3	http://www.ncbi.nlm.nih.gov/gene/?term=6604	"BAF60C, CRACD3, Rsc6p "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019207	66050	0610009B22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66050		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019208	66054	Cndp2	http://www.ncbi.nlm.nih.gov/gene/?term=66054	"0610010E05Rik, C76600, Cn2, Dip-2, Pep-1, Pep1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019209	66055	Sf3b6	http://www.ncbi.nlm.nih.gov/gene/?term=66055	"0610009D07Rik, 6030419K15Rik, AV001342, Sf3b14 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019210	66056	Zfp524	http://www.ncbi.nlm.nih.gov/gene/?term=66056	"0610012F07Rik, 2300009P13Rik, Znf524 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019211	66058	Tmem176a	http://www.ncbi.nlm.nih.gov/gene/?term=66058	"0610011I04Rik, AU040201, AU041743, Keg2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019212	6605	SMARCE1	http://www.ncbi.nlm.nih.gov/gene/?term=6605	BAF57	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019213	6605	SMARCE1	http://www.ncbi.nlm.nih.gov/gene/?term=6605	BAF57	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019214	66070	Cwc15	http://www.ncbi.nlm.nih.gov/gene/?term=66070	"0610040D20Rik, 2900052N06Rik, Ed1, c11orf5, mED1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019215	66074	Tmem167	http://www.ncbi.nlm.nih.gov/gene/?term=66074	"0610041E09Rik, 5730424F14Rik, AU041184, AW537806, ENSMUSG00000060669, Gm10085a, Tmem167 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019216	66074	Tmem167	http://www.ncbi.nlm.nih.gov/gene/?term=66074	"0610041E09Rik, 5730424F14Rik, AU041184, AW537806, ENSMUSG00000060669, Gm10085a, Tmem167 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019217	66075	Chchd3	http://www.ncbi.nlm.nih.gov/gene/?term=66075	"0610041L09Rik, 1700039J09Rik, AW558177 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019218	66078	Tsen34	http://www.ncbi.nlm.nih.gov/gene/?term=66078	"0610027F08Rik, Leng5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019219	6607	SMN2	http://www.ncbi.nlm.nih.gov/gene/?term=6607	"BCD541, C-BCD541, GEMIN1, SMNC, TDRD16B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019220	6607	SMN2	http://www.ncbi.nlm.nih.gov/gene/?term=6607	"BCD541, C-BCD541, GEMIN1, SMNC, TDRD16B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019221	6607	SMN2	http://www.ncbi.nlm.nih.gov/gene/?term=6607	"BCD541, C-BCD541, GEMIN1, SMNC, TDRD16B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019222	66083	Setd6	http://www.ncbi.nlm.nih.gov/gene/?term=66083	"0610039J04Rik, 3110004G14Rik, AI413388, C76402 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019223	66083	Setd6	http://www.ncbi.nlm.nih.gov/gene/?term=66083	"0610039J04Rik, 3110004G14Rik, AI413388, C76402 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019224	66084	Rmnd1	http://www.ncbi.nlm.nih.gov/gene/?term=66084	"0610042C05Rik, AA408137, AI462664, AW536662 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019225	66087	Emc3	http://www.ncbi.nlm.nih.gov/gene/?term=66087	"0610039A15Rik, AI225901, AW260416, Pob, Tmem111 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019226	66094	Lsm7	http://www.ncbi.nlm.nih.gov/gene/?term=66094	"0910001B06Rik, 1110033F18Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019227	66098	Chchd6	http://www.ncbi.nlm.nih.gov/gene/?term=66098	"0710001P09Rik, 1700021B03Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019228	6609	SMPD1	http://www.ncbi.nlm.nih.gov/gene/?term=6609	"ASM, ASMASE, NPD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019229	66101	Ppih	http://www.ncbi.nlm.nih.gov/gene/?term=66101	"1100001J08Rik, 2010111B15Rik, 4833408F11Rik, AI464484, CYP-20, CYPH, D4Wsu43e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019230	66105	Ube2d3	http://www.ncbi.nlm.nih.gov/gene/?term=66105	"1100001F19Rik, 9430029A22Rik, AA414951 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019231	66118	Sarnp	http://www.ncbi.nlm.nih.gov/gene/?term=66118	"1110005A23Rik, Cip29 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019232	66118	Sarnp	http://www.ncbi.nlm.nih.gov/gene/?term=66118	"1110005A23Rik, Cip29 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019233	6611	SMS	http://www.ncbi.nlm.nih.gov/gene/?term=6611	"MRSR, SPMSY, SRS, SpS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019234	6611	SMS	http://www.ncbi.nlm.nih.gov/gene/?term=6611	"MRSR, SPMSY, SRS, SpS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019235	66124	Josd2	http://www.ncbi.nlm.nih.gov/gene/?term=66124	1110007C05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019236	66126	Elof1	http://www.ncbi.nlm.nih.gov/gene/?term=66126	1110011K10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019237	6612	SUMO3	http://www.ncbi.nlm.nih.gov/gene/?term=6612	"SMT3A, SMT3H1, SUMO-3, Smt3B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019238	6612	SUMO3	http://www.ncbi.nlm.nih.gov/gene/?term=6612	"SMT3A, SMT3H1, SUMO-3, Smt3B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019239	6612	SUMO3	http://www.ncbi.nlm.nih.gov/gene/?term=6612	"SMT3A, SMT3H1, SUMO-3, Smt3B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019240	6613	SUMO2	http://www.ncbi.nlm.nih.gov/gene/?term=6613	"HSMT3, SMT3B, SMT3H2, SUMO3, Smt3A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019241	6613	SUMO2	http://www.ncbi.nlm.nih.gov/gene/?term=6613	"HSMT3, SMT3B, SMT3H2, SUMO3, Smt3A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019242	6613	SUMO2	http://www.ncbi.nlm.nih.gov/gene/?term=6613	"HSMT3, SMT3B, SMT3H2, SUMO3, Smt3A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019243	66153	Fbxo36	http://www.ncbi.nlm.nih.gov/gene/?term=66153	"0610008D19Rik, 1110020F21Rik, 2410002G19Rik, D1Ertd757e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019244	6615	SNAI1	http://www.ncbi.nlm.nih.gov/gene/?term=6615	"SLUGH2, SNA, SNAH, SNAIL, SNAIL1, dJ710H13.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019245	66163	Mrpl4	http://www.ncbi.nlm.nih.gov/gene/?term=66163	1110017G11Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019246	66167	Tma7	http://www.ncbi.nlm.nih.gov/gene/?term=66167	"1110017O22Rik, Ccdc72 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019247	6616	SNAP25	http://www.ncbi.nlm.nih.gov/gene/?term=6616	"CMS18, RIC-4, RIC4, SEC9, SNAP, SNAP-25, bA416N4.2, dJ1068F16.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019248	66170	Chchd5	http://www.ncbi.nlm.nih.gov/gene/?term=66170	"1110027L01Rik, AW045710 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019249	66171	Pgls	http://www.ncbi.nlm.nih.gov/gene/?term=66171	"1110030K05Rik, AI447866, Plgs "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019250	66171	Pgls	http://www.ncbi.nlm.nih.gov/gene/?term=66171	"1110030K05Rik, AI447866, Plgs "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019251	66172	Med11	http://www.ncbi.nlm.nih.gov/gene/?term=66172	"1110030J09Rik, AI465144, AW545069 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019252	66174	Nudt14	http://www.ncbi.nlm.nih.gov/gene/?term=66174	"1110030M18Rik, UGPPase "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019253	66177	Ubl5	http://www.ncbi.nlm.nih.gov/gene/?term=66177	"1110030M22Rik, beacon "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019254	66181	Nop10	http://www.ncbi.nlm.nih.gov/gene/?term=66181	"1110036B12Rik, NOP10P, Nola3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019255	66181	Nop10	http://www.ncbi.nlm.nih.gov/gene/?term=66181	"1110036B12Rik, NOP10P, Nola3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019256	66185	1110037F02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66185	"4930422M05Rik, Kiaa1429, mKIAA1429 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019257	6618	SNAPC2	http://www.ncbi.nlm.nih.gov/gene/?term=6618	"PTFDELTA, SNAP45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019258	6618	SNAPC2	http://www.ncbi.nlm.nih.gov/gene/?term=6618	"PTFDELTA, SNAP45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019259	66191	Ier3ip1	http://www.ncbi.nlm.nih.gov/gene/?term=66191	"1110057H19Rik, AI644142, AL022842, AL022863, AV026606 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019260	66194	Pycrl	http://www.ncbi.nlm.nih.gov/gene/?term=66194	"1110058B13Rik, 2700073G24Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019261	66196	Myo19	http://www.ncbi.nlm.nih.gov/gene/?term=66196	"1110055A02Rik, Myohd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019262	66197	Cks2	http://www.ncbi.nlm.nih.gov/gene/?term=66197	"1110038L14Rik, CKSHS2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019263	6619	SNAPC3	http://www.ncbi.nlm.nih.gov/gene/?term=6619	"PTFbeta, SNAP50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019264	6619	SNAPC3	http://www.ncbi.nlm.nih.gov/gene/?term=6619	"PTFbeta, SNAP50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019265	661	POLR3D	http://www.ncbi.nlm.nih.gov/gene/?term=661	"BN51T, RPC4, RPC53, TSBN51 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019266	66204	Acyp1	http://www.ncbi.nlm.nih.gov/gene/?term=66204	"1110039O14Rik, AI325944 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019267	66205	Cd302	http://www.ncbi.nlm.nih.gov/gene/?term=66205	"1110055L24Rik, AI159627 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019268	66212	Sec61b	http://www.ncbi.nlm.nih.gov/gene/?term=66212	"1190006C12Rik, AI326121, AW122942 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019269	66213	Med7	http://www.ncbi.nlm.nih.gov/gene/?term=66213	"1110063B05Rik, Crsp33, Crsp9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019270	66223	Mrpl35	http://www.ncbi.nlm.nih.gov/gene/?term=66223	1110066C01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019271	66226	Trappc2	http://www.ncbi.nlm.nih.gov/gene/?term=66226	"1110066L09Rik, 1810064C02Rik, AW496358, MIP-2A, Sedl, TRS20 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019272	6622	SNCA	http://www.ncbi.nlm.nih.gov/gene/?term=6622	"NACP, PARK1, PARK4, PD1 "	mRNA	Homo sapiens	25896939	Synapse	Nerve cell	qRT-PCR|Immunocytochemistry	"Consistent with the localization studies in the rat ENS, we observed similar staining pattern of a-syn in the human ENS decorating both enteric ganglia and nerve fibers. Again, the granular/punctuate a-syn immunoreactive signals co-localized with immunoreactive signals obtained for synaptophysin confirming the association of a-syn with the synaptic vesicle apparatus also within the human ENS. "
RLID00019273	6622	SNCA	http://www.ncbi.nlm.nih.gov/gene/?term=6622	"NACP, PARK1, PARK4, PD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019274	66231	Thoc7	http://www.ncbi.nlm.nih.gov/gene/?term=66231	Nif3l1bp1	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019275	66234	Msmo1	http://www.ncbi.nlm.nih.gov/gene/?term=66234	"1500001G16Rik, C78600, DESP4, ERG25, Sc4mol "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019276	66235	Eif1ax	http://www.ncbi.nlm.nih.gov/gene/?term=66235	"1500010B24Rik, AI426898, Eif1ay "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019277	66236	1500011B03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66236	"AI415201, AV141149, AW556386 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019278	6623	SNCG	http://www.ncbi.nlm.nih.gov/gene/?term=6623	"BCSG1, SR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019279	66244	Nemf	http://www.ncbi.nlm.nih.gov/gene/?term=66244	"1500011I12Rik, 4933405E14Rik, Sdccag1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019280	66245	Hspbp1	http://www.ncbi.nlm.nih.gov/gene/?term=66245	1500019G21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019281	66246	Osgep	http://www.ncbi.nlm.nih.gov/gene/?term=66246	"1500019L24Rik, GCPL-1, PRSMG1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019282	66249	Pno1	http://www.ncbi.nlm.nih.gov/gene/?term=66249	"1810003N24Rik, AA407421, AU015468, AU019495, AU042323, Emi3, Imi3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019283	6624	FSCN1	http://www.ncbi.nlm.nih.gov/gene/?term=6624	"FAN1, HSN, SNL, p55 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019284	6625	SNRNP70	http://www.ncbi.nlm.nih.gov/gene/?term=6625	"RNPU1Z, RPU1, SNRP70, Snp1, U1-70K, U170K, U1AP, U1RNP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019285	66268	Pigyl	http://www.ncbi.nlm.nih.gov/gene/?term=66268	"1810008A14Rik, PIG-Y, Pigy "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019286	6626	SNRPA	http://www.ncbi.nlm.nih.gov/gene/?term=6626	"Mud1, U1-A, U1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019287	6626	SNRPA	http://www.ncbi.nlm.nih.gov/gene/?term=6626	"Mud1, U1-A, U1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019288	66270	Fam134b	http://www.ncbi.nlm.nih.gov/gene/?term=66270	"1810015C04Rik, AU015349 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019289	66271	Tmem126a	http://www.ncbi.nlm.nih.gov/gene/?term=66271	1810020E01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019290	6627	SNRPA1	http://www.ncbi.nlm.nih.gov/gene/?term=6627	Lea1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019291	66286	Sec11c	http://www.ncbi.nlm.nih.gov/gene/?term=66286	"1810029G24Rik, Sec11l3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019292	6628	SNRPB	http://www.ncbi.nlm.nih.gov/gene/?term=6628	"CCMS, COD1, Sm-B/B', SmB/B', SmB/SmB', snRNP-B, SNRPB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019293	6628	SNRPB	http://www.ncbi.nlm.nih.gov/gene/?term=6628	"CCMS, COD, SNRPB1, Sm-B/B', SmB/B', SmB/SmB', snRNP-B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019294	66293	1810032O08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66293		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019295	6629	SNRPB2	http://www.ncbi.nlm.nih.gov/gene/?term=6629	"Msl1, U2B'' "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019296	6629	SNRPB2	http://www.ncbi.nlm.nih.gov/gene/?term=6629	Msl1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019297	662	BNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=662	"NIP1, SEC20, TRG-8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019298	66307	Isoc1	http://www.ncbi.nlm.nih.gov/gene/?term=66307	2610034N03Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019299	66308	Mplkip	http://www.ncbi.nlm.nih.gov/gene/?term=66308	"2810021B07Rik, C330007M08Rik, Ttdn1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019300	66309	Tmem128	http://www.ncbi.nlm.nih.gov/gene/?term=66309	2810021O14Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019301	66313	Smurf2	http://www.ncbi.nlm.nih.gov/gene/?term=66313	"2810411E22Rik, AI558114, AI649275 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019302	66315	Senp7	http://www.ncbi.nlm.nih.gov/gene/?term=66315	"2410152H17Rik, 2810413I22Rik, 2900036C23Rik, 6030449K19Rik, AI790676 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019303	6631	SNRPC	http://www.ncbi.nlm.nih.gov/gene/?term=6631	"U1C, Yhc1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019304	6631	SNRPC	http://www.ncbi.nlm.nih.gov/gene/?term=6631	"U1C, Yhc1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019305	6632	SNRPD1	http://www.ncbi.nlm.nih.gov/gene/?term=6632	"HsT2456, SMD1, SNRPD, Sm-D1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019306	6632	SNRPD1	http://www.ncbi.nlm.nih.gov/gene/?term=6632	"HsT2456, SMD1, SNRPD, Sm-D1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019307	6632	SNRPD1	http://www.ncbi.nlm.nih.gov/gene/?term=6632	"HsT2456, SMD1, SNRPD, Sm-D1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019308	66335	Atp6v1c1	http://www.ncbi.nlm.nih.gov/gene/?term=66335	"1700025B18Rik, U13839 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019309	66336	Cenpp	http://www.ncbi.nlm.nih.gov/gene/?term=66336	"1700022C02Rik, 4921518G09Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019310	6633	SNRPD2	http://www.ncbi.nlm.nih.gov/gene/?term=6633	"SMD2, SNRPD1, Sm-D2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019311	6633	SNRPD2	http://www.ncbi.nlm.nih.gov/gene/?term=6633	"SMD2, SNRPD1, Sm-D2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019312	6634	SNRPD3	http://www.ncbi.nlm.nih.gov/gene/?term=6634	"SMD3, Sm-D3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019313	66352	Blzf1	http://www.ncbi.nlm.nih.gov/gene/?term=66352	"1700030G05Rikl, Golgin-45, Jem-1, Blzf1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019314	66352	Blzf1	http://www.ncbi.nlm.nih.gov/gene/?term=66352	"1700030G05Rikl, Golgin-45, Jem-1, Blzf1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019315	66354	Snw1	http://www.ncbi.nlm.nih.gov/gene/?term=66354	"2310008B08Rik, AW048543, NCoA-62, SKIP, Skiip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019316	66355	Gmpr	http://www.ncbi.nlm.nih.gov/gene/?term=66355	"2310004P21Rik, AV028449, GMPR 1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019317	66356	Knop1	http://www.ncbi.nlm.nih.gov/gene/?term=66356	"2310008H09Rik, Tsg118 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019318	6635	SNRPE	http://www.ncbi.nlm.nih.gov/gene/?term=6635	"B-raf, HYPT11, SME, Sm-E "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019319	6635	SNRPE	http://www.ncbi.nlm.nih.gov/gene/?term=6635	"B-raf, HYPT11, SME, Sm-E "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019320	66361	Zfand1	http://www.ncbi.nlm.nih.gov/gene/?term=66361	"2310008M20Rik, AW048890 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019321	66368	Rtca	http://www.ncbi.nlm.nih.gov/gene/?term=66368	"2310009A18Rik, AI450277, RPC, Rtcd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019322	6636	SNRPF	http://www.ncbi.nlm.nih.gov/gene/?term=6636	"SMF, Sm-F, snRNP-F "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019323	6636	SNRPF	http://www.ncbi.nlm.nih.gov/gene/?term=6636	"SMF, Sm-F, snRNP-F "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019324	66374	2310011J03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66374	"AI452186, AW545358 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019325	66377	Ndufc1	http://www.ncbi.nlm.nih.gov/gene/?term=66377	"2310016K22Rik, KFYI "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019326	6637	SNRPG	http://www.ncbi.nlm.nih.gov/gene/?term=6637	"SMG, Sm-G "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019327	6637	SNRPG	http://www.ncbi.nlm.nih.gov/gene/?term=6637	"SMG, Sm-G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019328	66381	Rnf113a2	http://www.ncbi.nlm.nih.gov/gene/?term=66381	"2310020H19Rik, AI426758, Rnf113a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019329	66384	Srp19	http://www.ncbi.nlm.nih.gov/gene/?term=66384	2310020D23Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019330	66385	Ppp1r7	http://www.ncbi.nlm.nih.gov/gene/?term=66385	"2310014J01Rik, SDS22 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019331	66387	Nudt8	http://www.ncbi.nlm.nih.gov/gene/?term=66387	2310039H17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019332	6638	SNRPN	http://www.ncbi.nlm.nih.gov/gene/?term=6638	"HCERN3, PWCR, RT-LI, SM-D, SMN, SNRNP-N, SNURF-SNRPN, sm-N "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019333	66394	Nosip	http://www.ncbi.nlm.nih.gov/gene/?term=66394	"2310061K06Rik, CGI-25 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019334	66395	Ahnak	http://www.ncbi.nlm.nih.gov/gene/?term=66395	DY6	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019335	66395	Ahnak	http://www.ncbi.nlm.nih.gov/gene/?term=66395	DY6	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019336	66397	Sar1b	http://www.ncbi.nlm.nih.gov/gene/?term=66397	"2310075M17Rik, 2900019I22Rik, CMRD, Sara1b, Sara2, Sarb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019337	66398	Commd5	http://www.ncbi.nlm.nih.gov/gene/?term=66398	"2310065H03Rik, AI854466, D15Ertd81e, Hcarg "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019338	663	BNIP2	http://www.ncbi.nlm.nih.gov/gene/?term=663	"BNIP-2, NIP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019339	663	BNIP2	http://www.ncbi.nlm.nih.gov/gene/?term=663	"BNIP-2, NIP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019340	663	BNIP2	http://www.ncbi.nlm.nih.gov/gene/?term=663	"BNIP-2, NIP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019341	6640	SNTA1	http://www.ncbi.nlm.nih.gov/gene/?term=6640	"LQT12, SNT1, TACIP1, dJ1187J4.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019342	66410	Mterf3	http://www.ncbi.nlm.nih.gov/gene/?term=66410	"2410017I18Rik, Mterfd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019343	66413	Psmd6	http://www.ncbi.nlm.nih.gov/gene/?term=66413	2400006A19Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019344	66414	Ndufa12	http://www.ncbi.nlm.nih.gov/gene/?term=66414	"2410011G03Rik, AW112974 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019345	6641	SNTB1	http://www.ncbi.nlm.nih.gov/gene/?term=6641	"59-DAP, A1B, BSYN2, DAPA1B, SNT2, SNT2B1, TIP-43 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019346	66421	2410004B18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66421	4930572C24Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019347	66423	Coprs	http://www.ncbi.nlm.nih.gov/gene/?term=66423	"1700029I03Rik, 2410022L05Rik, AA409325, AI256813, C85432, Copr5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019348	66425	Pcp4l1	http://www.ncbi.nlm.nih.gov/gene/?term=66425	1500036F01Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019349	66427	Cyb5b	http://www.ncbi.nlm.nih.gov/gene/?term=66427	"1810044O22Rik, AU015618, Cyb5m "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019350	6642	SNX1	http://www.ncbi.nlm.nih.gov/gene/?term=6642	"HsT17379, VPS5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019351	6642	SNX1	http://www.ncbi.nlm.nih.gov/gene/?term=6642	"HsT17379, VPS5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019352	6642	SNX1	http://www.ncbi.nlm.nih.gov/gene/?term=6642	"HsT17379, VPS5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019353	6642	SNX1	http://www.ncbi.nlm.nih.gov/gene/?term=6642	"HsT17379, VPS5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019354	6642	SNX1	http://www.ncbi.nlm.nih.gov/gene/?term=6642	"HsT17379, VPS5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019355	66432	Slc7a6os	http://www.ncbi.nlm.nih.gov/gene/?term=66432	"2010007L18Rik, 2400002F02Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019356	66435	Uggt2	http://www.ncbi.nlm.nih.gov/gene/?term=66435	"1810064L21Rik, 3110001A05Rik, 3110027P15Rik, A230065J02Rik, AW047562, Ugcgl2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019357	66437	Fis1	http://www.ncbi.nlm.nih.gov/gene/?term=66437	"2010003O14Rik, Ttc11 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019358	6643	SNX2	http://www.ncbi.nlm.nih.gov/gene/?term=6643	TRG-9	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019359	6643	SNX2	http://www.ncbi.nlm.nih.gov/gene/?term=6643	TRG-9	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019360	6643	SNX2	http://www.ncbi.nlm.nih.gov/gene/?term=6643	TRG-9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019361	66441	Magohb	http://www.ncbi.nlm.nih.gov/gene/?term=66441	"2010012C16Rik, Mago, Magoh, Magoh-rs1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019362	66442	Spc25	http://www.ncbi.nlm.nih.gov/gene/?term=66442	"2600017H08Rik, 2610205L13Rik, Spbc25 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019363	66443	Tnfaip8l1	http://www.ncbi.nlm.nih.gov/gene/?term=66443	"2600017J23Rik, TIPE1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019364	66447	Mgst3	http://www.ncbi.nlm.nih.gov/gene/?term=66447	"2010012L10Rik, 2010306B17Rik, 2700004G04Rik, AA516734, GST-III "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019365	66449	Pam16	http://www.ncbi.nlm.nih.gov/gene/?term=66449	"2010110I09Rik, AV006767, CGI-136, Magmas, Tim16, Timm16 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019366	66455	Cnpy4	http://www.ncbi.nlm.nih.gov/gene/?term=66455	2610019P18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019367	6645	SNTB2	http://www.ncbi.nlm.nih.gov/gene/?term=6645	"D16S2531E, EST25263, SNT2B2, SNT3, SNTL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019368	6645	SNTB2	http://www.ncbi.nlm.nih.gov/gene/?term=6645	"D16S2531E, EST25263, SNT2B2, SNT3, SNTL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019369	6645	SNTB2	http://www.ncbi.nlm.nih.gov/gene/?term=6645	"D16S2531E, EST25263, SNT2B2, SNT3, SNTL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019370	6645	SNTB2	http://www.ncbi.nlm.nih.gov/gene/?term=6645	"D16S2531E, EST25263, SNT2B2, SNT3, SNTL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019371	6645	SNTB2	http://www.ncbi.nlm.nih.gov/gene/?term=6645	"D16S2531E, EST25263, SNT2B2, SNT3, SNTL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019372	66462	2810428I15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66462		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019373	6646	SOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6646	"ACACT, ACAT, ACAT-1, ACAT1, SOAT, STAT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019374	6646	SOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6646	"ACACT, ACAT, ACAT-1, ACAT1, SOAT, STAT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019375	664701	ZNF826P	http://www.ncbi.nlm.nih.gov/gene/?term=664701	ZNF826	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019376	664701	ZNF826P	http://www.ncbi.nlm.nih.gov/gene/?term=664701	ZNF826	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019377	66473	Ctrb1	http://www.ncbi.nlm.nih.gov/gene/?term=66473	"2200008D09Rik, AI504462, Ctrb, Prt-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019378	66475	Rps23	http://www.ncbi.nlm.nih.gov/gene/?term=66475	2410044J15Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019379	66475	Rps23	http://www.ncbi.nlm.nih.gov/gene/?term=66475	2410044J15Rik	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019380	664779	Zfp91Cntf	http://www.ncbi.nlm.nih.gov/gene/?term=664779	Zfp91-Cntf	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019381	6647	SOD1	http://www.ncbi.nlm.nih.gov/gene/?term=6647	"ALS, ALS1, HEL-S-44, IPOA, SOD, hSod1, homodimer "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019382	6647	SOD1	http://www.ncbi.nlm.nih.gov/gene/?term=6647	"ALS, ALS1, HEL-S-44, IPOA, SOD, hSod1, homodimer "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019383	6647	SOD1	http://www.ncbi.nlm.nih.gov/gene/?term=6647	"ALS, ALS1, HEL-S-44, IPOA, SOD, hSod1, homodimer "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019384	66480	Rpl15	http://www.ncbi.nlm.nih.gov/gene/?term=66480	2510008H07Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019385	66480	Rpl15	http://www.ncbi.nlm.nih.gov/gene/?term=66480	2510008H07Rik	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019386	66481	Rps21	http://www.ncbi.nlm.nih.gov/gene/?term=66481	"1810049N11Rik, 2410030A14Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019387	66481	Rps21	http://www.ncbi.nlm.nih.gov/gene/?term=66481	"1810049N11Rik, 2410030A14Rik "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019388	664829	Slx	http://www.ncbi.nlm.nih.gov/gene/?term=664829	"EG664958, Xmr "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00019389	66482	Exoc2	http://www.ncbi.nlm.nih.gov/gene/?term=66482	"2410030I24Rik, AI648199, Sec5, Sec5l1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019390	66489	Rpl35	http://www.ncbi.nlm.nih.gov/gene/?term=66489	2410039E09Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019391	6648	SOD2	http://www.ncbi.nlm.nih.gov/gene/?term=6648	"IPOB, MNSOD, MVCD6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019392	6648	SOD2	http://www.ncbi.nlm.nih.gov/gene/?term=6648	"IPOB, MNSOD, MVCD6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019393	664903	Rps15a-ps4	http://www.ncbi.nlm.nih.gov/gene/?term=664903	"Gm13253, Lethe, OTTMUSG00000011114 "	lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus.  "
RLID00019394	664903	Rps15a-ps4	http://www.ncbi.nlm.nih.gov/gene/664903	"Lethe, Gm13253, OTTMUSG00000011114 "	lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00019395	66492	Zmat2	http://www.ncbi.nlm.nih.gov/gene/?term=66492	"2610510D14Rik, 2900082I05Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019396	66494	Prelid1	http://www.ncbi.nlm.nih.gov/gene/?term=66494	"2610524G07Rik, Preli "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019397	664968	Tmem238	http://www.ncbi.nlm.nih.gov/gene/?term=664968	2210411K11Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019398	66496	Ppdpf	http://www.ncbi.nlm.nih.gov/gene/?term=66496	"0610012G23Rik, 2610317A05Rik, 2700038C09Rik, 3110053G12Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019399	66498	Dda1	http://www.ncbi.nlm.nih.gov/gene/?term=66498	"1500034J01Rik, 1700095J19Rik, R74921 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019400	6649	SOD3	http://www.ncbi.nlm.nih.gov/gene/?term=6649	EC-SOD	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019401	664	BNIP3	http://www.ncbi.nlm.nih.gov/gene/?term=664	NIP3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019402	664	BNIP3	http://www.ncbi.nlm.nih.gov/gene/?term=664	NIP3	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00019403	665033	Col6a5	http://www.ncbi.nlm.nih.gov/gene/?term=665033	"Col29a1, EG665033, Gm7455 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019404	66505	Zmynd11	http://www.ncbi.nlm.nih.gov/gene/?term=66505	"2210402G22Rik, BS69 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019405	66506	Psmg3	http://www.ncbi.nlm.nih.gov/gene/?term=66506	"1810042K04Rik, 4930403H09Rik, AI303239 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019406	66508	Lamtor1	http://www.ncbi.nlm.nih.gov/gene/?term=66508	"2400001E08Rik, Pdro, p18 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019407	665113	Tnik	http://www.ncbi.nlm.nih.gov/gene/?term=665113	"1500031A17Rik, 4831440I19Rik, AI451411, C530008O15Rik, C630040K21Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019408	66511	Chtop	http://www.ncbi.nlm.nih.gov/gene/?term=66511	"2500003M10Rik, Fop, Srag "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019409	6651	SON	http://www.ncbi.nlm.nih.gov/gene/?term=6651	"BASS1, C21orf50, DBP-5, NREBP3, SON "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019410	6651	SON	http://www.ncbi.nlm.nih.gov/gene/?term=6651	"BASS1, C21orf50, DBP-5, NREBP, SON3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019411	66522	Pgpep1	http://www.ncbi.nlm.nih.gov/gene/?term=66522	"2810003H13Rik, Gm19458, PAP-I, PGP, PGP-I, PGPI, Pcp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019412	6652	SORD	http://www.ncbi.nlm.nih.gov/gene/?term=6652	"HEL-S-95n1, SORD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019413	66530	Ubxn6	http://www.ncbi.nlm.nih.gov/gene/?term=66530	"1200008L11Rik, 2210415J11Rik, AU040909, Ubxd1, Ubxdc2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019414	6653	SORL1	http://www.ncbi.nlm.nih.gov/gene/?term=6653	"C11orf32, LR11, LRP9, SORLA, SorLA-1, gp250 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019415	6653	SORL1	http://www.ncbi.nlm.nih.gov/gene/?term=6653	"C11orf32, LR11, LRP9, SORLA, SorLA-1, gp250 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019416	6654	SOS1	http://www.ncbi.nlm.nih.gov/gene/?term=6654	"GF1, GGF1, GINGF, HGF, NS4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019417	66552	Sppl2a	http://www.ncbi.nlm.nih.gov/gene/?term=66552	"2010106G01Rik, C130089K23Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019418	66566	Ntpcr	http://www.ncbi.nlm.nih.gov/gene/?term=66566	"2310079N02Rik, AI449709 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019419	66568	Rwdd3	http://www.ncbi.nlm.nih.gov/gene/?term=66568	"2510027J23Rik, 3110037C01Rik, AI035684, AI662458, Rsume, X2CR1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019420	66569	Gdpd1	http://www.ncbi.nlm.nih.gov/gene/?term=66569	2610020H15Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019421	665797	Gm7788	http://www.ncbi.nlm.nih.gov/gene/?term=665797	EG665797	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019422	66579	2610007O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66579		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019423	6657	SOX2	http://www.ncbi.nlm.nih.gov/gene/?term=6657	"ANOP3, MCOPS3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019424	66589	Ube2v1	http://www.ncbi.nlm.nih.gov/gene/?term=66589	"0610011J09Rik, AI256840, CROC-1, CROC1, D7Bwg1382e, UEV-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019425	66595	Aste1	http://www.ncbi.nlm.nih.gov/gene/?term=66595	"1100001A21Rik, AV006403 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019426	66599	Rdm1	http://www.ncbi.nlm.nih.gov/gene/?term=66599	"2410008M22Rik, AW212028, Rad52b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019427	6659	SOX4	http://www.ncbi.nlm.nih.gov/gene/?term=6659	EVI16	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019428	6659	SOX4	http://www.ncbi.nlm.nih.gov/gene/?term=6659	EVI16	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019429	6659	SOX4	http://www.ncbi.nlm.nih.gov/gene/?term=6659	EVI16	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019430	665	BNIP3L	http://www.ncbi.nlm.nih.gov/gene/?term=665	"BNIP3a, NIX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019431	665	BNIP3L	http://www.ncbi.nlm.nih.gov/gene/?term=665	"BNIP3a, NIX "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00019432	665	BNIP3L	http://www.ncbi.nlm.nih.gov/gene/?term=665	"BNIP3a, NIX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019433	66602	1700020I14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66602	"1190006L01Rik, 4933437I03Rik, AI451541, AI585852, AW538376, AW558897, Cyrano "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019434	66603	Gemin2	http://www.ncbi.nlm.nih.gov/gene/?term=66603	"Sip1, gemin-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019435	66606	Lrrc57	http://www.ncbi.nlm.nih.gov/gene/?term=66606	"2810002D13Rik, AA407405 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019436	66609	Cryzl1	http://www.ncbi.nlm.nih.gov/gene/?term=66609	"2210407J23Rik, 2410006O11Rik, QOH-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019437	66614	Gpatch4	http://www.ncbi.nlm.nih.gov/gene/?term=66614	"2610029K21Rik, Gpatc4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019438	66617	Ntmt1	http://www.ncbi.nlm.nih.gov/gene/?term=66617	"2610205E22Rik, AL033331, AL033332, Mettl11a, NTM1A "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019439	666214	1700049E17Rik1	http://www.ncbi.nlm.nih.gov/gene/?term=666214	1700049E17Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019440	666231	Gm7993	http://www.ncbi.nlm.nih.gov/gene/?term=666231	EG666231	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019441	66625	Pnisr	http://www.ncbi.nlm.nih.gov/gene/?term=66625	"5730406M06Rik, AA673174, Pinsr, Sfrs18, Srsf18 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019442	66629	Golph3	http://www.ncbi.nlm.nih.gov/gene/?term=66629	"4733401N08Rik, 5730410D03Rik, AW413496 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019443	6662	SOX9	http://www.ncbi.nlm.nih.gov/gene/?term=6662	"CMD1, CMPD1, SRA1, SRXX2, SRXY10 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019444	666317	Prl2c1	http://www.ncbi.nlm.nih.gov/gene/?term=666317	Ghd22	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019445	66631	Mfsd14b	http://www.ncbi.nlm.nih.gov/gene/?term=66631	"5730414C17Rik, AU045608, AW539692, Hiatl1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019446	66632	Dph6	http://www.ncbi.nlm.nih.gov/gene/?term=66632	"5730421E18Rik, Atpbd4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019447	66632	Dph6	http://www.ncbi.nlm.nih.gov/gene/?term=66632	"5730421E18Rik, Atpbd4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019448	66634	Mcm8	http://www.ncbi.nlm.nih.gov/gene/?term=66634	5730432L01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019449	66640	Hoxaas2	http://www.ncbi.nlm.nih.gov/gene/?term=66640	"2810043O09Rik, 5730446D14Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019450	66641	Sike1	http://www.ncbi.nlm.nih.gov/gene/?term=66641	"2810005O12Rik, 5730470L24Rik, AI450236, AI839862, Sike, Sikeb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019451	66646	Rpe	http://www.ncbi.nlm.nih.gov/gene/?term=66646	"2810429B02Rik, 5730518J08Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019452	66647	Ndnl2	http://www.ncbi.nlm.nih.gov/gene/?term=66647	"5730494G16Rik, AI642138, BB044375, HCA4, Mageg1, Nsmce3, mage-g1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019453	666529	Gm8149	http://www.ncbi.nlm.nih.gov/gene/?term=666529	EG666529	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019454	66658	Ccdc51	http://www.ncbi.nlm.nih.gov/gene/?term=66658	"5730568A12Rik, AI551049 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019455	66660	Sltm	http://www.ncbi.nlm.nih.gov/gene/?term=66660	"5730455C01Rik, 5730555F13Rik, 9130215G10Rik, Met "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019456	66661	Srp72	http://www.ncbi.nlm.nih.gov/gene/?term=66661	"5730576P14Rik, 72kDa, AI132477, BC019196, C77589 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019457	66662	Fbxl12os	http://www.ncbi.nlm.nih.gov/gene/?term=66662	5730577I03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019458	66663	Uba5	http://www.ncbi.nlm.nih.gov/gene/?term=66663	"5730525G14Rik, AW240750, Ube1dc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019459	6666	SOX12	http://www.ncbi.nlm.nih.gov/gene/?term=6666	SOX22	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019460	6666	SOX12	http://www.ncbi.nlm.nih.gov/gene/?term=6666	SOX22	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019461	66671	Ccnh	http://www.ncbi.nlm.nih.gov/gene/?term=66671	"6330408H09Rik, AI661354, AV102684, AW538719 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019462	666737	4632427E13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=666737	AU015482	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019463	6667	SP1	http://www.ncbi.nlm.nih.gov/gene/?term=6667		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019464	6667	SP1	http://www.ncbi.nlm.nih.gov/gene/?term=6667		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019465	6667	SP1	http://www.ncbi.nlm.nih.gov/gene/?term=6667		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019466	66689	Klhl28	http://www.ncbi.nlm.nih.gov/gene/?term=66689	"2810440N09Rik, 4122402F11Rik, 4931401E10Rik, Btbd5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019467	6668	SP2	http://www.ncbi.nlm.nih.gov/gene/?term=6668		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019468	66691	Gapvd1	http://www.ncbi.nlm.nih.gov/gene/?term=66691	"2010005B09Rik, 4432404J10Rik, AW108497, Gapex-5, RAP6, RME-6, mKIAA1521 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019469	666	BOK	http://www.ncbi.nlm.nih.gov/gene/?term=666	"BCL2L9L, BOK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019470	666	BOK	http://www.ncbi.nlm.nih.gov/gene/?term=666	"BCL2L9, BOKL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019471	66705	Dnase1l2	http://www.ncbi.nlm.nih.gov/gene/?term=66705	4733401H14Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019472	6670	SP3	http://www.ncbi.nlm.nih.gov/gene/?term=6670	SPR2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019473	66713	Actr2	http://www.ncbi.nlm.nih.gov/gene/?term=66713	"4921510D23Rik, AA409782, Arp2, D6Ertd746e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019474	66719	4921522P10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66719		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019475	66724	Tab3	http://www.ncbi.nlm.nih.gov/gene/?term=66724	"4921526G09Rik, Map3k7ip3, mKIAA4135 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019476	667257	Gm8541	http://www.ncbi.nlm.nih.gov/gene/?term=667257	EG667257	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019477	66725	Lrrk2	http://www.ncbi.nlm.nih.gov/gene/?term=66725	"4921513O20Rik, 9330188B09Rik, AW561911, D630001M17Rik, Gm927, cI-46 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019478	667281	H60b	http://www.ncbi.nlm.nih.gov/gene/?term=667281	EG667281	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019479	6672	SP100	http://www.ncbi.nlm.nih.gov/gene/?term=6672	lysp100b	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019480	6672	SP100	http://www.ncbi.nlm.nih.gov/gene/?term=6672	lysp100b	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019481	66734	Map1lc3a	http://www.ncbi.nlm.nih.gov/gene/?term=66734	"1010001H21Rik, 4922501H04Rik, LC3, LC3a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019482	66736	Emc2	http://www.ncbi.nlm.nih.gov/gene/?term=66736	"4921531G14Rik, AV060620, AW209495, Ttc35 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019483	66740	4931417E11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66740		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019484	66748	Erich2	http://www.ncbi.nlm.nih.gov/gene/?term=66748	4933404M02Rik	mRNA	Mus musculus	26071953	Nucleus	Sperm	RT-PCR	"Within this set of RNAs, the Prm1 transcript, as well as Erich2 and Fam71e2 (formerly 4933404M02Rik and 4930401F20Rik, respectively), were previously identified within the mouse sperm nucleus by RT-PCR though their preferential localization within the gamete could not be inferred from that study (15).  "
RLID00019485	66753	Erlec1	http://www.ncbi.nlm.nih.gov/gene/?term=66753	4933407N01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019486	66759	4933425D22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66759	AI606871	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019487	6675	UAP1	http://www.ncbi.nlm.nih.gov/gene/?term=6675	"AGX, AGX1, AGX2, SPAG2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019488	6675	UAP1	http://www.ncbi.nlm.nih.gov/gene/?term=6675	"AGX, AGX1, AGX2, SPAG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019489	66775	Hacd4	http://www.ncbi.nlm.nih.gov/gene/?term=66775	"4933428I03Rik, Hcad4, Ptplad2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019490	66776	Pisd-ps3	http://www.ncbi.nlm.nih.gov/gene/?term=66776	4933439C20Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019491	6677	SPAM1	http://www.ncbi.nlm.nih.gov/gene/?term=6677	"HEL-S-96n, HYA1, HYAL1, HYAL3, HYAL5, PH-20, PH20, SPAG15 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019492	6677	SPAM1	http://www.ncbi.nlm.nih.gov/gene/?term=6677	"HEL-S-96n, HYA1, HYAL1, HYAL3, HYAL5, PH-20, PH20, SPAG15 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019493	66780	4933436I01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66780		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019494	66781	4933437F24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66781		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019495	6678	SPARC	http://www.ncbi.nlm.nih.gov/gene/?term=6678	"BM-40, OI17, ON "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019496	6678	SPARC	http://www.ncbi.nlm.nih.gov/gene/?term=6678	"BM-40, OI17, ON "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019497	667	DST	http://www.ncbi.nlm.nih.gov/gene/?term=667	"BP240, BPA, BPAG1, CATX-15, CATX15, D6S1101, DMH, DT, EBSB2, HSAN6, MACF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019498	667	DST	http://www.ncbi.nlm.nih.gov/gene/?term=667	"BP240, BPA, BPAG1, CATX-15, CATX15, D6S1101, DMH, DT, EBSB2, HSAN6, MACF2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019499	66809	Krt20	http://www.ncbi.nlm.nih.gov/gene/?term=66809	"9030623C06Rik, Ck-20, Ck20, K20, Krt21 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019500	66816	Thap2	http://www.ncbi.nlm.nih.gov/gene/?term=66816	"2900040O07Rik, 9030625G08Rik, AI450385, AI649097 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019501	66821	Bcs1l	http://www.ncbi.nlm.nih.gov/gene/?term=66821	9130022O19Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019502	66826	Taz	http://www.ncbi.nlm.nih.gov/gene/?term=66826	"5031411C02Rik, 9130012G04Rik, AW107266, AW552613, G4.5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019503	66832	Rsph3a	http://www.ncbi.nlm.nih.gov/gene/?term=66832	"1700012G05Rik, 4930524H12Rik, R74860, Rshl2, Rshl2a "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019504	668343	Gm9115	http://www.ncbi.nlm.nih.gov/gene/?term=668343	EG668343	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019505	66836	Tmem223	http://www.ncbi.nlm.nih.gov/gene/?term=66836	0610006I08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019506	66839	0610009O20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66839	"2700004E22Rik, Dele, Kiaa0141 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019507	6683	SPAST	http://www.ncbi.nlm.nih.gov/gene/?term=6683	"ADPSP, FSP2, SPG4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019508	6683	SPAST	http://www.ncbi.nlm.nih.gov/gene/?term=6683	"ADPSP, FSP2, SPG4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019509	668408	1700084K02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=668408		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019510	66848	Fuca2	http://www.ncbi.nlm.nih.gov/gene/?term=66848	"0610025O11Rik, 5530401P20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019511	66857	Plbd1	http://www.ncbi.nlm.nih.gov/gene/?term=66857	1100001H23Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019512	66857	Plbd1	http://www.ncbi.nlm.nih.gov/gene/?term=66857	1100001H23Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019513	66866	Nhlrc2	http://www.ncbi.nlm.nih.gov/gene/?term=66866	"1200003G01Rik, AI835049, AV002846, AW496455 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019514	66867	Hmg20a	http://www.ncbi.nlm.nih.gov/gene/?term=66867	"1200004E06Rik, 5730490E10Rik, Hmgxb1, Ibraf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019515	66869	Zfp869	http://www.ncbi.nlm.nih.gov/gene/?term=66869	1200003I07Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019516	66870	Serbp1	http://www.ncbi.nlm.nih.gov/gene/?term=66870	"1200009K13Rik, 9330147J08Rik, AL022786, Pairbp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019517	66874	Ncbp3	http://www.ncbi.nlm.nih.gov/gene/?term=66874	"1200014J11Rik, C130061O14Rik, C78393 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019518	66875	Swt1	http://www.ncbi.nlm.nih.gov/gene/?term=66875	"1200016B10Rik, C1orf26 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019519	668771	Gm9347	http://www.ncbi.nlm.nih.gov/gene/?term=668771	EG668771	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019520	66877	Crnkl1	http://www.ncbi.nlm.nih.gov/gene/?term=66877	"1200013P10Rik, 5730590A01Rik, C80326, crn "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019521	6687	SPG7	http://www.ncbi.nlm.nih.gov/gene/?term=6687	"CAR, CMAR, PGN, SPG5C "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019522	6687	SPG7	http://www.ncbi.nlm.nih.gov/gene/?term=6687	"CAR, CMAR, PGN, SPG5C "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019523	6687	SPG7	http://www.ncbi.nlm.nih.gov/gene/?term=6687	"CAR, CMAR, PGN, SPG5C "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019524	66880	Rsrc1	http://www.ncbi.nlm.nih.gov/gene/?term=66880	"1200013F24Rik, SRrp53 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019525	66881	Pcyox1	http://www.ncbi.nlm.nih.gov/gene/?term=66881	"1200015P13Rik, AI115532, AI448340, PCL1, Pcly "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019526	66884	Appbp2	http://www.ncbi.nlm.nih.gov/gene/?term=66884	"1300003O07Rik, AI465480, PAT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019527	66885	Acadsb	http://www.ncbi.nlm.nih.gov/gene/?term=66885	"1300003O09Rik, 2-MEBCAD, BB066609, SBCAD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019528	66887	Lonp2	http://www.ncbi.nlm.nih.gov/gene/?term=66887	"1300002A08Rik, AU015403, Lonp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019529	6688	SPI1	http://www.ncbi.nlm.nih.gov/gene/?term=6688	"OF, PU.1, SFPI1, SPI-1, SPI-A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019530	668917	Zfp133-ps	http://www.ncbi.nlm.nih.gov/gene/?term=668917	"OTTMUSG00000003825, Zfp133 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019531	66897	Naa16	http://www.ncbi.nlm.nih.gov/gene/?term=66897	"1300019C06Rik, Narg1l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019532	66898	Baiap2l1	http://www.ncbi.nlm.nih.gov/gene/?term=66898	"1300006M19Rik, AI585895, IRTKS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019533	66899	Fip1l1	http://www.ncbi.nlm.nih.gov/gene/?term=66899	"1300019H17Rik, Rje "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019534	6689	SPIB	http://www.ncbi.nlm.nih.gov/gene/?term=6689	SPI-B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019535	66905	Plin3	http://www.ncbi.nlm.nih.gov/gene/?term=66905	"1300012C15Rik, M6prbp1, Tip47 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019536	6690	SPINK1	http://www.ncbi.nlm.nih.gov/gene/?term=6690	"PCTT, PSTI, Spink3, TATI, TCP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019537	66910	Tmem107	http://www.ncbi.nlm.nih.gov/gene/?term=66910	"1110004B13Rik, 2810049P21Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019538	66911	Nudt16l1	http://www.ncbi.nlm.nih.gov/gene/?term=66911	"1110001K21Rik, 5330437I08Rik, Sdos "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019539	66912	Bzw2	http://www.ncbi.nlm.nih.gov/gene/?term=66912	"1110001I24Rik, Bdm2, HSPC028 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019540	66917	Chordc1	http://www.ncbi.nlm.nih.gov/gene/?term=66917	"1110001O09Rik, AA409036, Chp-1, morgana "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019541	66921	Prpf38b	http://www.ncbi.nlm.nih.gov/gene/?term=66921	"1110021E09Rik, AU018955 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019542	66923	Pbrm1	http://www.ncbi.nlm.nih.gov/gene/?term=66923	"2610016F04Rik, AI507524, BAF180, Pb1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019543	6692	SPINT1	http://www.ncbi.nlm.nih.gov/gene/?term=6692	"HAI, HAI1, MANSC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019544	66934	Dsn1	http://www.ncbi.nlm.nih.gov/gene/?term=66934	"1700022L09Rik, AW552447 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019545	66942	Ddx18	http://www.ncbi.nlm.nih.gov/gene/?term=66942	2310005B10Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019546	66942	Ddx18	http://www.ncbi.nlm.nih.gov/gene/?term=66942	2310005B10Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019547	66945	Sdha	http://www.ncbi.nlm.nih.gov/gene/?term=66945	"1500032O14Rik, 2310034D06Rik, 4921513A11, C81073, FP, SDH2, SDHF "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019548	66949	Trim59	http://www.ncbi.nlm.nih.gov/gene/?term=66949	"2310035M22Rik, 2700022F13Rik, Mrf1, TSBF1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019549	66950	Tmem206	http://www.ncbi.nlm.nih.gov/gene/?term=66950	"2310028N02Rik, AI118576 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019550	66950	Tmem206	http://www.ncbi.nlm.nih.gov/gene/?term=66950	"2310028N02Rik, AI118576 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019551	66960	Fam188a	http://www.ncbi.nlm.nih.gov/gene/?term=66960	"1810041E18Rik, 2310047O13Rik, 5830410F13Rik, AI447827, AW111958 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019552	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"2310043N10Rik, VINC "	lncRNA	Mus musculus	17270048	Nucleus	Liver cell	In situ hybridization	"In both the BLK CL.4 cell line and mouse liver, both Neat1 and Neat2/Malat-1 were both more than ten-fold enriched in nuclear fractions (Table ?(Table1).1) "
RLID00019553	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"2310043N10Rik, VINC "	lncRNA	Mus musculus	22070123	Nucleus	Kidney cell	In situ hybridization	"Here, we discuss the functions of a distinct group of vertebrate-specific lncRNAs, NEAT1/MENε/β/VINC, MALAT1/NEAT2, and Gomafu/RNCR2/MIAT, which accumulate abundantly within the nucleus as RNA components of specific nuclear bodies. "
RLID00019554	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"2310043N10Rik, VINC "	lncRNA	Mus musculus	22817891	Nucleus	Bone marrow Macrophage	Next-generation sequencing	"Cluster 7, for example, contains abundant transcripts in the chromatin, with much lower transcript levels in the nucleoplasm and cytoplasm relative to the other clusters. This cluster is dominated by annotated and unannotated non-coding transcripts and miRNA precursors. (The analysis excluded transcripts shorter than 400 nucleotides and therefore excluded mature miRNAs and many miRNA precursors.) Some non-coding RNAs, such as Xist, are highly enriched in the chromatin because they function at this location (Figure S2). Examples of other non-coding RNAs in Cluster 7 are Neat1 and Malat1/Neat2 (Figure S2). Further mining of the data sets may provide insights into the subcellular locations at which many non-coding RNAs function. Cluster 7 also includes transcripts from constitutive protein-coding genes that may be highly unstable and therefore present at low levels in the cytoplasm (e.g. Leng8 in Figure S2). "
RLID00019555	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"2310043N10Rik, VINC "	lncRNA	Mus musculus	21170033	Nucleus	Myoblast	In situ hybridization|qRT-PCR	"Using this system, we demonstrate that Menε/β ncRNAs are essential to initiate the de novo assembly of paraspeckles. These newly formed structures effectively harbor nuclear retained mRNAs confirming that they are bona fide functional paraspeckles. "
RLID00019556	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"2310043N10Rik, VINC "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019557	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"2310043N10Rik, VINC "	lncRNA	Mus musculus	22718948	Nucleus	Embryotem cell	In situ hybridization|Northern blot|qRT-PCR	"However, the cellular levels of another long, noncoding RNA--Neat1--which is an architectural component of nuclear bodies known as paraspeckles, were down-regulated in a particular set of tissues and cells lacking Malat1. "
RLID00019558	66966	Trit1	http://www.ncbi.nlm.nih.gov/gene/?term=66966	"2310075G14Rik, AI314189, AI314635, AV099619, IPT, MOD5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019559	66972	Slc25a23	http://www.ncbi.nlm.nih.gov/gene/?term=66972	"2310067G05Rik, SCaMC-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019560	66975	Trappc13	http://www.ncbi.nlm.nih.gov/gene/?term=66975	"2410002O22Rik, 2610524F24Rik, AI451892, AU017229 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019561	66977	Nuf2	http://www.ncbi.nlm.nih.gov/gene/?term=66977	"2410003C07Rik, AU044112, C85691, Cdca1, NUF2R "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019562	66978	Luc7l	http://www.ncbi.nlm.nih.gov/gene/?term=66978	"1810045C04Rik, 2410018D03Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019563	6697	SPR	http://www.ncbi.nlm.nih.gov/gene/?term=6697	SDR38C1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019564	66983	Zfp830	http://www.ncbi.nlm.nih.gov/gene/?term=66983	"2410003C20Rik, AV301118, AW048207, Ccdc16, Omcg1, Znf830 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019565	66985	Rassf7	http://www.ncbi.nlm.nih.gov/gene/?term=66985	"2400009B11Rik, AW210608 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019566	66990	Tmem134	http://www.ncbi.nlm.nih.gov/gene/?term=66990	"2410001H17Rik, AI463452 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019567	66993	Smarcd3	http://www.ncbi.nlm.nih.gov/gene/?term=66993	"1500001J14Rik, 2210409C08Rik, BAF60C "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019568	66997	Psmd12	http://www.ncbi.nlm.nih.gov/gene/?term=66997	"1500002F15Rik, AI480719, P55 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019569	66999	Med28	http://www.ncbi.nlm.nih.gov/gene/?term=66999	"1500003D12Rik, AI451633, AU045690, Eg1, FKSG20, magicin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019570	669	BPGM	http://www.ncbi.nlm.nih.gov/gene/?term=669	DPGM	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019571	669	BPGM	http://www.ncbi.nlm.nih.gov/gene/?term=669	DPGM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019572	67016	Tbc1d2b	http://www.ncbi.nlm.nih.gov/gene/?term=67016	"1810061M12Rik, AI480956, AV021536, AV023399, AW491493, mKIAA1055 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019573	67017	Fam210b	http://www.ncbi.nlm.nih.gov/gene/?term=67017	"2010011I20Rik, AI430961, AV108736 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019574	67019	Actr6	http://www.ncbi.nlm.nih.gov/gene/?term=67019	"2010200J04Rik, AU044443, Arp6, ArpX, CDA12 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019575	67025	Rpl11	http://www.ncbi.nlm.nih.gov/gene/?term=67025	2010203J19Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019576	67026	Thap4	http://www.ncbi.nlm.nih.gov/gene/?term=67026	2010320B01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019577	6702	SPRR2C	http://www.ncbi.nlm.nih.gov/gene/?term=6702		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019578	67031	Upf3a	http://www.ncbi.nlm.nih.gov/gene/?term=67031	"2600001C03Rik, 4930546M19Rik, RENT3A, UPF3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019579	67035	Dnajb4	http://www.ncbi.nlm.nih.gov/gene/?term=67035	"1700029A20Rik, 2010306G19Rik, 5730460G06Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019580	67037	Pmf1	http://www.ncbi.nlm.nih.gov/gene/?term=67037	"2600009M07Rik, AL033286, AW060657 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019581	67039	Rbm25	http://www.ncbi.nlm.nih.gov/gene/?term=67039	"2600011C06Rik, 2610015J01Rik, A130095G20Rik, AI159652, AL023075, AU043498, RNPC7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019582	67039	Rbm25	http://www.ncbi.nlm.nih.gov/gene/?term=67039	"2600011C06Rik, 2610015J01Rik, A130095G20Rik, AI159652, AL023075, AU043498, RNPC7 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019583	67040	Ddx17	http://www.ncbi.nlm.nih.gov/gene/?term=67040	"2610007K22Rik, A430025E01Rik, AI047725, C80929, Gm926, p72 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019584	67041	Oxct1	http://www.ncbi.nlm.nih.gov/gene/?term=67041	"2610008O03Rik, Oxct, Oxct2a, Scot-s "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019585	67042	Ift27	http://www.ncbi.nlm.nih.gov/gene/?term=67042	"2600013G09Rik, Rabl4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019586	67043	Syap1	http://www.ncbi.nlm.nih.gov/gene/?term=67043	"2010110O17Rik, AW011796 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019587	67045	Riok2	http://www.ncbi.nlm.nih.gov/gene/?term=67045	"2010110K24Rik, 2410085M17Rik "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019588	67045	Riok2	http://www.ncbi.nlm.nih.gov/gene/?term=67045	"2010110K24Rik, 2410085M17Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019589	67046	Tbc1d7	http://www.ncbi.nlm.nih.gov/gene/?term=67046	2610009C09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019590	67049	Pus3	http://www.ncbi.nlm.nih.gov/gene/?term=67049	"2610020J05Rik, 5730412F04Rik "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019591	67049	Pus3	http://www.ncbi.nlm.nih.gov/gene/?term=67049	"2610020J05Rik, 5730412F04Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019592	67050	Nkap	http://www.ncbi.nlm.nih.gov/gene/?term=67050	"2610020O08Rik, AA987160, AI849147, AL024236 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019593	67062	Slc25a53	http://www.ncbi.nlm.nih.gov/gene/?term=67062	"2310046F18Rik, 2810402A17Rik, AI448995, AI841128, Mcart6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019594	67062	Slc25a53	http://www.ncbi.nlm.nih.gov/gene/?term=67062	"2310046F18Rik, 2810402A17Rik, AI448995, AI841128, Mcart6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019595	6706	SPRR2G	http://www.ncbi.nlm.nih.gov/gene/?term=6706		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019596	67070	Lsm14a	http://www.ncbi.nlm.nih.gov/gene/?term=67070	"2700023B17Rik, AA407828, AU017544, Tral "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019597	67072	Cdc37l1	http://www.ncbi.nlm.nih.gov/gene/?term=67072	"2700033A15Rik, BB159850, Cdc37l, Harc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019598	67073	Pi4k2b	http://www.ncbi.nlm.nih.gov/gene/?term=67073	"2610042N09Rik, 4933409G22Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019599	67074	Mon2	http://www.ncbi.nlm.nih.gov/gene/?term=67074	"2610528O22Rik, AW495628, Sf21, mKIAA1040 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019600	67075	Magt1	http://www.ncbi.nlm.nih.gov/gene/?term=67075	"2410001C15Rik, 2610529C04Rik, 2810482I07Rik, IAG2, IAP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019601	67089	Psmc6	http://www.ncbi.nlm.nih.gov/gene/?term=67089	"2300001E01Rik, AI451058 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019602	6708	SPTA1	http://www.ncbi.nlm.nih.gov/gene/?term=6708	"EL2, HPP, HS3, SPH3, SPTA "	mRNA	Homo sapiens	10487838	Dendrite	Brain	In situ hybridization	"In addition, hybridization of [alpha]-spectrin mRNA in 10-day-old animals appeared as grain alignments along the dendritic shafts. "
RLID00019603	6708	SPTA1	http://www.ncbi.nlm.nih.gov/gene/?term=6708	"EL2, HPP, HS3, SPH3, SPTA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019604	67091	Trappc6a	http://www.ncbi.nlm.nih.gov/gene/?term=67091	"1810073E21Rik, 4930519D19Rik, AI480686, TRS33, mhyp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019605	67097	Rps10	http://www.ncbi.nlm.nih.gov/gene/?term=67097	2210402A09Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019606	6709	SPTAN1	http://www.ncbi.nlm.nih.gov/gene/?term=6709	"EIEE5, NEAS, SPTA2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019607	6709	SPTAN1	http://www.ncbi.nlm.nih.gov/gene/?term=6709	"EIEE5, NEAS, SPTA2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019608	6709	SPTAN1	http://www.ncbi.nlm.nih.gov/gene/?term=6709	"EIEE5, NEAS, SPTA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019609	670	BPHL	http://www.ncbi.nlm.nih.gov/gene/?term=670	"BPH-RP, MCNAA, VACVASE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019610	670	BPHL	http://www.ncbi.nlm.nih.gov/gene/?term=670	"BPH-RP, MCNAA, VACVASE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019611	67102	D16Ertd472e	http://www.ncbi.nlm.nih.gov/gene/?term=67102	"1700010I10Rik, 2310009O17Rik, E330003K22Rik, Eurl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019612	67102	D16Ertd472e	http://www.ncbi.nlm.nih.gov/gene/?term=67102	"1700010I10Rik, 2310009O17Rik, E330003K22Rik, Eurl "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019613	67105	Timm21	http://www.ncbi.nlm.nih.gov/gene/?term=67105	"1700034H14Rik, 2700002I20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019614	67106	Zbtb8os	http://www.ncbi.nlm.nih.gov/gene/?term=67106	"2010001H09Rik, 2310028N13Rik, AI851226, Arch, Archm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019615	67109	Zfp787	http://www.ncbi.nlm.nih.gov/gene/?term=67109	"2210018M03Rik, Znf787 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019616	67111	Naaa	http://www.ncbi.nlm.nih.gov/gene/?term=67111	"2210023K21Rik, 3830414F09Rik, Asahl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019617	67111	Naaa	http://www.ncbi.nlm.nih.gov/gene/?term=67111	"2210023K21Rik, 3830414F09Rik, Asahl "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019618	67115	Rpl14	http://www.ncbi.nlm.nih.gov/gene/?term=67115	"3100001N19Rik, AA407502, AL022816, CAG-ISL-7, CTG-B33, L14 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019619	67117	Dynlt3	http://www.ncbi.nlm.nih.gov/gene/?term=67117	"2310075M16Rik, AU042796, Tcte1l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019620	67117	Dynlt3	http://www.ncbi.nlm.nih.gov/gene/?term=67117	"2310075M16Rik, AU042796, Tcte1l "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019621	67117	Dynlt3	http://www.ncbi.nlm.nih.gov/gene/?term=67117	"2310075M16Rik, AU042796, Tcte1l "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00019622	67118	Bfar	http://www.ncbi.nlm.nih.gov/gene/?term=67118	"3010001A07Rik, AI666707, AW107665, Bar, Rnf47 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019623	6711	SPTBN1	http://www.ncbi.nlm.nih.gov/gene/?term=6711	"ELF, HEL102, SPTB2, betaSpII "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019624	6711	SPTBN1	http://www.ncbi.nlm.nih.gov/gene/?term=6711	"ELF, HEL102, SPTB2, betaSpII "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019625	6711	SPTBN1	http://www.ncbi.nlm.nih.gov/gene/?term=6711	"ELF, HEL102, SPTB2, betaSpII "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019626	67120	Ttc14	http://www.ncbi.nlm.nih.gov/gene/?term=67120	"2700016E08Rik, 4930434D01Rik, 4931403I22Rik, 4933402I15Rik, AI662468, AU014779, AW561908, cI-44, mKIAA1980 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019627	67121	Mastl	http://www.ncbi.nlm.nih.gov/gene/?term=67121	"2700091H24Rik, C88295, GW, GWL, MAST-L, THC2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019628	67126	Atp5e	http://www.ncbi.nlm.nih.gov/gene/?term=67126	"2410043G19Rik, ATPE, AV000645 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019629	6712	SPTBN2	http://www.ncbi.nlm.nih.gov/gene/?term=6712	"GTRAP41, SCA5, SCAR14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019630	67134	Nop56	http://www.ncbi.nlm.nih.gov/gene/?term=67134	"2310044F10Rik, Nol5a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019631	67138	Herc6	http://www.ncbi.nlm.nih.gov/gene/?term=67138	"1700121D12Rik, 2510038N07Rik, 4930427L17Rik, AI451296, CEB1, Herc5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019632	6713	SQLE	http://www.ncbi.nlm.nih.gov/gene/?term=6713		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019633	6713	SQLE	http://www.ncbi.nlm.nih.gov/gene/?term=6713		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019634	6713	SQLE	http://www.ncbi.nlm.nih.gov/gene/?term=6713		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019635	67141	Fbxo5	http://www.ncbi.nlm.nih.gov/gene/?term=67141	"2510044I10Rik, C85305, Emi1, Fbxo31 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019636	67144	Lrrc40	http://www.ncbi.nlm.nih.gov/gene/?term=67144	"2610040E16Rik, AI837674 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019637	67145	Tomm34	http://www.ncbi.nlm.nih.gov/gene/?term=67145	"2610100K07Rik, TOM34 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019638	6714	SRC	http://www.ncbi.nlm.nih.gov/gene/?term=6714	"ASV1, c-SRC, p60-Src, SRC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019639	67151	Psmd9	http://www.ncbi.nlm.nih.gov/gene/?term=67151	"1500011J20Rik, 2610202L11Rik, Bridge-1, P27 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019640	671535	Parp10	http://www.ncbi.nlm.nih.gov/gene/?term=671535		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019641	67155	Smarca2	http://www.ncbi.nlm.nih.gov/gene/?term=67155	"2610209L14Rik, SNF2alpha, Snf2l2, brahma, brm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019642	6715	SRD5A1	http://www.ncbi.nlm.nih.gov/gene/?term=6715	S5AR 1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019643	6715	SRD5A1	http://www.ncbi.nlm.nih.gov/gene/?term=6715	S5AR 1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019644	6715	SRD5A1	http://www.ncbi.nlm.nih.gov/gene/?term=6715	S5AR 1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019645	67161	Sclt1	http://www.ncbi.nlm.nih.gov/gene/?term=67161	"2610207F23Rik, 4931421F20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019646	67163	Ccdc47	http://www.ncbi.nlm.nih.gov/gene/?term=67163	"2610204L23Rik, C88307, asp4, calumin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019647	67166	Arl8b	http://www.ncbi.nlm.nih.gov/gene/?term=67166	"2610313E07Rik, 3100002J04Rik, Arl10c, gie1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019648	67168	Lpar6	http://www.ncbi.nlm.nih.gov/gene/?term=67168	"2610302I02Rik, P2ry5, P2y5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019649	67168	Lpar6	http://www.ncbi.nlm.nih.gov/gene/?term=67168	"2610302I02Rik, P2ry5, P2y5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019650	67178	Zmat5	http://www.ncbi.nlm.nih.gov/gene/?term=67178	"2610510L01Rik, D11Bwg0572e, D11Bwg1548e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019651	6717	SRI	http://www.ncbi.nlm.nih.gov/gene/?term=6717	"CP-22, CP22, SCN, V19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019652	6717	SRI	http://www.ncbi.nlm.nih.gov/gene/?term=6717	"CP-22, CP22, SCN, V19 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019653	6717	SRI	http://www.ncbi.nlm.nih.gov/gene/?term=6717	"CP-22, CP22, SCN, V19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019654	67186	Rplp2	http://www.ncbi.nlm.nih.gov/gene/?term=67186	2700049I22Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019655	67194	2700038G22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67194		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019656	67198	Spats2l	http://www.ncbi.nlm.nih.gov/gene/?term=67198	"2810022L02Rik, A230104H11Rik, AA987173, AI480531, AI842453, AW413586 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019657	67198	Spats2l	http://www.ncbi.nlm.nih.gov/gene/?term=67198	"2810022L02Rik, A230104H11Rik, AA987173, AI480531, AI842453, AW413586 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019658	67199	Pfdn1	http://www.ncbi.nlm.nih.gov/gene/?term=67199	"2700086I23Rik, AA408327, AU044714 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019659	67200	Ccdc77	http://www.ncbi.nlm.nih.gov/gene/?term=67200	"2400002C23Rik, 2700091N06Rik, AV168274 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019660	67201	Glod4	http://www.ncbi.nlm.nih.gov/gene/?term=67201	"1700082G03Rik, 2700085E05Rik, C81254 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019661	67204	Eif2s2	http://www.ncbi.nlm.nih.gov/gene/?term=67204	"2810026E11Rik, 38kDa, AA408636, AA571381, AA986487, AW822225, D2Ertd303e, EIF2, EIF2B "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019662	67204	Eif2s2	http://www.ncbi.nlm.nih.gov/gene/?term=67204	"2810026E11Rik, 38kDa, AA408636, AA571381, AA986487, AW822225, D2Ertd303e, EIF2, EIF2B "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019663	6720	SREBF1	http://www.ncbi.nlm.nih.gov/gene/?term=6720	"SREBP-1c, SREBP1, SREBP1a, bHLHd1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019664	6720	SREBF1	http://www.ncbi.nlm.nih.gov/gene/?term=6720	"SREBP-1c, SREBP1, SREBP1a, bHLHd1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019665	67211	Armc10	http://www.ncbi.nlm.nih.gov/gene/?term=67211	"2810037C14Rik, Svh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019666	6721	SREBF2	http://www.ncbi.nlm.nih.gov/gene/?term=6721	"SREBP-2, SREBP2, bHLHd2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019667	6721	SREBF2	http://www.ncbi.nlm.nih.gov/gene/?term=6721	"SREBP-2, SREBP2, bHLHd2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019668	67220	Plekho1	http://www.ncbi.nlm.nih.gov/gene/?term=67220	"2810052M02Rik, CKIP-1, Ckip1, JZA-20, Jza2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019669	67225	Rnpc3	http://www.ncbi.nlm.nih.gov/gene/?term=67225	"2810441O16Rik, AI447568, C030014B17Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019670	67229	Prpf18	http://www.ncbi.nlm.nih.gov/gene/?term=67229	2810441A10Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019671	6722	SRF	http://www.ncbi.nlm.nih.gov/gene/?term=6722	MCM1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019672	6722	SRF	http://www.ncbi.nlm.nih.gov/gene/?term=6722	MCM1	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00019673	6722	SRF	http://www.ncbi.nlm.nih.gov/gene/?term=6722	MCM1	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00019674	67231	Tbc1d20	http://www.ncbi.nlm.nih.gov/gene/?term=67231	"1110028I04Rik, 2810442O16Rik, AI414693, bs "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019675	67236	Cinp	http://www.ncbi.nlm.nih.gov/gene/?term=67236	"1810047K05Rik, 2810452K22Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019676	67239	Rpf2	http://www.ncbi.nlm.nih.gov/gene/?term=67239	"2810470K21Rik, AU040229, AU043242, Bxdc1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019677	6723	SRM	http://www.ncbi.nlm.nih.gov/gene/?term=6723	"PAPT, SPDSY, SPS1L1, SRM "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019678	6723	SRM	http://www.ncbi.nlm.nih.gov/gene/?term=6723	"PAPT, SPDSY, SPS1, SRML1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019679	67241	Smc6	http://www.ncbi.nlm.nih.gov/gene/?term=67241	"2810489L22Rik, 3830418C19Rik, AA990493, AU018782, AW742439, SMC-6l1, mKIAA4103, Smc6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019680	67245	Peli1	http://www.ncbi.nlm.nih.gov/gene/?term=67245	"2810468L03Rik, A930031K15Rik, AA409794, AI586297, D11Ertd676e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019681	67246	2810474O19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67246	"6720435I21Rik, AA536804, AU020969, GET, Kiaa1551 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019682	67246	2810474O19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67246	"6720435I21Rik, AA536804, AU020969, GET, Kiaa1551 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019683	67248	Rpl39	http://www.ncbi.nlm.nih.gov/gene/?term=67248	2810465O16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019684	67248	Rpl39	http://www.ncbi.nlm.nih.gov/gene/?term=67248	2810465O16Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019685	67249	Tbc1d19	http://www.ncbi.nlm.nih.gov/gene/?term=67249	2810453K03Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019686	672511	Rnf213	http://www.ncbi.nlm.nih.gov/gene/?term=672511	"6030403J01, D11Ertd759e, mKIAA1554 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019687	6725	SRMS	http://www.ncbi.nlm.nih.gov/gene/?term=6725	"C20orf148, SRM, dJ697K14.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019688	67263	Zswim6	http://www.ncbi.nlm.nih.gov/gene/?term=67263	"2900036G02Rik, mKIAA1577 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019689	67264	Ndufb8	http://www.ncbi.nlm.nih.gov/gene/?term=67264	"2900010I05Rik, AI987932 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019690	67266	Fam69a	http://www.ncbi.nlm.nih.gov/gene/?term=67266	"2900024C23Rik, AI315274 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019691	67266	Fam69a	http://www.ncbi.nlm.nih.gov/gene/?term=67266	"2900024C23Rik, AI315274 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019692	6726	SRP9	http://www.ncbi.nlm.nih.gov/gene/?term=6726	ALURBP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019693	6727	SRP14	http://www.ncbi.nlm.nih.gov/gene/?term=6727	ALURBP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019694	67281	Rpl37	http://www.ncbi.nlm.nih.gov/gene/?term=67281	3110005M08Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019695	67282	Ccdc53	http://www.ncbi.nlm.nih.gov/gene/?term=67282	"2900091E11Rik, 5730495F03Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019696	67283	Slc25a19	http://www.ncbi.nlm.nih.gov/gene/?term=67283	"2900089E13Rik, DNC, MUP1, TPC "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019697	67285	Cwc27	http://www.ncbi.nlm.nih.gov/gene/?term=67285	"3110009E13Rik, NY-CO-10, Sdccag10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019698	67286	Ift22	http://www.ncbi.nlm.nih.gov/gene/?term=67286	"3110017O03Rik, AI835745, AI847427, Rabl5 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019699	67288	Srek1ip1	http://www.ncbi.nlm.nih.gov/gene/?term=67288	"3110031B13Rik, AI462702, AV348305, AW121048, Sfrs12ip1, Srsf12ip1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019700	67289	3110021A11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67289		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019701	6728	SRP19	http://www.ncbi.nlm.nih.gov/gene/?term=6728		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019702	6728	SRP19	http://www.ncbi.nlm.nih.gov/gene/?term=6728		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019703	6728	SRP19	http://www.ncbi.nlm.nih.gov/gene/?term=6728		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019704	67291	Ccdc137	http://www.ncbi.nlm.nih.gov/gene/?term=67291	3110023B02Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019705	67292	Pigc	http://www.ncbi.nlm.nih.gov/gene/?term=67292	"3110030E07Rik, AW212108 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019706	67295	Rab3c	http://www.ncbi.nlm.nih.gov/gene/?term=67295	"2700062I01Rik, 3110015B08Rik, 3110037E15Rik, AI850886 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019707	67298	Gprasp1	http://www.ncbi.nlm.nih.gov/gene/?term=67298	"2210415K24Rik, 3110031O14Rik, C87852, GASP, GASP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019708	67299	Dock7	http://www.ncbi.nlm.nih.gov/gene/?term=67299	"3110056M06Rik, Gm430, m "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019709	6729	SRP54	http://www.ncbi.nlm.nih.gov/gene/?term=6729		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019710	6729	SRP54	http://www.ncbi.nlm.nih.gov/gene/?term=6729		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019711	672	BRCA1	http://www.ncbi.nlm.nih.gov/gene/?term=672	"BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4, PPP1R53, PSCP, RNF53 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019712	672	BRCA1	http://www.ncbi.nlm.nih.gov/gene/?term=672	"BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4, PPP1R53, PSCP, RNF53 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019713	672	BRCA1	http://www.ncbi.nlm.nih.gov/gene/?term=672	"BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4, PPP1R53, PSCP, RNF53 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019714	67300	Cltc	http://www.ncbi.nlm.nih.gov/gene/?term=67300	"3110065L21Rik, CHC, R74732 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019715	67302	Zc3h13	http://www.ncbi.nlm.nih.gov/gene/?term=67302	"2600010B19Rik, 3110050K21Rik, 4930570G11Rik, C87618 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019716	67306	Zc2hc1a	http://www.ncbi.nlm.nih.gov/gene/?term=67306	"3110050N22Rik, AI790358, AU023959, Fam164a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019717	6730	SRP68	http://www.ncbi.nlm.nih.gov/gene/?term=6730		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019718	6730	SRP68	http://www.ncbi.nlm.nih.gov/gene/?term=6730		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019719	6730	SRP68	http://www.ncbi.nlm.nih.gov/gene/?term=6730		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019720	67315	Ceacam12	http://www.ncbi.nlm.nih.gov/gene/?term=67315	"1600031J20Rik-C1, Ceacam12-C3, Ceacam12C1, Ceacam12C3, Ceacam12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019721	6731	SRP72	http://www.ncbi.nlm.nih.gov/gene/?term=6731	"BMFF, BMFS1, HEL103 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019722	6731	SRP72	http://www.ncbi.nlm.nih.gov/gene/?term=6731	"BMFF, BMFS1, HEL103 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019723	6731	SRP72	http://www.ncbi.nlm.nih.gov/gene/?term=6731	"BMFF, BMFS1, HEL103 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019724	67326	1700037H04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67326		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019725	6732	SRPK1	http://www.ncbi.nlm.nih.gov/gene/?term=6732	SFRSK1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019726	6732	SRPK1	http://www.ncbi.nlm.nih.gov/gene/?term=6732	SFRSK1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019727	67337	Cstf1	http://www.ncbi.nlm.nih.gov/gene/?term=67337	"1700057K18Rik, AI788832 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019728	6733	SRPK2	http://www.ncbi.nlm.nih.gov/gene/?term=6733	SFRSK2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019729	6733	SRPK2	http://www.ncbi.nlm.nih.gov/gene/?term=6733	SFRSK2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019730	67344	Tctex1d1	http://www.ncbi.nlm.nih.gov/gene/?term=67344	1700055O19Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019731	67345	Herc4	http://www.ncbi.nlm.nih.gov/gene/?term=67345	"1700056O17Rik, 4921531D01Rik, 9530080M15Rik, mKIAA1593 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019732	6734	SRPRA	http://www.ncbi.nlm.nih.gov/gene/?term=6734	"DP, SRPR, Sralpha "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019733	6734	SRPRA	http://www.ncbi.nlm.nih.gov/gene/?term=6734	"DP, SRPR, Sralpha "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019734	67367	Paxbp1	http://www.ncbi.nlm.nih.gov/gene/?term=67367	"1810007M14Rik, C21orf66, Gcfc, Gcfc1, Pax3/7bp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019735	67371	Gtf3c6	http://www.ncbi.nlm.nih.gov/gene/?term=67371	"2410016F19Rik, AU019813 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019736	67379	Dedd2	http://www.ncbi.nlm.nih.gov/gene/?term=67379	"2410050E11Rik, FLAME-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019737	67382	Brd3	http://www.ncbi.nlm.nih.gov/gene/?term=67382	"2410084F24Rik, AW060456, Fsrg2, ORFX, RINGL3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019738	67387	Unc50	http://www.ncbi.nlm.nih.gov/gene/?term=67387	"1110002A21Rik, GMH1, UNCL, URP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019739	6738	TROVE2	http://www.ncbi.nlm.nih.gov/gene/?term=6738	"RO60, RORNP, SSA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019740	6738	TROVE2	http://www.ncbi.nlm.nih.gov/gene/?term=6738	"RO60, RORNP, SSA2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019741	6738	TROVE2	http://www.ncbi.nlm.nih.gov/gene/?term=6738	"RO60, RORNP, SSA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019742	67392	4833420G17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67392	"2210017J06Rik, 5730533D17Rik, AW107518, C85193 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019743	67392	4833420G17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67392	"2210017J06Rik, 5730533D17Rik, AW107518, C85193 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019744	67394	4930404I05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67394		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019745	673	BRAF	http://www.ncbi.nlm.nih.gov/gene/?term=673	"B-RAF11, NS7, RAFB1, BRAF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019746	673	BRAF	http://www.ncbi.nlm.nih.gov/gene/?term=673	"B-RAF1, BRAF1, NS7, RAFB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019747	67414	Mfn1	http://www.ncbi.nlm.nih.gov/gene/?term=67414	"2310002F04Rik, 6330416C07Rik, D3Ertd265e, HR2, mKIAA4032 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019748	67418	Ppil4	http://www.ncbi.nlm.nih.gov/gene/?term=67418	"3732410E19Rik, 3830425H19Rik, AI788954, AW146233, PPIase "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019749	67419	3632451O06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67419	AU067705	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019750	6741	SSB	http://www.ncbi.nlm.nih.gov/gene/?term=6741	"LARP3, La, La/SSB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019751	6741	SSB	http://www.ncbi.nlm.nih.gov/gene/?term=6741	"LARP3, La, La/SSB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019752	67420	Far1	http://www.ncbi.nlm.nih.gov/gene/?term=67420	"2600011M19Rik, 2900034E22Rik, 3732409C05Rik, AI850429, Mlstd2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019753	67422	Dhdds	http://www.ncbi.nlm.nih.gov/gene/?term=67422	"3222401G21Rik, CIT, DS, HDS, W91638 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019754	67427	Rps20	http://www.ncbi.nlm.nih.gov/gene/?term=67427	"4632426K06Rik, Dsk4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019755	6742	SSBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6742	"Mt-SSB, SOSS-B1, SSBP, mtSSB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019756	6742	SSBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6742	"Mt-SSB, SOSS-B1, SSBP, mtSSB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019757	67437	Ssr3	http://www.ncbi.nlm.nih.gov/gene/?term=67437	"0610038P07Rik, AL022999, AU022074, AW553833, TRAPG "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019758	67440	Mtpap	http://www.ncbi.nlm.nih.gov/gene/?term=67440	"0610027A18Rik, AW551379, Papd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019759	67446	Dusp28	http://www.ncbi.nlm.nih.gov/gene/?term=67446	"0710001B24Rik, AV005521 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019760	6744	SSFA2	http://www.ncbi.nlm.nih.gov/gene/?term=6744	"CS-1, CS1, KRAP, SPAG13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019761	6744	SSFA2	http://www.ncbi.nlm.nih.gov/gene/?term=6744	"CS-1, CS1, KRAP, SPAG13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019762	67452	Pnpla8	http://www.ncbi.nlm.nih.gov/gene/?term=67452	"1200006O19Rik, AI467579, Ipla2(gamma) "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019763	67453	Slc25a46	http://www.ncbi.nlm.nih.gov/gene/?term=67453	"1200007B05Rik, AI325987 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019764	67454	Ikbip	http://www.ncbi.nlm.nih.gov/gene/?term=67454	"1200009F10Rik, 1700023M03Rik, D18354, Ikip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019765	67457	Frmd8	http://www.ncbi.nlm.nih.gov/gene/?term=67457	"1200004M23Rik, 2310035N23Rik, 4931429L16Rik, AU018809 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019766	67459	Nvl	http://www.ncbi.nlm.nih.gov/gene/?term=67459	1200009I24Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019767	6745	SSR1	http://www.ncbi.nlm.nih.gov/gene/?term=6745	TRAPA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019768	6745	SSR1	http://www.ncbi.nlm.nih.gov/gene/?term=6745	TRAPA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019769	6745	SSR1	http://www.ncbi.nlm.nih.gov/gene/?term=6745	TRAPA	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019770	6745	SSR1	http://www.ncbi.nlm.nih.gov/gene/?term=6745	TRAPA	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019771	6745	SSR1	http://www.ncbi.nlm.nih.gov/gene/?term=6745	TRAPA	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00019772	6745	SSR1	http://www.ncbi.nlm.nih.gov/gene/?term=6745	TRAPA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019773	67466	Pdcl	http://www.ncbi.nlm.nih.gov/gene/?term=67466	"1200011E13Rik, AW108059, PhLP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019774	67467	Gpalpp1	http://www.ncbi.nlm.nih.gov/gene/?term=67467	"1200011I18Rik, Kiaa1704 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019775	67468	Mmd	http://www.ncbi.nlm.nih.gov/gene/?term=67468	"1200017E07Rik, 1810073C06Rik, AA690185 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019776	6746	SSR2	http://www.ncbi.nlm.nih.gov/gene/?term=6746	"HSD25, TLAP, TRAP-BETA, TRAPB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019777	6746	SSR2	http://www.ncbi.nlm.nih.gov/gene/?term=6746	"HSD25, TLAP, TRAP-BETA, TRAPB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019778	67471	Gpatch1	http://www.ncbi.nlm.nih.gov/gene/?term=67471	"1300003A17Rik, ECGP, Gpatc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019779	67474	Snap29	http://www.ncbi.nlm.nih.gov/gene/?term=67474	"1300018G05Rik, AI891940, AU020222, BB131856, Gs32 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019780	6747	SSR3	http://www.ncbi.nlm.nih.gov/gene/?term=6747	TRAPG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019781	6747	SSR3	http://www.ncbi.nlm.nih.gov/gene/?term=6747	TRAPG	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019782	6747	SSR3	http://www.ncbi.nlm.nih.gov/gene/?term=6747	TRAPG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019783	67480	Cwc25	http://www.ncbi.nlm.nih.gov/gene/?term=67480	"1300013D05Rik, AA473636, Ccdc49, R75228 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019784	67486	Polr3g	http://www.ncbi.nlm.nih.gov/gene/?term=67486	"2310047G20Rik, AV275904, RPC32, RPC7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019785	67487	Dhx40	http://www.ncbi.nlm.nih.gov/gene/?term=67487	"2410016C14Rik, ARG147, DDX40, PAD "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019786	6748	SSR4	http://www.ncbi.nlm.nih.gov/gene/?term=6748	"CDG1Y, TRAPD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019787	6748	SSR4	http://www.ncbi.nlm.nih.gov/gene/?term=6748	"CDG1Y, TRAPD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019788	67490	Ufl1	http://www.ncbi.nlm.nih.gov/gene/?term=67490	"1810074P20Rik, AI429228, Kiaa0776, Maxer, Rcad, mKIAA0776 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019789	6749	SSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=6749	"FACT, FACT80, T160 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019790	6749	SSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=6749	"FACT, FACT80, T160 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019791	6749	SSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=6749	"FACT, FACT80, T160 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019792	67501	Ccdc50	http://www.ncbi.nlm.nih.gov/gene/?term=67501	C3orf6	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019793	67510	Tvp23b	http://www.ncbi.nlm.nih.gov/gene/?term=67510	"1810036I24Rik, Fam18b, Fam18b1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019794	67510	Tvp23b	http://www.ncbi.nlm.nih.gov/gene/?term=67510	"1810036I24Rik, Fam18b, Fam18b1 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019795	67511	Tmed9	http://www.ncbi.nlm.nih.gov/gene/?term=67511	2400003B06Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019796	67515	Ttc33	http://www.ncbi.nlm.nih.gov/gene/?term=67515	"2410099M07Rik, 2900001O04Rik, AI507072, AW538342, Osrf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019797	67516	Kctd4	http://www.ncbi.nlm.nih.gov/gene/?term=67516	"2210017A09Rik, AU017169 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019798	67524	1700095A21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67524		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019799	67528	Nudt7	http://www.ncbi.nlm.nih.gov/gene/?term=67528	"1300007B24Rik, 2210404C19Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019800	67529	Fgfr1op2	http://www.ncbi.nlm.nih.gov/gene/?term=67529	1500031J01Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019801	67531	5730408K05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67531	2610018C13Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019802	67532	Mfap1a	http://www.ncbi.nlm.nih.gov/gene/?term=67532	"4432409M24Rik, Mfap1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019803	67533	Ppfibp1	http://www.ncbi.nlm.nih.gov/gene/?term=67533	"4632409B19Rik, AW214454, AW261454 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019804	67533	Ppfibp1	http://www.ncbi.nlm.nih.gov/gene/?term=67533	"4632409B19Rik, AW214454, AW261454 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00019805	67534	Ttll4	http://www.ncbi.nlm.nih.gov/gene/?term=67534	"4632407P03Rik, AI451681, mKIAA0173 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019806	67552	H2afy3	http://www.ncbi.nlm.nih.gov/gene/?term=67552	4933432H23Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019807	67554	Slc25a30	http://www.ncbi.nlm.nih.gov/gene/?term=67554	"4933433D23Rik, AV025504, AV221431, AW319655, KMCP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019808	67557	Larp6	http://www.ncbi.nlm.nih.gov/gene/?term=67557	"5430431G03Rik, AI552438, Achn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019809	67561	Wdr48	http://www.ncbi.nlm.nih.gov/gene/?term=67561	"8430408H12Rik, Uaf1, mKIAA1449 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019810	67563	Narfl	http://www.ncbi.nlm.nih.gov/gene/?term=67563	"9030612I22Rik, AI504405, PRN "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019811	67575	4930430A15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67575		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019812	67580	Lrrc18	http://www.ncbi.nlm.nih.gov/gene/?term=67580	"4930442L21Rik, MTLR1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019813	675812	Zfp605	http://www.ncbi.nlm.nih.gov/gene/?term=675812	A830023I12Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019814	67581	Tbc1d23	http://www.ncbi.nlm.nih.gov/gene/?term=67581	"4930451A13Rik, AU015720, AU043671, AU043778, D030022P07Rik, W51689 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019815	67588	Rnf41	http://www.ncbi.nlm.nih.gov/gene/?term=67588	"2210404G21Rik, 4930511A05Rik, 4933415P08Rik, D10Ertd722e, FLRF, Nrdp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019816	67589	4930518J20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67589	AV209277	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019817	675	BRCA2	http://www.ncbi.nlm.nih.gov/gene/?term=675	"BRCC2, BROVCA2, FACD, FAD, FAD1, FANCD, FANCD1, GLM3, PNCA2, XRCC11 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019818	675	BRCA2	http://www.ncbi.nlm.nih.gov/gene/?term=675	"BRCC2, BROVCA2, FACD, FAD, FAD1, FANCD, FANCD1, GLM3, PNCA2, XRCC11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019819	67605	Akt1s1	http://www.ncbi.nlm.nih.gov/gene/?term=67605	"1110012J22Rik, AI227026, Lobe, Lobel, PRAS40 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019820	6760	SS18	http://www.ncbi.nlm.nih.gov/gene/?term=6760	"SSXT, SYT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019821	6760	SS18	http://www.ncbi.nlm.nih.gov/gene/?term=6760	"SSXT, SYT "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019822	6760	SS18	http://www.ncbi.nlm.nih.gov/gene/?term=6760	"SSXT, SYT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019823	6760	SS18	http://www.ncbi.nlm.nih.gov/gene/?term=6760	"SSXT, SYT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019824	67610	Rspry1	http://www.ncbi.nlm.nih.gov/gene/?term=67610	"4930470D19Rik, AI608258 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019825	67622	Mxra7	http://www.ncbi.nlm.nih.gov/gene/?term=67622	"1810057P16Rik, E130302J09Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019826	67629	Spc24	http://www.ncbi.nlm.nih.gov/gene/?term=67629	"2410030K01Rik, AV109292, Spbc24 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019827	67666	Hapln3	http://www.ncbi.nlm.nih.gov/gene/?term=67666	"4930554N11Rik, Lpr3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019828	67667	Alkbh8	http://www.ncbi.nlm.nih.gov/gene/?term=67667	"4930562C03Rik, 8030431D03Rik, 9430088N01Rik, Abh8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019829	67668	4930563N14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67668		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019830	67671	Rpl38	http://www.ncbi.nlm.nih.gov/gene/?term=67671	"0610025G13Rik, Rbt, Ts, Tss "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019831	67673	Tceb2	http://www.ncbi.nlm.nih.gov/gene/?term=67673	0610040H15Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019832	6767	ST13	http://www.ncbi.nlm.nih.gov/gene/?term=6767	"AAG2, FAM10A1, FAM10A4, HIP, HOP, HSPABP, HSPABP1, P48, PRO0786, SNC6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019833	6767	ST13	http://www.ncbi.nlm.nih.gov/gene/?term=6767	"AAG2, FAM10A1, FAM10A4, HIP, HOP, HSPABP, HSPABP1, P48, PRO0786, SNC6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019834	6767	ST13	http://www.ncbi.nlm.nih.gov/gene/?term=6767	"AAG2, FAM10A1, FAM10A4, HIP, HOP, HSPABP, HSPABP1, P48, PRO0786, SNC6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019835	67684	Luc7l3	http://www.ncbi.nlm.nih.gov/gene/?term=67684	"3300001P08Rik, Luc7a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019836	67689	Aldh3b1	http://www.ncbi.nlm.nih.gov/gene/?term=67689	"1700001N19Rik, ALDH4, ALDH7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019837	6768	ST14	http://www.ncbi.nlm.nih.gov/gene/?term=6768	"ARCI11, HAI, MT-SP1, MTSP1, PRSS14, SNC19, TADG15, TMPRSS14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019838	6768	ST14	http://www.ncbi.nlm.nih.gov/gene/?term=6768	"ARCI11, HAI, MT-SP1, MTSP1, PRSS14, SNC19, TADG15, TMPRSS14 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019839	67694	Ift74	http://www.ncbi.nlm.nih.gov/gene/?term=67694	"1700029H06Rik, Ccdc2, Cmg1, b2b796Clo "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019840	67702	Rnf149	http://www.ncbi.nlm.nih.gov/gene/?term=67702	"1600023E10Rik, AV037261, C76763, Gm15832, Greul4, OTTMUSG00000026591 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019841	67712	Slc25a37	http://www.ncbi.nlm.nih.gov/gene/?term=67712	"1700020E22Rik, 4930513O14Rik, 4930526G11Rik, AI848481, C330015G08Rik, Mfrn, Mfrn1, Mscp, frascati, mitoferrin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019842	67723	Cep83os	http://www.ncbi.nlm.nih.gov/gene/?term=67723	"4932415G12Rik, Ccdc41os1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019843	67726	Fam114a2	http://www.ncbi.nlm.nih.gov/gene/?term=67726	"1810073G14Rik, 9030624B09Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019844	67727	Stx17	http://www.ncbi.nlm.nih.gov/gene/?term=67727	"4833418L03Rik, 6330411F21Rik, 9030425C21Rik, AW048351 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019845	6772	STAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6772	"CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019846	6772	STAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6772	"CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019847	6772	STAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6772	"CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019848	6773	STAT2	http://www.ncbi.nlm.nih.gov/gene/?term=6773	"IMD44, ISGF-3, P113, STAT113 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019849	67741	4930579F01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67741		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019850	6774	STAT3	http://www.ncbi.nlm.nih.gov/gene/?term=6774	"ADMIO, APRF, HIES "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019851	6774	STAT3	http://www.ncbi.nlm.nih.gov/gene/?term=6774	"ADMIO, APRF, HIES "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019852	6775	STAT4	http://www.ncbi.nlm.nih.gov/gene/?term=6775	SLEB11	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019853	67760	Slc38a2	http://www.ncbi.nlm.nih.gov/gene/?term=67760	"5033402L14Rik, AI316867, ATA2, SAT2, mKIAA1382 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019854	67763	Prpsap1	http://www.ncbi.nlm.nih.gov/gene/?term=67763	"5730409F23Rik, PAP39 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019855	677679	SCARNA3	http://www.ncbi.nlm.nih.gov/gene/?term=677679	HBI-100	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019856	677681	SCARNA20	http://www.ncbi.nlm.nih.gov/gene/?term=677681	ACA66	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019857	67769	Gpatch2	http://www.ncbi.nlm.nih.gov/gene/?term=67769	"5830433G22Rik, 5830436K05Rik, AI427714, AI447508, AW107440, AW491060, Gpatc2 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019858	67769	Gpatch2	http://www.ncbi.nlm.nih.gov/gene/?term=67769	"5830433G22Rik, 5830436K05Rik, AI427714, AI447508, AW107440, AW491060, Gpatc2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019859	6776	STAT5A	http://www.ncbi.nlm.nih.gov/gene/?term=6776	"MGF, STAT5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019860	67772	Chd8	http://www.ncbi.nlm.nih.gov/gene/?term=67772	"5830451P18Rik, AU015341, Duplin, HELSNF1, mKIAA1564 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019861	67774	Borcs5	http://www.ncbi.nlm.nih.gov/gene/?term=67774	"5830457J20Rik, AW124643, Loh12cr1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019862	677763	SCARNA21	http://www.ncbi.nlm.nih.gov/gene/?term=677763	"ACA68A, SCARNA21 "	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019863	677765	SCARNA18	http://www.ncbi.nlm.nih.gov/gene/?term=677765	"SCARNA18A, U109 "	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019864	677766	SCARNA2	http://www.ncbi.nlm.nih.gov/gene/?term=677766	"HBII-382, mgU2-25/61 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019865	677767	SCARNA7	http://www.ncbi.nlm.nih.gov/gene/?term=677767	U90	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019866	677768	SCARNA13	http://www.ncbi.nlm.nih.gov/gene/?term=677768	U93	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019867	677768	SCARNA13	http://www.ncbi.nlm.nih.gov/gene/?term=677768	U93	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019868	67776	Vwa5a	http://www.ncbi.nlm.nih.gov/gene/?term=67776	"5830475I06Rik, AW552491, BCSC-1, E130119J22, Loh11cr2a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019869	677771	SCARNA4	http://www.ncbi.nlm.nih.gov/gene/?term=677771	ACA26	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019870	677772	SCARNA6	http://www.ncbi.nlm.nih.gov/gene/?term=677772	U88	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019871	677772	SCARNA6	http://www.ncbi.nlm.nih.gov/gene/?term=677772	U88	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019872	677772	SCARNA6	http://www.ncbi.nlm.nih.gov/gene/?term=677772	U88	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019873	677772	SCARNA6	http://www.ncbi.nlm.nih.gov/gene/?term=677772	U88	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"On the other hand, sdRNAs of only three Cajal body snoRNAs (SCARNA6, SCARNA15, SCARNA9L2) were represented in the subcellular libraries. "
RLID00019874	677774	SCARNA1	http://www.ncbi.nlm.nih.gov/gene/?term=677774	ACA35	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019875	677775	SCARNA5	http://www.ncbi.nlm.nih.gov/gene/?term=677775	U87	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019876	677776	SCARNA8	http://www.ncbi.nlm.nih.gov/gene/?term=677776	U92	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019877	677778	SCARNA15	http://www.ncbi.nlm.nih.gov/gene/?term=677778	ACA45	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019878	677778	SCARNA15	http://www.ncbi.nlm.nih.gov/gene/?term=677778	ACA45	snoRNA	Homo sapiens	25203660	Cytoplasm	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019879	677778	SCARNA15	http://www.ncbi.nlm.nih.gov/gene/?term=677778	ACA45	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"On the other hand, sdRNAs of only three Cajal body snoRNAs (SCARNA6, SCARNA15, SCARNA9L2) were represented in the subcellular libraries. "
RLID00019880	677778	SCARNA15	http://www.ncbi.nlm.nih.gov/gene/?term=677778	ACA45	snoRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019881	677780	SCARNA11	http://www.ncbi.nlm.nih.gov/gene/?term=677780	ACA57	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019882	677780	SCARNA11	http://www.ncbi.nlm.nih.gov/gene/?term=677780	ACA57	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019883	677781	SCARNA16	http://www.ncbi.nlm.nih.gov/gene/?term=677781	ACA47	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019884	677784	FAM138D	http://www.ncbi.nlm.nih.gov/gene/?term=677784	F379	lncRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00019885	67778	Zfp639	http://www.ncbi.nlm.nih.gov/gene/?term=67778	"6230400O18Rik, ANC-2H01, ZASC1, Znf639 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019886	677792	SNORA1	http://www.ncbi.nlm.nih.gov/gene/?term=677792	ACA1	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019887	677793	SNORA2A	http://www.ncbi.nlm.nih.gov/gene/?term=677793	ACA2A	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019888	677794	SNORA2B	http://www.ncbi.nlm.nih.gov/gene/?term=677794	ACA2b	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019889	677796	SNORA5C	http://www.ncbi.nlm.nih.gov/gene/?term=677796	ACA5c	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019890	677797	SNORA7B	http://www.ncbi.nlm.nih.gov/gene/?term=677797	ACA7B	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019891	6777	STAT5B	http://www.ncbi.nlm.nih.gov/gene/?term=6777	STAT5	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019892	6777	STAT5B	http://www.ncbi.nlm.nih.gov/gene/?term=6777	STAT5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019893	677801	SNORA14A	http://www.ncbi.nlm.nih.gov/gene/?term=677801	ACA14a	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019894	677802	SNORA14B	http://www.ncbi.nlm.nih.gov/gene/?term=677802	ACA14b	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019895	677803	SNORA15	http://www.ncbi.nlm.nih.gov/gene/?term=677803	"ACA15A, SNORA15 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019896	677804	SNORA17A	http://www.ncbi.nlm.nih.gov/gene/?term=677804	"ACA17, SNORA17 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019897	677805	SNORA18	http://www.ncbi.nlm.nih.gov/gene/?term=677805	ACA18	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019898	677805	SNORA18	http://www.ncbi.nlm.nih.gov/gene/?term=677805	ACA18	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019899	677806	SNORA20	http://www.ncbi.nlm.nih.gov/gene/?term=677806	ACA20	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019900	677806	SNORA20	http://www.ncbi.nlm.nih.gov/gene/?term=677806	ACA20	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019901	677808	SNORA23	http://www.ncbi.nlm.nih.gov/gene/?term=677808	ACA23	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019902	677809	SNORA24	http://www.ncbi.nlm.nih.gov/gene/?term=677809	"ACA24A, SNORA24 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019903	677809	SNORA24	http://www.ncbi.nlm.nih.gov/gene/?term=677809	"ACA24A, SNORA24 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019904	677810	SNORA26	http://www.ncbi.nlm.nih.gov/gene/?term=677810	HBI-6	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019905	677811	SNORA28	http://www.ncbi.nlm.nih.gov/gene/?term=677811	ACA28	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019906	677812	SNORA29	http://www.ncbi.nlm.nih.gov/gene/?term=677812	ACA29	snoRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00019907	677813	SNORA30	http://www.ncbi.nlm.nih.gov/gene/?term=677813	"ACA30A, SNORA30 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019908	677814	SNORA31	http://www.ncbi.nlm.nih.gov/gene/?term=677814	"ACA31A, SNORA31 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019909	677814	SNORA31	http://www.ncbi.nlm.nih.gov/gene/?term=677814	"ACA31A, SNORA31 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019910	677815	SNORA2C	http://www.ncbi.nlm.nih.gov/gene/?term=677815	"ACA34, MIR1291, SNORA34 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019911	677819	SNORA37	http://www.ncbi.nlm.nih.gov/gene/?term=677819	ACA37	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019912	677820	SNORA38	http://www.ncbi.nlm.nih.gov/gene/?term=677820	ACA38	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019913	677823	SNORA80E	http://www.ncbi.nlm.nih.gov/gene/?term=677823	"ACA42, SNORA42 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019914	677823	SNORA80E	http://www.ncbi.nlm.nih.gov/gene/?term=677823	"ACA42, SNORA42 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019915	677824	SNORA17B	http://www.ncbi.nlm.nih.gov/gene/?term=677824	"ACA43, SNORA43 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019916	677824	SNORA17B	http://www.ncbi.nlm.nih.gov/gene/?term=677824	"ACA43, SNORA43 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019917	677824	SNORA17B	http://www.ncbi.nlm.nih.gov/gene/?term=677824	"ACA43, SNORA43 "	snoRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019918	677825	SNORA44	http://www.ncbi.nlm.nih.gov/gene/?term=677825	ACA44	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019919	677826	SNORA3B	http://www.ncbi.nlm.nih.gov/gene/?term=677826	"ACA3-2, SNORA45, SNORA45B "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019920	677827	SNORA46	http://www.ncbi.nlm.nih.gov/gene/?term=677827	ACA46	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00019921	677827	SNORA46	http://www.ncbi.nlm.nih.gov/gene/?term=677827	ACA46	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019922	677827	SNORA46	http://www.ncbi.nlm.nih.gov/gene/?term=677827	ACA46	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019923	677828	SNORA47	http://www.ncbi.nlm.nih.gov/gene/?term=677828	HBI-115	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019924	677829	SNORA49	http://www.ncbi.nlm.nih.gov/gene/?term=677829	ACA49	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019925	677830	SNORA50A	http://www.ncbi.nlm.nih.gov/gene/?term=677830	"ACA50, SNORA50, SNORA76A "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019926	677832	SNORA53	http://www.ncbi.nlm.nih.gov/gene/?term=677832	ACA53	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019927	677832	SNORA53	http://www.ncbi.nlm.nih.gov/gene/?term=677832	ACA53	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019928	677832	SNORA53	http://www.ncbi.nlm.nih.gov/gene/?term=677832	ACA53	snRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019929	677833	SNORA54	http://www.ncbi.nlm.nih.gov/gene/?term=677833	ACA54	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019930	677834	SNORA55	http://www.ncbi.nlm.nih.gov/gene/?term=677834	ACA55	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019931	677837	SNORA60	http://www.ncbi.nlm.nih.gov/gene/?term=677837	ACA60	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019932	677838	SNORA61	http://www.ncbi.nlm.nih.gov/gene/?term=677838	ACA61	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019933	677838	SNORA61	http://www.ncbi.nlm.nih.gov/gene/?term=677838	ACA61	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019934	677839	SNORA71C	http://www.ncbi.nlm.nih.gov/gene/?term=677839	U71c	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019935	677840	SNORA71D	http://www.ncbi.nlm.nih.gov/gene/?term=677840	U71d	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019936	677841	SNORA74B	http://www.ncbi.nlm.nih.gov/gene/?term=677841	U19-2	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019937	677842	SNORA50C	http://www.ncbi.nlm.nih.gov/gene/?term=677842	"ACA62, SNORA76, SNORA76C "	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019938	677844	SNORA78	http://www.ncbi.nlm.nih.gov/gene/?term=677844	ACA64	snoRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00019939	677845	SNORA79	http://www.ncbi.nlm.nih.gov/gene/?term=677845	"ACA65A, SNORA79 "	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019940	677846	SNORA80A	http://www.ncbi.nlm.nih.gov/gene/?term=677846	"ACA67, SNORA80 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019941	677848	SNORD1A	http://www.ncbi.nlm.nih.gov/gene/?term=677848	"R38A, snR38A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019942	677849	SNORD1B	http://www.ncbi.nlm.nih.gov/gene/?term=677849	"R38B, snR38B "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019943	677849	SNORD1B	http://www.ncbi.nlm.nih.gov/gene/?term=677849	"R38B, snR38B "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00019944	677849	SNORD1B	http://www.ncbi.nlm.nih.gov/gene/?term=677849	"R38B, snR38B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019945	67785	Zmym4	http://www.ncbi.nlm.nih.gov/gene/?term=67785	"6330503C17Rik, AI480785, AW493829, CDIR, D630001M21, MYM, Zfp262, Znf262, mKIAA0425 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019946	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	8223259	Cytoskeleton	Oocyte	In situ hybridization	"Furthermore, Vg1 and Xcat-2 RNA appear to co-distribute to the cortex, a region particularly concentrated in cytoskeletal elements which include intermediate laments. "
RLID00019947	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	9148809	Cytoplasm	Oocyte	In situ hybridization	"Figure 3 Vg1 mRNA localization involves an interaction with the ER. (A) Vera cross-linking activity cosediments with ER membranes. Cytoplasmic extracts from pooled oocytes (stage IV through VI) were fractionated by sucrose density gradient sedimentation. (D) Endogenous Vg1 mRNA is associated with a subcompartment of the ER during localization. Endogenous Vg1 mRNA is distributed throughout the cytoplasm of early stage II oocytes (Fig. 3D), but at the transition between stages II and III (II/III) of oogenesis, Vg1 mRNA accumulates in a wedge-shaped region between the nucleus and vegetal cortex (Fig.3D) (5). As oogenesis proceeds to stage III, Vg1 mRNA labeling accumulates at the vegetal cortex (Fig. 3D) (5, 12,13). Before localization, Vg1 mRNA and the ER are probably not associated, because in stage II oocytes the Vg1 mRNA distribution is punctate and the ER is reticular (Fig. 3D). "
RLID00019948	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	9148809	Vegetal	Oocyte	In situ hybridization	"Figure 3 Vg1 mRNA localization involves an interaction with the ER. (A) Vera cross-linking activity cosediments with ER membranes. Cytoplasmic extracts from pooled oocytes (stage IV through VI) were fractionated by sucrose density gradient sedimentation. (D) Endogenous Vg1 mRNA is associated with a subcompartment of the ER during localization. Endogenous Vg1 mRNA is distributed throughout the cytoplasm of early stage II oocytes (Fig. 3D), but at the transition between stages II and III (II/III) of oogenesis, Vg1 mRNA accumulates in a wedge-shaped region between the nucleus and vegetal cortex (Fig.3D) (5). As oogenesis proceeds to stage III, Vg1 mRNA labeling accumulates at the vegetal cortex (Fig. 3D) (5, 12,13). Before localization, Vg1 mRNA and the ER are probably not associated, because in stage II oocytes the Vg1 mRNA distribution is punctate and the ER is reticular (Fig. 3D). "
RLID00019949	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	9545550	Mitochondrion	Oocyte	In situ hybridization	Whole-mount in situ hybridization with Xlsirt RNA probe in late stage 1 oocytes. The arrow points to the endogenous Xlsirt RNA localized in the METRO region of the mitochondrial cloud.
RLID00019950	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	9545550	Cytoplasm	Oocyte	In situ hybridization	"To help distinguish between these alternatives, we made several constructs in which we linked the Xlsirts localization signals to various regions of the full-length Vg1 mRNA (Fig. 1) and tested the ability of the chimeric RNAs to move to the mitochondrial cloud in stage 1 oocytes. Fig. 2. Localization of endogenous and exogenous Xlsirts and Vg1 RNAs in oocytes. (A) Whole-mount in situ hybridization with Xlsirt RNA probe in late stage 1 oocytes. The arrow points to the endogenous Xlsirt RNA localized in the METRO region of the mitochondrial cloud. (C) Whole mount in situ hybridization with Vg1 RNA probe in late stage 1 oocytes, Vg1 RNA is dispersed in the oocyte cytoplasm and is excluded from the mitochondrial cloud (arrow). (D) Injected Vg1 RNA spreads throughout the cytoplasm and is excluded from the mitochondrial cloud in late stage 1 oocytes (arrow). "
RLID00019951	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	15496522	Vegetal	Oocyte	Immunofluorescence	"We further showed that XStau proteins are transiently phosphorylated by the MAPK pathway during meiotic maturation, a period during which RNAs such as Vg1 RNA are released from their tight localization at the vegetal cortex. "
RLID00019952	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00019953	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	11309203	Vegetal	Oocyte	In situ hybridization	"The IVC retained mRNAs with a granular texture, and their distribution patterns resembled those of the whole oocyte. Vg1 was distributed in the entire cortex, whereas Xwnt-11 and Xcat-2 were both concentrated as a disc at the vegetal pole. "
RLID00019954	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	9545550	Endoplasmic reticulum	Oocyte	In situ hybridization	Fig. 4. Co-localization of ER and localized RNAs. (A) Stage 1 oocyte showing endogenous Vg1 RNA distributed throughout the cytoplasm (blue color) by in situ hybridization and the ER on the periphery of the mitochondrial cloud (red) by immunostaining with the GRP78 antibody (the arrow is pointing to the ER surrounding the cloud).
RLID00019955	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	11784070	Vegetal	Oocyte	In situ hybridization|RT-PCR	"While punctate staining for Vg1 mRNA was present at the vegetal cortex of uninjected oocytes, no localized Vg1 mRNA, either cortical or subcortical, was observed in the VegT-depleted oocytes (Figs. 3D and 3F). "
RLID00019956	677862	gdf1	http://www.ncbi.nlm.nih.gov/gene/?term=677862	"dvr-1, dvr1, gdf-1, vg1 "	mRNA	Xenopus laevis	23626739	Germ plasm	Oocyte	Microscopy	"We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs,Vg1 and VegT, also may localise into germ plasm. "
RLID00019957	67789	Dalrd3	http://www.ncbi.nlm.nih.gov/gene/?term=67789	"6330580J24Rik, C77829, mir-425 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019958	6778	STAT6	http://www.ncbi.nlm.nih.gov/gene/?term=6778	"D12S1644, IL-4-STAT, STAT6B, STAT6C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019959	67791	6530411M01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67791		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019960	67797	Snrnp48	http://www.ncbi.nlm.nih.gov/gene/?term=67797	"1110050F08Rik, 6530403A03Rik, C6orf151 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019961	67797	Snrnp48	http://www.ncbi.nlm.nih.gov/gene/?term=67797	"1110050F08Rik, 6530403A03Rik, C6orf151 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019962	677	ZFP36L1	http://www.ncbi.nlm.nih.gov/gene/?term=677	"BRF1, Berg36, ERF-1, ERF1, RNF162B, TIS11B, cMG1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019963	67803	Limd2	http://www.ncbi.nlm.nih.gov/gene/?term=67803	"0610025L06Rik, AI413966 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019964	67804	Snx2	http://www.ncbi.nlm.nih.gov/gene/?term=67804	0610030A03Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019965	6780	STAU1	http://www.ncbi.nlm.nih.gov/gene/?term=6780	"PPP1R150, STAU "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019966	6780	STAU1	http://www.ncbi.nlm.nih.gov/gene/?term=6780	"PPP1R150, STAU "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019967	6780	STAU1	http://www.ncbi.nlm.nih.gov/gene/?term=6780	"PPP1R150, STAU "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00019968	67821	Atp1b4	http://www.ncbi.nlm.nih.gov/gene/?term=67821	1110020B02Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019969	67824	Nmral1	http://www.ncbi.nlm.nih.gov/gene/?term=67824	"1110025F24Rik, AI256624 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019970	67826	Snap47	http://www.ncbi.nlm.nih.gov/gene/?term=67826	"1110031B06Rik, SNAP-47 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019971	6782	HSPA13	http://www.ncbi.nlm.nih.gov/gene/?term=6782	STCH	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00019972	6782	HSPA13	http://www.ncbi.nlm.nih.gov/gene/?term=6782	STCH	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019973	67830	Rer1	http://www.ncbi.nlm.nih.gov/gene/?term=67830	"1110060F11Rik, 5830454N22Rik, AU043380 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019974	67832	Brix1	http://www.ncbi.nlm.nih.gov/gene/?term=67832	"1110064N10Rik, Bxdc2, C76935 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019975	67838	Dnajb11	http://www.ncbi.nlm.nih.gov/gene/?term=67838	"1810031F23Rik, ABBP-2, AL024055, Dj9, ERdj3, ERj3p "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019976	6783	SULT1E1	http://www.ncbi.nlm.nih.gov/gene/?term=6783	"EST, EST-1, ST1E1, STE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019977	67841	Atg3	http://www.ncbi.nlm.nih.gov/gene/?term=67841	"2610016C12Rik, APG3, Apg3ll, PC3-96, Atg3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019978	67842	Nop9	http://www.ncbi.nlm.nih.gov/gene/?term=67842	2610027L16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019979	67845	Rnf115	http://www.ncbi.nlm.nih.gov/gene/?term=67845	"2610028E05Rik, AU042696, Zfp364 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019980	67848	Ddx55	http://www.ncbi.nlm.nih.gov/gene/?term=67848	"2810021H22Rik, mKIAA1595 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019981	6785	ELOVL4	http://www.ncbi.nlm.nih.gov/gene/?term=6785	"ADMD, CT118, ISQMR, SCA34, STGD2, STGD3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019982	67860	S100a16	http://www.ncbi.nlm.nih.gov/gene/?term=67860	"2300002L21Rik, AI325039, AI663996, DT1P1A7, S100F "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019983	67864	Yipf4	http://www.ncbi.nlm.nih.gov/gene/?term=67864	2310034L04Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019984	67868	Cela3b	http://www.ncbi.nlm.nih.gov/gene/?term=67868	"0910001F22Rik, 2310074F01Rik, AI504000, Ela3, Ela3b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00019985	6786	STIM1	http://www.ncbi.nlm.nih.gov/gene/?term=6786	"D11S4896E, GOK, IMD10, STRMK, TAM, TAM1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019986	67873	Mri1	http://www.ncbi.nlm.nih.gov/gene/?term=67873	2410018C20Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019987	67878	Tmem33	http://www.ncbi.nlm.nih.gov/gene/?term=67878	"1110006G02Rik, 1600019D15Rik, 2410089A21Rik, 2700052H22Rik, 5430406L04Rik, AA388285, AI314185, AI426615, db83 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019988	6787	NEK4	http://www.ncbi.nlm.nih.gov/gene/?term=6787	"NRK2, STK2, pp12301 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019989	67880	Dcxr	http://www.ncbi.nlm.nih.gov/gene/?term=67880	"0610038K04Rik, 1810027P18Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019990	67881	Mdp1	http://www.ncbi.nlm.nih.gov/gene/?term=67881	"1810034K20Rik, AI035604 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019991	67883	Uxs1	http://www.ncbi.nlm.nih.gov/gene/?term=67883	"1600025I13Rik, AI451869, AI649125, AW550562 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019992	67884	1810043G02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=67884	"AV026620, D10Jhu13e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019993	67886	Camsap2	http://www.ncbi.nlm.nih.gov/gene/?term=67886	"1600013L13Rik, 4930541M15Rik, Camsap1l1, mKIAA1078 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019994	67886	Camsap2	http://www.ncbi.nlm.nih.gov/gene/?term=67886	"1600013L13Rik, 4930541M15Rik, Camsap1l1, mKIAA1078 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019995	67887	Saraf	http://www.ncbi.nlm.nih.gov/gene/?term=67887	"1810045K07Rik, Tmem66 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019996	6788	STK3	http://www.ncbi.nlm.nih.gov/gene/?term=6788	"KRS1, MST2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00019997	6788	STK3	http://www.ncbi.nlm.nih.gov/gene/?term=6788	"KRS1, MST2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00019998	67897	Rnmt	http://www.ncbi.nlm.nih.gov/gene/?term=67897	"2610002P10Rik, AI848273, Rg7mt1, mKIAA0398 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00019999	67898	Pef1	http://www.ncbi.nlm.nih.gov/gene/?term=67898	"2600002E23Rik, Peflin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020000	6789	STK4	http://www.ncbi.nlm.nih.gov/gene/?term=6789	"KRS2, MST1, TIIAC, YSK3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020001	6789	STK4	http://www.ncbi.nlm.nih.gov/gene/?term=6789	"KRS2, MST1, TIIAC, YSK3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020002	6789	STK4	http://www.ncbi.nlm.nih.gov/gene/?term=6789	"KRS2, MST1, TIIAC, YSK3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020003	6789	STK4	http://www.ncbi.nlm.nih.gov/gene/?term=6789	"KRS2, MST1, TIIAC, YSK3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020004	6789	STK4	http://www.ncbi.nlm.nih.gov/gene/?term=6789	"KRS2, MST1, TIIAC, YSK3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020005	678	ZFP36L2	http://www.ncbi.nlm.nih.gov/gene/?term=678	"BRF2, ERF-2, ERF2, RNF162C, TIS11D "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020006	678	ZFP36L2	http://www.ncbi.nlm.nih.gov/gene/?term=678	"BRF2, ERF-2, ERF2, RNF162C, TIS11D "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020007	67903	Gipc1	http://www.ncbi.nlm.nih.gov/gene/?term=67903	"GIPC, Glut1CIP, Rgs19ip1, Semcap1, TIP-2, TaxIP2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020008	6790	AURKA	http://www.ncbi.nlm.nih.gov/gene/?term=6790	"AIK, ARK1, AURA, AURORA2, BTAK, PPP1R47, STK15, STK6, STK7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020009	6790	AURKA	http://www.ncbi.nlm.nih.gov/gene/?term=6790	"AIK, ARK1, AURA, AURORA2, BTAK, PPP1R47, STK15, STK6, STK7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020010	67920	Mak16	http://www.ncbi.nlm.nih.gov/gene/?term=67920	"2600016B03Rik, AI314911, Rbm13 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020011	67923	Tceb1	http://www.ncbi.nlm.nih.gov/gene/?term=67923	"2610043E24Rik, 2610301I15Rik, AA407206, AI987979, AW049146 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020012	6792	CDKL5	http://www.ncbi.nlm.nih.gov/gene/?term=6792	"CFAP247, EIEE2, ISSX, STK9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020013	67933	Hcfc2	http://www.ncbi.nlm.nih.gov/gene/?term=67933	"1700129L13Rik, AU019838 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020014	67939	Prorsd1	http://www.ncbi.nlm.nih.gov/gene/?term=67939	"2010316F05Rik, Ncrna00117, Prdxdd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020015	67943	Mesdc2	http://www.ncbi.nlm.nih.gov/gene/?term=67943	"2210015O11Rik, AW537813, mKIAA0081, mesd, msd "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020016	67944	Tex13a	http://www.ncbi.nlm.nih.gov/gene/?term=67944	1700025D03Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020017	67945	Rpl41	http://www.ncbi.nlm.nih.gov/gene/?term=67945	"1810055P16Rik, 2210411K19Rik "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020018	67945	Rpl41	http://www.ncbi.nlm.nih.gov/gene/?term=67945	"1810055P16Rik, 2210411K19Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020019	6794	STK11	http://www.ncbi.nlm.nih.gov/gene/?term=6794	"LKB1, PJS, hLKB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020020	67952	Tomm20	http://www.ncbi.nlm.nih.gov/gene/?term=67952	"1810060K07Rik, BB284719, Gm19268, MAS20, MOM19, TOM20, mKIAA0016 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020021	67955	Sugt1	http://www.ncbi.nlm.nih.gov/gene/?term=67955	"2410174K12Rik, SGT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020022	67956	Setd8	http://www.ncbi.nlm.nih.gov/gene/?term=67956	"2410195B05Rik, AA617402, AW536475, PR-SET7, PR/SET07 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020023	67958	U2surp	http://www.ncbi.nlm.nih.gov/gene/?term=67958	"2610101N10Rik, AU023006, Sr140 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020024	6795	AURKC	http://www.ncbi.nlm.nih.gov/gene/?term=6795	"AIE2, AIK3, ARK3, AurC, HEL-S-90, SPGF5, STK13, aurora-C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020025	67967	Pold3	http://www.ncbi.nlm.nih.gov/gene/?term=67967	"2410142G14Rik, C85233, P66, P68 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020026	67968	Ooep	http://www.ncbi.nlm.nih.gov/gene/?term=67968	"2410146L05Rik, Floped, Moep19, Sddr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020027	67972	Atp2b1	http://www.ncbi.nlm.nih.gov/gene/?term=67972	"2810442I22Rik, E130111D10Rik, Pmca1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020028	67974	Ccny	http://www.ncbi.nlm.nih.gov/gene/?term=67974	"1700025H17Rik, 3110050L10Rik, 4631402G10Rik, 5730405I09Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020029	67976	Trabd	http://www.ncbi.nlm.nih.gov/gene/?term=67976	"5730502D15Rik, AL023039 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020030	67980	Gnpda2	http://www.ncbi.nlm.nih.gov/gene/?term=67980	"4921523I18Rik, 4933412A11Rik, BB189630, GNPDA, Gnp2, Sb52, mKIAA4008 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020031	67981	Hormad1	http://www.ncbi.nlm.nih.gov/gene/?term=67981	"4921522K05Rik, Nohma "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020032	67988	Tmx3	http://www.ncbi.nlm.nih.gov/gene/?term=67988	"6430411B10Rik, A730024F05Rik, AV259382, Txndc10, mKIAA1830 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020033	67994	Mrps11	http://www.ncbi.nlm.nih.gov/gene/?term=67994	"0710005I03Rik, C79873 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020034	67996	Srsf6	http://www.ncbi.nlm.nih.gov/gene/?term=67996	"1210001E11Rik, AI314910, AW146126, Sfrs6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020035	68001	1110004E09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68001		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020036	68011	Snrpg	http://www.ncbi.nlm.nih.gov/gene/?term=68011	"2810024K17Rik, AL022803, SMG, sm-G, snRNP-G "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020037	68018	Col4a3bp	http://www.ncbi.nlm.nih.gov/gene/?term=68018	"2810404O15Rik, 9230101K08Rik, AU016711, CERT, GPBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020038	68026	2810417H13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68026	"AA409629, Ns5apt9, Ns5atp9, PAF15, Paf, mKIAA0101, p15(PAF) "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020039	68031	Rnf146	http://www.ncbi.nlm.nih.gov/gene/?term=68031	"2610509H23Rik, Iduna "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020040	68033	Cox19	http://www.ncbi.nlm.nih.gov/gene/?term=68033	"1810074D02Rik, 2810437L13Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020041	68035	Rbm42	http://www.ncbi.nlm.nih.gov/gene/?term=68035	"1700003D06Rik, 3100004P22Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020042	68037	2900093K20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68037		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020043	68040	Zfp593	http://www.ncbi.nlm.nih.gov/gene/?term=68040	"3110024A21Rik, AV062409, E130106C14Rik, ZNF593 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020044	68045	2700060E02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68045		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020045	6804	STX1A	http://www.ncbi.nlm.nih.gov/gene/?term=6804	"HPC-1, P35-1, STX1, SYN1A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020046	68050	Akirin1	http://www.ncbi.nlm.nih.gov/gene/?term=68050	6330407G11Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020047	68051	Nutf2	http://www.ncbi.nlm.nih.gov/gene/?term=68051	"2700067I02Rik, AI115459, AI413596, AW546000, Ntf2, Ntf3, PP15 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020048	68052	Rps13	http://www.ncbi.nlm.nih.gov/gene/?term=68052	2700063M04Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020049	68053	Ubxn2b	http://www.ncbi.nlm.nih.gov/gene/?term=68053	"3110003A22Rik, 6430407D20Rik, AI451665, p37 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020050	68058	Chd1l	http://www.ncbi.nlm.nih.gov/gene/?term=68058	"4432404A22Rik, Alc1, Snf2p "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020051	68059	Tm9sf2	http://www.ncbi.nlm.nih.gov/gene/?term=68059	"1500001N15Rik, AA536814, D14Ertd64e, P76 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020052	68066	Slc25a39	http://www.ncbi.nlm.nih.gov/gene/?term=68066	"3010027G13Rik, D11Ertd333e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020053	68067	3010026O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68067	"2900016G09Rik, AI851514, AW475975 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020054	68074	A930013F10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68074		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020055	68079	Pdcd2l	http://www.ncbi.nlm.nih.gov/gene/?term=68079	6030457N17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020056	68087	Dcakd	http://www.ncbi.nlm.nih.gov/gene/?term=68087	"3010024O21Rik, 6720485C15Rik, AI849483 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020057	68089	Arpc4	http://www.ncbi.nlm.nih.gov/gene/?term=68089	"20kDa, 5330419I20Rik, AI327076, p20-Arc "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020058	68094	Smarcc2	http://www.ncbi.nlm.nih.gov/gene/?term=68094	5930405J04Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020059	68095	Ociad1	http://www.ncbi.nlm.nih.gov/gene/?term=68095	"6030432N09Rik, AI481327, AW557942, Asrij, B230209J16Rik, BB021357, Emi2, Imi2, OCIA, TPA018 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020060	68099	Fam92a	http://www.ncbi.nlm.nih.gov/gene/?term=68099	"6720467C03Rik1, Fam92a "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020061	6809	STX3	http://www.ncbi.nlm.nih.gov/gene/?term=6809	STX3A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020062	68107	Cntd1	http://www.ncbi.nlm.nih.gov/gene/?term=68107	"1700051C09Rik, 4921513J16Rik, 5430417M23Rik, Cntd "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020063	68108	Snhg17	http://www.ncbi.nlm.nih.gov/gene/?term=68108	9430008C03Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020064	6810	STX4	http://www.ncbi.nlm.nih.gov/gene/?term=6810	"STX4A, p35-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020065	6810	STX4	http://www.ncbi.nlm.nih.gov/gene/?term=6810	"STX4A, p35-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020066	6811	STX5	http://www.ncbi.nlm.nih.gov/gene/?term=6811	"SED5A, STX5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020067	6811	STX5	http://www.ncbi.nlm.nih.gov/gene/?term=6811	"SED5, STX5A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020068	68127	B230217C12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68127	AI840637	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020069	6812	STXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6812	"MUNC18-1, NSEC1, P67, RBSEC1, UNC18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020070	68133	Gcsh	http://www.ncbi.nlm.nih.gov/gene/?term=68133	"1100001L02Rik, 5730591C18Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020071	68134	Upf3b	http://www.ncbi.nlm.nih.gov/gene/?term=68134	"5730594O13Rik, AI317193, AW541158, RENT3B, UPF3X "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020072	68135	Eif3h	http://www.ncbi.nlm.nih.gov/gene/?term=68135	"1110008A16Rik, 40kD, 9430017H16Rik, EIF3-P40, EIF3-gamma, Eif3s3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020073	68140	Tigd2	http://www.ncbi.nlm.nih.gov/gene/?term=68140	3632410O17Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020074	68142	Ino80	http://www.ncbi.nlm.nih.gov/gene/?term=68142	"2310079N15Rik, 4632409L19Rik, Inoc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020075	68142	Ino80	http://www.ncbi.nlm.nih.gov/gene/?term=68142	"2310079N15Rik, 4632409L19Rik, Inoc1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020076	68145	Etaa1	http://www.ncbi.nlm.nih.gov/gene/?term=68145	"5730466H23Rik, AA672646 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020077	6814	STXBP3	http://www.ncbi.nlm.nih.gov/gene/?term=6814	"MUNC18-3, MUNC18C, PSP, UNC-18C "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020078	6814	STXBP3	http://www.ncbi.nlm.nih.gov/gene/?term=6814	"MUNC18-3, MUNC18C, PSP, UNC-18C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020079	6814	STXBP3	http://www.ncbi.nlm.nih.gov/gene/?term=6814	"MUNC18-3, MUNC18C, PSP, UNC-18C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020080	68153	Gtf2e2	http://www.ncbi.nlm.nih.gov/gene/?term=68153	"34kDa, AI462509, C330006J08Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020081	68157	6720475J19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68157		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020082	6815	STYX	http://www.ncbi.nlm.nih.gov/gene/?term=6815		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020083	6815	STYX	http://www.ncbi.nlm.nih.gov/gene/?term=6815		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020084	6815	STYX	http://www.ncbi.nlm.nih.gov/gene/?term=6815		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020085	68161	A930005H10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68161		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020086	68162	A930003A15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68162	AI853191	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020087	68166	Spire1	http://www.ncbi.nlm.nih.gov/gene/?term=68166	"6030430B19Rik, AI415299, AU022898, AW550622, Spir-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020088	68168	A930009E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68168		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020089	68174	4930534H18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68174	AV040741	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020090	68180	Hyi	http://www.ncbi.nlm.nih.gov/gene/?term=68180	"2700033B16Rik, 6430559E15Rik, HT036 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020091	68185	Coa4	http://www.ncbi.nlm.nih.gov/gene/?term=68185	"5330414O08Rik, AI115477, AW047259, Chchd8, E2ig2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020092	68187	Fam135a	http://www.ncbi.nlm.nih.gov/gene/?term=68187	"4921533L14Rik, AI256732, AI835491 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020093	68188	Sympk	http://www.ncbi.nlm.nih.gov/gene/?term=68188	"1500016F02Rik, 4632415H16Rik, AA125406, AI449890, SPK, SYM "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020094	68189	5330431K02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68189		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020095	68193	Rpl24	http://www.ncbi.nlm.nih.gov/gene/?term=68193	"0610008L05Rik, Bst "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020096	68193	Rpl24	http://www.ncbi.nlm.nih.gov/gene/?term=68193	"0610008L05Rik, Bst "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00020097	68194	Ndufb4	http://www.ncbi.nlm.nih.gov/gene/?term=68194	"0610006N12Rik, 1300010H20Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020098	68194	Ndufb4	http://www.ncbi.nlm.nih.gov/gene/?term=68194	"0610006N12Rik, 1300010H20Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020099	68201	Ccdc34	http://www.ncbi.nlm.nih.gov/gene/?term=68201	"2810027O19Rik, 4930522P10Rik, AI596202 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020100	68205	Urm1	http://www.ncbi.nlm.nih.gov/gene/?term=68205	2900073H19Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020101	68205	Urm1	http://www.ncbi.nlm.nih.gov/gene/?term=68205	2900073H19Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020102	68209	Rnaseh2c	http://www.ncbi.nlm.nih.gov/gene/?term=68209	"1500026D16Rik, AYP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020103	68219	Nudt21	http://www.ncbi.nlm.nih.gov/gene/?term=68219	"25kDa, 3110048P04Rik, 5730530J16Rik, AU014860, AW549947, Cpsf5 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020104	6821	SUOX	http://www.ncbi.nlm.nih.gov/gene/?term=6821		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020105	68239	Krt42	http://www.ncbi.nlm.nih.gov/gene/?term=68239	"2410039E07Rik, K17n, Ka22, ecat6 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020106	68241	Fam195a	http://www.ncbi.nlm.nih.gov/gene/?term=68241	9530058B02Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020107	68246	1700112J05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68246	1700110A09Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020108	68250	Fam96a	http://www.ncbi.nlm.nih.gov/gene/?term=68250	5730536A07Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020109	68259	Ift80	http://www.ncbi.nlm.nih.gov/gene/?term=68259	"4921524P20Rik, Wdr56, mKIAA1374 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020110	68272	Rbm28	http://www.ncbi.nlm.nih.gov/gene/?term=68272	"2810480G15Rik, AI503051 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020111	68274	Toporsl	http://www.ncbi.nlm.nih.gov/gene/?term=68274	4930547C10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020112	6827	SUPT4H1	http://www.ncbi.nlm.nih.gov/gene/?term=6827	"SPT4, SPT4H, SUPT4H, Supt4a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020113	68281	4930430F08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68281	"4930571E09Rik, A730088G13Rik, AW551239, C430008C19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020114	68292	Stt3b	http://www.ncbi.nlm.nih.gov/gene/?term=68292	"1300006C19Rik, Simp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020115	68295	Aar2	http://www.ncbi.nlm.nih.gov/gene/?term=68295	0610011L14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020116	6829	SUPT5H	http://www.ncbi.nlm.nih.gov/gene/?term=6829	"SPT5, SPT5H, Tat-CT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020117	6829	SUPT5H	http://www.ncbi.nlm.nih.gov/gene/?term=6829	"SPT5, SPT5H, Tat-CT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020118	682	BSG	http://www.ncbi.nlm.nih.gov/gene/?term=682	"5F7, CD147, EMMPRIN, OK, TCSF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020119	682	BSG	http://www.ncbi.nlm.nih.gov/gene/?term=682	"5F7, CD147, EMMPRIN, OK, TCSF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020120	682	BSG	http://www.ncbi.nlm.nih.gov/gene/?term=682	"5F7, CD147, EMMPRIN, M6, OK, TCSF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020121	68308	4933406F09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68308	"1700007H14Rik, 4930429F21Rik, 4930570O04Rik, Gm3768 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020122	6830	SUPT6H	http://www.ncbi.nlm.nih.gov/gene/?term=6830	"SPT6, SPT6H, emb-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020123	68312	Gstm7	http://www.ncbi.nlm.nih.gov/gene/?term=68312	"0610005A07Rik, AI894236, Cd203c "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020124	68323	Nudt22	http://www.ncbi.nlm.nih.gov/gene/?term=68323	"0610006K04Rik, AI851793, AW545547 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020125	68328	Rab13	http://www.ncbi.nlm.nih.gov/gene/?term=68328	"0610007N03Rik, B230212B15Rik "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00020126	6832	SUPV3L1	http://www.ncbi.nlm.nih.gov/gene/?term=6832	SUV3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020127	6833	ABCC8	http://www.ncbi.nlm.nih.gov/gene/?term=6833	"ABC36, HHF1, HI, HRINS, MRP8, PHHI, SUR, SUR1, SUR1delta2, TNDM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020128	68347	0610011F06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68347		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020129	6834	SURF1	http://www.ncbi.nlm.nih.gov/gene/?term=6834	CMT4K	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020130	6834	SURF1	http://www.ncbi.nlm.nih.gov/gene/?term=6834	CMT4K	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020131	68350	Mul1	http://www.ncbi.nlm.nih.gov/gene/?term=68350	"0610009K11Rik, AV000801, Gide "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020132	68355	2010204K13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68355	"0610010M13Rik, Cip7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020133	6835	SURF2	http://www.ncbi.nlm.nih.gov/gene/?term=6835	SURF-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020134	6835	SURF2	http://www.ncbi.nlm.nih.gov/gene/?term=6835	SURF-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020135	68366	Tmem129	http://www.ncbi.nlm.nih.gov/gene/?term=68366	"0610039G24Rik, 2410015J15Rik, AA409575 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020136	6836	SURF4	http://www.ncbi.nlm.nih.gov/gene/?term=6836	ERV29	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020137	6836	SURF4	http://www.ncbi.nlm.nih.gov/gene/?term=6836	ERV29	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020138	68371	Pbld1	http://www.ncbi.nlm.nih.gov/gene/?term=68371	"0610038K03Rik, Mawbp, Pbld "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020139	68375	Ndufa8	http://www.ncbi.nlm.nih.gov/gene/?term=68375	"0610033L03Rik, AW261656 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020140	6837	MED22	http://www.ncbi.nlm.nih.gov/gene/?term=6837	"MED24, SURF5, surf-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020141	6838	SURF6	http://www.ncbi.nlm.nih.gov/gene/?term=6838	RRP14	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020142	6839	SUV39H1	http://www.ncbi.nlm.nih.gov/gene/?term=6839	"H3-K9-HMTase 1, KMT1A, MG44, SUV39H "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020143	6839	SUV39H1	http://www.ncbi.nlm.nih.gov/gene/?term=6839	"H3-K9-HMTase 1, KMT1A, MG44, SUV39H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020144	68404	Nrn1	http://www.ncbi.nlm.nih.gov/gene/?term=68404	"0710008J23Rik, Cpg15, Nrn "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020145	68404	Nrn1	http://www.ncbi.nlm.nih.gov/gene/?term=68404	"0710008J23Rik, Cpg15, Nrn "	mRNA	Mus musculus	26512708	Axon	ForeBrain	Immunoprecipitation|RIP-Chip	"HuD has also been implicated in axonal localization of other neuronal mRNAs including Tau, Neuritin/CPG15, Kv.1.1 and CaMKIIα mRNAs "
RLID00020146	68421	Lmbrd1	http://www.ncbi.nlm.nih.gov/gene/?term=68421	"0910001K20Rik, AV347960 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020147	68431	Fbxl15	http://www.ncbi.nlm.nih.gov/gene/?term=68431	"0710008C12Rik, Fbxo37 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020148	68436	Rpl34	http://www.ncbi.nlm.nih.gov/gene/?term=68436	1100001I22Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020149	68441	Rraga	http://www.ncbi.nlm.nih.gov/gene/?term=68441	"1300010C19Rik, AI255374, FIP-1, RAGA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020150	68449	Tbc1d10b	http://www.ncbi.nlm.nih.gov/gene/?term=68449	"1110003P22Rik, C87963 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020151	6844	VAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=6844	"SYB2, VAMP-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020152	6844	VAMP2	http://www.ncbi.nlm.nih.gov/gene/?term=6844	"SYB2, VAMP-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020153	6845	VAMP7	http://www.ncbi.nlm.nih.gov/gene/?term=6845	"SYBL1, TI-VAMP, TIVAMP, VAMP-7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020154	6845	VAMP7	http://www.ncbi.nlm.nih.gov/gene/?term=6845	"SYBL1, TI-VAMP, TIVAMP, VAMP-7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020155	68463	Mrpl14	http://www.ncbi.nlm.nih.gov/gene/?term=68463	"1110006I11Rik, AI846816, MRP-L32, Rpml32 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020156	68480	Card19	http://www.ncbi.nlm.nih.gov/gene/?term=68480	"1110007C09Rik, AI851695, Bincard "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020157	68481	Mpzl1	http://www.ncbi.nlm.nih.gov/gene/?term=68481	"1110007A10Rik, PZR "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020158	68497	Arel1	http://www.ncbi.nlm.nih.gov/gene/?term=68497	"1110018G07Rik, AI649076, AW610792, Kiaa0317, mKIAA0317 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020159	684	BST2	http://www.ncbi.nlm.nih.gov/gene/?term=684	"CD317, TETHERIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020160	684	BST2	http://www.ncbi.nlm.nih.gov/gene/?term=684	"CD317, TETHERIN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020161	68501	Nsmce2	http://www.ncbi.nlm.nih.gov/gene/?term=68501	"1110014D18Rik, AI661537 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020162	68505	Vps51	http://www.ncbi.nlm.nih.gov/gene/?term=68505	"1110014N23Rik, 3110057M17Rik, AI837850, Ffr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020163	6850	SYK	http://www.ncbi.nlm.nih.gov/gene/?term=6850	p72-Syk	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020164	68519	Eml1	http://www.ncbi.nlm.nih.gov/gene/?term=68519	"1110008N23Rik, A930030P13Rik, AA171013, AI847476, AI853955, ELP79, EMAP, EMAPL, heco "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020165	68520	Zfyve21	http://www.ncbi.nlm.nih.gov/gene/?term=68520	"1110013H04Rik, AW558780, C85416 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020166	68526	Gpr155	http://www.ncbi.nlm.nih.gov/gene/?term=68526	"1110017O10Rik, DEPDC3, F730029F15Rik, PGR22 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020167	68549	Sgol2a	http://www.ncbi.nlm.nih.gov/gene/?term=68549	"1110007N04Rik, 4932411A20Rik, 5730576N04Rik, AU018846, AV008062, D1Ertd8e, Sgol2, Tripin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020168	6854	SYN2	http://www.ncbi.nlm.nih.gov/gene/?term=6854	SYNII	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020169	68558	Ankra2	http://www.ncbi.nlm.nih.gov/gene/?term=68558	"1110004M18Rik, Ankra "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020170	68564	Nufip2	http://www.ncbi.nlm.nih.gov/gene/?term=68564	"1110001M19Rik, 9530056D24Rik, AI256692, AI461731, PIG1, mKIAA1321 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020171	6856	SYPL1	http://www.ncbi.nlm.nih.gov/gene/?term=6856	"H-SP1, SYPL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020172	6856	SYPL1	http://www.ncbi.nlm.nih.gov/gene/?term=6856	"H-SP1, SYPL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020173	6856	SYPL1	http://www.ncbi.nlm.nih.gov/gene/?term=6856	"H-SP1, SYPL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020174	68572	Ict1	http://www.ncbi.nlm.nih.gov/gene/?term=68572	"1110001A02Rik, 1110002E03Rik, MRP-L58 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020175	68576	Lamtor5	http://www.ncbi.nlm.nih.gov/gene/?term=68576	"1110003H18Rik, Hbxip, XIP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020176	6857	SYT1	http://www.ncbi.nlm.nih.gov/gene/?term=6857	"P65, SVP65, SYT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020177	68585	Rtn4	http://www.ncbi.nlm.nih.gov/gene/?term=68585	"1110020G17Rik, AA407876, AA409940, AA960376, ASY, C130026I10Rik, NOGO, NSP-CL, NgA, Nogo-A, Nogo-B, Nogo-C, mKIAA0886, mKIAA4153 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020178	68585	Rtn4	http://www.ncbi.nlm.nih.gov/gene/?term=68585	"1110020G17Rik, AA407876, AA409940, AA960376, ASY, C130026I10Rik, NOGO, NSP-CL, NgA, Nogo-A, Nogo-B, Nogo-C, mKIAA0886, mKIAA4153 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020179	68588	Cthrc1	http://www.ncbi.nlm.nih.gov/gene/?term=68588	1110014B07Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020180	68603	Pmvk	http://www.ncbi.nlm.nih.gov/gene/?term=68603	"1110011E12Rik, 2900002L22Rik, AV001327, PMK, PMKA, PMKASE "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020181	68611	Mrpl28	http://www.ncbi.nlm.nih.gov/gene/?term=68611	"1110015G04Rik, L28mt, MAAT1, MRP-L28, p15 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020182	6861	SYT5	http://www.ncbi.nlm.nih.gov/gene/?term=6861		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020183	68646	Nadk2	http://www.ncbi.nlm.nih.gov/gene/?term=68646	"MNADK, Nadkd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020184	68652	Tab2	http://www.ncbi.nlm.nih.gov/gene/?term=68652	"1110030N06Rik, A530078N03Rik, Map3k7ip2, mKIAA0733 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020185	68666	Svop	http://www.ncbi.nlm.nih.gov/gene/?term=68666	"1110030H18Rik, AI415691, msvop "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020186	6866	TAC3	http://www.ncbi.nlm.nih.gov/gene/?term=6866	"HH10, NKB, NKNB, PRO1155, ZNEUROK1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020187	6867	TACC1	http://www.ncbi.nlm.nih.gov/gene/?term=6867	Ga55	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020188	6867	TACC1	http://www.ncbi.nlm.nih.gov/gene/?term=6867	Ga55	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020189	68684	1110035D15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68684		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020190	6868	ADAM17	http://www.ncbi.nlm.nih.gov/gene/?term=6868	"ADAM18, CD156B, CSVP, NISBD, NISBD1, TACE "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020191	6868	ADAM17	http://www.ncbi.nlm.nih.gov/gene/?term=6868	"ADAM18, CD156B, CSVP, NISBD, NISBD1, TACE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020192	68693	Hnrnpul2	http://www.ncbi.nlm.nih.gov/gene/?term=68693	"1110031M08Rik, AI465155, Hnrpul2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020193	68695	Hddc3	http://www.ncbi.nlm.nih.gov/gene/?term=68695	"1110033O09Rik, C86475, MESH1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020194	6869	TACR1	http://www.ncbi.nlm.nih.gov/gene/?term=6869	"NK1R, NKIR, SPR, TAC1R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020195	686	BTD	http://www.ncbi.nlm.nih.gov/gene/?term=686		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020196	686	BTD	http://www.ncbi.nlm.nih.gov/gene/?term=686		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020197	68718	Rnf166	http://www.ncbi.nlm.nih.gov/gene/?term=68718	"1110031E24Rik, AW555115, Zfp313l "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020198	68724	Arl8a	http://www.ncbi.nlm.nih.gov/gene/?term=68724	"1110033P22Rik, Arl10b, gie2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020199	6872	TAF1	http://www.ncbi.nlm.nih.gov/gene/?term=6872	"BA2R, CCG1, CCGS, DYT3, DYT3/TAF1, KAT4, MRXS33, N-TAF1, NSCL2, OF, P250, TAF(II)250, TAF2A, TAFII-250, TAFII250, XDP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020200	68734	Smek1	http://www.ncbi.nlm.nih.gov/gene/?term=68734	"1110034C04Rik, BC064465, Ppp4r3a, mKIAA2010 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020201	68736	Tyw5	http://www.ncbi.nlm.nih.gov/gene/?term=68736	1110034B05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020202	6873	TAF2	http://www.ncbi.nlm.nih.gov/gene/?term=6873	"CIF150, MRT40B, TAFII150, TAF2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020203	6873	TAF2	http://www.ncbi.nlm.nih.gov/gene/?term=6873	"CIF150, MRT40, TAF2B, TAFII150 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020204	6874	TAF4	http://www.ncbi.nlm.nih.gov/gene/?term=6874	"TAF2C, TAF2C1A, TAFII130, TAFII135, TAF4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020205	6874	TAF4	http://www.ncbi.nlm.nih.gov/gene/?term=6874	"TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020206	68763	1110038B12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68763	"0610009C20Rik, 0910001G04Rik "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020207	68767	Wash1	http://www.ncbi.nlm.nih.gov/gene/?term=68767	"1110049F14Rik, ORF19, Wash "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020208	6876	TAGLN	http://www.ncbi.nlm.nih.gov/gene/?term=6876	"SM22, SMCC, TAGLN1, WS3-10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020209	68770	Phtf2	http://www.ncbi.nlm.nih.gov/gene/?term=68770	"1110054G21Rik, 9530062N20Rik, AI447096, C77923 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020210	68775	Atp6v1c2	http://www.ncbi.nlm.nih.gov/gene/?term=68775	1110038G14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020211	68786	1110059G02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68786		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020212	6878	TAF6	http://www.ncbi.nlm.nih.gov/gene/?term=6878	"MGC:8964, TAF(II)70, TAF(II)80, TAF2E, TAFII-70, TAFII-80, TAFII70, TAFII80, TAFII85 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020213	68792	Srpx2	http://www.ncbi.nlm.nih.gov/gene/?term=68792	"1110039C07Rik, SRP, SRPUL "	mRNA	Rattus norvegicus	10618370	Nucleolus	Fibroblast|NRK cell	In situ hybridization	"Additionally, SRP RNA is a member of a family of small nonribosomal RNAs found recently in the nucleolus, suggesting that the nucleolus is more plurifunctional than previously realized. These results demonstrate that SRP RNA and three SRP proteins visit the nucleolus, suggesting that partial SRP assembly, or another unidentified activity of the SRP components, occurs at the nucleolus. "
RLID00020214	68795	Ubr3	http://www.ncbi.nlm.nih.gov/gene/?term=68795	"1110059H15Rik, 4833421P10Rik, A130030D10Rik, AA409735, AA414972, AA422631, AI646861, AU016126, Zfp650, Znf650 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020215	6879	TAF7	http://www.ncbi.nlm.nih.gov/gene/?term=6879	"TAF2F, TAFII55 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020216	6879	TAF7	http://www.ncbi.nlm.nih.gov/gene/?term=6879	"TAF2F, TAFII55 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020217	6879	TAF7	http://www.ncbi.nlm.nih.gov/gene/?term=6879	"TAF2F, TAFII55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020218	687	KLF9	http://www.ncbi.nlm.nih.gov/gene/?term=687	"BTEB, BTEB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020219	68801	Elovl5	http://www.ncbi.nlm.nih.gov/gene/?term=68801	"1110059L23Rik, AI747313, AU043003, HELO1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020220	68817	Ddi2	http://www.ncbi.nlm.nih.gov/gene/?term=68817	"1110056G13Rik, 1700027M01Rik, 9130022E05Rik, AI604911, AU040698 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020221	6881	TAF10	http://www.ncbi.nlm.nih.gov/gene/?term=6881	"TAF2A, TAF2H, TAFII30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020222	6881	TAF10	http://www.ncbi.nlm.nih.gov/gene/?term=6881	"TAF2A, TAF2H, TAFII30 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020223	6881	TAF10	http://www.ncbi.nlm.nih.gov/gene/?term=6881	"TAF2A, TAF2H, TAFII30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020224	6882	TAF11	http://www.ncbi.nlm.nih.gov/gene/?term=6882	"MGC:15243, PRO2134, TAF2I, TAFII28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020225	6882	TAF11	http://www.ncbi.nlm.nih.gov/gene/?term=6882	"MGC:15243, PRO2134, TAF2I, TAFII28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020226	68832	Ldah	http://www.ncbi.nlm.nih.gov/gene/?term=68832	"1110057K04Rik, mLDAH "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020227	68837	Foxk2	http://www.ncbi.nlm.nih.gov/gene/?term=68837	"1110054H05Rik, 5730434B08Rik, 6230415M23Rik, ILF, Ilf1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020228	6883	TAF12	http://www.ncbi.nlm.nih.gov/gene/?term=6883	"TAF2J, TAFII20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020229	6883	TAF12	http://www.ncbi.nlm.nih.gov/gene/?term=6883	"TAF2J, TAFII20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020230	6883	TAF12	http://www.ncbi.nlm.nih.gov/gene/?term=6883	"TAF2J, TAFII20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020231	68842	Tulp4	http://www.ncbi.nlm.nih.gov/gene/?term=68842	"1110057P05Rik, 2210038L17Rik, Tusp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020232	68846	Rnf208	http://www.ncbi.nlm.nih.gov/gene/?term=68846	1110061N23Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020233	6884	TAF13	http://www.ncbi.nlm.nih.gov/gene/?term=6884	"TAF(II)18, TAF2K, TAFII-18, TAFII18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020234	68859	Smim1	http://www.ncbi.nlm.nih.gov/gene/?term=68859	"0610011H04Rik, 1190007F08Rik, 2700009I11Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020235	6885	MAP3K7	http://www.ncbi.nlm.nih.gov/gene/?term=6885	"MEKK7, TAK1, TGF1a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020236	6885	MAP3K7	http://www.ncbi.nlm.nih.gov/gene/?term=6885	"MEKK7, TAK1, TGF1a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020237	6886	TAL1	http://www.ncbi.nlm.nih.gov/gene/?term=6886	"SCL, TCL5, bHLHa17, tal-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020238	6888	TALDO1	http://www.ncbi.nlm.nih.gov/gene/?term=6888	"TAL, TAL-H, TALDOR, TALH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020239	688	KLF5	http://www.ncbi.nlm.nih.gov/gene/?term=688	"BTEB2, CKLF, IKLF "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020240	688	KLF5	http://www.ncbi.nlm.nih.gov/gene/?term=688	"BTEB2, CKLF, IKLF "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00020241	68904	Abhd13	http://www.ncbi.nlm.nih.gov/gene/?term=68904	"1110065L07Rik, AI463703, AI788994 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020242	68905	1110065H08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68905		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020243	689064	LOC689064	http://www.ncbi.nlm.nih.gov/gene/?term=689064		mRNA	Rattus norvegicus	19003354	Ribosome	Fibroblast	Hybridisation|Northern blot	Globin transcripts with the native globin 3'untranslated region or with the 3'untranslated region of c-myc are present in free/cytoskeletal-bound polysomes.
RLID00020244	6890	TAP1	http://www.ncbi.nlm.nih.gov/gene/?term=6890	"ABC17, ABCB2, APT1, D6S114E, PSF-1, PSF1, RING4*0102N, TAP1N, TAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020245	6890	TAP1	http://www.ncbi.nlm.nih.gov/gene/?term=6890	"ABC17, ABCB2, APT1, D6S114E, PSF-1, PSF1, RING4*0102N, TAP1N, TAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020246	6890	TAP1	http://www.ncbi.nlm.nih.gov/gene/?term=6890	"ABC17, ABCB2, APT1, D6S114E, PSF-1, PSF1, RING4, TAP1*0102N, TAP1N "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020247	68917	Hint2	http://www.ncbi.nlm.nih.gov/gene/?term=68917	1190005L05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020248	68918	1190005I06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68918		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020249	6891	TAP2	http://www.ncbi.nlm.nih.gov/gene/?term=6891	"ABC18, ABCB3, APT2, D6S217E, PSF-2, PSF2, RING11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020250	68927	Ptcd2	http://www.ncbi.nlm.nih.gov/gene/?term=68927	1190005P08Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020251	68929	Mospd3	http://www.ncbi.nlm.nih.gov/gene/?term=68929	"1190005J19Rik, 5133401H10Rik, Gtig2, R124 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020252	6892	TAPBP	http://www.ncbi.nlm.nih.gov/gene/?term=6892	"NGS17, TAPA, TPN, TPSN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020253	6892	TAPBP	http://www.ncbi.nlm.nih.gov/gene/?term=6892	"NGS17, TAPA, TPN, TPSN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020254	6892	TAPBP	http://www.ncbi.nlm.nih.gov/gene/?term=6892	"NGS17, TAPA, TPN, TPSN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020255	6892	TAPBP	http://www.ncbi.nlm.nih.gov/gene/?term=6892	"NGS17, TAPA, TPN, TPSN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020256	68938	Aspscr1	http://www.ncbi.nlm.nih.gov/gene/?term=68938	"1190006K01Rik, ASPC, ASPCR1, ASPL, ASPS, RCC17, TUG "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020257	68943	Pink1	http://www.ncbi.nlm.nih.gov/gene/?term=68943	"1190006F07Rik, AU042772, AW557854, BRPK, mFLJ00387 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020258	68944	Tmco1	http://www.ncbi.nlm.nih.gov/gene/?term=68944	"1190006A08Rik, 4930403O06Rik, AA109065, AU022572, ESTM39 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020259	68949	Zfos1	http://www.ncbi.nlm.nih.gov/gene/?term=68949	"1500012F01Rik, Zfas1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020260	68952	Fam57b	http://www.ncbi.nlm.nih.gov/gene/?term=68952	"1500016O10Rik, A330104J06Rik, AI413816, AW060769 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020261	6895	TARBP2	http://www.ncbi.nlm.nih.gov/gene/?term=6895	"LOQS, TRBP, TRBP1, TRBP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020262	68964	Ctc1	http://www.ncbi.nlm.nih.gov/gene/?term=68964	"1500010J02Rik, AAF-132, AAF132 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020263	68966	Ngdn	http://www.ncbi.nlm.nih.gov/gene/?term=68966	"1500001L15Rik, Ngd, neuroguidin "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020264	68968	Cdan1	http://www.ncbi.nlm.nih.gov/gene/?term=68968	"1500015A01Rik, AI448026, AW492297, CDA-I, CDA1, CDAI "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020265	68975	Med27	http://www.ncbi.nlm.nih.gov/gene/?term=68975	"1500015J03Rik, 2310042P07Rik, AA682045, Crsp8, D2Ertd434e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020266	6897	TARS	http://www.ncbi.nlm.nih.gov/gene/?term=6897	ThrRS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020267	68982	1500015A07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68982		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020268	6898	TAT	http://www.ncbi.nlm.nih.gov/gene/?term=6898		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020269	6898	TAT	http://www.ncbi.nlm.nih.gov/gene/?term=6898		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020270	68992	Zfp580	http://www.ncbi.nlm.nih.gov/gene/?term=68992	"1500015O20Rik, AI838225, Znf580 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020271	68995	Mcts1	http://www.ncbi.nlm.nih.gov/gene/?term=68995	"1500019M23Rik, MCT-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020272	689	BTF3	http://www.ncbi.nlm.nih.gov/gene/?term=689	"BETA-NACa, BTF3b, NACB, BTF3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020273	689	BTF3	http://www.ncbi.nlm.nih.gov/gene/?term=689	"BETA-NAC, BTF3a, BTF3b, NACB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020274	69002	1500026H17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69002		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020275	69009	Thap7	http://www.ncbi.nlm.nih.gov/gene/?term=69009	1810004B07Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020276	6901	TAZ	http://www.ncbi.nlm.nih.gov/gene/?term=6901	"BTHS, CMD3A, EFE, EFE2, G4.5, LVNCX, Taz1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020277	6901	TAZ	http://www.ncbi.nlm.nih.gov/gene/?term=6901	"BTHS, CMD3A, EFE, EFE2, G4.5, LVNCX, Taz1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020278	69025	1500032P08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69025		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020279	6902	TBCA	http://www.ncbi.nlm.nih.gov/gene/?term=6902		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020280	6902	TBCA	http://www.ncbi.nlm.nih.gov/gene/?term=6902		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020281	6902	TBCA	http://www.ncbi.nlm.nih.gov/gene/?term=6902		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020282	69034	Nupr1l	http://www.ncbi.nlm.nih.gov/gene/?term=69034	"1810010E01Rik, 4930579G22Rik, Nupr2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020283	69036	Zg16	http://www.ncbi.nlm.nih.gov/gene/?term=69036	"1810010M01Rik, AI593689, ZG16p "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020284	6903	TBCC	http://www.ncbi.nlm.nih.gov/gene/?term=6903	CFC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020285	69048	Slc30a5	http://www.ncbi.nlm.nih.gov/gene/?term=69048	"1810010K08Rik, AF233321, ZNT5, ZTL1, ZnT-5, Zntl1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020286	6904	TBCD	http://www.ncbi.nlm.nih.gov/gene/?term=6904	"SSD-1, tfcD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020287	69051	Pycr2	http://www.ncbi.nlm.nih.gov/gene/?term=69051	"1810018M05Rik, P5cr2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020288	69053	1810013L24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69053	"1110017P05Rik, 3010002C02Rik, AA792997, AW124177, Gm19906, R74903 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020289	69064	Fuom	http://www.ncbi.nlm.nih.gov/gene/?term=69064	"Fucu, Le51 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020290	69065	Chac1	http://www.ncbi.nlm.nih.gov/gene/?term=69065	1810008K03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020291	69077	Psmd11	http://www.ncbi.nlm.nih.gov/gene/?term=69077	"1700089D09Rik, 1810019E17Rik, 2610024G20Rik, 2810055C24Rik, C78232, P44.5, S9 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020292	6907	TBL1X	http://www.ncbi.nlm.nih.gov/gene/?term=6907	"EBI, SMAP55, TBL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020293	69080	Gmppa	http://www.ncbi.nlm.nih.gov/gene/?term=69080	1810012N01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020294	69082	Zc3h15	http://www.ncbi.nlm.nih.gov/gene/?term=69082	"1700006A17Rik, 1810012H02Rik, 2610312B22Rik, FM22, Ierepo4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020295	69085	Zcchc9	http://www.ncbi.nlm.nih.gov/gene/?term=69085	1810019C21Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020296	6908	TBP	http://www.ncbi.nlm.nih.gov/gene/?term=6908	"GTF2D, GTF2D1, HDL4, SCA17, TFIID "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020297	69090	Ascc1	http://www.ncbi.nlm.nih.gov/gene/?term=69090	"1810015P09Rik, AI550520, ASC1p50, CGI-18 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020298	69091	Vps26b	http://www.ncbi.nlm.nih.gov/gene/?term=69091	"1810012I05Rik, 2310075A12Rik, AI848392 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020299	69094	Tmem160	http://www.ncbi.nlm.nih.gov/gene/?term=69094	1810008O21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020300	6909	TBX2	http://www.ncbi.nlm.nih.gov/gene/?term=6909		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020301	69116	Ubr4	http://www.ncbi.nlm.nih.gov/gene/?term=69116	"1810009A16Rik, A930005E13Rik, D930005K06Rik, Gm1032, Gm1666, N28143, RBAF600, Zubr1, mKIAA0462, p600 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020302	69131	Cdk12	http://www.ncbi.nlm.nih.gov/gene/?term=69131	"1810022J16Rik, AI646528, Crk7, Crkrs, D11Ertd752e, Pksc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020303	69137	Vstm5	http://www.ncbi.nlm.nih.gov/gene/?term=69137	2200002K05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020304	691393	Oxa1l	http://www.ncbi.nlm.nih.gov/gene/?term=691393		mRNA	Rattus norvegicus	15485813	Ribosome	Hepatoma cell	qRT-PCR	"In agreement with previous studies, oxa1 mRNA was associated with the mitochondria-bound polysomes but unlike ucp2, oxa1 transcript did not bind K protein. "
RLID00020305	69149	Kbtbd3	http://www.ncbi.nlm.nih.gov/gene/?term=69149	"2200003A07Rik, Bklhd3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020306	69156	Comtd1	http://www.ncbi.nlm.nih.gov/gene/?term=69156	"1810030M08Rik, MT773 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020307	69159	Rhebl1	http://www.ncbi.nlm.nih.gov/gene/?term=69159	"1810036J22Rik, Rheb2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020308	6915	TBXA2R	http://www.ncbi.nlm.nih.gov/gene/?term=6915	"BDPLT13, TXA2-R "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020309	6915	TBXA2R	http://www.ncbi.nlm.nih.gov/gene/?term=6915	"BDPLT13, TXA2-R "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020310	6915	TBXA2R	http://www.ncbi.nlm.nih.gov/gene/?term=6915	"BDPLT13, TXA2-R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020311	69168	Bola1	http://www.ncbi.nlm.nih.gov/gene/?term=69168	1810037G04Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020312	6916	TBXAS1	http://www.ncbi.nlm.nih.gov/gene/?term=6916	"BDPLT14, CYP5, CYP5A1, GHOSAL, THAS, TS, TXAS, TXS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020313	6917	TCEA1	http://www.ncbi.nlm.nih.gov/gene/?term=6917	"GTF2S, SII, TCEA, TF2S, TFIIS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020314	6917	TCEA1	http://www.ncbi.nlm.nih.gov/gene/?term=6917	"GTF2S, SII, TCEA, TF2S, TFIIS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020315	69181	Dyrk2	http://www.ncbi.nlm.nih.gov/gene/?term=69181	1810038L18Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020316	69181	Dyrk2	http://www.ncbi.nlm.nih.gov/gene/?term=69181	1810038L18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020317	69186	Tmem256	http://www.ncbi.nlm.nih.gov/gene/?term=69186	"1810027O10Rik, 3110009M16Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020318	69188	Kmt2e	http://www.ncbi.nlm.nih.gov/gene/?term=69188	"1810033J14Rik, 9530077A04Rik, D230038D11Rik, Mll5, NKp44L "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020319	69188	Kmt2e	http://www.ncbi.nlm.nih.gov/gene/?term=69188	"1810033J14Rik, 9530077A04Rik, D230038D11Rik, Mll5, NKp44L "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020320	69195	Tmem121	http://www.ncbi.nlm.nih.gov/gene/?term=69195	"2410008J05Rik, Hole "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020321	6919	TCEA2	http://www.ncbi.nlm.nih.gov/gene/?term=6919	TFIIS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020322	69202	Ptms	http://www.ncbi.nlm.nih.gov/gene/?term=69202	2610009E16Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020323	692053	SNORD9	http://www.ncbi.nlm.nih.gov/gene/?term=692053	mgU6-53B	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020324	692057	SNORD12	http://www.ncbi.nlm.nih.gov/gene/?term=692057	"HBII-99, MIR1259, MIRN1259 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020325	692058	SNORD11	http://www.ncbi.nlm.nih.gov/gene/?term=692058	HBII-95	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020326	692075	SNORD6	http://www.ncbi.nlm.nih.gov/gene/?term=692075	mgh28S-2412	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020327	692075	SNORD6	http://www.ncbi.nlm.nih.gov/gene/?term=692075	mgh28S-2412	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020328	692076	SNORD7	http://www.ncbi.nlm.nih.gov/gene/?term=692076	"Z30, mgU6-47 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020329	692076	SNORD7	http://www.ncbi.nlm.nih.gov/gene/?term=692076	"Z30, mgU6-47 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020330	692076	SNORD7	http://www.ncbi.nlm.nih.gov/gene/?term=692076	"Z30, mgU6-47 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020331	69207	Srsf11	http://www.ncbi.nlm.nih.gov/gene/?term=69207	"0610009J05Rik, 2610019N13Rik, BF642805, Sfrs11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020332	692084	SNORD13	http://www.ncbi.nlm.nih.gov/gene/?term=692084	"RNU13A, U13, SNORD13 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020333	692084	SNORD13	http://www.ncbi.nlm.nih.gov/gene/?term=692084	"RNU13A, U13, SNORD13 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020334	692085	SNORD45C	http://www.ncbi.nlm.nih.gov/gene/?term=692085	U45C	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020335	692086	SNORD17	http://www.ncbi.nlm.nih.gov/gene/?term=692086	HBI-43	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020336	692086	SNORD17	http://www.ncbi.nlm.nih.gov/gene/?term=692086	HBI-43	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020337	692089	SNORD19	http://www.ncbi.nlm.nih.gov/gene/?term=692089	HBII-108	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020338	692090	SNORD59B	http://www.ncbi.nlm.nih.gov/gene/?term=692090	U59B	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020339	692090	SNORD59B	http://www.ncbi.nlm.nih.gov/gene/?term=692090	U59B	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020340	692093	SNORD62B	http://www.ncbi.nlm.nih.gov/gene/?term=692093	"U62, U62B "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020341	692093	SNORD62B	http://www.ncbi.nlm.nih.gov/gene/?term=692093	"U62, U62B "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020342	692093	SNORD62B	http://www.ncbi.nlm.nih.gov/gene/?term=692093	"U62, U62B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020343	692093	SNORD62B	http://www.ncbi.nlm.nih.gov/gene/?term=692093	"U62, U62B "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020344	6920	TCEA3	http://www.ncbi.nlm.nih.gov/gene/?term=6920	"TFIIS, TFIIS.H "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020345	692106	SNORD65	http://www.ncbi.nlm.nih.gov/gene/?term=692106	"HBII-135A, SNORD65 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020346	692107	SNORD66	http://www.ncbi.nlm.nih.gov/gene/?term=692107	HBII-142	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020347	692107	SNORD66	http://www.ncbi.nlm.nih.gov/gene/?term=692107	HBII-142	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020348	692107	SNORD66	http://www.ncbi.nlm.nih.gov/gene/?term=692107	HBII-142	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020349	692107	SNORD66	http://www.ncbi.nlm.nih.gov/gene/?term=692107	HBII-142	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020350	692107	SNORD66	http://www.ncbi.nlm.nih.gov/gene/?term=692107	HBII-142	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020351	692108	SNORD67	http://www.ncbi.nlm.nih.gov/gene/?term=692108	HBII-166	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020352	692108	SNORD67	http://www.ncbi.nlm.nih.gov/gene/?term=692108	HBII-166	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020353	692109	SNORD69	http://www.ncbi.nlm.nih.gov/gene/?term=692109	HBII-210	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020354	692109	SNORD69	http://www.ncbi.nlm.nih.gov/gene/?term=692109	HBII-210	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020355	692110	SNORD70	http://www.ncbi.nlm.nih.gov/gene/?term=692110	"HBII-234A, SNORD70 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020356	692111	SNORD71	http://www.ncbi.nlm.nih.gov/gene/?term=692111	"HBII-239, MIRN768, hsa-mir-768 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020357	692111	SNORD71	http://www.ncbi.nlm.nih.gov/gene/?term=692111	"HBII-239, MIRN768, hsa-mir-768 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020358	692111	SNORD71	http://www.ncbi.nlm.nih.gov/gene/?term=692111	"HBII-239, MIRN768, hsa-mir-768 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020359	692111	SNORD71	http://www.ncbi.nlm.nih.gov/gene/?term=692111	"HBII-239, MIRN768, hsa-mir-768 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020360	692111	SNORD71	http://www.ncbi.nlm.nih.gov/gene/?term=692111	"HBII-239, MIRN768, hsa-mir-768 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020361	692149	SCARNA14	http://www.ncbi.nlm.nih.gov/gene/?term=692149	U100	snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020362	692158	SNORA57	http://www.ncbi.nlm.nih.gov/gene/?term=692158	U99	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020363	692196	SNORD76	http://www.ncbi.nlm.nih.gov/gene/?term=692196	U76	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020364	692196	SNORD76	http://www.ncbi.nlm.nih.gov/gene/?term=692196	U76	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020365	692196	SNORD76	http://www.ncbi.nlm.nih.gov/gene/?term=692196	U76	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020366	692197	SNORD77	http://www.ncbi.nlm.nih.gov/gene/?term=692197	"SNORD77A, U77 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020367	692197	SNORD77	http://www.ncbi.nlm.nih.gov/gene/?term=692197	"SNORD77A, U77 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020368	692197	SNORD77	http://www.ncbi.nlm.nih.gov/gene/?term=692197	"SNORD77A, U77 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020369	692198	SNORD78	http://www.ncbi.nlm.nih.gov/gene/?term=692198	U78	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020370	692198	SNORD78	http://www.ncbi.nlm.nih.gov/gene/?term=692198	U78	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020371	692198	SNORD78	http://www.ncbi.nlm.nih.gov/gene/?term=692198	U78	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00020372	692198	SNORD78	http://www.ncbi.nlm.nih.gov/gene/?term=692198	U78	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020373	692198	SNORD78	http://www.ncbi.nlm.nih.gov/gene/?term=692198	U78	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020374	692199	SNORD84	http://www.ncbi.nlm.nih.gov/gene/?term=692199	U84	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020375	6921	TCEB1	http://www.ncbi.nlm.nih.gov/gene/?term=6921	"SIII, eloC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020376	6921	TCEB1	http://www.ncbi.nlm.nih.gov/gene/?term=6921	"SIII, eloC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020377	692200	SNORD103C	http://www.ncbi.nlm.nih.gov/gene/?term=692200	"HBII-251, SNORD85 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020378	692200	SNORD103C	http://www.ncbi.nlm.nih.gov/gene/?term=692200	"HBII-251, SNORD85 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020379	692202	SNORD88A	http://www.ncbi.nlm.nih.gov/gene/?term=692202	HBII-180A	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020380	692202	SNORD88A	http://www.ncbi.nlm.nih.gov/gene/?term=692202	HBII-180A	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020381	692205	SNORD89	http://www.ncbi.nlm.nih.gov/gene/?term=692205	HBII-289	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020382	692205	SNORD89	http://www.ncbi.nlm.nih.gov/gene/?term=692205	HBII-289	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020383	692205	SNORD89	http://www.ncbi.nlm.nih.gov/gene/?term=692205	HBII-289	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020384	692205	SNORD89	http://www.ncbi.nlm.nih.gov/gene/?term=692205	HBII-289	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020385	692206	SNORD90	http://www.ncbi.nlm.nih.gov/gene/?term=692206	HBII-295	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020386	692207	SNORD91A	http://www.ncbi.nlm.nih.gov/gene/?term=692207	HBII-296a	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020387	692207	SNORD91A	http://www.ncbi.nlm.nih.gov/gene/?term=692207	HBII-296a	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020388	692207	SNORD91A	http://www.ncbi.nlm.nih.gov/gene/?term=692207	HBII-296a	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020389	692208	SNORD91B	http://www.ncbi.nlm.nih.gov/gene/?term=692208	HBII-296b	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020390	692208	SNORD91B	http://www.ncbi.nlm.nih.gov/gene/?term=692208	HBII-296b	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020391	692208	SNORD91B	http://www.ncbi.nlm.nih.gov/gene/?term=692208	HBII-296b	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020392	692209	SNORD92	http://www.ncbi.nlm.nih.gov/gene/?term=692209	HBII-316	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020393	692209	SNORD92	http://www.ncbi.nlm.nih.gov/gene/?term=692209	HBII-316	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020394	692210	SNORD93	http://www.ncbi.nlm.nih.gov/gene/?term=692210	HBII-336	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020395	692210	SNORD93	http://www.ncbi.nlm.nih.gov/gene/?term=692210	HBII-336	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020396	692210	SNORD93	http://www.ncbi.nlm.nih.gov/gene/?term=692210	HBII-336	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020397	692210	SNORD93	http://www.ncbi.nlm.nih.gov/gene/?term=692210	HBII-336	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020398	692210	SNORD93	http://www.ncbi.nlm.nih.gov/gene/?term=692210	HBII-336	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020399	692211	SNORD98	http://www.ncbi.nlm.nih.gov/gene/?term=692211	HBII-419	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020400	692211	SNORD98	http://www.ncbi.nlm.nih.gov/gene/?term=692211	HBII-419	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020401	692211	SNORD98	http://www.ncbi.nlm.nih.gov/gene/?term=692211	HBII-419	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020402	692211	SNORD98	http://www.ncbi.nlm.nih.gov/gene/?term=692211	HBII-419	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020403	692212	SNORD99	http://www.ncbi.nlm.nih.gov/gene/?term=692212	HBII-420	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020404	692213	SNORD110	http://www.ncbi.nlm.nih.gov/gene/?term=692213	HBII-55	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020405	692213	SNORD110	http://www.ncbi.nlm.nih.gov/gene/?term=692213	HBII-55	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020406	692223	SNORD97	http://www.ncbi.nlm.nih.gov/gene/?term=692223	U97	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020407	692223	SNORD97	http://www.ncbi.nlm.nih.gov/gene/?term=692223	U97	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00020408	692223	SNORD97	http://www.ncbi.nlm.nih.gov/gene/?term=692223	U97	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020409	692225	SNORD94	http://www.ncbi.nlm.nih.gov/gene/?term=692225	U94	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020410	692225	SNORD94	http://www.ncbi.nlm.nih.gov/gene/?term=692225	U94	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020411	692225	SNORD94	http://www.ncbi.nlm.nih.gov/gene/?term=692225	U94	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020412	692225	SNORD94	http://www.ncbi.nlm.nih.gov/gene/?term=692225	U94	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020413	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020414	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00020415	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020416	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020417	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020418	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00020419	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020420	692227	SNORD104	http://www.ncbi.nlm.nih.gov/gene/?term=692227	U104	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020421	692229	SNORD105	http://www.ncbi.nlm.nih.gov/gene/?term=692229	U105	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020422	692229	SNORD105	http://www.ncbi.nlm.nih.gov/gene/?term=692229	U105	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020423	692229	SNORD105	http://www.ncbi.nlm.nih.gov/gene/?term=692229	U105	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020424	692229	SNORD105	http://www.ncbi.nlm.nih.gov/gene/?term=692229	U105	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020425	692232	SNORD3@	http://www.ncbi.nlm.nih.gov/gene/?term=692232	"U3, U3A, U3B "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020426	692232	SNORD3@	http://www.ncbi.nlm.nih.gov/gene/?term=692232	"U3, U3A, U3B "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020427	692232	SNORD3@	http://www.ncbi.nlm.nih.gov/gene/?term=692232	"U3, U3A, U3B "	snoRNA	Homo sapiens	25203660	Cytoplasm	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020428	692233	SNORD117	http://www.ncbi.nlm.nih.gov/gene/?term=692233	U83	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00020429	692233	SNORD117	http://www.ncbi.nlm.nih.gov/gene/?term=692233	U83	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020430	692233	SNORD117	http://www.ncbi.nlm.nih.gov/gene/?term=692233	U83	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00020431	692234	SNORD103A	http://www.ncbi.nlm.nih.gov/gene/?term=692234	U103	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020432	69236	2610034E01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69236		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020433	69237	Gtpbp4	http://www.ncbi.nlm.nih.gov/gene/?term=69237	"2610028C09Rik, Crfg, Gtpbp3, NGB, Nog1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020434	6923	TCEB2	http://www.ncbi.nlm.nih.gov/gene/?term=6923	"ELOB, SIII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020435	6923	TCEB2	http://www.ncbi.nlm.nih.gov/gene/?term=6923	"ELOB, SIII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020436	69241	Polr2d	http://www.ncbi.nlm.nih.gov/gene/?term=69241	"2310002G05Rik, 2610028L19Rik, HSRBP4, RBP4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020437	69253	Hspb2	http://www.ncbi.nlm.nih.gov/gene/?term=69253	"27kDa, 2810021G24Rik, HSP27, MKBP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020438	69257	Elf2	http://www.ncbi.nlm.nih.gov/gene/?term=69257	"2610036A20Rik, A230104O07Rik, AW111824, BB183398, EU32, NERF, NERF-1A, NERF-1B, NERF-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020439	6925	TCF4	http://www.ncbi.nlm.nih.gov/gene/?term=6925	"E2-2, FECD3, ITF-2, ITF2, PTHS, SEF-2, SEF2, SEF2-1, SEF2-1A, SEF2-1B, SEF2-1D, TCF-4, bHLHb19 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020440	6925	TCF4	http://www.ncbi.nlm.nih.gov/gene/?term=6925	"E2-2, FECD3, ITF-2, ITF2, PTHS, SEF-2, SEF2, SEF2-1, SEF2-1A, SEF2-1B, SEF2-1D, TCF-4, bHLHb19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020441	69260	Ing2	http://www.ncbi.nlm.nih.gov/gene/?term=69260	"2810011M06Rik, Ing1lb, P33ING2, Ing2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020442	69261	2810411K19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69261		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020443	6926	TBX3	http://www.ncbi.nlm.nih.gov/gene/?term=6926	"TBX3-ISO, UMS, XHL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020444	69270	Gins1	http://www.ncbi.nlm.nih.gov/gene/?term=69270	"2810418N01Rik, Gins4, PSF1, mKIAA0186 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020445	69276	Sec62	http://www.ncbi.nlm.nih.gov/gene/?term=69276	"3100002M17Rik, AI844545, AW545092, Dtrp1, HTP1, Tloc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020446	69296	Tmigd3	http://www.ncbi.nlm.nih.gov/gene/?term=69296	"1700001d09rik, 4930578J19Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020447	6929	TCF3	http://www.ncbi.nlm.nih.gov/gene/?term=6929	"E2A, E47, ITF1, TCF-3, VDIR, bHLHb21 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020448	6929	TCF3	http://www.ncbi.nlm.nih.gov/gene/?term=6929	"E2A, E47, ITF1, TCF-3, VDIR, bHLHb21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020449	6932	TCF7	http://www.ncbi.nlm.nih.gov/gene/?term=6932	TCF-1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020450	69350	1700003G18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69350	2610312K03Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020451	69354	Slc38a4	http://www.ncbi.nlm.nih.gov/gene/?term=69354	"1110012E16Rik, 1700012A18Rik, Ata3, mATA3, mNAT3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020452	6936	GCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=6936	"C2orf3, DNABF, GCF, TCF9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020453	6936	GCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=6936	"C2orf3, DNABF, GCF, TCF9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020454	6936	GCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=6936	"C2orf3, DNABF, GCF, TCF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020455	69371	Smco2	http://www.ncbi.nlm.nih.gov/gene/?term=69371	1700023A16Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020456	69372	Mocs3	http://www.ncbi.nlm.nih.gov/gene/?term=69372	"1700020H17Rik, Uba4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020457	6938	TCF12	http://www.ncbi.nlm.nih.gov/gene/?term=6938	"CRS3, HEB, HTF4, HsT17266, TCF-12, bHLHb20 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020458	6938	TCF12	http://www.ncbi.nlm.nih.gov/gene/?term=6938	"CRS3, HEB, HTF4, HsT17266, TCF-12, bHLHb20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020459	69421	1700022F17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69421		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020460	69423	1700019M22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69423		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020461	6942	TCF20	http://www.ncbi.nlm.nih.gov/gene/?term=6942	"AR1, SPBP, TCF-20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020462	69440	Dennd6b	http://www.ncbi.nlm.nih.gov/gene/?term=69440	"1700027J05Rik, AI414881, Fam116b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020463	69449	1700027A15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69449		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020464	6944	VPS72	http://www.ncbi.nlm.nih.gov/gene/?term=6944	"CFL1, Swc2, TCFL1, YL-1, YL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020465	6944	VPS72	http://www.ncbi.nlm.nih.gov/gene/?term=6944	"CFL1, Swc2, TCFL1, YL-1, YL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020466	69459	Ubl7	http://www.ncbi.nlm.nih.gov/gene/?term=69459	2300004C15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020467	6945	MLX	http://www.ncbi.nlm.nih.gov/gene/?term=6945	"MAD7, MXD7, TCFL4, bHLHd13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020468	6945	MLX	http://www.ncbi.nlm.nih.gov/gene/?term=6945	"MAD7, MXD7, TCFL4, bHLHd13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020469	6945	MLX	http://www.ncbi.nlm.nih.gov/gene/?term=6945	"MAD7, MXD7, TCFL4, bHLHd13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020470	69478	2300009A05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69478		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020471	6947	TCN1	http://www.ncbi.nlm.nih.gov/gene/?term=6947	"HC, TC-1, TC1, TCI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020472	69480	Ttc9	http://www.ncbi.nlm.nih.gov/gene/?term=69480		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020473	69489	2310007J06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69489		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020474	6948	TCN2	http://www.ncbi.nlm.nih.gov/gene/?term=6948	"D22S676, D22S750, II, TC, TC II, TC-2, TC2, TCII "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020475	6949	TCOF1	http://www.ncbi.nlm.nih.gov/gene/?term=6949	"MFD1, TCS, TCS1, treacle "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020476	6949	TCOF1	http://www.ncbi.nlm.nih.gov/gene/?term=6949	"MFD1, TCS, TCS1, treacle "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020477	694	BTG1	http://www.ncbi.nlm.nih.gov/gene/?term=694		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020478	694	BTG1	http://www.ncbi.nlm.nih.gov/gene/?term=694		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020479	69534	Avpi1	http://www.ncbi.nlm.nih.gov/gene/?term=69534	"2310008N12Rik, AA410041, VIT32, esu, mVIT32 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020480	69539	Trnp1	http://www.ncbi.nlm.nih.gov/gene/?term=69539	"2300002D11Rik, Trnp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020481	69546	Mapk1ip1	http://www.ncbi.nlm.nih.gov/gene/?term=69546	"2310009E07Rik, AU043776, MISS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020482	69587	Pcgf3	http://www.ncbi.nlm.nih.gov/gene/?term=69587	"2310035N15Rik, AI662857, D630042K08Rik, DONG1, E430039C14, RNF3A, Rnf3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020483	69617	Pitrm1	http://www.ncbi.nlm.nih.gov/gene/?term=69617	"2310012C15Rik, AA410010, MP-1, MP1, Ntup1, PreP, mKIAA1104 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020484	69632	Arhgef12	http://www.ncbi.nlm.nih.gov/gene/?term=69632	"2310014B11Rik, AU019857, Larg, mKIAA0382 "	mRNA	Mus musculus	18164504	Cell body	Hippocampus	RT-PCR	"In hippocampal neurons, IQ-ArfGEF/BRAG1 mRNA was localized not only at neuronal cell bodies but also at dendritic processes, indicating its dendritic transport and localization. "
RLID00020485	69632	Arhgef12	http://www.ncbi.nlm.nih.gov/gene/?term=69632	"2310014B11Rik, AU019857, Larg, mKIAA0382 "	mRNA	Mus musculus	18164504	Dendrite	Hippocampus	RT-PCR	"In hippocampal neurons, IQ-ArfGEF/BRAG1 mRNA was localized not only at neuronal cell bodies but also at dendritic processes, indicating its dendritic transport and localization. "
RLID00020486	69634	Clybl	http://www.ncbi.nlm.nih.gov/gene/?term=69634	"0610033J05Rik, 2310014M14Rik, AI256068, Clb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020487	69672	Txndc15	http://www.ncbi.nlm.nih.gov/gene/?term=69672	"2310047H23Rik, AI854086, C5orf14, UNQ335 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020488	69675	Pxdn	http://www.ncbi.nlm.nih.gov/gene/?term=69675	"2310075M15Rik, C85409, E330004E07, VPO1, mKIAA0230 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020489	69678	Atcayos	http://www.ncbi.nlm.nih.gov/gene/?term=69678	2310050B05Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020490	69694	Tatdn1	http://www.ncbi.nlm.nih.gov/gene/?term=69694	"2310079P03Rik, CDA11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020491	69713	Pin4	http://www.ncbi.nlm.nih.gov/gene/?term=69713	"2410002I22Rik, EPVH, Par14 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020492	69714	Tfpt	http://www.ncbi.nlm.nih.gov/gene/?term=69714	"2400004F01Rik, AI450389, Amida, FB1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020493	69716	Trip13	http://www.ncbi.nlm.nih.gov/gene/?term=69716	"2410002G23Rik, D13Ertd328e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020494	69723	Rpain	http://www.ncbi.nlm.nih.gov/gene/?term=69723	"2400006N03Rik, Rip "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020495	69724	Rnaseh2a	http://www.ncbi.nlm.nih.gov/gene/?term=69724	"2400006P09Rik, RNASEHI, RNHIA, RNHL "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020496	69731	Gemin7	http://www.ncbi.nlm.nih.gov/gene/?term=69731	"2400008I04Rik, AI120175, AI461688 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020497	69745	Pold4	http://www.ncbi.nlm.nih.gov/gene/?term=69745	"2410012M21Rik, AI463381, AW060307, Polds, p12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020498	69749	Epb41l4aos	http://www.ncbi.nlm.nih.gov/gene/?term=69749	"2410004N09Rik, Epb4.1l4aos "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020499	69757	Leng1	http://www.ncbi.nlm.nih.gov/gene/?term=69757	1500001K17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020500	69772	Bdh2	http://www.ncbi.nlm.nih.gov/gene/?term=69772	"1810026B04Rik, Dhrs6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020501	69774	Ms4a6b	http://www.ncbi.nlm.nih.gov/gene/?term=69774	1810027D10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020502	69786	Tprkb	http://www.ncbi.nlm.nih.gov/gene/?term=69786	"0610033G21Rik, 1810034M08Rik, Cgi-121, DRWMS1, mDRWMS1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020503	69798	1810044D09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69798		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020504	69816	Mzb1	http://www.ncbi.nlm.nih.gov/gene/?term=69816	"2010001M09Rik, AV064572, PACAP, pERp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020505	69829	2010001K21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69829		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020506	69863	Ttc39b	http://www.ncbi.nlm.nih.gov/gene/?term=69863	"1810054D07Rik, 9130422G05Rik, AI450603, AV103077, AW215585 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020507	69871	Ppp1r35	http://www.ncbi.nlm.nih.gov/gene/?term=69871	"2010007H12Rik, 2010011D20Rik, AL024004 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020508	69876	Thap3	http://www.ncbi.nlm.nih.gov/gene/?term=69876	"2010013E08Rik, 2210418H06Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020509	69885	Aunip	http://www.ncbi.nlm.nih.gov/gene/?term=69885	"2610002D18Rik, Clhc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020510	69887	2010100M03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69887		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020511	6988	TCTA	http://www.ncbi.nlm.nih.gov/gene/?term=6988		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020512	69895	Snhg8	http://www.ncbi.nlm.nih.gov/gene/?term=69895	"1110065M07Rik, 2010109N14Rik "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020513	6990	DYNLT3	http://www.ncbi.nlm.nih.gov/gene/?term=6990	"RP3, TCTE1L, TCTEX1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020514	6990	DYNLT3	http://www.ncbi.nlm.nih.gov/gene/?term=6990	"RP3, TCTE1L, TCTEX1L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020515	69917	Nabp2	http://www.ncbi.nlm.nih.gov/gene/?term=69917	"2610036N15Rik, Obfc2b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020516	69920	Polr2i	http://www.ncbi.nlm.nih.gov/gene/?term=69920	2810002B19Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020517	69922	Vrk2	http://www.ncbi.nlm.nih.gov/gene/?term=69922	"2810003O05Rik, AI447698 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020518	6992	PPP1R11	http://www.ncbi.nlm.nih.gov/gene/?term=6992	"CFAP255, HCG-V, HCGV, IPP3, TCTE5, TCTEX5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020519	6992	PPP1R11	http://www.ncbi.nlm.nih.gov/gene/?term=6992	"CFAP255, HCG-V, HCGV, IPP3, TCTE5, TCTEX5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020520	6993	DYNLT1	http://www.ncbi.nlm.nih.gov/gene/?term=6993	"CW-1, TCTEL1, tctex-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020521	69955	Fars2	http://www.ncbi.nlm.nih.gov/gene/?term=69955	"Fars1, pheRS "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020522	69957	Cdc16	http://www.ncbi.nlm.nih.gov/gene/?term=69957	"2700071J12Rik, 2810431D22Rik, APC6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020523	69961	Rpp25l	http://www.ncbi.nlm.nih.gov/gene/?term=69961	"2810432D09Rik, AW987258, Rppl25 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020524	69968	2810404F17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69968		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020525	6996	TDG	http://www.ncbi.nlm.nih.gov/gene/?term=6996	hTDG	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020526	6997	TDGF1	http://www.ncbi.nlm.nih.gov/gene/?term=6997	"CR, CRGF, CRIPTO "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020527	69981	Tmem30a	http://www.ncbi.nlm.nih.gov/gene/?term=69981	"2010200I23Rik, AW540225, Cdc50a, D9Wsu20e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020528	69986	1700025N23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69986		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020529	69987	1700026L06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69987	MAST	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020530	699	BUB1	http://www.ncbi.nlm.nih.gov/gene/?term=699	"BUB1AL, hBUB1, BUB1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020531	699	BUB1	http://www.ncbi.nlm.nih.gov/gene/?term=699	"BUB1A, BUB1L, hBUB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020532	70002	1700028E11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70002		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020533	70009	Ssty2	http://www.ncbi.nlm.nih.gov/gene/?term=70009	"1700029H17Rik, pc11 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020534	7001	PRDX2	http://www.ncbi.nlm.nih.gov/gene/?term=7001	"HEL-S-2a, NKEF-B, NKEFB, PRP, PRX2, PRXII, PTX1, TDPX1, TPX1, TSA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020535	7001	PRDX2	http://www.ncbi.nlm.nih.gov/gene/?term=7001	"HEL-S-2a, NKEF-B, NKEFB, PRP, PRX2, PRXII, PTX1, TDPX1, TPX1, TSA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020536	7001	PRDX2	http://www.ncbi.nlm.nih.gov/gene/?term=7001	"HEL-S-2a, NKEF-B, NKEFB, PRP, PRX2, PRXII, PTX1, TDPX1, TPX1, TSA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020537	70020	Ino80b	http://www.ncbi.nlm.nih.gov/gene/?term=70020	"2510009I23Rik, HMG1YL4, Hmga1l4, Papa1, Znhit4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020538	7003	TEAD1	http://www.ncbi.nlm.nih.gov/gene/?term=7003	"AA, NTEF-1, REF1, TCF-13, TCF13, TEAD-1, TEF-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020539	70044	Tut1	http://www.ncbi.nlm.nih.gov/gene/?term=70044	"2700038E08Rik, PAPD2, Rbm21, TUTase6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020540	7004	TEAD4	http://www.ncbi.nlm.nih.gov/gene/?term=7004	"EFTR-2, RTEF1, TCF13L1, TEF-3, TEF3, TEFR-1, hRTEF-1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020541	70052	Prpf4	http://www.ncbi.nlm.nih.gov/gene/?term=70052	"1600015H11Rik, AI874830, AW047464, bN189G18.1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020542	70083	Metrn	http://www.ncbi.nlm.nih.gov/gene/?term=70083	"1810034B16Rik, Hyrac "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020543	7009	TMBIM6	http://www.ncbi.nlm.nih.gov/gene/?term=7009	"BAXI1, BI-1, TEGT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020544	7009	TMBIM6	http://www.ncbi.nlm.nih.gov/gene/?term=7009	"BAXI1, BI-1, TEGT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020545	70118	Srrd	http://www.ncbi.nlm.nih.gov/gene/?term=70118	"2810002G02Rik, Srr1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020546	70120	Yars2	http://www.ncbi.nlm.nih.gov/gene/?term=70120	"2210023C10Rik, tyrRS "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020547	70122	Mllt3	http://www.ncbi.nlm.nih.gov/gene/?term=70122	"2210011H10Rik, 2610012I03Rik, 3830408D16Rik, Af9, D4Ertd321e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020548	70125	2210016H18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70125		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020549	70127	Dpf3	http://www.ncbi.nlm.nih.gov/gene/?term=70127	"2810403B03Rik, 6530402L11Rik, BAF45C, C78788, CERD4, cer-d4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020550	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020551	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	21963238	Nucleus	HeLa cell	Chip-seq	"TERC binding sites in the genome, which represents a large resource to study potential non-canonical functions of TERC RNA and telomerase (Table S2) "
RLID00020552	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	21381227	Nucleus	NIH3T3 cell	In situ hybridization	Nucleus with abnormal FISH pattern for hTERC was observed in 0.94-90.65% of SCC cells and in 0-85.59% of CIN III cells.
RLID00020553	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00020554	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00020555	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00020556	7012	TERC	http://www.ncbi.nlm.nih.gov/gene/?term=7012	"DKCA1, PFBMFT2, SCARNA19, TR, TRC3, hTR "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00020557	7013	TERF1	http://www.ncbi.nlm.nih.gov/gene/?term=7013	"PIN2, TRBF1, TRF, TRF1, hTRF1-AS, t-TRF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020558	7013	TERF1	http://www.ncbi.nlm.nih.gov/gene/?term=7013	"PIN2, TRBF1, TRF, TRF1, hTRF1-AS, t-TRF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020559	7013	TERF1	http://www.ncbi.nlm.nih.gov/gene/?term=7013	"PIN2, TRBF1, TRF, TRF1, hTRF1-AS, t-TRF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020560	70141	2210414I22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70141		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020561	7014	TERF2	http://www.ncbi.nlm.nih.gov/gene/?term=7014	"TRBF2, TRF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020562	7014	TERF2	http://www.ncbi.nlm.nih.gov/gene/?term=7014	"TRBF2, TRF2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020563	7014	TERF2	http://www.ncbi.nlm.nih.gov/gene/?term=7014	"TRBF2, TRF2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020564	7014	TERF2	http://www.ncbi.nlm.nih.gov/gene/?term=7014	"TRBF2, TRF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020565	7016	TESK1	http://www.ncbi.nlm.nih.gov/gene/?term=7016		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020566	7016	TESK1	http://www.ncbi.nlm.nih.gov/gene/?term=7016		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020567	70186	Fam162a	http://www.ncbi.nlm.nih.gov/gene/?term=70186	"2310056P07Rik, HGTD-P "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00020568	70189	2010015P12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70189	AI605416	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020569	7018	TF	http://www.ncbi.nlm.nih.gov/gene/?term=7018	"HEL-S-71p, PRO1557, PRO2086, TFQTL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020570	7019	TFAM	http://www.ncbi.nlm.nih.gov/gene/?term=7019	"MTTF1, MTTFA, TCF6, TCF6L1, TCF6L2, TCF6L3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020571	7019	TFAM	http://www.ncbi.nlm.nih.gov/gene/?term=7019	"MTTF1, MTTFA, TCF6, TCF6L1, TCF6L2, TCF6L3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020572	701	BUB1B	http://www.ncbi.nlm.nih.gov/gene/?term=701	"BUB1beta, BUBR1, Bub1A, MAD3L, MVA1, SSK1, hBUBR1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020573	701	BUB1B	http://www.ncbi.nlm.nih.gov/gene/?term=701	"BUB1beta, BUBR1, Bub1A, MAD3L, MVA1, SSK1, hBUBR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020574	701	BUB1B	http://www.ncbi.nlm.nih.gov/gene/?term=701	"BUB1beta, BUBR1, Bub1A, MAD3L, MVA1, SSK1, hBUBR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020575	70205	2310068C19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70205		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020576	70208	Med23	http://www.ncbi.nlm.nih.gov/gene/?term=70208	"130kDa, 3000002A17Rik, Crsp3, ESTM7, Sur2, X83317, mKIAA1216 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020577	70209	Tmem143	http://www.ncbi.nlm.nih.gov/gene/?term=70209	"2310076O21Rik, AI481604 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020578	7020	TFAP2A	http://www.ncbi.nlm.nih.gov/gene/?term=7020	"AP-2, AP-2alpha, AP2TF, BOFS, TFAP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020579	70218	Kif18b	http://www.ncbi.nlm.nih.gov/gene/?term=70218	3000004C01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020580	7021	TFAP2B	http://www.ncbi.nlm.nih.gov/gene/?term=7021	"AP-2B, AP2-B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020581	70223	Nars	http://www.ncbi.nlm.nih.gov/gene/?term=70223	"3010001M15Rik, AA960128, ASNRS, C78150 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020582	7022	TFAP2C	http://www.ncbi.nlm.nih.gov/gene/?term=7022	"AP2-GAMMA, ERF1, TFAP2G, hAP-2g "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020583	70235	Poc1a	http://www.ncbi.nlm.nih.gov/gene/?term=70235	"2510040D07Rik, Wdr51a, cha "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020584	70237	Bhlhb9	http://www.ncbi.nlm.nih.gov/gene/?term=70237	2700087I09Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020585	70238	Rnf168	http://www.ncbi.nlm.nih.gov/gene/?term=70238	3110001H15Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020586	70239	Gtf3c5	http://www.ncbi.nlm.nih.gov/gene/?term=70239	"2700084A09Rik, TFIIIC63, TFiiiC2-63 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020587	7023	TFAP4	http://www.ncbi.nlm.nih.gov/gene/?term=7023	"AP-4, bHLHc41 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020588	7023	TFAP4	http://www.ncbi.nlm.nih.gov/gene/?term=7023	"AP-4, bHLHc41 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020589	70247	Psmd1	http://www.ncbi.nlm.nih.gov/gene/?term=70247	"2410026J11Rik, P112, S1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020590	7024	TFCP2	http://www.ncbi.nlm.nih.gov/gene/?term=7024	"LBP1C, LSF, LSF1D, SEF, TFCP2C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020591	7026	NR2F2	http://www.ncbi.nlm.nih.gov/gene/?term=7026	"ARP1, CHTD4, COUPTFB, COUPTFII, NF-E3, NR2F1, SVP40, TFCOUP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020592	7026	NR2F2	http://www.ncbi.nlm.nih.gov/gene/?term=7026	"ARP1, CHTD4, COUPTFB, COUPTFII, NF-E3, NR2F1, SVP40, TFCOUP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020593	7027	TFDP1	http://www.ncbi.nlm.nih.gov/gene/?term=7027	"DILC, DP1, DRTF1, Dp-1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020594	7027	TFDP1	http://www.ncbi.nlm.nih.gov/gene/?term=7027	"DILC, DP1, DRTF1, Dp-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020595	70285	Rpf1	http://www.ncbi.nlm.nih.gov/gene/?term=70285	"2210420E24Rik, 2310066N05Rik, Bxdc5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020596	70295	2610011I18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70295		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020597	70296	Tbc1d13	http://www.ncbi.nlm.nih.gov/gene/?term=70296	"2600014A06Rik, BC025586 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020598	70297	Gcc2	http://www.ncbi.nlm.nih.gov/gene/?term=70297	"0610043A03Rik, 2210420P05Rik, 2600014C01Rik, AW112121, mKIAA0336 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020599	70299	2610012C04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70299		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020600	7029	TFDP2	http://www.ncbi.nlm.nih.gov/gene/?term=7029	DP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020601	7030	TFE3	http://www.ncbi.nlm.nih.gov/gene/?term=7030	"RCCP2, RCCX1, TFEA, bHLHe33 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020602	7031	TFF1	http://www.ncbi.nlm.nih.gov/gene/?term=7031	"BCEI, D21S21, HP1.A, HPS2, pNR-2, pS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020603	7031	TFF1	http://www.ncbi.nlm.nih.gov/gene/?term=7031	"BCEI, D21S21, HP1.A, HPS2, pNR-2, pS2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020604	70335	Reep6	http://www.ncbi.nlm.nih.gov/gene/?term=70335	"0610011M24Rik, Dp1l1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020605	7033	TFF3	http://www.ncbi.nlm.nih.gov/gene/?term=7033	"ITF, P1B, TFI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020606	7033	TFF3	http://www.ncbi.nlm.nih.gov/gene/?term=7033	"ITF, P1B, TFI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020607	70349	Copb1	http://www.ncbi.nlm.nih.gov/gene/?term=70349	2610019B04Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020608	70350	Basp1	http://www.ncbi.nlm.nih.gov/gene/?term=70350	"2610024P12Rik, CAP-23, CAP23, Ckap3, NAP-22, NAP22 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020609	70351	Ppp4r1	http://www.ncbi.nlm.nih.gov/gene/?term=70351	"3110001J10Rik, Pp4r1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020610	70359	Gtpbp3	http://www.ncbi.nlm.nih.gov/gene/?term=70359	"2410009F13Rik, AI607903 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020611	7035	TFPI	http://www.ncbi.nlm.nih.gov/gene/?term=7035	"EPI, LACI, TFI1, TFPI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020612	7035	TFPI	http://www.ncbi.nlm.nih.gov/gene/?term=7035	"EPI, LACI, TFI1, TFPI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020613	7035	TFPI	http://www.ncbi.nlm.nih.gov/gene/?term=7035	"EPI, LACI, TFI1, TFPI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020614	70361	Lman1	http://www.ncbi.nlm.nih.gov/gene/?term=70361	"2610020P13Rik, AI326273, AU043785, C730041J05, ERGIC53, F5F8D, MCFD1, MR60, P58, gp58 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020615	7036	TFR2	http://www.ncbi.nlm.nih.gov/gene/?term=7036	"HFE3, TFRC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020616	70378	1810073G21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70378		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020617	7037	TFRC	http://www.ncbi.nlm.nih.gov/gene/?term=7037	"CD71, IMD46, T9, TFR, TFR1, TR, TRFR, p90 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020618	7037	TFRC	http://www.ncbi.nlm.nih.gov/gene/?term=7037	"CD71, IMD46, T9, TFR, TFR1, TR, TRFR, p90 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020619	7037	TFRC	http://www.ncbi.nlm.nih.gov/gene/?term=7037	"CD71, IMD46, T9, TFR, TFR1, TR, TRFR, p90 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020620	7037	TFRC	http://www.ncbi.nlm.nih.gov/gene/?term=7037	"CD71, IMD46, T9, TFR, TFR1, TR, TRFR, p90 "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00020621	7037	TFRC	http://www.ncbi.nlm.nih.gov/gene/?term=7037	"CD71, IMD46, T9, TFR, TFR1, TR, TRFR, p90 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020622	70383	Cox10	http://www.ncbi.nlm.nih.gov/gene/?term=70383	"2410004F01Rik, AU042636 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020623	70385	Spdl1	http://www.ncbi.nlm.nih.gov/gene/?term=70385	"1700018I02Rik, 2600001J17Rik, 2810049B11Rik, AA409762, Ccdc99 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020624	70394	Kptn	http://www.ncbi.nlm.nih.gov/gene/?term=70394	"2310042D10Rik, 2E4, C030013F01Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020625	70396	Asnsd1	http://www.ncbi.nlm.nih.gov/gene/?term=70396	2210409M21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020626	70397	Tmem70	http://www.ncbi.nlm.nih.gov/gene/?term=70397	"1110020A09Rik, 2210416J16Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020627	7039	TGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7039	TFGA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020628	7040	TGFB1	http://www.ncbi.nlm.nih.gov/gene/?term=7040	"CED, DPD1, LAP, TGFB, TGFbeta "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020629	70417	Megf10	http://www.ncbi.nlm.nih.gov/gene/?term=70417	"3000002B06Rik, Gm331 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00020630	7041	TGFB1I1	http://www.ncbi.nlm.nih.gov/gene/?term=7041	"ARA55, HIC-5, HIC5, TSC-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020631	70420	Arpin	http://www.ncbi.nlm.nih.gov/gene/?term=70420	2610034B18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020632	70422	Ints2	http://www.ncbi.nlm.nih.gov/gene/?term=70422	"2810417D08Rik, AA408260, AI987735, mKIAA1287 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020633	70428	Polr3b	http://www.ncbi.nlm.nih.gov/gene/?term=70428	"2700078H01Rik, A330032P03Rik, C85372, RPC2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020634	70428	Polr3b	http://www.ncbi.nlm.nih.gov/gene/?term=70428	"2700078H01Rik, A330032P03Rik, C85372, RPC2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020635	7042	TGFB2	http://www.ncbi.nlm.nih.gov/gene/?term=7042	"LDS4, TGF-beta2 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00020636	7042	TGFB2	http://www.ncbi.nlm.nih.gov/gene/?term=7042	"LDS4, TGF-beta2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020637	7042	TGFB2	http://www.ncbi.nlm.nih.gov/gene/?term=7042	"LDS4, TGF-beta2 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00020638	70432	Rufy2	http://www.ncbi.nlm.nih.gov/gene/?term=70432	"2610111M19Rik, AI844453, Denn, LZ-FYVE, ZFYVE13 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020639	70439	Taf15	http://www.ncbi.nlm.nih.gov/gene/?term=70439	"2610111C21Rik, 68kDa, TAFII68, Taf2n "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020640	7043	TGFB3	http://www.ncbi.nlm.nih.gov/gene/?term=7043	"ARVD, ARVD1, LDS5, RNHF, TGF-beta3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020641	7044	LEFTY2	http://www.ncbi.nlm.nih.gov/gene/?term=7044	"EBAF, LEFTA, LEFTYA, TGFB4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020642	70454	Cenpl	http://www.ncbi.nlm.nih.gov/gene/?term=70454	"2610300B10Rik, AW121806, AW550697, CENP-L "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020643	70454	Cenpl	http://www.ncbi.nlm.nih.gov/gene/?term=70454	"2610300B10Rik, AW121806, AW550697, CENP-L "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020644	7045	TGFBI	http://www.ncbi.nlm.nih.gov/gene/?term=7045	"BIGH3, CDB1, CDG2, CDGG1, CSD, CSD1, CSD2, CSD3, EBMD, LCD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020645	70466	Ckap2l	http://www.ncbi.nlm.nih.gov/gene/?term=70466	"2010016H04Rik, 2610318C08Rik, AV070319, radmis, rdm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020646	7046	TGFBR1	http://www.ncbi.nlm.nih.gov/gene/?term=7046	"AAT5, ACVRLK4, ALK-5, ALK5, ESS1, LDS1, LDS1A, LDS2A, MSSE, SKR4, TGFR-1, tbetaR-I "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020647	7046	TGFBR1	http://www.ncbi.nlm.nih.gov/gene/?term=7046	"AAT5, ACVRLK4, ALK-5, ALK5, ESS1, LDS1, LDS1A, LDS2A, MSSE, SKR4, TGFR-1, tbetaR-I "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020648	70472	Atad2	http://www.ncbi.nlm.nih.gov/gene/?term=70472	2610509G12Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020649	70474	5730405A10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70474		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020650	70478	Mipep	http://www.ncbi.nlm.nih.gov/gene/?term=70478	"5730405E07Rik, MIP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020651	70488	5730405O12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70488		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020652	70489	5730405O15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70489		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020653	7048	TGFBR2	http://www.ncbi.nlm.nih.gov/gene/?term=7048	"AAT3, FAA3, LDS1B, LDS2, LDS2B, MFS2, RIIC, TAAD2, TGFR-2, TGFbeta-RII "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020654	70495	Atp6ap2	http://www.ncbi.nlm.nih.gov/gene/?term=70495	"(P)RR, 5730403E06Rik, APT6M8-9, ATP6M8-9, Atp6ip2, M8-9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020655	7049	TGFBR3	http://www.ncbi.nlm.nih.gov/gene/?term=7049	"BGCAN, betaglycan "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020656	70508	Bbx	http://www.ncbi.nlm.nih.gov/gene/?term=70508	"5530401J07Rik, 5730403O13Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020657	70509	5730405N03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70509		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020658	7050	TGIF1	http://www.ncbi.nlm.nih.gov/gene/?term=7050	"HPE4, TGIF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020659	70516	5730408A14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70516		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020660	7052	TGM2	http://www.ncbi.nlm.nih.gov/gene/?term=7052	"G-ALPHA-h, GNAH, HEL-S-45, TG2, TGC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020661	70551	Tmtc4	http://www.ncbi.nlm.nih.gov/gene/?term=70551	"4930403J22Rik, 5730419O14Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020662	70556	Slc25a33	http://www.ncbi.nlm.nih.gov/gene/?term=70556	"5730438N18Rik, Pnc1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020663	70561	Txndc16	http://www.ncbi.nlm.nih.gov/gene/?term=70561	"5730420B22Rik, C77647 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020664	70572	Ipo5	http://www.ncbi.nlm.nih.gov/gene/?term=70572	"1110011C18Rik, 5730478E03Rik, AA409333, C76941, IMB3, Kpnb3, Ranbp5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020665	70574	Cpm	http://www.ncbi.nlm.nih.gov/gene/?term=70574	"1110060I01Rik, 5730456K23Rik, AA589379, E030045M14Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020666	70575	Gfod2	http://www.ncbi.nlm.nih.gov/gene/?term=70575	5730466C23Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020667	70579	Zc3h11a	http://www.ncbi.nlm.nih.gov/gene/?term=70579	"1110003F06Rik, 5730454B08Rik, G630041M05Rik, Zc3hdc11a, Zc3hh11a, mKIAA0663 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020668	70579	Zc3h11a	http://www.ncbi.nlm.nih.gov/gene/?term=70579	"1110003F06Rik, 5730454B08Rik, G630041M05Rik, Zc3hdc11a, Zc3hh11a, mKIAA0663 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020669	70584	Pak4	http://www.ncbi.nlm.nih.gov/gene/?term=70584	"5730488L07Rik, AW555722, mKIAA1142 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020670	70599	Ssfa2	http://www.ncbi.nlm.nih.gov/gene/?term=70599	"5730488C15Rik, CS-1, CS1, KRAP, SPAG13, mKIAA1927 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020671	7059	THBS3	http://www.ncbi.nlm.nih.gov/gene/?term=7059	TSP3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020672	705	BYSL	http://www.ncbi.nlm.nih.gov/gene/?term=705	BYSTIN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020673	705	BYSL	http://www.ncbi.nlm.nih.gov/gene/?term=705	BYSTIN	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020674	705	BYSL	http://www.ncbi.nlm.nih.gov/gene/?term=705	BYSTIN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020675	70619	5730510P18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70619		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020676	70625	Med26	http://www.ncbi.nlm.nih.gov/gene/?term=70625	"5730493L18Rik, AI414941, AW495270, Crsp7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020677	7064	THOP1	http://www.ncbi.nlm.nih.gov/gene/?term=7064	"EP24.15, MEPD_HUMAN, MP78, TOP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020678	70650	Zcchc8	http://www.ncbi.nlm.nih.gov/gene/?term=70650	5730565F05Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020679	7066	THPO	http://www.ncbi.nlm.nih.gov/gene/?term=7066	"MGDF, MKCSF, ML, MPLLG, THCYT1, TPO "	mRNA	Homo sapiens	25063809	Ribosome	HeLa cell	qRT-PCR	Figure 1: Endoplasmic reticulum-associated mRNAs are partitioned between detergent-resistant and detergent-sensitive membrane domains. Data are collected from Figure 1.
RLID00020680	70673	Prdm16	http://www.ncbi.nlm.nih.gov/gene/?term=70673	"5730557K01Rik, csp1, mel1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020681	70675	Vcpip1	http://www.ncbi.nlm.nih.gov/gene/?term=70675	"4932442A08, 5730421J18Rik, 5730538E15Rik, VCIP135, mKIAA1850 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020682	70675	Vcpip1	http://www.ncbi.nlm.nih.gov/gene/?term=70675	"4932442A08, 5730421J18Rik, 5730538E15Rik, VCIP135, mKIAA1850 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00020683	70676	Gulp1	http://www.ncbi.nlm.nih.gov/gene/?term=70676	"3110030A04Rik, 5730529O06Rik, CED-6, Ced6, GULP, Gulp-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020684	7067	THRA	http://www.ncbi.nlm.nih.gov/gene/?term=7067	"AR7, CHNG6, EAR7, ERB-T-1, ERBA, ERBA1, NR1A11, THRA2, c-ERBA-1, THRA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020685	7067	THRA	http://www.ncbi.nlm.nih.gov/gene/?term=7067	"AR7, CHNG6, EAR7, ERB-T-1, ERBA, ERBA1, NR1A1, THRA1, THRA2, c-ERBA-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020686	70683	Utp20	http://www.ncbi.nlm.nih.gov/gene/?term=70683	"3830408P06Rik, AA617408, Drim, mDRIM, mDRIN "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020687	70693	Adgra3	http://www.ncbi.nlm.nih.gov/gene/?term=70693	"3830613O22Rik, AU044632, Gpr125, Tem5-like "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020688	70699	Nup205	http://www.ncbi.nlm.nih.gov/gene/?term=70699	"3830404O05Rik, AV248391, mKIAA0225 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020689	706	TSPO	http://www.ncbi.nlm.nih.gov/gene/?term=706	"BPBS, BZRP, DBI, IBP, MBR, PBR, PBS, PKBS, PTBR, mDRC, pk18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020690	7070	THY1	http://www.ncbi.nlm.nih.gov/gene/?term=7070	"CD90, CDw90 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020691	7071	KLF10	http://www.ncbi.nlm.nih.gov/gene/?term=7071	"EGR-alpha, EGRA, TIEG, TIEG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020692	7072	TIA1	http://www.ncbi.nlm.nih.gov/gene/?term=7072	"TIA-1, WDM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020693	7072	TIA1	http://www.ncbi.nlm.nih.gov/gene/?term=7072	"TIA-1, WDM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020694	7073	TIAL1	http://www.ncbi.nlm.nih.gov/gene/?term=7073	"TCBP, TIAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020695	7073	TIAL1	http://www.ncbi.nlm.nih.gov/gene/?term=7073	"TCBP, TIAR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020696	70747	Tspan2	http://www.ncbi.nlm.nih.gov/gene/?term=70747	"6330415F13Rik, B230119D02Rik, tspan-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020697	70757	Hacd2	http://www.ncbi.nlm.nih.gov/gene/?term=70757	"6330408J20Rik, AI255777, AI481689, Hcad2, Ptplb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020698	7075	TIE1	http://www.ncbi.nlm.nih.gov/gene/?term=7075	"JTK14, TIE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020699	70760	6330417A16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70760		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020700	7076	TIMP1	http://www.ncbi.nlm.nih.gov/gene/?term=7076	"CLGI, EPA, EPO, HCI, TIMP, TIMP-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020701	7076	TIMP1	http://www.ncbi.nlm.nih.gov/gene/?term=7076	"CLGI, EPA, EPO, HCI, TIMP, TIMP-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020702	7076	TIMP1	http://www.ncbi.nlm.nih.gov/gene/?term=7076	"CLGI, EPA, EPO, HCI, TIMP, TIMP-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020703	7077	TIMP2	http://www.ncbi.nlm.nih.gov/gene/?term=7077	"CSC-21K, DDC8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020704	7077	TIMP2	http://www.ncbi.nlm.nih.gov/gene/?term=7077	"CSC-21K, DDC8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020705	7077	TIMP2	http://www.ncbi.nlm.nih.gov/gene/?term=7077	"CSC-21K, DDC8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020706	70788	Klhl30	http://www.ncbi.nlm.nih.gov/gene/?term=70788	4631423F02Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020707	7078	TIMP3	http://www.ncbi.nlm.nih.gov/gene/?term=7078	"HSMRK222, K222, K222TA2, SFD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020708	7078	TIMP3	http://www.ncbi.nlm.nih.gov/gene/?term=7078	"HSMRK222, K222, K222TA2, SFD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020709	70790	Ubr5	http://www.ncbi.nlm.nih.gov/gene/?term=70790	"Edd, Edd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020710	70791	Hars2	http://www.ncbi.nlm.nih.gov/gene/?term=70791	"4631412B19Rik, HARSR, HO3, Harsl "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020711	70796	Zdhhc1	http://www.ncbi.nlm.nih.gov/gene/?term=70796	4432412D04Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020712	70799	Cep192	http://www.ncbi.nlm.nih.gov/gene/?term=70799	"4631422C13Rik, D430014P18Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020713	7079	TIMP4	http://www.ncbi.nlm.nih.gov/gene/?term=7079		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020714	70804	Pgrmc2	http://www.ncbi.nlm.nih.gov/gene/?term=70804	"4631434O19Rik, 5730409G06Rik, DG6, PMBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020715	70808	4632415L05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70808	AI662792	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020716	70809	Clec2g	http://www.ncbi.nlm.nih.gov/gene/?term=70809	"4632413B12Rik, Clr-c, Clr-d, Clrc, Clrd, Clrx, Ddv10, Ocilrp1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020717	7080	NKX2-1	http://www.ncbi.nlm.nih.gov/gene/?term=7080	"BCH, BHC, NK-2, NKX2.1, NKX2A, NMTC1, T/EBP, TEBP, TITF1, TTF-1, TTF1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020718	70810	Krt25	http://www.ncbi.nlm.nih.gov/gene/?term=70810	"4631426H08Rik, Ka38a, mIRSa1, Krt25 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020719	70821	4921507P07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70821	TISP74	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020720	70825	4633401L03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70825		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020721	70831	Krtap31-1	http://www.ncbi.nlm.nih.gov/gene/?term=70831	"4733401H21Rik, AI506529 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020722	70834	Spag9	http://www.ncbi.nlm.nih.gov/gene/?term=70834	"3110018C07Rik, 4733401I23Rik, 4831406C20Rik, AW552012, JLP, JSAP2, JSAP2a, Jip4, Mapk8ip4, syd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020723	7083	TK1	http://www.ncbi.nlm.nih.gov/gene/?term=7083	TK2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020724	7083	TK1	http://www.ncbi.nlm.nih.gov/gene/?term=7083	TK2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020725	7083	TK1	http://www.ncbi.nlm.nih.gov/gene/?term=7083	TK2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020726	7084	TK2	http://www.ncbi.nlm.nih.gov/gene/?term=7084	"MTDPS2, MTTK, SCA31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020727	7084	TK2	http://www.ncbi.nlm.nih.gov/gene/?term=7084	"MTDPS2, MTTK, SCA31 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020728	70853	Vwa3b	http://www.ncbi.nlm.nih.gov/gene/?term=70853	"4921511C04Rik, A230074B11Rik, Gm555 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020729	70859	Lrrc63	http://www.ncbi.nlm.nih.gov/gene/?term=70859	4921509B22Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020730	70861	Akr1cl	http://www.ncbi.nlm.nih.gov/gene/?term=70861	"4921521F21Rik, AI451536, AI503553 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020731	7086	TKT	http://www.ncbi.nlm.nih.gov/gene/?term=7086	"HEL-S-48, HEL107, TK1, TKT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020732	7087	ICAM5	http://www.ncbi.nlm.nih.gov/gene/?term=7087	"TLCN, TLN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020733	70881	Nt5c1b	http://www.ncbi.nlm.nih.gov/gene/?term=70881	"4921514H13Rik, AIRP, CN-IB, cN1B "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020734	70885	Ints10	http://www.ncbi.nlm.nih.gov/gene/?term=70885	"4921521J11Rik, AI462004 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020735	70888	4921521C08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70888		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020736	7088	TLE1	http://www.ncbi.nlm.nih.gov/gene/?term=7088	"ESG, ESG1, GRG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020737	70891	Spdya	http://www.ncbi.nlm.nih.gov/gene/?term=70891	"4921517J08Rik, 4930548B21Rik, GS4, MLZ-465, Spdy1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020738	70895	4921511E07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70895		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020739	7089	TLE2	http://www.ncbi.nlm.nih.gov/gene/?term=7089	"ESG, ESG2, GRG2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020740	7089	TLE2	http://www.ncbi.nlm.nih.gov/gene/?term=7089	"ESG, ESG2, GRG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020741	708	C1QBP	http://www.ncbi.nlm.nih.gov/gene/?term=708	"GC1QBP, HABP1, SF2p32, gC1Q-R, gC1qR, p32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020742	7090	TLE3	http://www.ncbi.nlm.nih.gov/gene/?term=7090	"ESG, ESG3, GRG3, HsT18976 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020743	7091	TLE4	http://www.ncbi.nlm.nih.gov/gene/?term=7091	"BCE-1, BCE1, E(spI), ESG, ESG4, GRG4, Grg-4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020744	70941	4921539E11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=70941		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020745	7094	TLN1	http://www.ncbi.nlm.nih.gov/gene/?term=7094	"ILWEQ, TLN "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020746	70957	Stamos	http://www.ncbi.nlm.nih.gov/gene/?term=70957	4921530L18Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020747	7095	SEC62	http://www.ncbi.nlm.nih.gov/gene/?term=7095	"Dtrp1, HTP1, TLOC1, TP-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020748	7095	SEC62	http://www.ncbi.nlm.nih.gov/gene/?term=7095	"Dtrp1, HTP1, TLOC1, TP-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020749	7095	SEC62	http://www.ncbi.nlm.nih.gov/gene/?term=7095	"Dtrp1, HTP1, TLOC1, TP-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020750	7095	SEC62	http://www.ncbi.nlm.nih.gov/gene/?term=7095	"Dtrp1, HTP1, TLOC1, TP-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020751	70974	Pgm2l1	http://www.ncbi.nlm.nih.gov/gene/?term=70974	"4931406N15Rik, AI553438, BM32A "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020752	70997	Spef1	http://www.ncbi.nlm.nih.gov/gene/?term=70997	"4931426K16Rik, Clamp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020753	70998	Phf6	http://www.ncbi.nlm.nih.gov/gene/?term=70998	"2700007B13Rik, 4931428F02Rik, mKIAA1823 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020754	70999	Naa40	http://www.ncbi.nlm.nih.gov/gene/?term=70999	"4931433E08Rik, AU023197, Nat11 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020755	70	ACTC1	http://www.ncbi.nlm.nih.gov/gene/?term=70	"ACTC, ASD5, CMD1R, CMH11, LVNC4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020756	70	ACTC1	http://www.ncbi.nlm.nih.gov/gene/?term=70	"ACTC, ASD5, CMD1R, CMH11, LVNC4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020757	70	ACTC1	http://www.ncbi.nlm.nih.gov/gene/?term=70	"ACTC, ASD5, CMD1R, CMH11, LVNC4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020758	7100	TLR5	http://www.ncbi.nlm.nih.gov/gene/?term=7100	"MELIOS, SLE1, SLEB1, TIL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020759	71018	4933404K13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71018		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020760	71025	4933402C05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71025		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020761	71029	4933402C06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71029		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020762	7102	TSPAN7	http://www.ncbi.nlm.nih.gov/gene/?term=7102	"A15, CCG-B7, CD231, DXS1692E, MRX58, MXS1, TALLA-1, TM4SF2, TM4SF2b "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020763	71030	4933403O08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71030		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020764	7103	TSPAN8	http://www.ncbi.nlm.nih.gov/gene/?term=7103	"CO-029, TM4SF3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020765	7103	TSPAN8	http://www.ncbi.nlm.nih.gov/gene/?term=7103	"CO-029, TM4SF3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020766	71041	Pcgf6	http://www.ncbi.nlm.nih.gov/gene/?term=71041	"4933407A11Rik, AI604840, MBLR, Rnf134 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020767	71057	4933402J10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71057		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020768	7105	TSPAN6	http://www.ncbi.nlm.nih.gov/gene/?term=7105	"T245, TM4SF6, TSPAN-6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020769	71063	Zfp597	http://www.ncbi.nlm.nih.gov/gene/?term=71063	"4933407K12Rik, AI462383, AI666357 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020770	71067	4933411E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71067		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020771	71069	Stox2	http://www.ncbi.nlm.nih.gov/gene/?term=71069	"4933409N07Rik, AI449080, AI835114, mKIAA1392 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020772	7106	TSPAN4	http://www.ncbi.nlm.nih.gov/gene/?term=7106	"NAG-2, NAG2, TETRASPAN, TM4SF7, TSPAN-4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020773	7106	TSPAN4	http://www.ncbi.nlm.nih.gov/gene/?term=7106	"NAG-2, NAG2, TETRASPAN, TM4SF7, TSPAN-4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020774	71076	4933422E07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71076		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020775	7107	GPR137B	http://www.ncbi.nlm.nih.gov/gene/?term=7107	TM7SF1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020776	7107	GPR137B	http://www.ncbi.nlm.nih.gov/gene/?term=7107	TM7SF1	mRNA	Homo sapiens	19175411	Ribosome	T-cell|SeAx	qRT-PCR	"Using quantitative real-time RT-PCR we evaluated, whether mRNAs coding for differently located proteins are selectively enriched in one of the two analysed compartments, namely free versus membrane-associated polysomes. We selected genes coding for proteins located in the plasma membrane (GPR137B), secreted proteins (TIC2, IBP2, PAI) and cytosolic proteins (the house keeping genes GAPDH and HMBS). In fact, the distribution of the specific mRNA was as predicted ( Fig. 1): The average ratio of specific mRNA at bound ribosomes versus free ribosomes was 1 ? 4.4 for the housekeeping genes (GAPDH and HMBS) and 13.3 ? 1 for genes coding for membrane-bound or secreted proteins. Ratios for genes coding for cytosolic proteins were always below 0.6 and those for membrane or secreted genes were always above 1. The highest values were observed for PAI in MyLa (57 ? 1) and GPR137B in SeAx (34 ? 1), while the lowest ratios were detected for HMBS (1 ? 55) and GAPDH (1 ? 12) in HuT78. "
RLID00020777	7107	GPR137B	http://www.ncbi.nlm.nih.gov/gene/?term=7107	TM7SF1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020778	7107	GPR137B	http://www.ncbi.nlm.nih.gov/gene/?term=7107	TM7SF1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020779	7108	TM7SF2	http://www.ncbi.nlm.nih.gov/gene/?term=7108	"ANG1, DHCR14A, NET47 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020780	71093	Atoh8	http://www.ncbi.nlm.nih.gov/gene/?term=71093	"4933425C05Rik, Hath6, Math6, bHLHa21, okadin "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020781	7109	TRAPPC10	http://www.ncbi.nlm.nih.gov/gene/?term=7109	"EHOC-1, EHOC1, GT334, TMEM1, TRS130, TRS30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020782	710	SERPING1	http://www.ncbi.nlm.nih.gov/gene/?term=710	"C1IN, C1INH, C1NH, HAE1, HAE2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020783	71101	Uvssa	http://www.ncbi.nlm.nih.gov/gene/?term=71101	"4933407H18Rik, D330017J19Rik, Kiaa1530, mKIAA1530 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020784	7110	TMF1	http://www.ncbi.nlm.nih.gov/gene/?term=7110	"ARA160, TMF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020785	7111	TMOD1	http://www.ncbi.nlm.nih.gov/gene/?term=7111	"D9S57E, ETMOD, TMOD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020786	7111	TMOD1	http://www.ncbi.nlm.nih.gov/gene/?term=7111	"D9S57E, ETMOD, TMOD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020787	7112	TMPO	http://www.ncbi.nlm.nih.gov/gene/?term=7112	"CMD1T, LAP2, LEMD4, PRO0868, TP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020788	7112	TMPO	http://www.ncbi.nlm.nih.gov/gene/?term=7112	"CMD1T, LAP2, LEMD4, PRO0868, TP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020789	71135	4933411O13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71135		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020790	71137	Rfx4	http://www.ncbi.nlm.nih.gov/gene/?term=71137	"4933412G19Rik, NYD-sp10 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020791	7113	TMPRSS2	http://www.ncbi.nlm.nih.gov/gene/?term=7113	"PP9284, PRSS10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020792	71145	Scara5	http://www.ncbi.nlm.nih.gov/gene/?term=71145	"4932433F15Rik, 4933425F03Rik, AV278087, Tesr "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020793	71148	Mier1	http://www.ncbi.nlm.nih.gov/gene/?term=71148	"4933425I22Rik, 5830411K19Rik, er1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020794	7114	TMSB4X	http://www.ncbi.nlm.nih.gov/gene/?term=7114	"FX, PTMB4, TB4X, TMSB4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020795	7114	TMSB4X	http://www.ncbi.nlm.nih.gov/gene/?term=7114	"FX, PTMB4, TB4X, TMSB4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020796	7114	TMSB4X	http://www.ncbi.nlm.nih.gov/gene/?term=7114	"FX, PTMB4, TB4X, TMSB4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020797	71151	Eri2	http://www.ncbi.nlm.nih.gov/gene/?term=71151	"4933424N09Rik, Exod1, mKIAA1504 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020798	71175	Nipbl	http://www.ncbi.nlm.nih.gov/gene/?term=71175	Idn3	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020799	71177	Asun	http://www.ncbi.nlm.nih.gov/gene/?term=71177	"4933424B01Rik, Spata30 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020800	71181	4933411E06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71181		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020801	71190	4933425M03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71190		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020802	71213	Cage1	http://www.ncbi.nlm.nih.gov/gene/?term=71213	"4933427I01Rik, Ctag3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020803	71223	Gpr15	http://www.ncbi.nlm.nih.gov/gene/?term=71223	4933439K08Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020804	71237	4933435G04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71237		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020805	7123	CLEC3B	http://www.ncbi.nlm.nih.gov/gene/?term=7123	"TN, TNA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020806	7124	TNF	http://www.ncbi.nlm.nih.gov/gene/?term=7124	"DIF-alpha, TNFA, TNFSF2, TNLG1F, TNF "	mRNA	Homo sapiens	26000482	Ribosome	HeLa cell	qRT-PCR	"Because Il6, Tnf, and Ptgs2 mRNAs present in polysomal fractions rapidly increased in response to IL-1 b stimulation in HeLa cells and then decreased at later time points ( Figures 3 H and S7 C), we hypothesized that the contribu- tion of translation-dependent decay by Reg1 changes in the time course of BMM activation.  "
RLID00020807	71268	Lrrfip2	http://www.ncbi.nlm.nih.gov/gene/?term=71268	"5133400F20Rik, AI850587 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020808	7126	TNFAIP1	http://www.ncbi.nlm.nih.gov/gene/?term=7126	"B12, B61, BTBD34, EDP1, hBACURD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020809	71270	4933438K21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71270		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020810	71279	Slc29a3	http://www.ncbi.nlm.nih.gov/gene/?term=71279	"4933435C21Rik, AW987637, Ent3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020811	7127	TNFAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=7127	"B94, EXOC3L3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020812	7127	TNFAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=7127	"B94, EXOC3L3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020813	71288	4933440K10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71288		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020814	7128	TNFAIP3	http://www.ncbi.nlm.nih.gov/gene/?term=7128	"A20, AISBL, OTUD7C, TNFA1P2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020815	71299	4933439N06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71299		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020816	71301	4930593A02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71301	4933440I01Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020817	7132	TNFRSF1A	http://www.ncbi.nlm.nih.gov/gene/?term=7132	"CD120a, FPF, MS5, TBP1, TNF-R, TNF-R-I, TNF-R55, TNFAR, TNFR1, TNFR1-d2, TNFR55, TNFR60, p55, p55-R, p60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020818	7132	TNFRSF1A	http://www.ncbi.nlm.nih.gov/gene/?term=7132	"CD120a, FPF, MS5, TBP1, TNF-R, TNF-R-I, TNF-R55, TNFAR, TNFR1, TNFR1-d2, TNFR55, TNFR60, p55, p55-R, p60 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020819	7133	TNFRSF1B	http://www.ncbi.nlm.nih.gov/gene/?term=7133	"CD120b, TBPII, TNF-R-II, TNF-R75, TNFBR, TNFR1B, TNFR2, TNFR80, p75, p75TNFR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020820	7133	TNFRSF1B	http://www.ncbi.nlm.nih.gov/gene/?term=7133	"CD120b, TBPII, TNF-R-II, TNF-R75, TNFBR, TNFR1B, TNFR2, TNFR80, p75, p75TNFR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020821	71340	Riok1	http://www.ncbi.nlm.nih.gov/gene/?term=71340	"3110046C13Rik, 5430416A05Rik, Ad034 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020822	7135	TNNI1	http://www.ncbi.nlm.nih.gov/gene/?term=7135	"SSTNI, TNN1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020823	7135	TNNI1	http://www.ncbi.nlm.nih.gov/gene/?term=7135	"SSTNI, TNN1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020824	7135	TNNI1	http://www.ncbi.nlm.nih.gov/gene/?term=7135	"SSTNI, TNN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020825	71360	5530401D11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71360		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020826	71361	Aifm2	http://www.ncbi.nlm.nih.gov/gene/?term=71361	"5430437E11Rik, Amid, D730001I10Rik, PRG3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020827	71367	Chst9	http://www.ncbi.nlm.nih.gov/gene/?term=71367	5430438D01Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020828	71371	Arid5b	http://www.ncbi.nlm.nih.gov/gene/?term=71371	"4930580B11, 5430435G07Rik, AI467247, Desrt, Mrf2, Mrf2alpha, Mrf2beta "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020829	71382	Pex1	http://www.ncbi.nlm.nih.gov/gene/?term=71382	"5430414H02Rik, E330005K07Rik, ZWS1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020830	71389	Chd6	http://www.ncbi.nlm.nih.gov/gene/?term=71389	"5430439G14Rik, 6330406J24Rik, CHD-6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020831	71393	Kctd6	http://www.ncbi.nlm.nih.gov/gene/?term=71393	"5430433B02Rik, AU044285 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020832	71409	Fmnl2	http://www.ncbi.nlm.nih.gov/gene/?term=71409	"5430425K04Rik, Man "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020833	71420	5530400N10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71420		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020834	71445	5530601H04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71445	AI835882	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020835	71452	Ankrd40	http://www.ncbi.nlm.nih.gov/gene/?term=71452	"1110011C06Rik, 5530600A18Rik, Gcap15 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020836	71456	8430401P03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71456		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020837	71458	Bcor	http://www.ncbi.nlm.nih.gov/gene/?term=71458	"2900008C10Rik, 5830466J11Rik, 8430401K06RikR, D930024N20Rik, mKIAA1575, Bcor "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020838	7148	TNXB	http://www.ncbi.nlm.nih.gov/gene/?term=7148	"EDS3, HXBL, TENX, TN-X, TNX, TNXB1, TNXB2, TNXBS, VUR8, XB, XBS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020839	714	C1QC	http://www.ncbi.nlm.nih.gov/gene/?term=714	"C1Q-C, C1QG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020840	71514	Sfpq	http://www.ncbi.nlm.nih.gov/gene/?term=71514	"1110004P21Rik, 2810416M14Rik, 5730453G22Rik, 9030402K04Rik, AU021830, D4Ertd314e, Gm12940, OTTMUSG00000009329, PSF, REP1 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020841	71514	Sfpq	http://www.ncbi.nlm.nih.gov/gene/?term=71514	"1110004P21Rik, 2810416M14Rik, 5730453G22Rik, 9030402K04Rik, AU021830, D4Ertd314e, Gm12940, OTTMUSG00000009329, PSF, REP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020842	71514	Sfpq	http://www.ncbi.nlm.nih.gov/gene/?term=71514	"1110004P21Rik, 2810416M14Rik, 5730453G22Rik, 9030402K04Rik, AU021830, D4Ertd314e, Gm12940, OTTMUSG00000009329, PSF, REP1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020843	71521	Pds5a	http://www.ncbi.nlm.nih.gov/gene/?term=71521	"9030416H16Rik, E230024D05Rik, mKIAA0648 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020844	71523	8430429K09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71523		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020845	71524	8430432A02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71524		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020846	71534	9030408N04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71534		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020847	7153	TOP2A	http://www.ncbi.nlm.nih.gov/gene/?term=7153	"TOP2, TP2A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020848	7153	TOP2A	http://www.ncbi.nlm.nih.gov/gene/?term=7153	"TOP2, TP2A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020849	7155	TOP2B	http://www.ncbi.nlm.nih.gov/gene/?term=7155	"TOPIIB, top2beta "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020850	71565	9030418E23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71565		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020851	7156	TOP3A	http://www.ncbi.nlm.nih.gov/gene/?term=7156	"TOP3, ZGRF7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020852	7156	TOP3A	http://www.ncbi.nlm.nih.gov/gene/?term=7156	"TOP3, ZGRF7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020853	7157	TP53	http://www.ncbi.nlm.nih.gov/gene/?term=7157	"BCC7, LFS1, P53, TRP53 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020854	7157	TP53	http://www.ncbi.nlm.nih.gov/gene/?term=7157	"BCC7, LFS1, P53, TRP53 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020855	71581	9130015A21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71581	"100043575, Gm4527 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020856	71599	Senp8	http://www.ncbi.nlm.nih.gov/gene/?term=71599	"9130010J17Rik, AU020827, Den1, Nedp1, Prsc2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020857	7159	TP53BP2	http://www.ncbi.nlm.nih.gov/gene/?term=7159	"53BP2, ASPP2, BBP, P53BP2, PPP1R13A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020858	7159	TP53BP2	http://www.ncbi.nlm.nih.gov/gene/?term=7159	"53BP2, ASPP2, BBP, P53BP2, PPP1R13A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020859	71611	9130022K11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71611		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020860	7162	TPBG	http://www.ncbi.nlm.nih.gov/gene/?term=7162	"5T4, 5T4AG, M6P1, WAIF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020861	7162	TPBG	http://www.ncbi.nlm.nih.gov/gene/?term=7162	"5T4, 5T4AG, M6P1, WAIF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020862	7163	TPD52	http://www.ncbi.nlm.nih.gov/gene/?term=7163	"D52, N8L, PC-1, PrLZ, hD52 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020863	71643	Zgrf1	http://www.ncbi.nlm.nih.gov/gene/?term=71643	"4930422G04Rik, AI448607 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020864	7164	TPD52L1	http://www.ncbi.nlm.nih.gov/gene/?term=7164	D53	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020865	71653	Shtn1	http://www.ncbi.nlm.nih.gov/gene/?term=71653	"4930506M07Rik, Kiaa1598, Shootin1, mKIAA1598 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020866	7165	TPD52L2	http://www.ncbi.nlm.nih.gov/gene/?term=7165	"D54, TPD54 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020867	7165	TPD52L2	http://www.ncbi.nlm.nih.gov/gene/?term=7165	"D54, TPD54 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020868	7165	TPD52L2	http://www.ncbi.nlm.nih.gov/gene/?term=7165	"D54, TPD54 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020869	71660	Rarres2	http://www.ncbi.nlm.nih.gov/gene/?term=71660	"0610007L05Rik, AI303516 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020870	71670	Acy3	http://www.ncbi.nlm.nih.gov/gene/?term=71670	"0610006H10Rik, AA3, AAIII, AW107362, Acy-3, HCBP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020871	71676	0610012D04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71676		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020872	7167	TPI1	http://www.ncbi.nlm.nih.gov/gene/?term=7167	"HEL-S-49, TIM, TPI, TPID "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020873	7167	TPI1	http://www.ncbi.nlm.nih.gov/gene/?term=7167	"HEL-S-49, TIM, TPI, TPID "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020874	7168	TPM1	http://www.ncbi.nlm.nih.gov/gene/?term=7168	"C15orf13, CMD1Y, CMH3, HEL-S-265, HTM-alpha, LVNC9, TMSA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020875	7168	TPM1	http://www.ncbi.nlm.nih.gov/gene/?term=7168	"C15orf13, CMD1Y, CMH3, HEL-S-265, HTM-alpha, LVNC9, TMSA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020876	7168	TPM1	http://www.ncbi.nlm.nih.gov/gene/?term=7168	"C15orf13, CMD1Y, CMH3, HEL-S-265, HTM-alpha, LVNC9, TMSA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020877	7169	TPM2	http://www.ncbi.nlm.nih.gov/gene/?term=7169	"AMCD1, DA1, DA2B, HEL-S-273, NEM4, TMSB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020878	716	C1S	http://www.ncbi.nlm.nih.gov/gene/?term=716		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020879	716	C1S	http://www.ncbi.nlm.nih.gov/gene/?term=716		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020880	71701	Pnpt1	http://www.ncbi.nlm.nih.gov/gene/?term=71701	"1200003F12Rik, Old35, PNPase, Pnptl1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020881	71702	Cdc5l	http://www.ncbi.nlm.nih.gov/gene/?term=71702	"1200002I02Rik, AA408004, PCDC5RP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020882	71706	Slc46a3	http://www.ncbi.nlm.nih.gov/gene/?term=71706	1200006F02Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020883	7170	TPM3	http://www.ncbi.nlm.nih.gov/gene/?term=7170	"CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020884	7170	TPM3	http://www.ncbi.nlm.nih.gov/gene/?term=7170	"CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020885	7170	TPM3	http://www.ncbi.nlm.nih.gov/gene/?term=7170	"CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020886	71710	Lrrcc1	http://www.ncbi.nlm.nih.gov/gene/?term=71710	"1200008A14Rik, 4932441F23Rik, AI195358, AI447421 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020887	71711	Mus81	http://www.ncbi.nlm.nih.gov/gene/?term=71711	"1200008A18Rik, AI182501, AW045863 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020888	71713	Cdc40	http://www.ncbi.nlm.nih.gov/gene/?term=71713	"1200003H23Rik, EHB3, PRP17 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020889	71718	Telo2	http://www.ncbi.nlm.nih.gov/gene/?term=71718	"1200003M09Rik, AI415602, Tel2, mKIAA0683 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020890	7171	TPM4	http://www.ncbi.nlm.nih.gov/gene/?term=7171	HEL-S-108	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020891	7171	TPM4	http://www.ncbi.nlm.nih.gov/gene/?term=7171	HEL-S-108	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020892	7171	TPM4	http://www.ncbi.nlm.nih.gov/gene/?term=7171	HEL-S-108	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020893	71726	Smug1	http://www.ncbi.nlm.nih.gov/gene/?term=71726	"1200013B09Rik, A930006H09Rik, C85220 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020894	71728	Stk11ip	http://www.ncbi.nlm.nih.gov/gene/?term=71728	"1200014D22Rik, BB131189, LIP1, LKB1IP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020895	71729	Rgs12	http://www.ncbi.nlm.nih.gov/gene/?term=71729	"1200016K18Rik, 4632412M04Rik, AI481290, E130309H11 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020896	7172	TPMT	http://www.ncbi.nlm.nih.gov/gene/?term=7172		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020897	7172	TPMT	http://www.ncbi.nlm.nih.gov/gene/?term=7172		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020898	7172	TPMT	http://www.ncbi.nlm.nih.gov/gene/?term=7172		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020899	7172	TPMT	http://www.ncbi.nlm.nih.gov/gene/?term=7172		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020900	7172	TPMT	http://www.ncbi.nlm.nih.gov/gene/?term=7172		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020901	71745	Cul2	http://www.ncbi.nlm.nih.gov/gene/?term=71745	"1300003D18Rik, 4932411N15Rik, AI327301, mKIAA4106 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020902	7174	TPP2	http://www.ncbi.nlm.nih.gov/gene/?term=7174	"TPP-2, TPPII "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020903	7174	TPP2	http://www.ncbi.nlm.nih.gov/gene/?term=7174	"TPP-2, TPPII "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020904	7174	TPP2	http://www.ncbi.nlm.nih.gov/gene/?term=7174	"TPP-2, TPPII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020905	71753	Tmprss6	http://www.ncbi.nlm.nih.gov/gene/?term=71753	1300008A22Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020906	7175	TPR	http://www.ncbi.nlm.nih.gov/gene/?term=7175		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020907	7175	TPR	http://www.ncbi.nlm.nih.gov/gene/?term=7175		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020908	7175	TPR	http://www.ncbi.nlm.nih.gov/gene/?term=7175		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020909	71767	Tysnd1	http://www.ncbi.nlm.nih.gov/gene/?term=71767	1300019N10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020910	7178	TPT1	http://www.ncbi.nlm.nih.gov/gene/?term=7178	"HRF, TCTP, p02, p23 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020911	71791	Cpa4	http://www.ncbi.nlm.nih.gov/gene/?term=71791	"1110019K20Rik, AV009555 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020912	71795	Pitpnc1	http://www.ncbi.nlm.nih.gov/gene/?term=71795	"1110020B03Rik, 5830436L09Rik, AI662802, AI851387, C330017I21Rik, Dnr411, RDGBB, RDGBB1, rdgB-beta "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020913	71799	Ptcd1	http://www.ncbi.nlm.nih.gov/gene/?term=71799	1110069M14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020914	7179	TPTE	http://www.ncbi.nlm.nih.gov/gene/?term=7179	"CT44, PTEN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020915	717	C2	http://www.ncbi.nlm.nih.gov/gene/?term=717	"ARMD14, CO2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020916	71803	Slc25a18	http://www.ncbi.nlm.nih.gov/gene/?term=71803	"1500015I14Rik, AW125787 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020917	7180	CRISP2	http://www.ncbi.nlm.nih.gov/gene/?term=7180	"CRISP-2, CT36, GAPDL5, TPX1, TSP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020918	71811	2610027H17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71811		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020919	71817	Tmem50a	http://www.ncbi.nlm.nih.gov/gene/?term=71817	"3200001F09Rik, CAM, Smp1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020920	71819	Kif23	http://www.ncbi.nlm.nih.gov/gene/?term=71819	"3110001D19Rik, C87313, CHO1, Knsl5, MKLP-1, MKLP1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020921	7181	NR2C1	http://www.ncbi.nlm.nih.gov/gene/?term=7181	TR2	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020922	7181	NR2C1	http://www.ncbi.nlm.nih.gov/gene/?term=7181	TR2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020923	71820	Wdr34	http://www.ncbi.nlm.nih.gov/gene/?term=71820	3200002I06Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020924	71826	1700001F09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71826	Gm10377	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020925	7182	NR2C2	http://www.ncbi.nlm.nih.gov/gene/?term=7182	"TAK1, TR4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020926	71832	Csl	http://www.ncbi.nlm.nih.gov/gene/?term=71832	1700007H16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020927	71833	Dcaf7	http://www.ncbi.nlm.nih.gov/gene/?term=71833	"1700012F10Rik, 2610037L01Rik, C86529, HAN11, Wdr68 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020928	71833	Dcaf7	http://www.ncbi.nlm.nih.gov/gene/?term=71833	"1700012F10Rik, 2610037L01Rik, C86529, HAN11, Wdr68 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020929	71834	Zbtb43	http://www.ncbi.nlm.nih.gov/gene/?term=71834	"1700010E06Rik, Zfp297b, mKIAA0414 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020930	71835	Lancl2	http://www.ncbi.nlm.nih.gov/gene/?term=71835	1700003F10Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020931	71841	Tcp11x2	http://www.ncbi.nlm.nih.gov/gene/?term=71841	"1700008I05Rik, C77164, TCP11, Tcp11l3 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020932	71843	R3hcc1	http://www.ncbi.nlm.nih.gov/gene/?term=71843	"1700020M16Rik, AA407796 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020933	71846	Syce2	http://www.ncbi.nlm.nih.gov/gene/?term=71846	"1700013H19Rik, AA407907, Cesc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020934	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020935	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	12923260	Endoplasmic reticulum	T-cell line Jurkat	Northern blot	"In this report, we use multiple cell fractionation protocols, in combination with cDNA microarray, nuclease protection, and Northern blot analyses, to assess the distribution of mRNAs between free and ER-bound ribosomes. We find a broad representation of mRNAs encoding soluble proteins in the ER fraction, with a subset of such mRNAs displaying substantial ER partitioning. In addition, we present evidence that membrane-bound ribosomes engage in the translation of mRNAs encoding soluble proteins. Single-cell in situ hybridization analysis of the subcellular distribution of mRNAs encoding ER-localized and soluble proteins identify two overall patterns of mRNA distribution in the cell-endoplasmic reticular and cytosolic. FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells.  "
RLID00020936	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	12923260	Endoplasmic reticulum	Embryo	-	"These data were not unique to murine (NIH-3T3) cells; identical distribution patterns were observed in HEK293 cells, a human embryonic cell line (T. Zheng and C.V. Nicchitta, unpubl.). "
RLID00020937	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. mRNAs for resident proteins of the ER lumen, including BiP, calreticulin, and GRP94, were also highly enriched on membrane-bound polysomes. "
RLID00020938	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	18192611	Ribosome	HeLa cell	Northern blot	FIGURE 2. Subcellular mRNA distribution in SRP54 knock-down HeLa cell lines. (A) Total RNA from control HeLa (H) or SRP54 (54) stable knock-down cells was analyzed by Northern blot. (B) Cell surface expression of DR4 was determined by flow cytometry using no primary antibody (control) or DR4 antibody. (C) Cells were fractionated by sequential detergent extraction into cytosol (lane C) or membrane-bound (lane M) fractions. RNA isolated from total cells (lane T) or cell fractions was analyzed by Northern blot using the probes listed in Materials and Methods. Data are collected from Figure 2.
RLID00020939	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	21431749	Endoplasmic reticulum	HEK293 cell	Northern blot	"Similarly, Northern blot analysis of the mRNA composition of the cytosol and membrane fractions show that the cytosol fraction is enriched for mRNAs encoding histone (H3F3A) and GAPDH, whereas the membrane fraction is enriched in mRNAs encoding ER resident proteins, such as GRP94 and calreticulin (Fig. 2 B). "
RLID00020940	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00020941	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020942	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/7184	"ECGP, GP96, TRA1, GRP94, HEL35, HEL-S-125m "	mRNA	Homo sapiens	25063809	Ribosome	HeLa cell	qRT-PCR	Figure 1: Endoplasmic reticulum-associated mRNAs are partitioned between detergent-resistant and detergent-sensitive membrane domains. Data are collected from Figure 1.
RLID00020943	7184	HSP90B1	http://www.ncbi.nlm.nih.gov/gene/?term=7184	"ECGP, GP96, TRA1, GRP94, HEL35, HEL-S-125m "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00020944	71853	Pdia6	http://www.ncbi.nlm.nih.gov/gene/?term=71853	"1700015E05Rik, AL023058, C77895, CaBP5, P5, Txndc7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020945	7185	TRAF1	http://www.ncbi.nlm.nih.gov/gene/?term=7185	"EBI6, MGC:10353 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020946	71865	Fbxo30	http://www.ncbi.nlm.nih.gov/gene/?term=71865	"1700026A16Rik, MUSA1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020947	7186	TRAF2	http://www.ncbi.nlm.nih.gov/gene/?term=7186	"MGC:45012, TRAP, TRAP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020948	71870	Cfap45	http://www.ncbi.nlm.nih.gov/gene/?term=71870	"1700028D05Rik, Ccdc19, Nesg1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020949	71876	Cenpu	http://www.ncbi.nlm.nih.gov/gene/?term=71876	"1700029A22Rik, Mlf1ip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020950	7187	TRAF3	http://www.ncbi.nlm.nih.gov/gene/?term=7187	"CAP-1, CAP1, CD40bp, CRAF1, IIAE5, LAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020951	71888	Krt33a	http://www.ncbi.nlm.nih.gov/gene/?term=71888	2310015J09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020952	71889	Epn3	http://www.ncbi.nlm.nih.gov/gene/?term=71889	2310022G12Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020953	7188	TRAF5	http://www.ncbi.nlm.nih.gov/gene/?term=7188	"MGC:39780, RNF84 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020954	71891	Cdadc1	http://www.ncbi.nlm.nih.gov/gene/?term=71891	"2310010M10Rik, AI449174, AI463398, BB130816, NYD-SP15 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020955	7189	TRAF6	http://www.ncbi.nlm.nih.gov/gene/?term=7189	"MGC:3310, RNF85 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020956	71900	Tmem106b	http://www.ncbi.nlm.nih.gov/gene/?term=71900	"2310036D22Rik, 5830455K21Rik, 6430519M21Rik, AI428776, AI661344 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020957	71901	Fam219a	http://www.ncbi.nlm.nih.gov/gene/?term=71901	2310028H24Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020958	71902	Cand1	http://www.ncbi.nlm.nih.gov/gene/?term=71902	"2310038O07Rik, 6330512O03Rik, AI195005, AI846556, D10Ertd516e, Tp120a, mKIAA0829 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020959	71903	Ces2f	http://www.ncbi.nlm.nih.gov/gene/?term=71903	"2310038E17Rik, A430088E12 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020960	71914	Antxr2	http://www.ncbi.nlm.nih.gov/gene/?term=71914	"2310046B19Rik, AW561899, CMG-2, CMG2, cI-35 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020961	71916	Dus4l	http://www.ncbi.nlm.nih.gov/gene/?term=71916	"2310069P03Rik, 2700089B10Rik, AI482040, Pp35 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020962	71919	Rpap3	http://www.ncbi.nlm.nih.gov/gene/?term=71919	"2310042P20Rik, D15Ertd682e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020963	71920	Epgn	http://www.ncbi.nlm.nih.gov/gene/?term=71920	"2310069M11Rik, epigen "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020964	71921	2310058N22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71921		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020965	71923	Borcs6	http://www.ncbi.nlm.nih.gov/gene/?term=71923	2310047M10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020966	71924	Tube1	http://www.ncbi.nlm.nih.gov/gene/?term=71924	"2310061K05Rik, AI551343, Tube "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020967	71927	Itfg1	http://www.ncbi.nlm.nih.gov/gene/?term=71927	"2310047C21Rik, AI314457, Cda08, D8Wsu49e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020968	71929	Tmem123	http://www.ncbi.nlm.nih.gov/gene/?term=71929	2310075C12Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020969	71934	Car13	http://www.ncbi.nlm.nih.gov/gene/?term=71934	"2310075C21Rik, Ca13 "	mRNA	Mus musculus	20820888	Cytosol	Gland tissue	qRT-PCR	"In the present study, we examined the mRNA expression of all 13 enzymatically active CA isozymes by qRT-PCR in the mouse harderian gland. As shown in Fig. 1, nine of the 13 isozymes were detected in the harderian gland tissue at the mRNA level. Four isoforms were cytosolic (Car2, Car3, Car7, and Car13), three were membrane-associated (Car4, Car12, and Car15), one was mitochondrial (Car5b), and one was secreted (Car6). "
RLID00020970	71946	Endod1	http://www.ncbi.nlm.nih.gov/gene/?term=71946	"2210414F18Rik, 2310067E08Rik, C85344 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020971	71952	2410016O06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=71952	"MAPJD, NO66 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020972	71956	Rnf135	http://www.ncbi.nlm.nih.gov/gene/?term=71956	"0610037N03Rik, 2410006N06Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020973	71960	Myh14	http://www.ncbi.nlm.nih.gov/gene/?term=71960	"2400004E04Rik, II-C, NHMCII, NMHC II-C "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020974	71962	Gatsl3	http://www.ncbi.nlm.nih.gov/gene/?term=71962	2410008K03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020975	71963	Cdca4	http://www.ncbi.nlm.nih.gov/gene/?term=71963	"2410018C03Rik, HEPP, SEI-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020976	71966	Nkiras2	http://www.ncbi.nlm.nih.gov/gene/?term=71966	"2410003M04Rik, 4930527H08Rik, D630018G21Rik, KBRAS2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020977	71971	Zswim1	http://www.ncbi.nlm.nih.gov/gene/?term=71971	"2410003H12Rik, AI850991, BB046916 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020978	71972	Dnmbp	http://www.ncbi.nlm.nih.gov/gene/?term=71972	"2410003L07Rik, 2410003M15Rik, TUBA "	mRNA	Mus musculus	22817891	Cytoplasm	Bone marrow Macrophage	Next-generation sequencing	"Cluster 11, by contrast, contains abundant cytoplasmic transcripts, with fewer transcripts in the chromatin and nucleoplasm. This cluster includes genes that are likely to encode highly stable mRNAs, such as Actb (beta-actin) and Tuba (alpha-tubulin). "
RLID00020979	71981	Tdrd12	http://www.ncbi.nlm.nih.gov/gene/?term=71981	"2410004F06Rik, 2410070K17Rik, ECAT8, EG434165, G1-476-14, repro23 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020980	71983	Tmco6	http://www.ncbi.nlm.nih.gov/gene/?term=71983	2410015B03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020981	71984	Sars2	http://www.ncbi.nlm.nih.gov/gene/?term=71984	"2410015F05Rik, D7Ertd353e, SerRS, SerRSmt "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020982	71985	Acad10	http://www.ncbi.nlm.nih.gov/gene/?term=71985	2410021P16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020983	71988	Esco2	http://www.ncbi.nlm.nih.gov/gene/?term=71988	"2410004I17Rik, D030072L07Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020984	71	ACTG1	http://www.ncbi.nlm.nih.gov/gene/?term=71	"ACT, ACTG, BRWS2, DFNA20, DFNA26, HEL-176 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020985	71	ACTG1	http://www.ncbi.nlm.nih.gov/gene/?term=71	"ACT, ACTG, BRWS2, DFNA20, DFNA26, HEL-176 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020986	71	ACTG1	http://www.ncbi.nlm.nih.gov/gene/?term=71	"ACT, ACTG, BRWS2, DFNA20, DFNA26, HEL-176 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00020987	72007	Fndc3b	http://www.ncbi.nlm.nih.gov/gene/?term=72007	"1600019O04Rik, AW550168, Fad104, mKIAA4164 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020988	7200	TRH	http://www.ncbi.nlm.nih.gov/gene/?term=7200	"Pro-TRH, TRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00020989	72012	1600020E01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72012		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020990	72020	Zfp654	http://www.ncbi.nlm.nih.gov/gene/?term=72020	"1600021C16Rik, 1810008K20Rik, Znf654 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020991	72033	Tsc22d2	http://www.ncbi.nlm.nih.gov/gene/?term=72033	"1810043J12Rik, 5530402M19Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020992	72039	Mccc1	http://www.ncbi.nlm.nih.gov/gene/?term=72039	"1810045E08Rik, 2310058B18Rik, MCCalpha, Mcca, R75106 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020993	7203	CCT3	http://www.ncbi.nlm.nih.gov/gene/?term=7203	"CCT-gamma, CCTG, PIG48, TCP-1-gamma, TRIC5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020994	72042	Cotl1	http://www.ncbi.nlm.nih.gov/gene/?term=72042	"1810074P22Rik, 2010004C08Rik, Clp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020995	72047	Ddx42	http://www.ncbi.nlm.nih.gov/gene/?term=72047	"1810047H21Rik, AW319508, AW556242, B430002H05Rik, RHELP, RNAHP, SF3b125 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020996	72047	Ddx42	http://www.ncbi.nlm.nih.gov/gene/?term=72047	"1810047H21Rik, AW319508, AW556242, B430002H05Rik, RHELP, RNAHP, SF3b125 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00020997	7204	TRIO	http://www.ncbi.nlm.nih.gov/gene/?term=7204	"ARHGEF23, tgat "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00020998	72050	Kdelc1	http://www.ncbi.nlm.nih.gov/gene/?term=72050	"1810049A15Rik, 5730416C13Rik, EP58, Kdel1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00020999	7205	TRIP6	http://www.ncbi.nlm.nih.gov/gene/?term=7205	"OIP-1, OIP1, TRIP-6i2, ZRP-1, TRIP6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021000	7205	TRIP6	http://www.ncbi.nlm.nih.gov/gene/?term=7205	"OIP-1, OIP1, TRIP-6, TRIP6i2, ZRP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021001	72061	2010111I01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72061	"2300006M17Rik, AP-O, Aopep, mir-23b, mir-24-1, mir-27b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021002	72065	Rap2c	http://www.ncbi.nlm.nih.gov/gene/?term=72065	"2010200P20Rik, AI194294, AL022976 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021003	72068	Cnot2	http://www.ncbi.nlm.nih.gov/gene/?term=72068	"2600016M12Rik, 2810470K03Rik, AA537049, AA959607, AW557563, C79650 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021004	7206	TRK-TTT3-5	http://www.ncbi.nlm.nih.gov/gene/?term=7206	"TRK-TTT3-4, TRK1, TRNAK1 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00021005	7206	TRK-TTT3-5	http://www.ncbi.nlm.nih.gov/gene/?term=7206	"TRK-TTT3-4, TRK1, TRNAK1 "	tRNA	Homo sapiens	25690653	Cytoplasm	P493-6 cell	qRT-PCR	"To validate the isolation of nuclear and cytoplasmic fractions, the enrichment of 3 nuclear (ANRIL, MIAT, XIST) and 3 cytoplasmic (RPPH1, DANCR, tRNA-Lys) RNAs was analyzed by qRT-PCR. "
RLID00021006	72074	Anks4b	http://www.ncbi.nlm.nih.gov/gene/?term=72074	"2010013E14Rik, AI956809, Harp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021007	72083	Mzt2	http://www.ncbi.nlm.nih.gov/gene/?term=72083	"2410018G20Rik, 2610001E06Rik, Fam128, Fam128b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021008	72085	Osgepl1	http://www.ncbi.nlm.nih.gov/gene/?term=72085	"2610001M19Rik, AA416452 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021009	72087	2010015M23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72087		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021010	72091	Snhg7	http://www.ncbi.nlm.nih.gov/gene/?term=72091	"2610002F03Rik, AI427062 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021011	72096	Mettl10	http://www.ncbi.nlm.nih.gov/gene/?term=72096	2010208K18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021012	72098	Tmem68	http://www.ncbi.nlm.nih.gov/gene/?term=72098	"2010300G19Rik, AA408325, AW123402 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021013	720	C4A	http://www.ncbi.nlm.nih.gov/gene/?term=720	"C4, C4A2, C4A3, C4A4, C4A6, C4AD, C4S, CO4, CPAMD2, RG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021014	72107	Dscc1	http://www.ncbi.nlm.nih.gov/gene/?term=72107	"2010006I05Rik, 2600005O03Rik, Dcc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021015	7210	TRX-CAT1-2	http://www.ncbi.nlm.nih.gov/gene/?term=7210	"RNTMI1, RNTMI2, RNTMT1, TRM1, TRM2, TRMI2, TRNAM1, TRNAMI2, TRX-CAT1-3 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00021016	72117	Naa50	http://www.ncbi.nlm.nih.gov/gene/?term=72117	"2600005K24Rik, 2810441M03Rik, AW112078, Mak3, Mak3p, Nat13, Nat5, San "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021017	72123	Ccdc71l	http://www.ncbi.nlm.nih.gov/gene/?term=72123	"2010109K11Rik, AV375874 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021018	72124	Seh1l	http://www.ncbi.nlm.nih.gov/gene/?term=72124	"2610007A16Rik, AW540070, SEC13L, SEH1A, SEH1B, Seh1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021019	72124	Seh1l	http://www.ncbi.nlm.nih.gov/gene/?term=72124	"2610007A16Rik, AW540070, SEC13L, SEH1A, SEH1B, Seh1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021020	72129	Pex13	http://www.ncbi.nlm.nih.gov/gene/?term=72129	2610008O20Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021021	72131	2010310C07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72131		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021022	72133	Trub1	http://www.ncbi.nlm.nih.gov/gene/?term=72133	"2610009I02Rik, 9030425C13Rik, AI448235, BB118943, C76870 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021023	72144	Slc37a3	http://www.ncbi.nlm.nih.gov/gene/?term=72144	"2610507O21Rik, AU044904 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021024	72148	Tdrp	http://www.ncbi.nlm.nih.gov/gene/?term=72148	2610019F03Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021025	72154	Zfp157	http://www.ncbi.nlm.nih.gov/gene/?term=72154	"2610020C11Rik, A630094N24Rik, AI327407, mszf12, mszf23-1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021026	72155	Cenpn	http://www.ncbi.nlm.nih.gov/gene/?term=72155	"2610510J17Rik, AI426416, AW545024 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021027	72175	Mfsd8	http://www.ncbi.nlm.nih.gov/gene/?term=72175	"2810423E13Rik, AI836898, AV142426, Cln7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021028	72183	Snx6	http://www.ncbi.nlm.nih.gov/gene/?term=72183	"2010006G21Rik, 2610032J07Rik, 2810425K19Rik, AU018928, C85963 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021029	72185	Dbndd1	http://www.ncbi.nlm.nih.gov/gene/?term=72185	"2810427I04Rik, D8Ertd590e "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021030	72193	Scaf11	http://www.ncbi.nlm.nih.gov/gene/?term=72193	"1110061H03Rik, 2610510E10Rik, AI462454, CASP11, SIP1, SRRP129, Sfrs2ip, Srsf2ip, mKIAA3013 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021031	72194	Fbxl20	http://www.ncbi.nlm.nih.gov/gene/?term=72194	"2610511F20Rik, 4632423N09Rik, AI849362, AL117906, C86145, Fbl2, Scr, mKIAA4147 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021032	72198	Skiv2l2	http://www.ncbi.nlm.nih.gov/gene/?term=72198	"2610528A15Rik, mKIAA0052 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021033	72207	1700003K11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72207		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021034	7220	TRPC1	http://www.ncbi.nlm.nih.gov/gene/?term=7220	"HTRP-1, TRP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021035	7220	TRPC1	http://www.ncbi.nlm.nih.gov/gene/?term=7220	"HTRP-1, TRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021036	72229	1700003G13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72229		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021037	72242	Psg21	http://www.ncbi.nlm.nih.gov/gene/?term=72242	"1600019C01Rik, 1600025N01Rik, 1600026N13Rik, cea8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021038	72245	1700018M17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72245		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021039	72246	1700030C12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72246	ENSMUSG00000073112	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021040	72258	Kcnk10	http://www.ncbi.nlm.nih.gov/gene/?term=72258	"1700024D23Rik, 3010005K24Rik, Trek2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021041	72265	Tram1	http://www.ncbi.nlm.nih.gov/gene/?term=72265	"1810049E02Rik, TRAMP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021042	72269	Cda	http://www.ncbi.nlm.nih.gov/gene/?term=72269	2210401N16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021043	7226	TRPM2	http://www.ncbi.nlm.nih.gov/gene/?term=7226	"EREG1, KNP3, LTRPC2, LTrpC-2, NUDT9H, NUDT9L1, TRPC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021044	72278	Ccpg1	http://www.ncbi.nlm.nih.gov/gene/?term=72278	"1700030B06Rik, 1810073J13Rik, 9430028F23Rik, AI426686, AI875170, CPR8, D9Ertd392e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021045	7227	TRPS1	http://www.ncbi.nlm.nih.gov/gene/?term=7227	"GC79, LGCR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021046	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	17270048	Nucleus	Liver cell	In situ hybridization	"In both the BLK CL.4 cell line and mouse liver, both Neat1 and Neat2/Malat-1 were both more than ten-fold enriched in nuclear fractions (Table ?(Table1).1) "
RLID00021047	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	20729808	Nucleus	Bone osteosarcoma epithelial cell	Microarray	Malat1 RNA is expressed in numerous tissues and is highly abundant in neurons. It is enriched in nuclear speckles only when RNA polymerase II-dependent transcription is active. 
RLID00021048	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	22817891	Nucleus	Bone marrow Macrophage	Next-generation sequencing	"Cluster 7, for example, contains abundant transcripts in the chromatin, with much lower transcript levels in the nucleoplasm and cytoplasm relative to the other clusters. This cluster is dominated by annotated and unannotated non-coding transcripts and miRNA precursors. (The analysis excluded transcripts shorter than 400 nucleotides and therefore excluded mature miRNAs and many miRNA precursors.) Some non-coding RNAs, such as Xist, are highly enriched in the chromatin because they function at this location (Figure S2). Examples of other non-coding RNAs in Cluster 7 are Neat1 and Malat1/Neat2 (Figure S2). Further mining of the data sets may provide insights into the subcellular locations at which many non-coding RNAs function. Cluster 7 also includes transcripts from constitutive protein-coding genes that may be highly unstable and therefore present at low levels in the cytoplasm (e.g. Leng8 in Figure S2). "
RLID00021049	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021050	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021051	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	22718948	Nucleus	Embryotem cell	In situ hybridization|Northern blot|qRT-PCR	"Malat1 localizes to one type of these nuclear bodies, known as nuclear speckles, which contain various pre-mRNA splicing regulators, including uridine-rich small nuclear RNA-protein complexes (UsnRNPs) and the serine- and arginine-rich (SR) family of splicing factors, which are involved in exon recognition and alternative splicing (for review, see Hall et al. 2006; Spector and Lamond 2011). "
RLID00021052	72289	Malat1	http://www.ncbi.nlm.nih.gov/gene/?term=72289	"2210401K01Rik, 9430072K23Rik, AI647968, Neat2 "	lncRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"We then analyzed the abundance of several lncRNAs, namely Malat1, Meg3, Rmst, Xist and Miat. All of these lncRNAs were present in the axonal compartment.  "
RLID00021053	722	C4BPA	http://www.ncbi.nlm.nih.gov/gene/?term=722	"C4BP, PRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021054	72301	1810041L15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72301	Kiaa1644	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021055	72313	Fryl	http://www.ncbi.nlm.nih.gov/gene/?term=72313	"2010313D22Rik, 2310004H21Rik, 2510002A14Rik, 9030227G01Rik, mKIAA0826 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021056	72313	Fryl	http://www.ncbi.nlm.nih.gov/gene/?term=72313	"2010313D22Rik, 2310004H21Rik, 2510002A14Rik, 9030227G01Rik, mKIAA0826 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021057	7231	TRR-ACG1-2	http://www.ncbi.nlm.nih.gov/gene/?term=7231	"TRNAR2, TRR-ACG1-3, TRR2 "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00021058	72323	Asb6	http://www.ncbi.nlm.nih.gov/gene/?term=72323	"2510004M11Rik, AA409356 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021059	72333	Palld	http://www.ncbi.nlm.nih.gov/gene/?term=72333	"2410003B16Rik, 6030492A02 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021060	72333	Palld	http://www.ncbi.nlm.nih.gov/gene/?term=72333	"2410003B16Rik, 6030492A02 "	mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00021061	72341	Elp6	http://www.ncbi.nlm.nih.gov/gene/?term=72341	"2610001P13Rik, 2610002I17Rik, AV159994, Tmem103 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021062	72343	2600002B07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72343	AI586157	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021063	72344	Usp36	http://www.ncbi.nlm.nih.gov/gene/?term=72344	"2700002L06Rik, mKIAA1453 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021064	72349	Dusp3	http://www.ncbi.nlm.nih.gov/gene/?term=72349	"2210015O03Rik, 5031436O03Rik, T-DSP11, VHR "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021065	7234	TRU-TCA1-1	http://www.ncbi.nlm.nih.gov/gene/?term=7234	"TRNAU1, TRSP, tRNA(Sec) "	tRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00021066	72357	2210016L21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72357		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021067	72399	Brap	http://www.ncbi.nlm.nih.gov/gene/?term=72399	"3010002G07Rik, BRAP2, IMP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021068	72415	Sgol1	http://www.ncbi.nlm.nih.gov/gene/?term=72415	"3300001M08Rik, C81037, Sgo1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021069	72429	Dnajc25	http://www.ncbi.nlm.nih.gov/gene/?term=72429	"2010109C08Rik, 2010203O07Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021070	72433	Rab38	http://www.ncbi.nlm.nih.gov/gene/?term=72433	"2310011F14Rik, AU043391, cht "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021071	72454	Ccdc71	http://www.ncbi.nlm.nih.gov/gene/?term=72454	2600016J21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021072	72459	Htatsf1	http://www.ncbi.nlm.nih.gov/gene/?term=72459	"1600023H17Rik, 2600017A12Rik, 2700077B20Rik, TAT-SF1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021073	72462	Rrp1b	http://www.ncbi.nlm.nih.gov/gene/?term=72462	"2600005C20Rik, D030064A17, Kiaa0179, mKIAA0179 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021074	72477	Tmem87b	http://www.ncbi.nlm.nih.gov/gene/?term=72477	"2610301K12Rik, 2810431I02Rik, AU014804 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021075	7247	TSN	http://www.ncbi.nlm.nih.gov/gene/?term=7247	"BCLF-1, C3PO, RCHF1, REHF-1, TBRBP, TRSLN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021076	7247	TSN	http://www.ncbi.nlm.nih.gov/gene/?term=7247	"BCLF-1, C3PO, RCHF1, REHF-1, TBRBP, TRSLN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021077	7247	TSN	http://www.ncbi.nlm.nih.gov/gene/?term=7247	"BCLF-1, C3PO, RCHF1, REHF-1, TBRBP, TRSLN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021078	72480	Tspyl4	http://www.ncbi.nlm.nih.gov/gene/?term=72480	"2610102M01Rik, B230210I21Rik, D10Bwg0791e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021079	72482	Acbd6	http://www.ncbi.nlm.nih.gov/gene/?term=72482	"0610010G04Rik, 2610100E10Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021080	7248	TSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7248	"LAM, TSC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021081	72493	2610202C22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72493		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021082	7249	TSC2	http://www.ncbi.nlm.nih.gov/gene/?term=7249	"LAM, PPP1R160, TSC4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021083	72504	Taf4b	http://www.ncbi.nlm.nih.gov/gene/?term=72504	"105kDa, 2610524B04Rik, 4932409F03Rik, AW987595, TAFII-105, TAFII105, Taf2c2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021084	72511	2610316D01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72511		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021085	72515	Wdr43	http://www.ncbi.nlm.nih.gov/gene/?term=72515	"2610318G08Rik, AU020887, AV024208, Wrd43, mKIAA0007 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021086	7251	TSG101	http://www.ncbi.nlm.nih.gov/gene/?term=7251	"TSG10, VPS23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021087	7251	TSG101	http://www.ncbi.nlm.nih.gov/gene/?term=7251	"TSG10, VPS23 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021088	7251	TSG101	http://www.ncbi.nlm.nih.gov/gene/?term=7251	"TSG10, VPS23 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021089	72535	Aldh1b1	http://www.ncbi.nlm.nih.gov/gene/?term=72535	2700007F14Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021090	72539	2700008E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72539		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021091	72545	2700008G24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72545		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021092	72560	Naalad2	http://www.ncbi.nlm.nih.gov/gene/?term=72560	"2700022G20Rik, D9Ertd285e, Folh1b, GCP3, GCPIII, NAADALASE2, NAALADASE2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021093	72567	Bclaf1	http://www.ncbi.nlm.nih.gov/gene/?term=72567	"2610102K23Rik, 2700025J07Rik, 2810454G14Rik, 5730534O06Rik, AI450190, AW556225, Btf, mKIAA0164 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021094	72568	Lin9	http://www.ncbi.nlm.nih.gov/gene/?term=72568	"2700022J23Rik, Bara, Lin-9, TGS, TGS1, mLin-9 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021095	72569	Bbs5	http://www.ncbi.nlm.nih.gov/gene/?term=72569	"1700049I01Rik, 2700023J09Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021096	7257	TSNAX	http://www.ncbi.nlm.nih.gov/gene/?term=7257	TRAX	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021097	7257	TSNAX	http://www.ncbi.nlm.nih.gov/gene/?term=7257	TRAX	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021098	72584	Cul4b	http://www.ncbi.nlm.nih.gov/gene/?term=72584	"2700050M05Rik, AA409770, CUL-4B, mKIAA0695 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021099	72585	Lypd1	http://www.ncbi.nlm.nih.gov/gene/?term=72585	"2700050C12Rik, AI853408, C530008O16Rik, Lynx2, Lypdc1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021100	72599	Pdia5	http://www.ncbi.nlm.nih.gov/gene/?term=72599	"2700053F16Rik, AU015525, Pdir "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021101	7259	TSPYL1	http://www.ncbi.nlm.nih.gov/gene/?term=7259	TSPYL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021102	7259	TSPYL1	http://www.ncbi.nlm.nih.gov/gene/?term=7259	TSPYL	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021103	7259	TSPYL1	http://www.ncbi.nlm.nih.gov/gene/?term=7259	TSPYL	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021104	7259	TSPYL1	http://www.ncbi.nlm.nih.gov/gene/?term=7259	TSPYL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021105	72605	Car10	http://www.ncbi.nlm.nih.gov/gene/?term=72605	"2700029L05Rik, BB085816, Ca10 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021106	72607	Usp13	http://www.ncbi.nlm.nih.gov/gene/?term=72607	"2700071E21Rik, AI848077, ISOT3, IsoT-3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021107	7260	TSSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7260		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021108	7260	TSSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7260		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021109	72611	Zfp655	http://www.ncbi.nlm.nih.gov/gene/?term=72611	"2700038I16Rik, 9030409O18Rik, mKIAA4222 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021110	72612	2700029M09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72612	C230006B22Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021111	72621	Pdzd11	http://www.ncbi.nlm.nih.gov/gene/?term=72621	"1810012H22Rik, 2310079D11Rik, 2700099C19Rik, AI854765, Pdzk11 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021112	7262	PHLDA2	http://www.ncbi.nlm.nih.gov/gene/?term=7262	"BRW1C, BWR1C, HLDA2, IPL, TSSC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021113	7262	PHLDA2	http://www.ncbi.nlm.nih.gov/gene/?term=7262	"BRW1C, BWR1C, HLDA2, IPL, TSSC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021114	72634	Tdrkh	http://www.ncbi.nlm.nih.gov/gene/?term=72634	"2700091C21Rik, Tdrd2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021115	7263	TST	http://www.ncbi.nlm.nih.gov/gene/?term=7263	RDS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021116	7263	TST	http://www.ncbi.nlm.nih.gov/gene/?term=7263	RDS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021117	72649	Tmem209	http://www.ncbi.nlm.nih.gov/gene/?term=72649	"2700094F01Rik, AI428435 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021118	7264	TSTA3	http://www.ncbi.nlm.nih.gov/gene/?term=7264	"FX, P35B, SDR4E1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021119	7264	TSTA3	http://www.ncbi.nlm.nih.gov/gene/?term=7264	"FX, P35B, SDR4E1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021120	72650	2810006K23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72650		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021121	72654	Ccdc12	http://www.ncbi.nlm.nih.gov/gene/?term=72654	"2700094L05Rik, C76605 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021122	72655	Snhg5	http://www.ncbi.nlm.nih.gov/gene/?term=72655	"2810026P18Rik, 4933428I09Rik, mU50HG-b "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021123	72656	Ints8	http://www.ncbi.nlm.nih.gov/gene/?term=72656	"2810013E07Rik, AV063769, D130008D20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021124	72658	2700097O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72658	AW552125	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021125	7265	TTC1	http://www.ncbi.nlm.nih.gov/gene/?term=7265	TPR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021126	7265	TTC1	http://www.ncbi.nlm.nih.gov/gene/?term=7265	TPR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021127	72662	Dis3	http://www.ncbi.nlm.nih.gov/gene/?term=72662	2810028N01Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021128	72666	2810047J09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72666		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021129	72667	Zfp444	http://www.ncbi.nlm.nih.gov/gene/?term=72667	"2810031J10Rik, 6230401O10Rik, mFLJ00134 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021130	72669	2810032G03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72669	AI461720	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021131	7266	DNAJC7	http://www.ncbi.nlm.nih.gov/gene/?term=7266	"DJ11, DJC7, TPR2, TTC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021132	72674	Adipor1	http://www.ncbi.nlm.nih.gov/gene/?term=72674	"2810031L11Rik, ACDCR1, CGI-45, Paqr1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021133	7267	TTC3	http://www.ncbi.nlm.nih.gov/gene/?term=7267	"DCRR1, RNF105, TPRDIII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021134	72692	Hnrnpll	http://www.ncbi.nlm.nih.gov/gene/?term=72692	"2510028H02Rik, 2810036L13Rik, AI256697, AI852082, Hnrpll "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021135	72697	2810043O03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72697		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021136	72699	Lime1	http://www.ncbi.nlm.nih.gov/gene/?term=72699	"2810038K19Rik, LIME "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021137	726	CAPN5	http://www.ncbi.nlm.nih.gov/gene/?term=726	"ADNIV, HTRA3, VRNI, nCL-3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021138	72713	Angptl1	http://www.ncbi.nlm.nih.gov/gene/?term=72713	"2810039D03Rik, ANG3, ANGPT3, ANGY, ARP1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021139	72716	2810047C21Rik1	http://www.ncbi.nlm.nih.gov/gene/?term=72716	"100042870, 2810047C21Rik, AA683836, Gm4082 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021140	72720	Zfp248	http://www.ncbi.nlm.nih.gov/gene/?term=72720	"2810037F07Rik, E130106N01Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021141	72723	Zfp74	http://www.ncbi.nlm.nih.gov/gene/?term=72723	"2810054M15Rik, KRAB8, Zfp66, Znf569, mszf21, mszf77 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021142	72727	B3gat3	http://www.ncbi.nlm.nih.gov/gene/?term=72727	2810405M13Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021143	72735	Eldr	http://www.ncbi.nlm.nih.gov/gene/?term=72735	"2810442I21Rik, 4930500E12Rik, Fabl "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021144	72739	Zkscan3	http://www.ncbi.nlm.nih.gov/gene/?term=72739	"2810435N07Rik, AA408594, AI132359, Skz1, Zf47, Zfp-47, Zfp306, Zfp307, mszf35 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021145	7273	TTN	http://www.ncbi.nlm.nih.gov/gene/?term=7273	"CMD1G, CMH9, CMPD4, EOMFC, HMERF, LGMD2J, MYLK5, TMD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021146	7273	TTN	http://www.ncbi.nlm.nih.gov/gene/?term=7273	"CMD1G, CMH9, CMPD4, EOMFC, HMERF, LGMD2J, MYLK5, TMD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021147	72745	Tmem161b	http://www.ncbi.nlm.nih.gov/gene/?term=72745	"2810446P07Rik, AI843389 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021148	72748	Hdhd3	http://www.ncbi.nlm.nih.gov/gene/?term=72748	2810435D12Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021149	72759	Tmem135	http://www.ncbi.nlm.nih.gov/gene/?term=72759	"2810439K08Rik, AW319712, PMP52 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021150	727676	SNORD118	http://www.ncbi.nlm.nih.gov/gene/?term=727676	U8	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00021151	727676	SNORD118	http://www.ncbi.nlm.nih.gov/gene/?term=727676	U8	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021152	727676	SNORD118	http://www.ncbi.nlm.nih.gov/gene/?term=727676	U8	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021153	72772	Rint1	http://www.ncbi.nlm.nih.gov/gene/?term=72772	"1500019C06Rik, 2810450M21Rik, Rint-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021154	72775	Fance	http://www.ncbi.nlm.nih.gov/gene/?term=72775	"2810451D06Rik, AI415634, AW209126 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021155	7277	TUBA4A	http://www.ncbi.nlm.nih.gov/gene/?term=7277	"ALS22, H2-ALPHA, TUBA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021156	7277	TUBA4A	http://www.ncbi.nlm.nih.gov/gene/?term=7277	"ALS22, H2-ALPHA, TUBA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021157	72787	Ndc1	http://www.ncbi.nlm.nih.gov/gene/?term=72787	"2810475A17Rik, AI450313, Tmem48, sks "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021158	727897	MUC5B	http://www.ncbi.nlm.nih.gov/gene/?term=727897	"MG1, MUC-5B, MUC5, MUC9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021159	727940	RHOXF2B	http://www.ncbi.nlm.nih.gov/gene/?term=727940		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021160	72801	2810488O17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72801		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021161	7280	TUBB2A	http://www.ncbi.nlm.nih.gov/gene/?term=7280	"CDCBM5, TUBB, TUBB2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021162	72820	2810461L16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72820		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021163	72825	Mon1a	http://www.ncbi.nlm.nih.gov/gene/?term=72825	2810468K17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021164	72826	Fam76b	http://www.ncbi.nlm.nih.gov/gene/?term=72826	"2810485I05Rik, C78303 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021165	72828	Ubash3b	http://www.ncbi.nlm.nih.gov/gene/?term=72828	"2810457I06Rik, BB125008, TULA-2, p70 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021166	728294	D2HGDH	http://www.ncbi.nlm.nih.gov/gene/?term=728294	D2HGD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021167	7283	TUBG1	http://www.ncbi.nlm.nih.gov/gene/?term=7283	"CDCBM4, GCP-1, TUBG, TUBGCP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021168	7283	TUBG1	http://www.ncbi.nlm.nih.gov/gene/?term=7283	"CDCBM4, GCP-1, TUBG, TUBGCP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021169	7283	TUBG1	http://www.ncbi.nlm.nih.gov/gene/?term=7283	"CDCBM4, GCP-1, TUBG, TUBGCP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021170	728409	LINC01548	http://www.ncbi.nlm.nih.gov/gene/?term=728409	C21orf54	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00021171	728448	PPIEL	http://www.ncbi.nlm.nih.gov/gene/?term=728448	PPIEP1	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021172	728464	METTL24	http://www.ncbi.nlm.nih.gov/gene/?term=728464	"C6orf186, dJ71D21.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021173	728464	METTL24	http://www.ncbi.nlm.nih.gov/gene/?term=728464	"C6orf186, dJ71D21.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021174	728492	SERF1B	http://www.ncbi.nlm.nih.gov/gene/?term=728492	"FAM2B, H4F5C, h4F5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021175	728492	SERF1B	http://www.ncbi.nlm.nih.gov/gene/?term=728492	"FAM2B, H4F5C, h4F5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021176	728492	SERF1B	http://www.ncbi.nlm.nih.gov/gene/?term=728492	"FAM2B, H4F5C, h4F5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021177	728492	SERF1B	http://www.ncbi.nlm.nih.gov/gene/?term=728492	"FAM2B, H4F5C, h4F5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021178	7284	TUFM	http://www.ncbi.nlm.nih.gov/gene/?term=7284	"COXPD4, EF-TuMT, EFTU, P43 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021179	728509	RPS19P7	http://www.ncbi.nlm.nih.gov/gene/?term=728509	RPS19_3_1038	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021180	728568	C12orf73	http://www.ncbi.nlm.nih.gov/gene/?term=728568		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021181	728577	CNTNAP3B	http://www.ncbi.nlm.nih.gov/gene/?term=728577		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021182	728609	SDHAP3	http://www.ncbi.nlm.nih.gov/gene/?term=728609	"SDHACL, SDHAL "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021183	728621	CCDC30	http://www.ncbi.nlm.nih.gov/gene/?term=728621	"PFD6L, PFDN6L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021184	728621	CCDC30	http://www.ncbi.nlm.nih.gov/gene/?term=728621	"PFD6L, PFDN6L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021185	728655	HULC	http://www.ncbi.nlm.nih.gov/gene/?term=728655	"HCCAT1, LINC00078, NCRNA00078 "	lncRNA	Homo sapiens	17241883	Cytoplasm	Hepatoma cell	qRT-PCR|Next generation sequencing	"HULC is present in the cytoplasm, where it copurifies with ribosomes. siRNA-mediated knockdown of HULC RNA in 2 HCC cell lines altered the expression of several genes, 5 of which were known to be affected in HCC, suggesting a role for HULC in post-transcriptional modulation of gene expression. "
RLID00021186	728655	HULC	http://www.ncbi.nlm.nih.gov/gene/?term=728655	"HCCAT1, LINC00078, NCRNA00078 "	lncRNA	Homo sapiens	25332394	Cytoplasm	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/HULC/
RLID00021187	72865	Cxx1c	http://www.ncbi.nlm.nih.gov/gene/?term=72865	"2900027G03Rik, Mar8.1, Mart8a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021188	728661	SLC35E2B	http://www.ncbi.nlm.nih.gov/gene/?term=728661	SLC35E2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021189	728661	SLC35E2B	http://www.ncbi.nlm.nih.gov/gene/?term=728661	SLC35E2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021190	728689	EIF3CL	http://www.ncbi.nlm.nih.gov/gene/?term=728689		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021191	728689	EIF3CL	http://www.ncbi.nlm.nih.gov/gene/?term=728689		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021192	7286	TUFT1	http://www.ncbi.nlm.nih.gov/gene/?term=7286		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021193	7286	TUFT1	http://www.ncbi.nlm.nih.gov/gene/?term=7286		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021194	7286	TUFT1	http://www.ncbi.nlm.nih.gov/gene/?term=7286		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021195	72873	Bbof1	http://www.ncbi.nlm.nih.gov/gene/?term=72873	"2900006K08Rik, AI427784, Ccdc176 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021196	728819	C1GALT1C1L	http://www.ncbi.nlm.nih.gov/gene/?term=728819		mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00021197	728819	C1GALT1C1L	http://www.ncbi.nlm.nih.gov/gene/?term=728819		mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00021198	728841	NBPF8	http://www.ncbi.nlm.nih.gov/gene/?term=728841	NBPF8P	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021199	72892	2900018K06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72892		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021200	728953	RPS19P3	http://www.ncbi.nlm.nih.gov/gene/?term=728953	RPS19_4_1350	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021201	72895	Setd5	http://www.ncbi.nlm.nih.gov/gene/?term=72895	"2900045N06Rik, C330007C20, C85544, mKIAA1757 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021202	7289	TULP3	http://www.ncbi.nlm.nih.gov/gene/?term=7289	TUBL3	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021203	729082	OIP5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=729082	cyrano	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021204	7290	HIRA	http://www.ncbi.nlm.nih.gov/gene/?term=7290	"DGCR1, TUP1, TUPLE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021205	72915	2900017F05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72915		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021206	729359	PLIN4	http://www.ncbi.nlm.nih.gov/gene/?term=729359	"KIAA1881, S3-12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021207	72937	2900008C10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72937		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021208	729396	GAGE12J	http://www.ncbi.nlm.nih.gov/gene/?term=729396	GAGE11	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021209	72940	2900022M12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72940		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021210	729422	GAGE12C	http://www.ncbi.nlm.nih.gov/gene/?term=729422	GAGE-12B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021211	729431	GAGE12E	http://www.ncbi.nlm.nih.gov/gene/?term=729431	GAGE-12B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021212	729442	GAGE12H	http://www.ncbi.nlm.nih.gov/gene/?term=729442		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021213	729447	GAGE2A	http://www.ncbi.nlm.nih.gov/gene/?term=729447	"CT4.2, GAGE-2, GAGE-2A, GAGE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021214	72949	Ccnt2	http://www.ncbi.nlm.nih.gov/gene/?term=72949	"2900041I18Rik, C81304, CycT2, CycT2a, CycT2b "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021215	729515	TMEM242	http://www.ncbi.nlm.nih.gov/gene/?term=729515	"BM033, C6orf35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021216	729515	TMEM242	http://www.ncbi.nlm.nih.gov/gene/?term=729515	"BM033, C6orf35 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021217	729540	RGPD6	http://www.ncbi.nlm.nih.gov/gene/?term=729540	"RGP6, RGPD7, RanBP2L1, RanBP2L2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021218	729540	RGPD6	http://www.ncbi.nlm.nih.gov/gene/?term=729540	"RGP6, RGPD7, RanBP2L1, RanBP2L2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021219	72958	Zfp493	http://www.ncbi.nlm.nih.gov/gene/?term=72958	"2900054J07Rik, Rslcan12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021220	7295	TXN	http://www.ncbi.nlm.nih.gov/gene/?term=7295	"TRDX, TRX, TRX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021221	729614	FLJ37453	http://www.ncbi.nlm.nih.gov/gene/?term=729614		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021222	72962	Tymp	http://www.ncbi.nlm.nih.gov/gene/?term=72962	"2900072D10Rik, Ecgf1, PD-ECGF, PDECGF, Pdgfec "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021223	729648	ZNF812P	http://www.ncbi.nlm.nih.gov/gene/?term=729648	ZNF812	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021224	729665	CCDC175	http://www.ncbi.nlm.nih.gov/gene/?term=729665	"C14orf38, c14_5395 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021225	7296	TXNRD1	http://www.ncbi.nlm.nih.gov/gene/?term=7296	"GRIM-12, TR, TR1, TRXR1, TXNR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021226	7296	TXNRD1	http://www.ncbi.nlm.nih.gov/gene/?term=7296	"GRIM-12, TR, TR1, TRXR1, TXNR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021227	7296	TXNRD1	http://www.ncbi.nlm.nih.gov/gene/?term=7296	"GRIM-12, TR, TR1, TRXR1, TXNR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021228	7297	TYK2	http://www.ncbi.nlm.nih.gov/gene/?term=7297	"IMD35, JTK1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021229	7297	TYK2	http://www.ncbi.nlm.nih.gov/gene/?term=7297	"IMD35, JTK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021230	72983	2900052O17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72983		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021231	729852	UMAD1	http://www.ncbi.nlm.nih.gov/gene/?term=729852	"RPA3-AS1, RPA3OS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021232	72987	2900057C01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72987		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021233	72989	2900074G08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=72989		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021234	7298	TYMS	http://www.ncbi.nlm.nih.gov/gene/?term=7298	"HST422, TMS, TS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021235	7298	TYMS	http://www.ncbi.nlm.nih.gov/gene/?term=7298	"HST422, TMS, TS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021236	729948	CDC26P1	http://www.ncbi.nlm.nih.gov/gene/?term=729948	CDC26P	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021237	729956	SHISA7	http://www.ncbi.nlm.nih.gov/gene/?term=729956		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021238	729967	MORN2	http://www.ncbi.nlm.nih.gov/gene/?term=729967	"BLOCK27, MOPT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021239	729991	BORCS8	http://www.ncbi.nlm.nih.gov/gene/?term=729991	MEF2BNB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021240	72999	Insig2	http://www.ncbi.nlm.nih.gov/gene/?term=72999	"2900053I11Rik, C730043J18Rik, Insig-2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021241	72	ACTG2	http://www.ncbi.nlm.nih.gov/gene/?term=72	"ACT, ACTA3, ACTE, ACTL3, ACTSG, VSCM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021242	73008	2900073C16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73008		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021243	730092	RRN3P1	http://www.ncbi.nlm.nih.gov/gene/?term=730092		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021244	730094	C16orf52	http://www.ncbi.nlm.nih.gov/gene/?term=730094		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021245	730101	LOC730101	http://www.ncbi.nlm.nih.gov/gene/?term=730101		lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021246	7301	TYRO3	http://www.ncbi.nlm.nih.gov/gene/?term=7301	"BYK, Dtk, Etk-2, RSE, Rek, Sky, Tif "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021247	73020	2900073C17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73020		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021248	73032	Ttc9b	http://www.ncbi.nlm.nih.gov/gene/?term=73032	2900074C18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021249	730394	GTF2H2C_2	http://www.ncbi.nlm.nih.gov/gene/?term=730394	GTF2H2D	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021250	730394	GTF2H2C_2	http://www.ncbi.nlm.nih.gov/gene/?term=730394	GTF2H2D	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021251	73047	Camk2n2	http://www.ncbi.nlm.nih.gov/gene/?term=73047	2900075A18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021252	7305	TYROBP	http://www.ncbi.nlm.nih.gov/gene/?term=7305	"DAP12, KARAP, PLOSL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021253	7307	U2AF1	http://www.ncbi.nlm.nih.gov/gene/?term=7307	"FP793, RN, RNU2AF1, U2AF35, U2AFBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021254	7307	U2AF1	http://www.ncbi.nlm.nih.gov/gene/?term=7307	"FP793, RN, RNU2AF1, U2AF35, U2AFBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021255	73080	2900084O13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73080		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021256	73082	3100003M19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73082		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021257	73093	3110006O06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73093		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021258	730	C7	http://www.ncbi.nlm.nih.gov/gene/?term=730		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021259	73100	2900092D14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73100		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021260	7311	UBA52	http://www.ncbi.nlm.nih.gov/gene/?term=7311	"CEP52, HUBCEP52, L40, RPL40 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021261	7311	UBA52	http://www.ncbi.nlm.nih.gov/gene/?term=7311	"CEP52, HUBCEP52, L40, RPL40 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021262	7311	UBA52	http://www.ncbi.nlm.nih.gov/gene/?term=7311	"CEP52, HUBCEP52, L40, RPL40 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021263	7311	UBA52	http://www.ncbi.nlm.nih.gov/gene/?term=7311	"CEP52, HUBCEP52, L40, RPL40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021264	73121	Fam101a	http://www.ncbi.nlm.nih.gov/gene/?term=73121	"3110032G18Rik, cfm, cfm2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021265	73130	Tmed5	http://www.ncbi.nlm.nih.gov/gene/?term=73130	"3110020O18Rik, 4432412D15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021266	73130	Tmed5	http://www.ncbi.nlm.nih.gov/gene/?term=73130	"3110020O18Rik, 4432412D15Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021267	73137	Prrc1	http://www.ncbi.nlm.nih.gov/gene/?term=73137	"1190002C06Rik, 2310058D16Rik, 3110038B19Rik, 9430085A19Rik "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021268	73137	Prrc1	http://www.ncbi.nlm.nih.gov/gene/?term=73137	"1190002C06Rik, 2310058D16Rik, 3110038B19Rik, 9430085A19Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021269	73139	Cenpv	http://www.ncbi.nlm.nih.gov/gene/?term=73139	"3110013H01Rik, AA671303, Prr6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021270	7314	UBB	http://www.ncbi.nlm.nih.gov/gene/?term=7314	HEL-S-50	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021271	73158	Larp1	http://www.ncbi.nlm.nih.gov/gene/?term=73158	"1810024J12Rik, 3110040D16Rik, Larp, mKIAA0731 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021272	73162	Otud3	http://www.ncbi.nlm.nih.gov/gene/?term=73162	3110030K17Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021273	7316	UBC	http://www.ncbi.nlm.nih.gov/gene/?term=7316	HMG20	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021274	73178	Wasl	http://www.ncbi.nlm.nih.gov/gene/?term=73178	"2900021I12Rik, 3110031I02Rik, N-WASP "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021275	7317	UBA1	http://www.ncbi.nlm.nih.gov/gene/?term=7317	"A1S9, A1S9T, A1ST, AMCX1, CFAP124, GXP1, POC20, SMAX2A, UBE1, UBE1X, UBA1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021276	7317	UBA1	http://www.ncbi.nlm.nih.gov/gene/?term=7317	"A1S9, A1S9T, A1ST, AMCX1, CFAP124, GXP1, POC20, SMAX2A, UBE1, UBE1X, UBA1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021277	7317	UBA1	http://www.ncbi.nlm.nih.gov/gene/?term=7317	"A1S9, A1S9T, A1ST, AMCX1, CFAP124, GXP1, POC20, SMAX2, UBA1A, UBE1, UBE1X "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021278	73186	3110045A19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73186		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021279	7318	UBA7	http://www.ncbi.nlm.nih.gov/gene/?term=7318	"D8, UBA1B, UBE1L, UBE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021280	73192	Xpot	http://www.ncbi.nlm.nih.gov/gene/?term=73192	"1110004L07Rik, 3110065H13Rik, AI452076, C79645, EXPORTIN-T "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021281	7319	UBE2A	http://www.ncbi.nlm.nih.gov/gene/?term=7319	"HHR6A, MRXS30, MRXSN, RAD6A, UBC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021282	7319	UBE2A	http://www.ncbi.nlm.nih.gov/gene/?term=7319	"HHR6A, MRXS30, MRXSN, RAD6A, UBC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021283	7320	UBE2B	http://www.ncbi.nlm.nih.gov/gene/?term=7320	"E2-17kDa, HHR6B, HR6B, RAD6B, UBC2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021284	7320	UBE2B	http://www.ncbi.nlm.nih.gov/gene/?term=7320	"E2-17kDa, HHR6B, HR6B, RAD6B, UBC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021285	732253	TDRG1	http://www.ncbi.nlm.nih.gov/gene/?term=732253	LINC00532	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021286	7322	UBE2D2	http://www.ncbi.nlm.nih.gov/gene/?term=7322	"E2(17)KB2, PUBC1, UBC4, UBC4/5, UBCH4, UBCH5B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021287	7322	UBE2D2	http://www.ncbi.nlm.nih.gov/gene/?term=7322	"E2(17)KB2, PUBC1, UBC4, UBC4/5, UBCH4, UBCH5B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021288	73233	Zfp942	http://www.ncbi.nlm.nih.gov/gene/?term=73233	3110048L19Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021289	73233	Zfp942	http://www.ncbi.nlm.nih.gov/gene/?term=73233	3110048L19Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021290	73238	3110049I03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73238		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021291	7323	UBE2D3	http://www.ncbi.nlm.nih.gov/gene/?term=7323	"E2(17)KB3, UBC4/5, UBCH5C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021292	73255	1700026J12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73255		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021293	73262	1700036O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73262		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021294	7326	UBE2G1	http://www.ncbi.nlm.nih.gov/gene/?term=7326	"E217K, UBC7, UBE2G "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021295	7326	UBE2G1	http://www.ncbi.nlm.nih.gov/gene/?term=7326	"E217K, UBC7, UBE2G "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021296	7326	UBE2G1	http://www.ncbi.nlm.nih.gov/gene/?term=7326	"E217K, UBC7, UBE2G "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021297	73274	Gpbp1	http://www.ncbi.nlm.nih.gov/gene/?term=73274	"1700034P14Rik, AU019836, D230035M11Rik, Gpbp, mGPBP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021298	73276	1700037J18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73276		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021299	7327	UBE2G2	http://www.ncbi.nlm.nih.gov/gene/?term=7327	UBC7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021300	7327	UBE2G2	http://www.ncbi.nlm.nih.gov/gene/?term=7327	UBC7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021301	732802	zein	http://www.ncbi.nlm.nih.gov/gene/732802		mRNA	Zea mays	11910012	Endoplasmic reticulum	Endosperm	In situ hybridization	"We analyzed the distribution of mRNAs encoding the 22-kD alpha-zein and the 27-kD gamma-zein proteins on cisternal and protein body rough endoplasmic reticulum membranes. In situ hybridization revealed similar frequencies of the mRNAs in both regions of the endoplasmic reticulum, indicating that the transcripts are distributed more or less randomly. "
RLID00021302	73288	Vps50	http://www.ncbi.nlm.nih.gov/gene/?term=73288	"1700034M03Rik, 8430415E05Rik, BLM, C87205, Ccdc132, mKIAA1861 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021303	7328	UBE2H	http://www.ncbi.nlm.nih.gov/gene/?term=7328	"E2-20K, GID3, UBC8, UBCH, UBCH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021304	7328	UBE2H	http://www.ncbi.nlm.nih.gov/gene/?term=7328	"E2-20K, GID3, UBC8, UBCH, UBCH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021305	7329	UBE2I	http://www.ncbi.nlm.nih.gov/gene/?term=7329	"C358B7.1, P18, UBC9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021306	7329	UBE2I	http://www.ncbi.nlm.nih.gov/gene/?term=7329	"C358B7.1, P18, UBC9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021307	73310	1700044K19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73310		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021308	7332	UBE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=7332	"E2-F1, L-UBC, UBCH7, UbcM4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021309	7332	UBE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=7332	"E2-F1, L-UBC, UBCH7, UbcM4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021310	7332	UBE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=7332	"E2-F1, L-UBC, UBCH7, UbcM4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021311	7332	UBE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=7332	"E2-F1, L-UBC, UBCH7, UbcM4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021312	7334	UBE2N	http://www.ncbi.nlm.nih.gov/gene/?term=7334	"HEL-S-71, UBC13, UBCHBEN, UBC13, UbcH-ben, UbcH13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021313	7334	UBE2N	http://www.ncbi.nlm.nih.gov/gene/?term=7334	"HEL-S-71, UBC13, UBCHBEN, UBC13, UbcH-ben, UbcH13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021314	7334	UBE2N	http://www.ncbi.nlm.nih.gov/gene/?term=7334	"HEL-S-71, UBC13, UBCHBEN, UBC13, UbcH-ben, UbcH13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021315	73363	1700056E22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73363		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021316	7336	UBE2V2	http://www.ncbi.nlm.nih.gov/gene/?term=7336	"DDVIT1, DDVit-1, EDAF-1, EDPF-1, EDPF1, MMS2, UEV-2, UEV2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021317	7336	UBE2V2	http://www.ncbi.nlm.nih.gov/gene/?term=7336	"DDVIT1, DDVit-1, EDAF-1, EDPF-1, EDPF1, MMS2, UEV-2, UEV2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021318	7336	UBE2V2	http://www.ncbi.nlm.nih.gov/gene/?term=7336	"DDVIT1, DDVit-1, EDAF-1, EDPF-1, EDPF1, MMS2, UEV-2, UEV2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021319	73373	Phospho2	http://www.ncbi.nlm.nih.gov/gene/?term=73373	"1700048E23Rik, AI661517, AU021728, AV006103, Phos2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021320	73378	1700060L04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73378		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021321	7337	UBE3A	http://www.ncbi.nlm.nih.gov/gene/?term=7337	"ANCR, AS, E6-AP, EPVE6AP, HPVE6A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021322	7337	UBE3A	http://www.ncbi.nlm.nih.gov/gene/?term=7337	"ANCR, AS, E6-AP, EPVE6AP, HPVE6A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021323	734060	mogat1	http://www.ncbi.nlm.nih.gov/gene/?term=734060	"dgat2l, dgat2l1 "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00021324	73408	1700065L07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73408		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021325	7341	SUMO1	http://www.ncbi.nlm.nih.gov/gene/?term=7341	"DAP1, GMP1, OFC10, PIC1, SENP2, SMT3, SMT3C, SMT3H3, UBL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021326	7341	SUMO1	http://www.ncbi.nlm.nih.gov/gene/?term=7341	"DAP1, GMP1, OFC10, PIC1, SENP2, SMT3, SMT3C, SMT3H3, UBL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021327	7341	SUMO1	http://www.ncbi.nlm.nih.gov/gene/?term=7341	"DAP1, GMP1, OFC10, PIC1, SENP2, SMT3, SMT3C, SMT3H3, UBL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021328	734240	trib1	http://www.ncbi.nlm.nih.gov/gene/?term=734240	"c8fw, gig2, skip1, trb1, tribbles "	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00021329	73429	Hoxd3os1	http://www.ncbi.nlm.nih.gov/gene/?term=73429	"1700064D17Rik, 1700109F18Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021330	73435	Tex35	http://www.ncbi.nlm.nih.gov/gene/?term=73435	1700057K13Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021331	73437	1700064F23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73437		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021332	7343	UBTF	http://www.ncbi.nlm.nih.gov/gene/?term=7343	"NOR-90, UBF, UBF-1, UBF1, UBF2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021333	734470	cpeb1-b	http://www.ncbi.nlm.nih.gov/gene/?term=734470	CPEB	mRNA	Xenopus laevis	11081630	Mitotic spindle	Embryo	Whole mount In Situ Hybridization	"CPEB, Maskin, and Cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. "
RLID00021334	73447	Wdr13	http://www.ncbi.nlm.nih.gov/gene/?term=73447	"1700060B08Rik, 5730411P10Rik, DXHXS7467e, W51679, mMg21 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021335	7345	UCHL1	http://www.ncbi.nlm.nih.gov/gene/?term=7345	"HEL-117, HEL-S-53, NDGOA, PARK5, PGP 9.5, PGP9.5, PGP95, Uch-L1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021336	7345	UCHL1	http://www.ncbi.nlm.nih.gov/gene/?term=7345	"HEL-117, HEL-S-53, NDGOA, PARK5, PGP 9.5, PGP9.5, PGP95, Uch-L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021337	73463	Als2cr11	http://www.ncbi.nlm.nih.gov/gene/?term=73463	"1700052H20Rik, 4930408G06Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021338	73473	Iws1	http://www.ncbi.nlm.nih.gov/gene/?term=73473	"1700069O15Rik, 3000008H23, AL117927, AW214353 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021339	7347	UCHL3	http://www.ncbi.nlm.nih.gov/gene/?term=7347	UCH-L3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021340	7347	UCHL3	http://www.ncbi.nlm.nih.gov/gene/?term=7347	UCH-L3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021341	73483	1700074A11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73483		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021342	734998	farp2	http://www.ncbi.nlm.nih.gov/gene/?term=734998		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00021343	734	OSGIN2	http://www.ncbi.nlm.nih.gov/gene/?term=734	"C8orf1, hT41 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021344	7351	UCP2	http://www.ncbi.nlm.nih.gov/gene/?term=7351	"BMIQ4, SLC25A8, UCPH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021345	73526	Speer4b	http://www.ncbi.nlm.nih.gov/gene/?term=73526	"1700081O22Rik, SPEER-4B "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021346	735301	SNHG9	http://www.ncbi.nlm.nih.gov/gene/?term=735301	NCRNA00062	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021347	7353	UFD1L	http://www.ncbi.nlm.nih.gov/gene/?term=7353	UFD1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021348	7353	UFD1L	http://www.ncbi.nlm.nih.gov/gene/?term=7353	UFD1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021349	7353	UFD1L	http://www.ncbi.nlm.nih.gov/gene/?term=7353	UFD1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021350	7354404	Yeti	http://www.ncbi.nlm.nih.gov/gene/?term=7354404	"Dmel_CG40218, 41Aa, BEST:GH01620, BcDNA:RE36623, CG40218, Dmel\CG40218, GroupI, l(2)41Aa, l(2)EMS31, l(2R)B, l(2R)EMS-31 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00021351	7354465	CG42232	http://www.ncbi.nlm.nih.gov/gene/?term=7354465	"Dmel_ CG14896, CG14897, Dmel\CG42232, Dmel_CG14896, Dmel_CG14897, anon-EST:Liang-1.14, clone 1.14 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00021352	73545	1700094D03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73545		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021353	7355	SLC35A2	http://www.ncbi.nlm.nih.gov/gene/?term=7355	"CDG2M, CDGX, UDP-Gal-Tr, UGALT, UGAT, UGT, UGT1, UGT2, UGTL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021354	7355	SLC35A2	http://www.ncbi.nlm.nih.gov/gene/?term=7355	"CDG2M, CDGX, UDP-Gal-Tr, UGALT, UGAT, UGT, UGT1, UGT2, UGTL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021355	73577	1700102F20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73577		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021356	7357	UGCG	http://www.ncbi.nlm.nih.gov/gene/?term=7357	"GCS, GLCT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021357	7357	UGCG	http://www.ncbi.nlm.nih.gov/gene/?term=7357	"GCS, GLCT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021358	7357	UGCG	http://www.ncbi.nlm.nih.gov/gene/?term=7357	"GCS, GLCT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021359	73582	Camkmt	http://www.ncbi.nlm.nih.gov/gene/?term=73582	"1700106N22Rik, AI480743, AV099781, CLNMT, CaM KMT "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021360	73589	1700101I19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73589		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021361	7358	UGDH	http://www.ncbi.nlm.nih.gov/gene/?term=7358	"GDH, UDP-GlcDH, UDPGDH, UGD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021362	7358	UGDH	http://www.ncbi.nlm.nih.gov/gene/?term=7358	"GDH, UDP-GlcDH, UDPGDH, UGD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021363	7358	UGDH	http://www.ncbi.nlm.nih.gov/gene/?term=7358	"GDH, UDP-GlcDH, UDPGDH, UGD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021364	73603	Trp53tg5	http://www.ncbi.nlm.nih.gov/gene/?term=73603	1700126L10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021365	7360	UGP2	http://www.ncbi.nlm.nih.gov/gene/?term=7360	"UDPG, UDPGP, UDPGP2, UGP1, UGPP1, UGPP2, pHC379 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021366	7360	UGP2	http://www.ncbi.nlm.nih.gov/gene/?term=7360	"UDPG, UDPGP, UDPGP2, UGP1, UGPP1, UGPP2, pHC379 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021367	7360	UGP2	http://www.ncbi.nlm.nih.gov/gene/?term=7360	"UDPG, UDPGP, UDPGP2, UGP1, UGPP1, UGPP2, pHC379 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021368	73628	1700125G02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73628		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021369	7364	UGT2B7	http://www.ncbi.nlm.nih.gov/gene/?term=7364	"UDPGT 2B9, UDPGT2B7, UDPGTH2, UGT2B9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021370	73668	Ttc21b	http://www.ncbi.nlm.nih.gov/gene/?term=73668	"2410066K11Rik, Thm1, aln, mKIAA1992 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021371	73674	Wdr75	http://www.ncbi.nlm.nih.gov/gene/?term=73674	"1300003A18Rik, 2410118I19Rik, C77608 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021372	73674	Wdr75	http://www.ncbi.nlm.nih.gov/gene/?term=73674	"1300003A18Rik, 2410118I19Rik, C77608 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021373	73680	Zbtb8a	http://www.ncbi.nlm.nih.gov/gene/?term=73680	"2410081M15Rik, AI480941 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021374	73681	Trmt11	http://www.ncbi.nlm.nih.gov/gene/?term=73681	"2410075D05Rik, 3110045I18Rik, AW213713 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021375	7368	UGT8	http://www.ncbi.nlm.nih.gov/gene/?term=7368	"CGT, UGT4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021376	7368	UGT8	http://www.ncbi.nlm.nih.gov/gene/?term=7368	"CGT, UGT4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021377	73692	2410089E03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73692	"4732468D17Rik, Hug, Jbts17, b2b012Clo "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021378	7369	UMOD	http://www.ncbi.nlm.nih.gov/gene/?term=7369	"ADMCKD2, FJHN, HNFJ, HNFJ1, MCKD2, THGP, THP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021379	73708	Dppa3	http://www.ncbi.nlm.nih.gov/gene/?term=73708	"2410075G02Rik, PCG7, PGC7, Stella "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021380	7371	UCK2	http://www.ncbi.nlm.nih.gov/gene/?term=7371	"TSA903, UK, UMPK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021381	7371	UCK2	http://www.ncbi.nlm.nih.gov/gene/?term=7371	"TSA903, UK, UMPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021382	73724	Mcee	http://www.ncbi.nlm.nih.gov/gene/?term=73724	1110007A04Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021383	7372	UMPS	http://www.ncbi.nlm.nih.gov/gene/?term=7372	OPRT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021384	7372	UMPS	http://www.ncbi.nlm.nih.gov/gene/?term=7372	OPRT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021385	7372	UMPS	http://www.ncbi.nlm.nih.gov/gene/?term=7372	OPRT	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021386	7372	UMPS	http://www.ncbi.nlm.nih.gov/gene/?term=7372	OPRT	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021387	7372	UMPS	http://www.ncbi.nlm.nih.gov/gene/?term=7372	OPRT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021388	73737	1110008P14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73737	C79326	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00021389	73739	Cby1	http://www.ncbi.nlm.nih.gov/gene/?term=73739	"1110014P06Rik, CBY, PGEA14, Pgea1, arb1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021390	7373	COL14A1	http://www.ncbi.nlm.nih.gov/gene/?term=7373	UND	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021391	7373	COL14A1	http://www.ncbi.nlm.nih.gov/gene/?term=7373	UND	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021392	73744	Man2c1	http://www.ncbi.nlm.nih.gov/gene/?term=73744	1110025H24Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021393	73747	1110034G24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73747		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021394	7374	UNG	http://www.ncbi.nlm.nih.gov/gene/?term=7374	"DGU, HIGM4, HIGM5, UDG1, UNG15, UNG2, UNG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021395	7375	USP4	http://www.ncbi.nlm.nih.gov/gene/?term=7375	"UNP, Unph "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021396	7375	USP4	http://www.ncbi.nlm.nih.gov/gene/?term=7375	"UNP, Unph "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021397	73766	4833420D23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73766		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021398	7376	NR1H2	http://www.ncbi.nlm.nih.gov/gene/?term=7376	"LXR-b, LXRB, NER, NER-I, RIP15, UNR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021399	7376	NR1H2	http://www.ncbi.nlm.nih.gov/gene/?term=7376	"LXR-b, LXRB, NER, NER-I, RIP15, UNR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021400	73786	4930429L21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73786		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021401	7378	UPP1	http://www.ncbi.nlm.nih.gov/gene/?term=7378	"UDRPASE, UP, UPASE, UPP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021402	73792	4930401G09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73792		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021403	73794	4930402M22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73794		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021404	73804	Kif2c	http://www.ncbi.nlm.nih.gov/gene/?term=73804	"4930402F02Rik, ESTM5, Knsl6, MCAK, X83316 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021405	73817	4930404F17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73817		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021406	7381	UQCRB	http://www.ncbi.nlm.nih.gov/gene/?term=7381	"MC3DN3, QCR7, QP-C, QPC, UQBC, UQBP, UQCR6, UQPC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021407	7381	UQCRB	http://www.ncbi.nlm.nih.gov/gene/?term=7381	"MC3DN3, QCR7, QP-C, QPC, UQBC, UQBP, UQCR6, UQPC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021408	73824	Snhg6	http://www.ncbi.nlm.nih.gov/gene/?term=73824	1110008H02Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021409	73847	Fam110a	http://www.ncbi.nlm.nih.gov/gene/?term=73847	"1700008J10Rik, 5430432M24Rik, AI747080 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021410	7384	UQCRC1	http://www.ncbi.nlm.nih.gov/gene/?term=7384	"D3S3191, QCR1, UQCR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021411	7384	UQCRC1	http://www.ncbi.nlm.nih.gov/gene/?term=7384	"D3S3191, QCR1, UQCR1 "	mRNA	Homo sapiens	23500070	Mitochondrion	SH-SY5Y cell	Fluorescence in situ hybridization	"These results demonstrate that TMEM126A mRNA is an MLR, with asymmetric localization to the mitochondrial surface similar to UQCRC1 mRNA, which is known to encode a mitochondrial protein of the IM.  "
RLID00021412	7385	UQCRC2	http://www.ncbi.nlm.nih.gov/gene/?term=7385	"MC3DN5, QCR2, UQCR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021413	7385	UQCRC2	http://www.ncbi.nlm.nih.gov/gene/?term=7385	"MC3DN5, QCR2, UQCR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021414	73868	4930415N12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73868		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021415	7386	UQCRFS1	http://www.ncbi.nlm.nih.gov/gene/?term=7386	"RIP1, RIS1, RISP, UQCR5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021416	7386	UQCRFS1	http://www.ncbi.nlm.nih.gov/gene/?term=7386	"RIP1, RIS1, RISP, UQCR5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021417	73884	Zdbf2	http://www.ncbi.nlm.nih.gov/gene/?term=73884	"4930431J08Rik, 9330107J05Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021418	7388	UQCRH	http://www.ncbi.nlm.nih.gov/gene/?term=7388	"QCR6, UQCR8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021419	7389	UROD	http://www.ncbi.nlm.nih.gov/gene/?term=7389	"PCT, UPD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021420	7389	UROD	http://www.ncbi.nlm.nih.gov/gene/?term=7389	"PCT, UPD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021421	7389	UROD	http://www.ncbi.nlm.nih.gov/gene/?term=7389	"PCT, UPD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021422	738	VPS51	http://www.ncbi.nlm.nih.gov/gene/?term=738	"ANG2, ANG3, C11orf2, C11orf3, FFR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021423	73902	Psmb11	http://www.ncbi.nlm.nih.gov/gene/?term=73902	"5830406J20Rik, beta5t "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021424	7390	UROS	http://www.ncbi.nlm.nih.gov/gene/?term=7390	UROIIIS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021425	7390	UROS	http://www.ncbi.nlm.nih.gov/gene/?term=7390	UROIIIS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021426	73916	Ift57	http://www.ncbi.nlm.nih.gov/gene/?term=73916	"4833420A15Rik, Esrrbl1, Hippi, MHS4R2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021427	7391	USF1	http://www.ncbi.nlm.nih.gov/gene/?term=7391	"FCHL, FCHL1, HYPLIP1, MLTF, MLTFI, UEF, bHLHb11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021428	7392	USF2	http://www.ncbi.nlm.nih.gov/gene/?term=7392	"FIP, bHLHb12 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021429	7392	USF2	http://www.ncbi.nlm.nih.gov/gene/?term=7392	"FIP, bHLHb12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021430	73948	4930415P13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73948		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021431	73966	4930449I21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73966		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021432	73985	4930445N18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73985	3010027C24Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021433	73988	4930438A08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73988		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021434	7398	USP1	http://www.ncbi.nlm.nih.gov/gene/?term=7398	UBP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021435	7398	USP1	http://www.ncbi.nlm.nih.gov/gene/?term=7398	UBP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021436	74006	Dnm1l	http://www.ncbi.nlm.nih.gov/gene/?term=74006	"6330417M19Rik, AI450666, Dlp1, Dnmlp1, Drp1, python "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021437	74011	Slc25a27	http://www.ncbi.nlm.nih.gov/gene/?term=74011	"3632410G24Rik, 9430092A03Rik, D530043E16Rik, Ucp4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021438	74012	Rap2b	http://www.ncbi.nlm.nih.gov/gene/?term=74012	"4021402C18Rik, AA408554 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021439	74014	3732407C23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74014		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021440	74026	Msl1	http://www.ncbi.nlm.nih.gov/gene/?term=74026	"2810017F12Rik, 4121402D02Rik, 4930463F05Rik, AA682082, Msl-1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021441	7402	UTRN	http://www.ncbi.nlm.nih.gov/gene/?term=7402	"DMDL, DRP, DRP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021442	7402	UTRN	http://www.ncbi.nlm.nih.gov/gene/?term=7402	"DMDL, DRP, DRP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021443	7402	UTRN	http://www.ncbi.nlm.nih.gov/gene/?term=7402	"DMDL, DRP, DRP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021444	7402	UTRN	http://www.ncbi.nlm.nih.gov/gene/?term=7402	"DMDL, DRP, DRP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021445	7402	UTRN	http://www.ncbi.nlm.nih.gov/gene/?term=7402	"DMDL, DRP, DRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021446	74034	4632404H12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74034		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021447	74034	4632404H12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74034		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021448	7403	KDM6A	http://www.ncbi.nlm.nih.gov/gene/?term=7403	"KABUK2, UTX, bA386N14.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021449	74042	4921501E09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74042	PHF8	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021450	74044	Ttf2	http://www.ncbi.nlm.nih.gov/gene/?term=74044	"4632434F22Rik, 8030447N19, AV218430 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021451	74046	4632432E15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74046	Gm38310	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021452	7404	UTY	http://www.ncbi.nlm.nih.gov/gene/?term=7404	"KDM6AL1, UTY "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021453	7404	UTY	http://www.ncbi.nlm.nih.gov/gene/?term=7404	"KDM6AL1, UTY "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021454	74050	4921525O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74050		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021455	74053	Grip1	http://www.ncbi.nlm.nih.gov/gene/?term=74053	"4931400F03Rik, GRIP, eb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021456	74055	Plce1	http://www.ncbi.nlm.nih.gov/gene/?term=74055	"4933403A21Rik, PLCepsilon, Plce, mKIAA1516 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021457	74059	4933406G16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74059		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021458	7405	UVRAG	http://www.ncbi.nlm.nih.gov/gene/?term=7405	"DHTX, VPS38, p63 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021459	7405	UVRAG	http://www.ncbi.nlm.nih.gov/gene/?term=7405	"DHTX, VPS38, p63 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021460	74061	4933404K08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74061		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021461	74068	Asz1	http://www.ncbi.nlm.nih.gov/gene/?term=74068	"4933400N19Rik, Gasz, ORF3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021462	7407	VARS	http://www.ncbi.nlm.nih.gov/gene/?term=7407	"G7A1, VARS2, VARS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021463	7407	VARS	http://www.ncbi.nlm.nih.gov/gene/?term=7407	"G7A1, VARS2, VARS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021464	7407	VARS	http://www.ncbi.nlm.nih.gov/gene/?term=7407	"G7A, VARS1, VARS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021465	74081	Cep350	http://www.ncbi.nlm.nih.gov/gene/?term=74081	"4933409L06Rik, 6430546F08Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021466	74081	Cep350	http://www.ncbi.nlm.nih.gov/gene/?term=74081	"4933409L06Rik, 6430546F08Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021467	74085	4933414I06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74085		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021468	74086	4933411D12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74086		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021469	7408	VASP	http://www.ncbi.nlm.nih.gov/gene/?term=7408		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021470	7408	VASP	http://www.ncbi.nlm.nih.gov/gene/?term=7408		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021471	74096	Hvcn1	http://www.ncbi.nlm.nih.gov/gene/?term=74096	"0610039P13Rik, AI450555, BTS, HV1, Vsop., mVSOP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021472	7409	VAV1	http://www.ncbi.nlm.nih.gov/gene/?term=7409	VAV	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021473	740	MRPL49	http://www.ncbi.nlm.nih.gov/gene/?term=740	"C11orf4, L49mt, MRP-L49, NOF, NOF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021474	740	MRPL49	http://www.ncbi.nlm.nih.gov/gene/?term=740	"C11orf4, L49mt, MRP-L49, NOF, NOF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021475	740	MRPL49	http://www.ncbi.nlm.nih.gov/gene/?term=740	"C11orf4, L49mt, MRP-L49, NOF, NOF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021476	74100	Arpp21	http://www.ncbi.nlm.nih.gov/gene/?term=74100	"0710001E13Rik, AI853636, ARPP-21, D9Bwg1012e, R3hdm3, Tarpp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021477	74102	Slc35a5	http://www.ncbi.nlm.nih.gov/gene/?term=74102	"1010001J06Rik, AU021179, BB097433, D16Ertd450e, D730043G07Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021478	74106	Dcaf6	http://www.ncbi.nlm.nih.gov/gene/?term=74106	"1200006M05Rik, Iqwd1, PC326 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021479	74107	Cep55	http://www.ncbi.nlm.nih.gov/gene/?term=74107	"1200008O12Rik, 2700032M20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021480	7410	VAV2	http://www.ncbi.nlm.nih.gov/gene/?term=7410	VAV-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021481	74111	Rbm19	http://www.ncbi.nlm.nih.gov/gene/?term=74111	"1200009A02Rik, AV302714, NPO "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021482	74112	Usp16	http://www.ncbi.nlm.nih.gov/gene/?term=74112	"1200004E02Rik, 2810483I07Rik, 6330514E22Rik, UBPM "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021483	74114	Crot	http://www.ncbi.nlm.nih.gov/gene/?term=74114	1200003H03Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021484	74117	Actr3	http://www.ncbi.nlm.nih.gov/gene/?term=74117	"1200003A09Rik, Arp3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021485	7411	VBP1	http://www.ncbi.nlm.nih.gov/gene/?term=7411	"HIBBJ46, PFD3, PFDN3, VBP-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021486	7411	VBP1	http://www.ncbi.nlm.nih.gov/gene/?term=7411	"HIBBJ46, PFD3, PFDN3, VBP-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021487	7411	VBP1	http://www.ncbi.nlm.nih.gov/gene/?term=7411	"HIBBJ46, PFD3, PFDN3, VBP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021488	74120	Zfp263	http://www.ncbi.nlm.nih.gov/gene/?term=74120	"1200014J04Rik, AI326880, AU020888, NT2, mFPM315 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021489	74123	Foxp4	http://www.ncbi.nlm.nih.gov/gene/?term=74123	"1200010K03Rik, 2310007G05Rik, mFKHLA "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021490	74125	Armc8	http://www.ncbi.nlm.nih.gov/gene/?term=74125	"1200015K23Rik, Gid5, HSPC056 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021491	74132	Rnf6	http://www.ncbi.nlm.nih.gov/gene/?term=74132	"1200013I08Rik, 5730419H05Rik, AA537053 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021492	74143	Opa1	http://www.ncbi.nlm.nih.gov/gene/?term=74143	"1200011N24Rik, AI225888, AI847218, lilr3, mKIAA0567 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021493	7414	VCL	http://www.ncbi.nlm.nih.gov/gene/?term=7414	"CMD1W, CMH15, HEL114, MV, MVCL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021494	7414	VCL	http://www.ncbi.nlm.nih.gov/gene/?term=7414	"CMD1W, CMH15, HEL114, MV, MVCL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021495	7414	VCL	http://www.ncbi.nlm.nih.gov/gene/?term=7414	"CMD1W, CMH15, HEL114, MV, MVCL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021496	74150	Slc35f5	http://www.ncbi.nlm.nih.gov/gene/?term=74150	"1300003P13Rik, AI646727 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021497	7415	VCP	http://www.ncbi.nlm.nih.gov/gene/?term=7415	"ALS14, CMT2Y, HEL-220, HEL-S-70, IBMPFD, IBMPFD1, TERA, p97 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021498	74164	Nfx1	http://www.ncbi.nlm.nih.gov/gene/?term=74164	"1300017N15Rik, 3000003M19Rik, NFX.1, TEG-42, Tex42 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021499	74167	Nudt9	http://www.ncbi.nlm.nih.gov/gene/?term=74167	"1190002C07Rik, ADPR-PPase, AI462474 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021500	7416	VDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=7416	"PORIN, VDAC-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021501	7416	VDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=7416	"PORIN, VDAC-1 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00021502	7416	VDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=7416	"PORIN, VDAC-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021503	74173	Rab10os	http://www.ncbi.nlm.nih.gov/gene/?term=74173	"1700012B15Rik, 1810036A22Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021504	74173	Rab10os	http://www.ncbi.nlm.nih.gov/gene/?term=74173	"1700012B15Rik, 1810036A22Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021505	7417	VDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=7417	POR	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021506	7417	VDAC2	http://www.ncbi.nlm.nih.gov/gene/?term=7417	POR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021507	74182	Gpcpd1	http://www.ncbi.nlm.nih.gov/gene/?term=74182	"2310004G06Rik, 2310032D16Rik, AU015213, Gde5, Prei4, mKIAA1434 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021508	74185	Gbe1	http://www.ncbi.nlm.nih.gov/gene/?term=74185	"2310045H19Rik, 2810426P10Rik, D16Ertd536e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021509	74187	Katnb1	http://www.ncbi.nlm.nih.gov/gene/?term=74187	"2410003J24Rik, KAT "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021510	74196	Ttc27	http://www.ncbi.nlm.nih.gov/gene/?term=74196	2610511O17Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021511	7419	VDAC3	http://www.ncbi.nlm.nih.gov/gene/?term=7419	"HD-VDAC3, VDAC-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021512	7419	VDAC3	http://www.ncbi.nlm.nih.gov/gene/?term=7419	"HD-VDAC3, VDAC-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021513	741	ZNHIT2	http://www.ncbi.nlm.nih.gov/gene/?term=741	"C11orf5, FON "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021514	74203	Eif4enif1	http://www.ncbi.nlm.nih.gov/gene/?term=74203	"2610509L04Rik, A930019J01Rik, AA410001, AU021239, Clast4, D11Ertd166e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021515	74205	Acsl3	http://www.ncbi.nlm.nih.gov/gene/?term=74205	"2610510B12Rik, Acs3, C85929, Facl3, Pro2194 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021516	7421	VDR	http://www.ncbi.nlm.nih.gov/gene/?term=7421	"NR1I1, PPP1R163 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021517	7421	VDR	http://www.ncbi.nlm.nih.gov/gene/?term=7421	"NR1I1, PPP1R163 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021518	74222	Sept14	http://www.ncbi.nlm.nih.gov/gene/?term=74222	1700016K13Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021519	7422	VEGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7422	"MVCD1, VEGF, VPF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021520	7422	VEGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7422	"MVCD1, VEGF, VPF "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00021521	7422	VEGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7422	"MVCD1, VEGF, VPF "	mRNA	Homo sapiens	25063809	Ribosome	HeLa cell	qRT-PCR	Figure 1: Endoplasmic reticulum-associated mRNAs are partitioned between detergent-resistant and detergent-sensitive membrane domains. Data are collected from Figure 1.
RLID00021522	7422	VEGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7422	"MVCD1, VEGF, VPF "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00021523	7422	VEGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7422	"MVCD1, VEGF, VPF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021524	7422	VEGFA	http://www.ncbi.nlm.nih.gov/gene/?term=7422	"VPF, VEGF, MVCD1 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00021525	7423	VEGFB	http://www.ncbi.nlm.nih.gov/gene/?term=7423	"VEGFL, VRF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021526	7423	VEGFB	http://www.ncbi.nlm.nih.gov/gene/?term=7423	"VEGFL, VRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021527	74244	Atg7	http://www.ncbi.nlm.nih.gov/gene/?term=74244	"1810013K23Rik, Agp7, Apg7ll, Gm21553, Atg7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021528	74246	Gale	http://www.ncbi.nlm.nih.gov/gene/?term=74246	"2310002A12Rik, AI323962 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021529	74249	Lrrc2	http://www.ncbi.nlm.nih.gov/gene/?term=74249	"2400002D05Rik, 4933431K03Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021530	7424	VEGFC	http://www.ncbi.nlm.nih.gov/gene/?term=7424	"Flt4-L, LMPH1D, VRP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021531	7424	VEGFC	http://www.ncbi.nlm.nih.gov/gene/?term=7424	"Flt4-L, LMPH1D, VRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021532	74251	Ankrd9	http://www.ncbi.nlm.nih.gov/gene/?term=74251	2500003O20Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021533	74252	Armc1	http://www.ncbi.nlm.nih.gov/gene/?term=74252	"2310016N05Rik, 2900046P06Rik, 3110009G21Rik, AA409258, AW048872, Arcp, C330014L16Rik "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021534	74256	Cyld	http://www.ncbi.nlm.nih.gov/gene/?term=74256	"2010013M14Rik, 2900009M21Rik, C130039D01Rik, CDMT, CYLD1, EAC, mKIAA0849 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00021535	74280	1700084F23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74280	"1700003E18Rik, 4930589D02Rik "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021536	7428	VHL	http://www.ncbi.nlm.nih.gov/gene/?term=7428	"HRCA1, RCA11, pVHL, VHL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021537	7428	VHL	http://www.ncbi.nlm.nih.gov/gene/?term=7428	"HRCA1, RCA11, pVHL, VHL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021538	7428	VHL	http://www.ncbi.nlm.nih.gov/gene/?term=7428	"HRCA1, RCA11, pVHL, VHL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021539	7428	VHL	http://www.ncbi.nlm.nih.gov/gene/?term=7428	"HRCA1, RCA11, pVHL, VHL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021540	7428	VHL	http://www.ncbi.nlm.nih.gov/gene/?term=7428	"HRCA1, RCA1, VHL1, pVHL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021541	74298	1700108I11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74298		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021542	7429	VIL1	http://www.ncbi.nlm.nih.gov/gene/?term=7429	"D2S1471, VIL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021543	7430	EZR	http://www.ncbi.nlm.nih.gov/gene/?term=7430	"CVIL, CVL, HEL-S-105, VIL2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021544	7430	EZR	http://www.ncbi.nlm.nih.gov/gene/?term=7430	"CVIL, CVL, HEL-S-105, VIL2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021545	7430	EZR	http://www.ncbi.nlm.nih.gov/gene/?term=7430	"CVIL, CVL, HEL-S-105, VIL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021546	74315	Rnf145	http://www.ncbi.nlm.nih.gov/gene/?term=74315	"3732413I11Rik, TMRF1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021547	7431	VIM	http://www.ncbi.nlm.nih.gov/gene/?term=7431	"CTRCT30, HEL113 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021548	7431	VIM	http://www.ncbi.nlm.nih.gov/gene/?term=7431	"CTRCT30, HEL113 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021549	74320	Wdr33	http://www.ncbi.nlm.nih.gov/gene/?term=74320	"1110001N06Rik, 2310011G05Rik, 2810021O11Rik, 8430413N20Rik, WDC146 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021550	74325	Cltb	http://www.ncbi.nlm.nih.gov/gene/?term=74325	2310046E19Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021551	74326	Hnrnpr	http://www.ncbi.nlm.nih.gov/gene/?term=74326	"2610003J05Rik, 2610528B01Rik, Hnrpr "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021552	74330	Dnajc14	http://www.ncbi.nlm.nih.gov/gene/?term=74330	"5730551F12Rik, DNAJ, DRIP78, HDJ3, LIP6 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021553	74333	A330040F15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74333		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021554	74340	Ahcyl2	http://www.ncbi.nlm.nih.gov/gene/?term=74340	"4631427C17Rik, AI227036, Adohcyase3, mKIAA0828 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021555	74347	Tldc1	http://www.ncbi.nlm.nih.gov/gene/?term=74347	"4632415K11Rik, Kiaa1609 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021556	7434	VIPR2	http://www.ncbi.nlm.nih.gov/gene/?term=7434	"C16DUPq36.3, DUP7q36.3, PACAP-R-3, PACAP-R3, VIP-R-2, VPAC2, VPAC2R, VPCAP2R "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021557	7434	VIPR2	http://www.ncbi.nlm.nih.gov/gene/?term=7434	"C16DUPq36.3, DUP7q36.3, PACAP-R-3, PACAP-R3, VIP-R-2, VPAC2, VPAC2R, VPCAP2R "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021558	74355	Smchd1	http://www.ncbi.nlm.nih.gov/gene/?term=74355	"4931400A14Rik, AW554188, MommeD1, mKIAA0650 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021559	74356	4931428F04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74356	"AI426165, Kiaa0895l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021560	74360	Cep57	http://www.ncbi.nlm.nih.gov/gene/?term=74360	"3110002L15Rik, 4921510P06Rik, 4931428M20Rik, AI467480, Tsp57, mKIAA0092 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021561	7436	VLDLR	http://www.ncbi.nlm.nih.gov/gene/?term=7436	"CAMRQ1, CARMQ1, CHRMQ1, VLDL-RCH, VLDLR "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00021562	74388	Dpp8	http://www.ncbi.nlm.nih.gov/gene/?term=74388	"2310004I03Rik, 4932434F09Rik, AI666706, DPP VIII "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021563	74388	Dpp8	http://www.ncbi.nlm.nih.gov/gene/?term=74388	"2310004I03Rik, 4932434F09Rik, AI666706, DPP VIII "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021564	74392	Specc1l	http://www.ncbi.nlm.nih.gov/gene/?term=74392	"4930470P14Rik, 4932439K10Rik, 9530057A13Rik, AI317249, Cytsa, mKIAA0376 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021565	74399	Duxf3	http://www.ncbi.nlm.nih.gov/gene/?term=74399	4933403O03Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021566	74401	4933406J08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74401	TERB2	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021567	74410	Ttll11	http://www.ncbi.nlm.nih.gov/gene/?term=74410	"4932702F08Rik, 4933424A20Rik, AU043211, D2Ertd624e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021568	7442	TRPV1	http://www.ncbi.nlm.nih.gov/gene/?term=7442	VR1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021569	7442	TRPV1	http://www.ncbi.nlm.nih.gov/gene/?term=7442	VR1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021570	74437	4933402E13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74437		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021571	7443	VRK1	http://www.ncbi.nlm.nih.gov/gene/?term=7443	"PCH1, PCH1A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021572	7443	VRK1	http://www.ncbi.nlm.nih.gov/gene/?term=7443	"PCH1, PCH1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021573	7443	VRK1	http://www.ncbi.nlm.nih.gov/gene/?term=7443	"PCH1, PCH1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021574	7444	VRK2	http://www.ncbi.nlm.nih.gov/gene/?term=7444		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021575	74451	Pgs1	http://www.ncbi.nlm.nih.gov/gene/?term=74451	"2610019F11Rik, 4933424M23Rik, SAF "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021576	74455	Nsun6	http://www.ncbi.nlm.nih.gov/gene/?term=74455	"4933403D21Rik, 4933414E04Rik, NOPD1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021577	74467	Pus10	http://www.ncbi.nlm.nih.gov/gene/?term=74467	"2810013G11Rik, 4933435A13Rik, AU014648, C77560, Ccdc139 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021578	74474	5230400M06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74474		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021579	74479	Snx11	http://www.ncbi.nlm.nih.gov/gene/?term=74479	"4933439F10Rik, A930041K09Rik, AI117694 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021580	7448	VTN	http://www.ncbi.nlm.nih.gov/gene/?term=7448	"V75, VN, VNT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021581	74493	Tnks2	http://www.ncbi.nlm.nih.gov/gene/?term=74493	"5430432P15Rik, AA517131, AI662480, ARTD6, TNKS-2, Tank2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021582	74498	Gorasp1	http://www.ncbi.nlm.nih.gov/gene/?term=74498	"5430411C10Rik, GOLPH5, GRASP65, P65 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021583	74507	5530400K19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74507		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021584	74522	Morc2a	http://www.ncbi.nlm.nih.gov/gene/?term=74522	"8430403M08Rik, Zcwcc1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021585	74528	Mgme1	http://www.ncbi.nlm.nih.gov/gene/?term=74528	"8430406I07Rik, AI426476 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021586	74530	9030612E09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74530		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021587	74533	Gzf1	http://www.ncbi.nlm.nih.gov/gene/?term=74533	"8430437G08Rik, Zfp336, mGZF1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021588	74536	9030409C19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74536		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021589	74538	9030409K20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74538		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021590	7453	WARS	http://www.ncbi.nlm.nih.gov/gene/?term=7453	"GAMMA-2, IFI53, IFP53 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021591	7453	WARS	http://www.ncbi.nlm.nih.gov/gene/?term=7453	"GAMMA-2, IFI53, IFP53 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021592	7453	WARS	http://www.ncbi.nlm.nih.gov/gene/?term=7453	"GAMMA-2, IFI53, IFP53 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021593	74545	9030417H13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74545		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021594	7454	WAS	http://www.ncbi.nlm.nih.gov/gene/?term=7454	"IMD2, SCNX, THC, THC1, WASP, WASPA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021595	74554	9130002K18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74554		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021596	74561	Nkx6-3	http://www.ncbi.nlm.nih.gov/gene/?term=74561	"9130417I07Rik, Nkx6.3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021597	7456	WIPF1	http://www.ncbi.nlm.nih.gov/gene/?term=7456	"PRPL-2, WAS2, WASPIP, WIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021598	74570	Zkscan1	http://www.ncbi.nlm.nih.gov/gene/?term=74570	"5930429A01Rik, 9130423L19Rik, 9230118B16Rik, AI646829, AI788588, C87323, KOX18, PHZ-37, ZNF139 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021599	74580	Pyroxd2	http://www.ncbi.nlm.nih.gov/gene/?term=74580	"3830409H07Rik, 4833409A17Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021600	74583	4833411I10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74583		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021601	74587	4833422B07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74587		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021602	74587	4833422B07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74587		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021603	7458	EIF4H	http://www.ncbi.nlm.nih.gov/gene/?term=7458	"WBSCR1, WSCR1, eIF-4H "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021604	7458	EIF4H	http://www.ncbi.nlm.nih.gov/gene/?term=7458	"WBSCR1, WSCR1, eIF-4H "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021605	74600	Mrpl47	http://www.ncbi.nlm.nih.gov/gene/?term=74600	"4833424P18Rik, CGI-204, ENSMUSG00000051761, Gm9859, L47mt, MRP-L47, MTF/L47, NCM1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021606	74601	4833427F10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74601		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021607	7461	CLIP2	http://www.ncbi.nlm.nih.gov/gene/?term=7461	"CLIP, CLIP-115, CYLN2, WBSCR3, WBSCR4, WSCR3, WSCR4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021608	7461	CLIP2	http://www.ncbi.nlm.nih.gov/gene/?term=7461	"CLIP, CLIP-115, CYLN2, WBSCR3, WBSCR4, WSCR3, WSCR4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021609	74658	4930445G23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74658		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021610	7465	WEE1	http://www.ncbi.nlm.nih.gov/gene/?term=7465	"WEE1Ahu, WEE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021611	74672	4930449A18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74672		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021612	74673	Spdye4a	http://www.ncbi.nlm.nih.gov/gene/?term=74673	"4930445A17Rik, 4930451F05Rik, RINGO E4A, Spdy2, Spdye4, Spy/Ringo B, spdyb "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021613	74676	4930456A14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74676		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021614	74682	Wdr35	http://www.ncbi.nlm.nih.gov/gene/?term=74682	"4930459M12Rik, 4931430C06, mKIAA1336 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021615	7468	WHSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7468	"MMSET, NSD2, REIIBP, TRX5, WHS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021616	7468	WHSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7468	"MMSET, NSD2, REIIBP, TRX5, WHS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021617	7468	WHSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7468	"MMSET, NSD2, REIIBP, TRX5, WHS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021618	7468	WHSC1	http://www.ncbi.nlm.nih.gov/gene/?term=7468	"MMSET, NSD2, REIIBP, TRX5, WHS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021619	74693	4930509J09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74693		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021620	746	TMEM258	http://www.ncbi.nlm.nih.gov/gene/?term=746	C11orf10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021621	746	TMEM258	http://www.ncbi.nlm.nih.gov/gene/?term=746	C11orf10	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021622	74704	4930518I15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74704		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021623	74707	4930521G14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74707		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021624	74718	Snx16	http://www.ncbi.nlm.nih.gov/gene/?term=74718	"4930522N22Rik, AI117577, AI747675 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021625	74730	5830413G11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74730		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021626	74737	Pcf11	http://www.ncbi.nlm.nih.gov/gene/?term=74737	"2500001H09Rik, 5730417B17Rik, C77803 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021627	74741	C2cd5	http://www.ncbi.nlm.nih.gov/gene/?term=74741	"5730419I09Rik, C030008B15Rik, CDP138 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021628	7474	WNT5A	http://www.ncbi.nlm.nih.gov/gene/?term=7474	hWNT5A	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021629	74753	Trmo	http://www.ncbi.nlm.nih.gov/gene/?term=74753	"5830415F09Rik, AV014846, Nap1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021630	74764	Klc4	http://www.ncbi.nlm.nih.gov/gene/?term=74764	"1200014P03Rik, AA408085, AW146303, Knsl8 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021631	74778	Rrp7a	http://www.ncbi.nlm.nih.gov/gene/?term=74778	"1110014J01Rik, AA408146, Kheg1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021632	747	DAGLA	http://www.ncbi.nlm.nih.gov/gene/?term=747	"C11orf11, DAGL(ALPHA), DAGLALPHA, NSDDR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021633	7481	WNT11	http://www.ncbi.nlm.nih.gov/gene/?term=7481	HWNT11	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021634	74838	Naa15	http://www.ncbi.nlm.nih.gov/gene/?term=74838	"5730450D16Rik, 6330400I15, ASTBDN, Narg1, Tbdn-1, mNAT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021635	74841	Usp38	http://www.ncbi.nlm.nih.gov/gene/?term=74841	"4631402N15Rik, 4833420O05Rik, AA536967, AU044701, AW544820, mKIAA1891 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021636	74857	4930448O17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74857		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021637	7485	WRB	http://www.ncbi.nlm.nih.gov/gene/?term=7485	"CHD5, GET1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021638	7485	WRB	http://www.ncbi.nlm.nih.gov/gene/?term=7485	"CHD5, GET1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021639	74867	4930445B03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74867		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021640	74869	4930447G04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74869		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021641	7486	WRN	http://www.ncbi.nlm.nih.gov/gene/?term=7486	"RECQ3, RECQL2, RECQL3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021642	74873	4930443G03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74873	Gm44273	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021643	74886	4930445K14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74886		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021644	74896	4930405A10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74896	4930456G20Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021645	7490	WT1	http://www.ncbi.nlm.nih.gov/gene/?term=7490	"AWT1, EWS-WT1, GUD, NPHS4, WAGR, WIT-2, WT33 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021646	74914	Cylc2	http://www.ncbi.nlm.nih.gov/gene/?term=74914	4930488P18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021647	74936	4930474B08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74936		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021648	7494	XBP1	http://www.ncbi.nlm.nih.gov/gene/?term=7494	"TREB-5, TREB5, XBP-1, XBP2 "	mRNA	Homo sapiens	26068456	Nucleus	MCF-7|293T|T47D |3T3 cell	RT-PCR	"Our results reveal the presence of basal unconventional splicing of XBP1 mRNA in the nucleus that also requires inositol-requiring transmembrane kinase and endonuclease 1a (IRE1a) and can occur independently of acute ER stress. Furthermore, we confirm that acute ER stress induces the splicing of XBP1 mRNA predominantly occurring in the cytoplasm, but it also promotes the splicing in the nucleus. "
RLID00021649	7494	XBP1	http://www.ncbi.nlm.nih.gov/gene/?term=7494	"TREB-5, TREB5, XBP-1, XBP2 "	mRNA	Homo sapiens	26068456	Cytoplasm	MCF-7|293T|T47D |3T3 cell	RT-PCR	"Our results reveal the presence of basal unconventional splicing of XBP1 mRNA in the nucleus that also requires inositol-requiring transmembrane kinase and endonuclease 1a (IRE1a) and can occur independently of acute ER stress. Furthermore, we confirm that acute ER stress induces the splicing of XBP1 mRNA predominantly occurring in the cytoplasm, but it also promotes the splicing in the nucleus. "
RLID00021650	7494	XBP1	http://www.ncbi.nlm.nih.gov/gene/?term=7494	"TREB-5, TREB5, XBP-1, XBP2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021651	74957	4930486N12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74957		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021652	74972	4930500A05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74972		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021653	74978	Lrriq1	http://www.ncbi.nlm.nih.gov/gene/?term=74978	"4930503E15Rik, Gm1557 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021654	74996	Usp47	http://www.ncbi.nlm.nih.gov/gene/?term=74996	"4930502N04Rik, A630020C16Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021655	75004	4930467D19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75004		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021656	75036	4930488B01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75036	"AI844408, R74771 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021657	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	11440993	Nucleus	Embryonic stem cell	In situ hybridization|RT-PCR	These results identify for the first time a dual function for Tsix as both a repressor of the steady-state level of Xist expression and as a regulator of the distribution of Xist RNA within the nucleus. 
RLID00021658	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	12900550	Nucleus	Somatic cell	In situ hybridization|RT-PCR	"XIST transcripts remain in the nucleus, and their specific localization to the inactive X is important for silencing; however, it is not known how these transcripts localize to the inactive X chromosome.  "
RLID00021659	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	1423611	Nucleus	Lymphoblast|Fibroblast	In situ hybridization	"Consistent with this, fluorescence in situ hybridization experiments demonstrate localization of XIST RNA within the nucleus to a position indistinguishable from the X inactivation-associated Barr body. "
RLID00021660	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	16682630	Nucleus	Fibroblast	In situ hybridization	"We have shown that XIST RNA remains in the nucleus, functionally associated with the inactive chromatin, forming an interphase territory coincident with Xi. "
RLID00021661	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	17146760	Nucleus	Breast|Ovarian cancer cell	In situ hybridization|qRT-PCR	"Recently, it was reported that BRCA1 supports localization of XIST RNA to the inactive X chromosome (Xi) in women. "
RLID00021662	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	25332394	Nucleus	-	lncRNAdb	Data are collected from lncRNAdb database: http://www.lncrnadb.org/xist/
RLID00021663	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	19571010	Nucleus	HFF|HLF|HeLa cell	Fluorescence in situ hybridization	"Figure 3b: Subcellular localization analysis of lincRNAs by RNA FISH demonstrates localization of lincRNAs to the nucleus. Each panel represents the in situ hybridization of �0 fluorescently labeled DNA oligos with complementarity to the interrogated lincRNA. RNA FISH experiments were performed in male hFF for each represented lincRNA (XIST, HOTAIR, TUG-1, lincMKLN-1, lincFOXF1, and lincSFPQ), and also in female hLF for XIST (XX). White “speckles�indicate the subcellular localization of each lincRNA. The nuclear compartment is demarked by DAPI staining (purple). "
RLID00021664	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	8636206	Nucleus	Epithelial line	In situ hybridization	The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. 
RLID00021665	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	9560241	Nucleus	4F5 cell	RT-PCR	We isolated RNA from nuclear and cytoplasmic extracts and found by RT-PCR that the spliced XIST RNA was localized properly to the nuclear fraction in the 4F5 cells (Fi.4).
RLID00021666	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	25690653	Nucleus	P493-6 cell	qRT-PCR	"To validate the isolation of nuclear and cytoplasmic fractions, the enrichment of 3 nuclear (ANRIL, MIAT, XIST) and 3 cytoplasmic (RPPH1, DANCR, tRNA-Lys) RNAs was analyzed by qRT-PCR. "
RLID00021667	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66 "	lncRNA	Homo sapiens	22955988	Nucleus	Brain	Microarray	"We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3  were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold). "
RLID00021668	7504	XK	http://www.ncbi.nlm.nih.gov/gene/?term=7504	"KX, MCLDS, NA, NAC, X1k, XKR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021669	75052	4930509B17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75052		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021670	75062	Sf3a3	http://www.ncbi.nlm.nih.gov/gene/?term=75062	"4930512K19Rik, 60kDa "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021671	75068	4930513N24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75068		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021672	7507	XPA	http://www.ncbi.nlm.nih.gov/gene/?term=7507	"XP1, XPAC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021673	75083	Usp50	http://www.ncbi.nlm.nih.gov/gene/?term=75083	"1700086G18Rik, 4930511O11Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021674	75086	4930520P13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75086		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021675	7508	XPC	http://www.ncbi.nlm.nih.gov/gene/?term=7508	"RAD4, XP3, XPCC, p125 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021676	75103	4930518I17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75103		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021677	751071	METTL12	http://www.ncbi.nlm.nih.gov/gene/?term=751071	U99HG	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021678	75108	4930513N20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75108		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021679	7511	XPNPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=7511	"APP1, SAMP, XPNPEP, XPNPEPL, XPNPEPL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021680	7511	XPNPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=7511	"APP1, SAMP, XPNPEP, XPNPEPL, XPNPEPL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021681	7511	XPNPEP1	http://www.ncbi.nlm.nih.gov/gene/?term=7511	"APP1, SAMP, XPNPEP, XPNPEPL, XPNPEPL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021682	75137	Rprd2	http://www.ncbi.nlm.nih.gov/gene/?term=75137	"2810036A19Rik, 4930535B03Rik, 6720469I21Rik, AL022841, AL022940, AU021304, BB077382, mKIAA0460 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021683	75139	Gm38397	http://www.ncbi.nlm.nih.gov/gene/?term=75139		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021684	7514	XPO1	http://www.ncbi.nlm.nih.gov/gene/?term=7514	"CRM1, emb, exp1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021685	7514	XPO1	http://www.ncbi.nlm.nih.gov/gene/?term=7514	"CRM1, emb, exp1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021686	7514	XPO1	http://www.ncbi.nlm.nih.gov/gene/?term=7514	"CRM1, emb, exp1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021687	75154	4930542M03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75154		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021688	75155	4930529K09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75155	4930507G21Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021689	7515	XRCC1	http://www.ncbi.nlm.nih.gov/gene/?term=7515	RCC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021690	7516	XRCC2	http://www.ncbi.nlm.nih.gov/gene/?term=7516		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021691	7516	XRCC2	http://www.ncbi.nlm.nih.gov/gene/?term=7516		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021692	7516	XRCC2	http://www.ncbi.nlm.nih.gov/gene/?term=7516		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021693	7517	XRCC3	http://www.ncbi.nlm.nih.gov/gene/?term=7517	CMM6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021694	751865	Sap25	http://www.ncbi.nlm.nih.gov/gene/?term=751865		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021695	75188	1700009J07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75188	4930535B06Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021696	7518	XRCC4	http://www.ncbi.nlm.nih.gov/gene/?term=7518	SSMED	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021697	75194	4930527A07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75194		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021698	75203	4930539N22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75203		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021699	75204	Orly	http://www.ncbi.nlm.nih.gov/gene/?term=75204	"4930529H12Rik, 4933412F11Rik, Asty(rec) "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021700	7520	XRCC5	http://www.ncbi.nlm.nih.gov/gene/?term=7520	"KARP-1, KARP1, KU80, KUB2, Ku86, NFIV "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021701	7520	XRCC5	http://www.ncbi.nlm.nih.gov/gene/?term=7520	"KARP-1, KARP1, KU80, KUB2, Ku86, NFIV "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021702	75210	Prr3	http://www.ncbi.nlm.nih.gov/gene/?term=75210	"4930540G07Rik, Cat56 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021703	75211	4930542D17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75211		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021704	75220	4930535I16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75220		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021705	75221	Dpp3	http://www.ncbi.nlm.nih.gov/gene/?term=75221	"4930533O14Rik, C86324 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021706	75252	4930555G21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75252		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021707	7525	YES1	http://www.ncbi.nlm.nih.gov/gene/?term=7525	"HsT441, P61-YES, Yes, c-yes "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021708	7525	YES1	http://www.ncbi.nlm.nih.gov/gene/?term=7525	"HsT441, P61-YES, Yes, c-yes "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021709	7525	YES1	http://www.ncbi.nlm.nih.gov/gene/?term=7525	"HsT441, P61-YES, Yes, c-yes "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021710	7525	YES1	http://www.ncbi.nlm.nih.gov/gene/?term=7525	"HsT441, P61-YES, Yes, c-yes "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021711	75269	4930564D02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75269		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021712	75275	Tmco5b	http://www.ncbi.nlm.nih.gov/gene/?term=75275	4930563P21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021713	75284	Bcdin3d	http://www.ncbi.nlm.nih.gov/gene/?term=75284	"4930556P03Rik, AV138748 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021714	7528	YY1	http://www.ncbi.nlm.nih.gov/gene/?term=7528	"DELTA, INO80S, NF-E1, UCRBP, YIN-YANG-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021715	7528	YY1	http://www.ncbi.nlm.nih.gov/gene/?term=7528	"DELTA, INO80S, NF-E1, UCRBP, YIN-YANG-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021716	7528	YY1	http://www.ncbi.nlm.nih.gov/gene/?term=7528	"DELTA, INO80S, NF-E1, UCRBP, YIN-YANG-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021717	7529	YWHAB	http://www.ncbi.nlm.nih.gov/gene/?term=7529	"GW128, HEL-S-1, HS1, KCIP-1, YWHAA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021718	75302	Asxl2	http://www.ncbi.nlm.nih.gov/gene/?term=75302	"4930556B16Rik, mKIAA1685 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021719	75304	4930563E22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75304		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021720	75305	Ankrd53	http://www.ncbi.nlm.nih.gov/gene/?term=75305	4930564N15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021721	75316	Taf1d	http://www.ncbi.nlm.nih.gov/gene/?term=75316	"2810003M17Rik, 4930553M18Rik, 5930426I11Rik, Josd3, TAF(I)41, TAFI41 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021722	7531	YWHAE	http://www.ncbi.nlm.nih.gov/gene/?term=7531	"14-3-3E, HEL2, KCIP-1, MDCR, MDS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021723	7531	YWHAE	http://www.ncbi.nlm.nih.gov/gene/?term=7531	"14-3-3E, HEL2, KCIP-1, MDCR, MDS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021724	7531	YWHAE	http://www.ncbi.nlm.nih.gov/gene/?term=7531	"14-3-3E, HEL2, KCIP-1, MDCR, MDS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021725	75320	Etnk1	http://www.ncbi.nlm.nih.gov/gene/?term=75320	"1110061E11Rik, 4930555L11Rik, AI195356, AI841245, C80956, D6Ertd3e, EKI1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021726	75326	4930563J15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75326		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021727	7532	YWHAG	http://www.ncbi.nlm.nih.gov/gene/?term=7532	"14-3-3GAMMA, PPP1R170 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021728	7532	YWHAG	http://www.ncbi.nlm.nih.gov/gene/?term=7532	"14-3-3GAMMA, PPP1R170 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021729	7532	YWHAG	http://www.ncbi.nlm.nih.gov/gene/?term=7532	"14-3-3GAMMA, PPP1R170 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021730	75335	4930549O18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75335		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021731	75339	Mphosph8	http://www.ncbi.nlm.nih.gov/gene/?term=75339	"1500035L22Rik, 4930548G07Rik, AU040635 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021732	7533	YWHAH	http://www.ncbi.nlm.nih.gov/gene/?term=7533	YWHA1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021733	7533	YWHAH	http://www.ncbi.nlm.nih.gov/gene/?term=7533	YWHA1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021734	7533	YWHAH	http://www.ncbi.nlm.nih.gov/gene/?term=7533	YWHA1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021735	75349	4930556J02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75349		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021736	7534	YWHAZ	http://www.ncbi.nlm.nih.gov/gene/?term=7534	"14-3-3-zeta, HEL-S-3, HEL-S-93, HEL4, KCIP-1, YWHAD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021737	7534	YWHAZ	http://www.ncbi.nlm.nih.gov/gene/?term=7534	"14-3-3-zeta, HEL-S-3, HEL-S-93, HEL4, KCIP-1, YWHAD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021738	7534	YWHAZ	http://www.ncbi.nlm.nih.gov/gene/?term=7534	"14-3-3-zeta, HEL-S-3, HEL-S-93, HEL4, KCIP-1, YWHAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021739	75364	4930549P19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75364		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021740	7536	SF1	http://www.ncbi.nlm.nih.gov/gene/?term=7536	"BBP, D11S636, MBBP, ZCCHC25, ZFM1, ZNF162 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021741	7536	SF1	http://www.ncbi.nlm.nih.gov/gene/?term=7536	"BBP, D11S636, MBBP, ZCCHC25, ZFM1, ZNF162 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021742	75373	4930597O21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75373		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021743	75387	Sirt4	http://www.ncbi.nlm.nih.gov/gene/?term=75387	4930596O17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021744	75410	Kmt2b	http://www.ncbi.nlm.nih.gov/gene/?term=75410	"2610014H22Rik, Mll2, Wbp7, mKIAA0304 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021745	75415	Arhgap12	http://www.ncbi.nlm.nih.gov/gene/?term=75415	2810011M08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021746	75416	Nop14	http://www.ncbi.nlm.nih.gov/gene/?term=75416	"2610033H07Rik, Nol14 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021747	7541	ZBTB14	http://www.ncbi.nlm.nih.gov/gene/?term=7541	"ZF5, ZFP-161, ZFP-5, ZFP161, ZNF478 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021748	75420	Secisbp2	http://www.ncbi.nlm.nih.gov/gene/?term=75420	"2210413N07Rik, 2810012K13Rik, SBP2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021749	75424	Zfp820	http://www.ncbi.nlm.nih.gov/gene/?term=75424	2610036F08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021750	7542	ZFPL1	http://www.ncbi.nlm.nih.gov/gene/?term=7542	"D11S750, MCG4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021751	75437	1700006E09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75437		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021752	7543	ZFX	http://www.ncbi.nlm.nih.gov/gene/?term=7543	ZNF926	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021753	75452	Ascc2	http://www.ncbi.nlm.nih.gov/gene/?term=75452	"1700011I11Rik, 2610034L15Rik, AI482016, ASC1p100, AW046480 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021754	75458	Cklf	http://www.ncbi.nlm.nih.gov/gene/?term=75458	"1700001C14Rik, 1810018M11Rik, C32, CKLF1, CKLF3, CKLF4, CKLF52, Cklf6, HSPC224, UCK-1, Cklf "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021755	7546	ZIC2	http://www.ncbi.nlm.nih.gov/gene/?term=7546	HPE5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021756	754	PTTG1IP	http://www.ncbi.nlm.nih.gov/gene/?term=754	"C21orf1, C21orf3, PBF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021757	754	PTTG1IP	http://www.ncbi.nlm.nih.gov/gene/?term=754	"C21orf1, C21orf3, PBF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021758	75514	1700013H16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75514	"Slx2, Xlr6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021759	7551	ZNF3	http://www.ncbi.nlm.nih.gov/gene/?term=7551	"A8-51, HF.12, KOX25, PP838, Zfp113 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021760	7551	ZNF3	http://www.ncbi.nlm.nih.gov/gene/?term=7551	"A8-51, HF.12, KOX25, PP838, Zfp113 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021761	75530	Lyrm7	http://www.ncbi.nlm.nih.gov/gene/?term=75530	"1700024C24Rik, 9330147L21Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021762	75547	Akap13	http://www.ncbi.nlm.nih.gov/gene/?term=75547	"1700026G02Rik, 5730522G15Rik, 5830460E08Rik, AKAP-Lbc, BRX, Ht31, LBC, PROTO-LB, PROTO-LBC "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021763	7555	CNBP	http://www.ncbi.nlm.nih.gov/gene/?term=7555	"CNBP1, DM2, PROMM, RNF163, ZCCHC22, ZNF9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021764	7555	CNBP	http://www.ncbi.nlm.nih.gov/gene/?term=7555	"CNBP1, DM2, PROMM, RNF163, ZCCHC22, ZNF9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021765	7555	CNBP	http://www.ncbi.nlm.nih.gov/gene/?term=7555	"CNBP1, DM2, PROMM, RNF163, ZCCHC22, ZNF9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021766	7555	CNBP	http://www.ncbi.nlm.nih.gov/gene/?term=7555	"CNBP1, DM2, PROMM, RNF163, ZCCHC22, ZNF9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021767	7555	CNBP	http://www.ncbi.nlm.nih.gov/gene/?term=7555	"CNBP1, DM2, PROMM, RNF163, ZCCHC22, ZNF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021768	75560	Ep400	http://www.ncbi.nlm.nih.gov/gene/?term=75560	"1700020J09Rik, AU023439, mDomino, mKIAA1498, p400 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021769	75565	Sgf29	http://www.ncbi.nlm.nih.gov/gene/?term=75565	"1700023O11Rik, 9530025I05Rik, Ccdc101 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021770	75580	Zbtb4	http://www.ncbi.nlm.nih.gov/gene/?term=75580	"2310026P19Rik, 9230111I22Rik, mKIAA1538 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021771	75596	Prl7b1	http://www.ncbi.nlm.nih.gov/gene/?term=75596	"1600014J19Rik, Ghd17, PLP-N, Prlpn "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021772	7559	ZNF12	http://www.ncbi.nlm.nih.gov/gene/?term=7559	"GIOT-3, HZF11, KOX3, ZNF325 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021773	75604	Tm4sf5	http://www.ncbi.nlm.nih.gov/gene/?term=75604	"2010003F10Rik, AI323987 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021774	75607	Wnk2	http://www.ncbi.nlm.nih.gov/gene/?term=75607	"1810073P09Rik, AW122246, ESTM15, X83337, mKIAA1760 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021775	75612	Gns	http://www.ncbi.nlm.nih.gov/gene/?term=75612	"2610016K11Rik, AU042285, C87209, G6S, N28088 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021776	75613	Med25	http://www.ncbi.nlm.nih.gov/gene/?term=75613	"2610034E13Rik, 2610529E18Rik, ESTM2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021777	75614	Rab26os	http://www.ncbi.nlm.nih.gov/gene/?term=75614	2610019E17Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021778	75616	Smim15	http://www.ncbi.nlm.nih.gov/gene/?term=75616	2810008M24Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021779	75617	Rps25	http://www.ncbi.nlm.nih.gov/gene/?term=75617	2810009D21Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021780	75617	Rps25	http://www.ncbi.nlm.nih.gov/gene/?term=75617	2810009D21Rik	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00021781	75619	Fastkd2	http://www.ncbi.nlm.nih.gov/gene/?term=75619	2810421I24Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021782	7561	ZNF14	http://www.ncbi.nlm.nih.gov/gene/?term=7561	"GIOT-4, KOX6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021783	75620	Kxd1	http://www.ncbi.nlm.nih.gov/gene/?term=75620	"0610030B01Rik, 2810422J05Rik, C78305 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021784	75627	Snapc1	http://www.ncbi.nlm.nih.gov/gene/?term=75627	"2700033G17Rik, AU015787 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021785	7562	ZNF708	http://www.ncbi.nlm.nih.gov/gene/?term=7562	"KOX8, ZNF15, ZNF15L1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021786	7562	ZNF708	http://www.ncbi.nlm.nih.gov/gene/?term=7562	"KOX8, ZNF15, ZNF15L1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021787	75638	1700008O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75638		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021788	75646	Rai14	http://www.ncbi.nlm.nih.gov/gene/?term=75646	"1700008J19Rik, 1700020L11Rik, Ankycorbin, Norpeg, mKIAA1334 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021789	75657	Speer4a	http://www.ncbi.nlm.nih.gov/gene/?term=75657	"1700027N01Rik, SPEER-4A "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021790	75659	Wdr54	http://www.ncbi.nlm.nih.gov/gene/?term=75659	1700030E05Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021791	75660	Lin37	http://www.ncbi.nlm.nih.gov/gene/?term=75660	1810054G18Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021792	75669	Pik3r4	http://www.ncbi.nlm.nih.gov/gene/?term=75669	"2210010O15Rik, C730038E05Rik, C85833, D9Ertd418e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021793	7566	ZNF18	http://www.ncbi.nlm.nih.gov/gene/?term=7566	"HDSG1, KOX11, ZKSCAN6, ZNF535, ZSCAN38, Zfp535 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021794	7566	ZNF18	http://www.ncbi.nlm.nih.gov/gene/?term=7566	"HDSG1, KOX11, ZKSCAN6, ZNF535, ZSCAN38, Zfp535 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021795	75677	Cldn22	http://www.ncbi.nlm.nih.gov/gene/?term=75677	"2210404A22Rik, 5330431C14Rik, 9530051B05Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021796	75692	Nr2c2ap	http://www.ncbi.nlm.nih.gov/gene/?term=75692	2310073E15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021797	7569	ZNF182	http://www.ncbi.nlm.nih.gov/gene/?term=7569	"HHZ150, KOX14, ZNF21, Zfp182 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021798	75706	Krt24	http://www.ncbi.nlm.nih.gov/gene/?term=75706	"2310058N18Rik, 2310075C18Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021799	75717	Cul5	http://www.ncbi.nlm.nih.gov/gene/?term=75717	"4921514I20Rik, 8430423K24Rik, AI852817, C030032G03Rik, C330021I08Rik, VACM-1, VACM1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021800	7571	ZNF23	http://www.ncbi.nlm.nih.gov/gene/?term=7571	"KOX16, ZNF359, ZNF612, Zfp612 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021801	75725	Phf14	http://www.ncbi.nlm.nih.gov/gene/?term=75725	"1110001C23Rik, 4932409F11Rik, 5730446A07Rik, AA623952, AV297001, mKIAA0783 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021802	7572	ZNF24	http://www.ncbi.nlm.nih.gov/gene/?term=7572	"KOX17, RSG-A, ZNF191, ZSCAN3, Zfp191 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021803	7572	ZNF24	http://www.ncbi.nlm.nih.gov/gene/?term=7572	"KOX17, RSG-A, ZNF191, ZSCAN3, Zfp191 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021804	75731	Idnk	http://www.ncbi.nlm.nih.gov/gene/?term=75731	5133401N09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021805	75734	Mff	http://www.ncbi.nlm.nih.gov/gene/?term=75734	"5230400G24Rik, AI314724 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021806	75736	Bcl2l12	http://www.ncbi.nlm.nih.gov/gene/?term=75736	"2810475P17Rik, 5430429M05Rik, Bcl-L12, Bcl2-L12 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021807	75745	Rian	http://www.ncbi.nlm.nih.gov/gene/?term=75745	"5530401N18Rik, C130089L09Rik, Meg8 "	lncRNA	Mus musculus	11481034	Nucleus	Embryos cell	In situ hybridization|RT-PCR	"The Rian transcript did not have any apparent open reading frame, and its transcript was exclusively localized to the nucleus. "
RLID00021808	75745	Rian	http://www.ncbi.nlm.nih.gov/gene/?term=75745	"5530401N18Rik, C130089L09Rik, Meg8 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021809	7574	ZNF26	http://www.ncbi.nlm.nih.gov/gene/?term=7574	"HEL-179, KOX20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021810	75751	Ipo4	http://www.ncbi.nlm.nih.gov/gene/?term=75751	"8430408O15Rik, AA409693, Imp4a, RanBP4 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021811	75753	Klf17	http://www.ncbi.nlm.nih.gov/gene/?term=75753	"7420700M05Rik, AA420409, AU043468, C85123, D4Ertd561e, Gzf, Zfp393 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021812	75754	9030607L02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75754		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021813	75763	Dcaf17	http://www.ncbi.nlm.nih.gov/gene/?term=75763	"2810055O12Rik, 4833418A01Rik, A030004A10Rik, A930009G19Rik, AI448937 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021814	75764	Slx1b	http://www.ncbi.nlm.nih.gov/gene/?term=75764	"1110030E23Rik, 2410170E21Rik, 4833422P03Rik, AI853643, Giyd1, Giyd2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021815	75767	Rab11fip1	http://www.ncbi.nlm.nih.gov/gene/?term=75767	"2010200K21Rik, 4833414G05Rik, Rcp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021816	7576	ZNF28	http://www.ncbi.nlm.nih.gov/gene/?term=7576	KOX24	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021817	75775	4930402K13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75775		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021818	75786	Ckap5	http://www.ncbi.nlm.nih.gov/gene/?term=75786	"3110043H24Rik, 4930432B04Rik, D730027C18Rik, T25636, mKIAA0097 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021819	75797	4930435N07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75797		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021820	757	TMEM50B	http://www.ncbi.nlm.nih.gov/gene/?term=757	"C21orf4, HCVP7TP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021821	757	TMEM50B	http://www.ncbi.nlm.nih.gov/gene/?term=757	"C21orf4, HCVP7TP3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021822	75801	4930447C04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75801	"4921504I02Rik, A930035O15Rik, Six6OS, Six6as, Six6os1 "	mRNA	Mus musculus	15703187	Nucleus	Embryonic tissue	In situ hybridization|RT-PCR	"We detected the expression in adult retina (postnatal day 30, P30) of Six3OS, Six6OS, Otx2OS, CrxOS and RaxOS (Fig. 3 and data not shown). In general, these transcripts were all expressed at higher levels in the inner nuclear layer (INL) and in the ganglion cell layer (GCL).  "
RLID00021823	75805	Nln	http://www.ncbi.nlm.nih.gov/gene/?term=75805	"4930472G13Rik, C79345 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021824	7580	ZNF32	http://www.ncbi.nlm.nih.gov/gene/?term=7580	KOX30	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021825	7580	ZNF32	http://www.ncbi.nlm.nih.gov/gene/?term=7580	KOX30	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021826	7581	ZNF33A	http://www.ncbi.nlm.nih.gov/gene/?term=7581	"KOX2, KOX31, KOX5, NF11A, ZNF11, ZNF11A, ZNF33, ZZAPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021827	75838	4930560O18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75838		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021828	75841	Rnf139	http://www.ncbi.nlm.nih.gov/gene/?term=75841	4930555P18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021829	75842	4930556H04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75842		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021830	7584	ZNF35	http://www.ncbi.nlm.nih.gov/gene/?term=7584	"HF.10, HF10, Zfp105 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021831	75858	Speer4cos	http://www.ncbi.nlm.nih.gov/gene/?term=75858	"4930568L21Rik, SPEER-7, Speer7-ps, Speer7-ps1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021832	7586	ZKSCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=7586	"9130423L19Rik, KOX18, PHZ-37, ZNF139, ZNF36, ZSCAN33 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021833	7586	ZKSCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=7586	"9130423L19Rik, KOX18, PHZ-37, ZNF139, ZNF36, ZSCAN33 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021834	7586	ZKSCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=7586	"9130423L19Rik, KOX18, PHZ-37, ZNF139, ZNF36, ZSCAN33 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021835	75872	4930568E02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75872		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021836	7587	ZNF37A	http://www.ncbi.nlm.nih.gov/gene/?term=7587	"KOX21, ZNF37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021837	75937	4930594M17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75937		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021838	75938	4930570E01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75938		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021839	7593	MZF1	http://www.ncbi.nlm.nih.gov/gene/?term=7593	"MZF-1B, ZFP98, ZNF42, ZSCAN6, MZF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021840	7593	MZF1	http://www.ncbi.nlm.nih.gov/gene/?term=7593	"MZF-1, MZF1B, ZFP98, ZNF42, ZSCAN6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021841	7594	ZNF43	http://www.ncbi.nlm.nih.gov/gene/?term=7594	"HTF6, KOX27, ZNF39L1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021842	7594	ZNF43	http://www.ncbi.nlm.nih.gov/gene/?term=7594	"HTF6, KOX27, ZNF39L1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021843	7594	ZNF43	http://www.ncbi.nlm.nih.gov/gene/?term=7594	"HTF6, KOX27, ZNF39L1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021844	75957	Mir17hg	http://www.ncbi.nlm.nih.gov/gene/?term=75957	"5033413D16Rik, Mirhg1, OTTMUSG00000033261, mir-17-92 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021845	75964	Trappc8	http://www.ncbi.nlm.nih.gov/gene/?term=75964	"5033403J15Rik, AI845423, D030074E01Rik, Trs85, mKIAA1012 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021846	75974	Dock11	http://www.ncbi.nlm.nih.gov/gene/?term=75974	"5033414A21Rik, 8030476J24, Zizimin2, sph238 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021847	75986	Agmat	http://www.ncbi.nlm.nih.gov/gene/?term=75986	5033405N08Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021848	75990	5033421B08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=75990		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021849	759	CA1	http://www.ncbi.nlm.nih.gov/gene/?term=759	"CA-I, CAB, Car1, HEL-S-11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021850	76007	Zmym2	http://www.ncbi.nlm.nih.gov/gene/?term=76007	"5830413P05Rik, FIM, MYM, RAMP, SCLL, Zfp198, Znf198 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021851	76013	5830407E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76013		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021852	76016	5730406G12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76016		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021853	76017	5830411K02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76017		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021854	76022	Gon4l	http://www.ncbi.nlm.nih.gov/gene/?term=76022	"1500041I23Rik, 2610100B20Rik, 3632445O20Rik, 5430404N14Rik, AA387005 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021855	76036	5830431N17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76036		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021856	76044	Ncapg2	http://www.ncbi.nlm.nih.gov/gene/?term=76044	"5830426I05Rik, Luzp5, Mtb, mCAP-G2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021857	76045	5830449F15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76045		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021858	76047	5830433M15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76047		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021859	76051	Ganc	http://www.ncbi.nlm.nih.gov/gene/?term=76051	"5830445O15Rik, 9330160A12, mFLJ00088 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021860	76053	5830426K05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76053		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021861	76055	Mgea5	http://www.ncbi.nlm.nih.gov/gene/?term=76055	"2810009A20Rik, 4833427O07Rik, 5830447M11Rik, AA408215, Hy5, Ncoat, OGA, mKIAA0679 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021862	76066	5830435N17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76066		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021863	760	CA2	http://www.ncbi.nlm.nih.gov/gene/?term=760	"CA-II, CAC, CAII, Car2, HEL-76, HEL-S-282 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021864	760	CA2	http://www.ncbi.nlm.nih.gov/gene/?term=760	"CA-II, CAC, CAII, Car2, HEL-76, HEL-S-282 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021865	76105	5830456J23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76105		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021866	76105	5830456J23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76105		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021867	76123	Gpsm2	http://www.ncbi.nlm.nih.gov/gene/?term=76123	"6230410J09Rik, LGN, Pins "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021868	76130	Las1l	http://www.ncbi.nlm.nih.gov/gene/?term=76130	"1810030A06Rik, 5830482G23Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021869	76141	6230414M07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76141		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021870	76156	Fam131b	http://www.ncbi.nlm.nih.gov/gene/?term=76156	"6330503C03Rik, 6530406I18Rik, AV277466 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021871	76179	Usp31	http://www.ncbi.nlm.nih.gov/gene/?term=76179	"6330567E21Rik, mKIAA1203 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021872	76195	6330590E21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76195		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021873	76199	Med13l	http://www.ncbi.nlm.nih.gov/gene/?term=76199	"2210413I17Rik, 6330591G05Rik, 9030618F05Rik, Thrap2, Trap240L, mKIAA1025 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021874	76203	6430605C03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76203		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021875	7620	ZNF69	http://www.ncbi.nlm.nih.gov/gene/?term=7620	"Cos5, hZNF3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021876	7620	ZNF69	http://www.ncbi.nlm.nih.gov/gene/?term=7620	"Cos5, hZNF3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021877	76213	6530406A20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76213		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021878	76214	6430710M23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76214		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021879	76217	Jakmip2	http://www.ncbi.nlm.nih.gov/gene/?term=76217	"6430702L21Rik, AI850334, D930046L20Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021880	76219	Arxes1	http://www.ncbi.nlm.nih.gov/gene/?term=76219	"6530401D17Rik, Spc22/23, Spcs3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021881	7621	ZNF70	http://www.ncbi.nlm.nih.gov/gene/?term=7621	Cos17	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021882	76222	Magef1	http://www.ncbi.nlm.nih.gov/gene/?term=76222	6430590I03Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021883	76223	Agbl3	http://www.ncbi.nlm.nih.gov/gene/?term=76223	"2900053G10Rik, 4930431N21Rik, 6530406M24Rik, CCP3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021884	76229	Vmn2r29	http://www.ncbi.nlm.nih.gov/gene/?term=76229	6430701C03Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021885	76246	Rtf1	http://www.ncbi.nlm.nih.gov/gene/?term=76246	"2900005O08Rik, 6530416A09Rik, AI853581, AU043144, AW553985, Gtl7, cbp82 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021886	76251	Ercc6l2	http://www.ncbi.nlm.nih.gov/gene/?term=76251	"0610007P08Rik, 1700019D06Rik, 9330134C04Rik, Rad26l, Sr278 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021887	7625	ZNF74	http://www.ncbi.nlm.nih.gov/gene/?term=7625	"COS52, ZFP520, ZNF520, hZNF7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021888	76260	Ttc8	http://www.ncbi.nlm.nih.gov/gene/?term=76260	"0610012F22Rik, AV001447, BBS8 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021889	76273	Ndfip2	http://www.ncbi.nlm.nih.gov/gene/?term=76273	"0710001O20Rik, 2810436B12Rik, 9130207N19Rik, N4wbp5a, mKIAA1165 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021890	7627	ZNF75A	http://www.ncbi.nlm.nih.gov/gene/?term=7627		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021891	76281	Tax1bp3	http://www.ncbi.nlm.nih.gov/gene/?term=76281	"1300011C24Rik, TIP-1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021892	76295	Atp11b	http://www.ncbi.nlm.nih.gov/gene/?term=76295	"1110019I14Rik, ATPIF, ATPIR, mKIAA0956 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021893	76299	Erp44	http://www.ncbi.nlm.nih.gov/gene/?term=76299	"1110001E24Rik, AI849526, AL033348, Txndc4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021894	7629	ZNF76	http://www.ncbi.nlm.nih.gov/gene/?term=7629	"D6S229E, ZNF523, Zfp523 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021895	76302	Pcnp	http://www.ncbi.nlm.nih.gov/gene/?term=76302	"1110018D06Rik, AI647035 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021896	76308	Rab1b	http://www.ncbi.nlm.nih.gov/gene/?term=76308	1110011F09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021897	76311	1110019D14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76311		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021898	76368	2610028L16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76368		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021899	76376	Slc24a2	http://www.ncbi.nlm.nih.gov/gene/?term=76376	"2810021B17Rik, 6330417K15Rik, AI847460, Nckx2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021900	76390	Zfp735	http://www.ncbi.nlm.nih.gov/gene/?term=76390	1700012C15Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021901	76390	Zfp735	http://www.ncbi.nlm.nih.gov/gene/?term=76390	1700012C15Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021902	76416	Znrd1as	http://www.ncbi.nlm.nih.gov/gene/?term=76416	"1700022C21Rik, AI746295, Znrd1-as "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021903	76425	Gid8	http://www.ncbi.nlm.nih.gov/gene/?term=76425	"2310003C23Rik, 4833420G11Rik, AI451474, Twa1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021904	76429	Lhpp	http://www.ncbi.nlm.nih.gov/gene/?term=76429	2310007H09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021905	76448	Ppp1r18	http://www.ncbi.nlm.nih.gov/gene/?term=76448	"2310014H01Rik, AA407849, AI450394 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021906	7644	ZNF91	http://www.ncbi.nlm.nih.gov/gene/?term=7644	"HPF7, HTF10 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021907	76454	Fbxo31	http://www.ncbi.nlm.nih.gov/gene/?term=76454	"1110003O08Rik, 2310046N15Rik, Fbx14, Fbxo14 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021908	76455	2310067E19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76455		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021909	76457	Ccdc134	http://www.ncbi.nlm.nih.gov/gene/?term=76457	"2310042L06Rik, AW208859 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021910	76478	Haus8	http://www.ncbi.nlm.nih.gov/gene/?term=76478	"2410004L22Rik, Hice1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021911	76482	3110002H16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76482	"2400010D15Rik, Mic-1, Mic1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021912	76485	Glt8d1	http://www.ncbi.nlm.nih.gov/gene/?term=76485	"2410004H05Rik, 5430414N14Rik, AI450005 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021913	76498	Paqr4	http://www.ncbi.nlm.nih.gov/gene/?term=76498	1500004C10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021914	76501	Commd9	http://www.ncbi.nlm.nih.gov/gene/?term=76501	"1810029F08Rik, AA409293 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021915	76508	Ube2d-ps	http://www.ncbi.nlm.nih.gov/gene/?term=76508	"1600028I17Rik, 2210015D19Rik, AI596465 "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021916	76510	Trappc9	http://www.ncbi.nlm.nih.gov/gene/?term=76510	"1810044A24Rik, 2900005P22Rik, 4632408O18Rik, Ibp, Nibp, TRS130, mKIAA1882 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021917	76522	Lsm8	http://www.ncbi.nlm.nih.gov/gene/?term=76522	"2010003I05Rik, AW214405, Naa38 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021918	76524	Cln6	http://www.ncbi.nlm.nih.gov/gene/?term=76524	"1810065L06Rik, AW743417, D9Bwg1455e, nclf "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021919	76533	2010106G04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76533		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021920	76559	Atg2b	http://www.ncbi.nlm.nih.gov/gene/?term=76559	"2410024A21Rik, AI047755, AI503411, AW558123, C030004M05Rik, C630028L02Rik, mKIAA4067 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021921	76581	2510001I10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76581		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021922	76582	Ipo11	http://www.ncbi.nlm.nih.gov/gene/?term=76582	"1700081H05Rik, 2510001A17Rik, AI314624, AW555235, E330021B14Rik, Ranbp11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021923	76585	Lce1i	http://www.ncbi.nlm.nih.gov/gene/?term=76585	2310069N01Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021924	76594	Dnajc18	http://www.ncbi.nlm.nih.gov/gene/?term=76594	"2700075B01Rik, AU041129 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021925	76610	1700063K16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76610		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021926	76613	1700069B07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76613		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021927	76614	Immt	http://www.ncbi.nlm.nih.gov/gene/?term=76614	"1700082C19Rik, D830041H16Rik, HMP, P87, P87/89, P89 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021928	76627	Prr30	http://www.ncbi.nlm.nih.gov/gene/?term=76627	1700110M21Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021929	76634	1700110C19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76634		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021930	76671	5330406M23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76671		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021931	76682	1500002K03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76682		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). "
RLID00021932	76686	Clip3	http://www.ncbi.nlm.nih.gov/gene/?term=76686	"1500005P14Rik, AI844915, Clipr-59 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021933	76687	Spcs3	http://www.ncbi.nlm.nih.gov/gene/?term=76687	1810011E08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021934	76690	1500037F05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76690		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021935	76707	Clasp1	http://www.ncbi.nlm.nih.gov/gene/?term=76707	"1700030C23Rik, 5730583A19Rik, B130045P17Rik, CLASP1alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021936	76709	Arpc2	http://www.ncbi.nlm.nih.gov/gene/?term=76709	"2210023N03Rik, 34kDa, p34-Arc "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021937	76725	2010003D24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76725		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021938	76740	Efr3a	http://www.ncbi.nlm.nih.gov/gene/?term=76740	"A130089M23Rik, BB071175, C76891, C920006C10Rik, D030063F01Rik, mKIAA0143 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021939	76747	Dapl1	http://www.ncbi.nlm.nih.gov/gene/?term=76747	"2310032F03Rik, EEDA "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021940	7675	ZNF121	http://www.ncbi.nlm.nih.gov/gene/?term=7675	"D19S204, ZHC32, ZNF20 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021941	76763	Mospd2	http://www.ncbi.nlm.nih.gov/gene/?term=76763	2410013I23Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021942	76775	Slc10a7	http://www.ncbi.nlm.nih.gov/gene/?term=76775	"2410193C02Rik, P7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021943	76784	Mtif2	http://www.ncbi.nlm.nih.gov/gene/?term=76784	"2310038D14Rik, 2410112O06Rik, IF-2(Mt), IF-2mt, IF2(mt) "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021944	76789	Mzt1	http://www.ncbi.nlm.nih.gov/gene/?term=76789	"2410129H14Rik, AI120158, Mozart1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021945	7678	ZNF124	http://www.ncbi.nlm.nih.gov/gene/?term=7678	"HZF-16, HZF16, ZK7 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021946	7678	ZNF124	http://www.ncbi.nlm.nih.gov/gene/?term=7678	"HZF-16, HZF16, ZK7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021947	76794	Man2c1os	http://www.ncbi.nlm.nih.gov/gene/?term=76794	"2410133F24Rik, AI851351 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021948	76798	Srrm4os	http://www.ncbi.nlm.nih.gov/gene/?term=76798	2410137F16Rik	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021949	767	CA8	http://www.ncbi.nlm.nih.gov/gene/?term=767	"CA-RP, CA-VIII, CALS, CAMRQ3, CARP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021950	767	CA8	http://www.ncbi.nlm.nih.gov/gene/?term=767	"CA-VIII, CALS, CAMRQ3, CARP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021951	76800	Usp42	http://www.ncbi.nlm.nih.gov/gene/?term=76800	"2410140K03Rik, 3110031A07Rik, A630018G05Rik, D5Ertd591e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021952	76803	2410141K09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76803	"4930482J15Rik, Ayu21-35, Gt(pU21)35Imeg "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021953	76804	Kdm4c	http://www.ncbi.nlm.nih.gov/gene/?term=76804	"2410141F18Rik, AA517467, Gasc1, Jmjd2c "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021954	76813	Armc6	http://www.ncbi.nlm.nih.gov/gene/?term=76813	"2410153K17Rik, AW554412 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021955	768211	RELL1	http://www.ncbi.nlm.nih.gov/gene/?term=768211		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021956	768211	RELL1	http://www.ncbi.nlm.nih.gov/gene/?term=768211		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021957	768211	RELL1	http://www.ncbi.nlm.nih.gov/gene/?term=768211		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00021958	768420	COTL1	http://www.ncbi.nlm.nih.gov/gene/?term=768420		mRNA	Gallus gallus	19951325	Axon	Oculomotor nerve|Retina	In situ hybridization	"C-Coactosin mRNA is expressed in the oculomotor and trochlear nuclei and axon of oculomotor nerve (E, I) and trigeminal nerve (A, B). "
RLID00021959	76843	Dtl	http://www.ncbi.nlm.nih.gov/gene/?term=76843	"2810047L02Rik, 5730564G15Rik, L2dtl, Ramp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021960	76846	Rps9	http://www.ncbi.nlm.nih.gov/gene/?term=76846	"3010033P07Rik, AL022771, AL022885 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021961	76857	Spopl	http://www.ncbi.nlm.nih.gov/gene/?term=76857	"4921517N04Rik, AU014935, BB233739, E430033K04Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021962	76863	Dcun1d5	http://www.ncbi.nlm.nih.gov/gene/?term=76863	"3110001A18Rik, 4833420K19Rik, AW060460, D430047L21Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021963	76877	Rab36	http://www.ncbi.nlm.nih.gov/gene/?term=76877	"6330593L16Rik, AW047545 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021964	76878	6330582A15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76878		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021965	76892	Rnft1	http://www.ncbi.nlm.nih.gov/gene/?term=76892	"0610013E23Rik, AV007605 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021966	76893	Cers2	http://www.ncbi.nlm.nih.gov/gene/?term=76893	"0610013I17Rik, AI225939, Lass2, TRH3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021967	76895	Bicd2	http://www.ncbi.nlm.nih.gov/gene/?term=76895		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021968	768	CA9	http://www.ncbi.nlm.nih.gov/gene/?term=768	"CAIX, MN "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00021969	76900	Ssbp4	http://www.ncbi.nlm.nih.gov/gene/?term=76900	"1210002E11Rik, AW743380, Sspb4 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021970	7690	ZNF131	http://www.ncbi.nlm.nih.gov/gene/?term=7690	"ZBTB35, pHZ-10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021971	76916	Timmdc1	http://www.ncbi.nlm.nih.gov/gene/?term=76916	"2810021C21Rik, 4930455C21Rik, AV135763 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021972	7692	ZNF133	http://www.ncbi.nlm.nih.gov/gene/?term=7692	"ZNF150, pHZ-13, pHZ-66 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021973	76932	Arfip2	http://www.ncbi.nlm.nih.gov/gene/?term=76932	"2310002N04Rik, POR, Por1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021974	76936	Hnrnpm	http://www.ncbi.nlm.nih.gov/gene/?term=76936	"2610023M21Rik, AA409009, Hnrpm, mKIAA4193 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021975	7693	ZNF134	http://www.ncbi.nlm.nih.gov/gene/?term=7693	pHZ-15	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021976	76967	2700049A03Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76967	"Ta3, Talpid3, mKIAA0586 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021977	76969	Chst1	http://www.ncbi.nlm.nih.gov/gene/?term=76969	"2610008E20Rik, AW125896, C6ST, GST-1, Gst1, KSGAL6ST "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021978	76971	Sult2a8	http://www.ncbi.nlm.nih.gov/gene/?term=76971	2810007J24Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021979	76972	Snhg20	http://www.ncbi.nlm.nih.gov/gene/?term=76972	2810008D09Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021980	76976	Arxes2	http://www.ncbi.nlm.nih.gov/gene/?term=76976	"2900062L11Rik, Spc22/23, Spcs3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021981	7697	ZNF138	http://www.ncbi.nlm.nih.gov/gene/?term=7697	pHZ-32	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021982	76982	3110035E14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76982	"AI415019, AV164974, R75066 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021983	77015	Mpped2	http://www.ncbi.nlm.nih.gov/gene/?term=77015	"239Fb, 2700082O15Rik, AV354767, AW060960 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021984	7701	ZNF142	http://www.ncbi.nlm.nih.gov/gene/?term=7701	pHZ-49	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021985	77027	4432414F05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77027		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021986	77031	Slc9a8	http://www.ncbi.nlm.nih.gov/gene/?term=77031	"1200006P13Rik, 6430709P13Rik, AI182282, NHE-8, NHE8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021987	77038	Arfgap2	http://www.ncbi.nlm.nih.gov/gene/?term=77038	"2310032E02Rik, Zfp289 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021988	77038	Arfgap2	http://www.ncbi.nlm.nih.gov/gene/?term=77038	"2310032E02Rik, Zfp289 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021989	77041	Arsk	http://www.ncbi.nlm.nih.gov/gene/?term=77041	"2810429K17Rik, 4833414G15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021990	77045	Bcl7a	http://www.ncbi.nlm.nih.gov/gene/?term=77045	"4432415N06Rik, AI448316 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021991	77048	Cep83	http://www.ncbi.nlm.nih.gov/gene/?term=77048	"2600001G24Rik, 4921537D05Rik, 5730513H21Rik, Ccdc41 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021992	77053	Sun1	http://www.ncbi.nlm.nih.gov/gene/?term=77053	"4632417G13Rik, 5730434D03Rik, Unc84a, mKIAA0810 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00021993	77059	4931408D14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77059		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00021994	7705	ZNF146	http://www.ncbi.nlm.nih.gov/gene/?term=7705	OZF	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00021995	7705	ZNF146	http://www.ncbi.nlm.nih.gov/gene/?term=7705	OZF	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021996	7705	ZNF146	http://www.ncbi.nlm.nih.gov/gene/?term=7705	OZF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021997	7706	TRIM25	http://www.ncbi.nlm.nih.gov/gene/?term=7706	"EFP, RNF147, Z147, ZNF147 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00021998	7706	TRIM25	http://www.ncbi.nlm.nih.gov/gene/?term=7706	"EFP, RNF147, Z147, ZNF147 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00021999	7707	ZNF148	http://www.ncbi.nlm.nih.gov/gene/?term=7707	"BERF-1, BFCOL1, HT-BETA, ZBP-89, ZFP148, pHZ-52 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022000	7707	ZNF148	http://www.ncbi.nlm.nih.gov/gene/?term=7707	"BERF-1, BFCOL1, HT-BETA, ZBP-89, ZFP148, pHZ-52 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022001	77087	Ankrd11	http://www.ncbi.nlm.nih.gov/gene/?term=77087	"2410104C19Rik, 3010027A04Rik, 6330578C09Rik, 9530048I21Rik, AA930108, Gm176, Yod "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022002	77088	3010031K01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77088		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022003	77090	Ocel1	http://www.ncbi.nlm.nih.gov/gene/?term=77090	"9430098E02Rik, AI326022, AI593544 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022004	77097	Tanc2	http://www.ncbi.nlm.nih.gov/gene/?term=77097	"3526402J09Rik, 5730590C14Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022005	7709	ZBTB17	http://www.ncbi.nlm.nih.gov/gene/?term=7709	"MIZ-1, ZNF151, ZNF60, pHZ-67 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022006	770	CA11	http://www.ncbi.nlm.nih.gov/gene/?term=770	CARPX1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022007	77106	Tmem181a	http://www.ncbi.nlm.nih.gov/gene/?term=77106	"5930418K15Rik, C76977, Gpr178, Tmem181, mKIAA1423 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022008	77106	Tmem181a	http://www.ncbi.nlm.nih.gov/gene/?term=77106	"5930418K15Rik, C76977, Gpr178, Tmem181, mKIAA1423 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022009	77113	Klhl2	http://www.ncbi.nlm.nih.gov/gene/?term=77113	"6030411N21Rik, ABP-KELCH, AU020744, Mav "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022010	77116	Mtmr2	http://www.ncbi.nlm.nih.gov/gene/?term=77116	6030445P13Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022011	77128	Crebrf	http://www.ncbi.nlm.nih.gov/gene/?term=77128	"A930001N09Rik, LRF "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022012	7716	VEZF1	http://www.ncbi.nlm.nih.gov/gene/?term=7716	"DB1, ZNF161 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022013	7716	VEZF1	http://www.ncbi.nlm.nih.gov/gene/?term=7716	"DB1, ZNF161 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022014	77189	A430105J06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77189		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022015	7718	ZNF165	http://www.ncbi.nlm.nih.gov/gene/?term=7718	"CT53, LD65, ZSCAN7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022016	77198	4930407I19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77198		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022017	771	CA12	http://www.ncbi.nlm.nih.gov/gene/?term=771	"CAXII, HsT18816 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022018	77200	5430403G16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77200	ENSMUSG00000072763	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022019	77210	8030448I15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77210		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022020	77216	A930002H02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77216		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022021	77247	9430006E15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77247		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022022	77248	9430014N10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77248		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022023	7726	TRIM26	http://www.ncbi.nlm.nih.gov/gene/?term=7726	"AFP, RNF95, ZNF173 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022024	7727	ZNF174	http://www.ncbi.nlm.nih.gov/gene/?term=7727	ZSCAN8	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022025	7727	ZNF174	http://www.ncbi.nlm.nih.gov/gene/?term=7727	ZSCAN8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022026	77289	9430034F23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77289		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022027	77301	9430031J08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77301		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022028	77304	9430068D22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77304		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022029	77311	C030011I16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77311		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022030	77352	Axdnd1	http://www.ncbi.nlm.nih.gov/gene/?term=77352	"9430070O13Rik, Gm979 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022031	77365	9430083B18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77365		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022032	77371	Sec24a	http://www.ncbi.nlm.nih.gov/gene/?term=77371		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022033	7737	RNF113A	http://www.ncbi.nlm.nih.gov/gene/?term=7737	"Cwc24, RNF113, TTD5, ZNF183 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022034	7738	ZNF184	http://www.ncbi.nlm.nih.gov/gene/?term=7738	kr-ZNF3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022035	7738	ZNF184	http://www.ncbi.nlm.nih.gov/gene/?term=7738	kr-ZNF3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022036	77393	9530006C21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77393		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022037	77406	9530004M16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77406		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022038	77415	C030015E24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77415		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022039	7741	ZSCAN26	http://www.ncbi.nlm.nih.gov/gene/?term=7741	"SRE-ZBP, SREZBP, ZNF187 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022040	77439	9530025L08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77439		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022041	77440	9430087N24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77440		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022042	77463	C030014O09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77463		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022043	7746	ZSCAN9	http://www.ncbi.nlm.nih.gov/gene/?term=7746	"PRD51, ZNF193 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022044	77479	C030040K24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77479		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022045	77481	C030048H21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77481		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022046	7748	ZNF195	http://www.ncbi.nlm.nih.gov/gene/?term=7748	"HRF1, ZNFP104 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022047	7748	ZNF195	http://www.ncbi.nlm.nih.gov/gene/?term=7748	"HRF1, ZNFP104 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022048	7748	ZNF195	http://www.ncbi.nlm.nih.gov/gene/?term=7748	"HRF1, ZNFP104 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022049	77492	8030456M14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77492		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022050	7750	ZMYM2	http://www.ncbi.nlm.nih.gov/gene/?term=7750	"FIM, MYM, RAMP, SCLL, ZNF198 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022051	7750	ZMYM2	http://www.ncbi.nlm.nih.gov/gene/?term=7750	"FIM, MYM, RAMP, SCLL, ZNF198 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022052	77511	9330185C12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77511		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022053	77519	Zfp266	http://www.ncbi.nlm.nih.gov/gene/?term=77519	"5330440G10Rik, 5730601F06Rik, AW552317 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022054	7752	ZNF200	http://www.ncbi.nlm.nih.gov/gene/?term=7752		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022055	7753	ZNF202	http://www.ncbi.nlm.nih.gov/gene/?term=7753	"ZKSCAN10, ZSCAN42 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022056	7753	ZNF202	http://www.ncbi.nlm.nih.gov/gene/?term=7753	"ZKSCAN10, ZSCAN42 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022057	77544	8030479D07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77544		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022058	7756	ZNF207	http://www.ncbi.nlm.nih.gov/gene/?term=7756	"BuGZ, hBuGZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022059	77579	Myh10	http://www.ncbi.nlm.nih.gov/gene/?term=77579	"5730504C04Rik, 9330167F11Rik, Fltn, Myhn-2, Myhn2, NMHC II-B, NMHC-B, NMHCII-B, NMMHC II-b, NMMHC-B, NMMHC-IIB, SMemb, mKIAA3005 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022060	7757	ZNF208	http://www.ncbi.nlm.nih.gov/gene/?term=7757	"PMIDP, ZNF95 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022061	7757	ZNF208	http://www.ncbi.nlm.nih.gov/gene/?term=7757	"PMIDP, ZNF95 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022062	77591	Ddx10	http://www.ncbi.nlm.nih.gov/gene/?term=77591	"4632415A01Rik, AI646054 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022063	77596	Adgrf1	http://www.ncbi.nlm.nih.gov/gene/?term=77596	"5031409J19Rik, Gpr110, KPG_009 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022064	775	CACNA1C	http://www.ncbi.nlm.nih.gov/gene/?term=775	"CACH2, CACN2, CACNL1A1, CCHL1A1, CaV1.2, LQT8, TS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022065	77605	H2afv	http://www.ncbi.nlm.nih.gov/gene/?term=77605	"C530002L11Rik, H2a.z-2, H2av "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022066	77610	C330002G04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77610		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022067	77612	C030038I04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77612		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022068	77622	Apex2	http://www.ncbi.nlm.nih.gov/gene/?term=77622	"C430040P13Rik, ape2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022069	77634	Snapc3	http://www.ncbi.nlm.nih.gov/gene/?term=77634	"1810020H02Rik, 4930558A07Rik, 5031401C21Rik, AI414457, E030018J20Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022070	7763	ZFAND5	http://www.ncbi.nlm.nih.gov/gene/?term=7763	"ZA20D2A, ZNF216, ZFAND5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022071	7763	ZFAND5	http://www.ncbi.nlm.nih.gov/gene/?term=7763	"ZA20D2A, ZNF216, ZFAND5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022072	7763	ZFAND5	http://www.ncbi.nlm.nih.gov/gene/?term=7763	"ZA20D2A, ZNF216, ZFAND5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022073	7764	ZNF217	http://www.ncbi.nlm.nih.gov/gene/?term=7764	ZABC1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022074	77656	C430045I18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77656	C78534	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022075	77656	C430045I18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77656	C78534	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022076	77683	Ehmt1	http://www.ncbi.nlm.nih.gov/gene/?term=77683	"9230102N17Rik, D330003E03, Eu-HMTase1, GLP, GLP1, KMT1D, mKIAA1876 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022077	7769	ZNF226	http://www.ncbi.nlm.nih.gov/gene/?term=7769		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022078	776	CACNA1D	http://www.ncbi.nlm.nih.gov/gene/?term=776	"CACH3, CACN4, CACNL1A2, CCHL1A2, Cav1.3, PASNA, SANDD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022079	77700	9130208D14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77700		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022080	77702	9130201A16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77702		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022081	77707	9130604C24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77707	AW554730	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022082	77708	9130223C08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77708		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022083	77719	6030458A19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77719		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022084	77724	6030460B20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77724		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022085	77755	A230103L15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77755		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022086	77760	A230106O10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77760		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022087	77761	9230118N01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77761		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022088	77766	Elp4	http://www.ncbi.nlm.nih.gov/gene/?term=77766	"A330107A17Rik, Paxneb "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022089	7776	ZNF236	http://www.ncbi.nlm.nih.gov/gene/?term=7776	"ZNF236AB, ZNF236 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022090	7776	ZNF236	http://www.ncbi.nlm.nih.gov/gene/?term=7776	"ZNF236AB, ZNF236 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022091	77777	Ulbp1	http://www.ncbi.nlm.nih.gov/gene/?term=77777	"A430108B07Rik, MULT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022092	77781	Epm2aip1	http://www.ncbi.nlm.nih.gov/gene/?term=77781	"A930003G21Rik, mKIAA0766 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022093	77782	Polq	http://www.ncbi.nlm.nih.gov/gene/?term=77782	A430110D14Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022094	77790	A930006J02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77790		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022095	77799	Sla2	http://www.ncbi.nlm.nih.gov/gene/?term=77799	"A930009E21Rik, AI430952, SLAP-2, SLAP2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022096	7779	SLC30A1	http://www.ncbi.nlm.nih.gov/gene/?term=7779	"ZNT1, ZRC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022097	7779	SLC30A1	http://www.ncbi.nlm.nih.gov/gene/?term=7779	"ZNT1, ZRC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022098	77803	Fam159b	http://www.ncbi.nlm.nih.gov/gene/?term=77803	A930021C24Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022099	77813	A930012N16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77813	C78811	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022100	7781	SLC30A3	http://www.ncbi.nlm.nih.gov/gene/?term=7781	ZNT3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022101	77825	A930027M08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77825		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022102	7782	SLC30A4	http://www.ncbi.nlm.nih.gov/gene/?term=7782	"ZNT4, znT-4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022103	7782	SLC30A4	http://www.ncbi.nlm.nih.gov/gene/?term=7782	"ZNT4, znT-4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022104	77838	A930036M01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77838		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022105	77841	Far2os2	http://www.ncbi.nlm.nih.gov/gene/?term=77841	B230104C08Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022106	7784	ZP3	http://www.ncbi.nlm.nih.gov/gene/?term=7784	"ZP3AB, ZPC, Zp-3, ZP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022107	77850	B830007D08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77850		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022108	77857	9430065F17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77857	E130110G22Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022109	77877	6030458C11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77877		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022110	77884	6720427H10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77884		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022111	77889	Lbh	http://www.ncbi.nlm.nih.gov/gene/?term=77889	"1810009F10Rik, 6720416L16Rik "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022112	779157	slc12a9	http://www.ncbi.nlm.nih.gov/gene/?term=779157	cip1	mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00022113	7791	ZYX	http://www.ncbi.nlm.nih.gov/gene/?term=7791	"ESP-2, HED-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022114	77938	Fam53b	http://www.ncbi.nlm.nih.gov/gene/?term=77938	"A930008G19Rik, mKIAA0140 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022115	77942	A930006A01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77942		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022116	77951	Cyp20a1	http://www.ncbi.nlm.nih.gov/gene/?term=77951	"A930011N14Rik, Cypm "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022117	77963	Hook1	http://www.ncbi.nlm.nih.gov/gene/?term=77963	"A930033L17Rik, azh "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022118	77967	A930036I15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77967		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022119	77968	A930041D05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77968		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022120	77972	A930037G07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77972		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022121	779853	aen	http://www.ncbi.nlm.nih.gov/gene/?term=779853	"isg20l1, xaen "	mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00022122	77988	D730047N16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77988		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022123	7798	LUZP1	http://www.ncbi.nlm.nih.gov/gene/?term=7798	LUZP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022124	77991	D730048M19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77991		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022125	77996	Cutal	http://www.ncbi.nlm.nih.gov/gene/?term=77996	D730039F16Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022126	7799	PRDM2	http://www.ncbi.nlm.nih.gov/gene/?term=7799	"HUMHOXY1, KMT8, MTB-ZF, RIZ, RIZ1, RIZ2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022127	78010	4930465I24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78010		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022128	780193	acp6	http://www.ncbi.nlm.nih.gov/gene/?term=780193		mRNA	Xenopus tropicalis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00022129	7802	DNALI1	http://www.ncbi.nlm.nih.gov/gene/?term=7802	"P28, dJ423B22.5, hp28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022130	7803	PTP4A1	http://www.ncbi.nlm.nih.gov/gene/?term=7803	"HH72, PRL-1, PRL1, PTP(CAAX1), PTPCAAX1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022131	7803	PTP4A1	http://www.ncbi.nlm.nih.gov/gene/?term=7803	"HH72, PRL-1, PRL1, PTP(CAAX1), PTPCAAX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022132	7804	LRP8	http://www.ncbi.nlm.nih.gov/gene/?term=7804	"APOER2, HSZ75190, LRP-8, MCI1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022133	7804	LRP8	http://www.ncbi.nlm.nih.gov/gene/?term=7804	"APOER2, HSZ75190, LRP-8, MCI1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022134	7805	LAPTM5	http://www.ncbi.nlm.nih.gov/gene/?term=7805	CLAST6	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022135	780776	TVP23A	http://www.ncbi.nlm.nih.gov/gene/?term=780776	"FAM18A, YDR084C "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022136	780776	TVP23A	http://www.ncbi.nlm.nih.gov/gene/?term=780776	"FAM18A, YDR084C "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022137	78078	9230108I15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78078		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022138	780851	SNORD3A	http://www.ncbi.nlm.nih.gov/gene/?term=780851	"RNU3, U3 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022139	780851	SNORD3A	http://www.ncbi.nlm.nih.gov/gene/?term=780851	"RNU3, U3 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022140	780851	SNORD3A	http://www.ncbi.nlm.nih.gov/gene/?term=780851	"RNU3, U3 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022141	780852	SNORD3B-2	http://www.ncbi.nlm.nih.gov/gene/?term=780852	"U3-2B, U3b2 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022142	780852	SNORD3B-2	http://www.ncbi.nlm.nih.gov/gene/?term=780852	"U3-2B, U3b2 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022143	780852	SNORD3B-2	http://www.ncbi.nlm.nih.gov/gene/?term=780852	"U3-2B, U3b2 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022144	780853	SNORD3C	http://www.ncbi.nlm.nih.gov/gene/?term=780853	U3-3	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022145	780853	SNORD3C	http://www.ncbi.nlm.nih.gov/gene/?term=780853	U3-3	snoRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00022146	780853	SNORD3C	http://www.ncbi.nlm.nih.gov/gene/?term=780853	U3-3	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022147	780853	SNORD3C	http://www.ncbi.nlm.nih.gov/gene/?term=780853	U3-3	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022148	780854	SNORD3D	http://www.ncbi.nlm.nih.gov/gene/?term=780854	U3-4	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022149	780854	SNORD3D	http://www.ncbi.nlm.nih.gov/gene/?term=780854	U3-4	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022150	780854	SNORD3D	http://www.ncbi.nlm.nih.gov/gene/?term=780854	U3-4	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022151	780	DDR1	http://www.ncbi.nlm.nih.gov/gene/?term=780	"CAK, CD167, DDR, EDDR1, HGK2, MCK10, NEP, NTRK4, PTK3, PTK3A, RTK6, TRKE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022152	780	DDR1	http://www.ncbi.nlm.nih.gov/gene/?term=780	"CAK, CD167, DDR, EDDR1, HGK2, MCK10, NEP, NTRK4, PTK3, PTK3A, RTK6, TRKE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022153	78100	Msantd4	http://www.ncbi.nlm.nih.gov/gene/?term=78100	"8430410K20Rik, Mysantd4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022154	78102	8430426J06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78102		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022155	78107	4930425F17Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78107		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022156	7812	CSDE1	http://www.ncbi.nlm.nih.gov/gene/?term=7812	"D1S155E, UNR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022157	7812	CSDE1	http://www.ncbi.nlm.nih.gov/gene/?term=7812	"D1S155E, UNR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022158	7813	EVI5	http://www.ncbi.nlm.nih.gov/gene/?term=7813	"EVI-5, NB4S "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022159	7813	EVI5	http://www.ncbi.nlm.nih.gov/gene/?term=7813	"EVI-5, NB4S "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022160	7813	EVI5	http://www.ncbi.nlm.nih.gov/gene/?term=7813	"EVI-5, NB4S "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022161	78195	4930528J18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78195		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022162	781	CACNA2D1	http://www.ncbi.nlm.nih.gov/gene/?term=781	"CACNA2, CACNL2A, CCHL2A, LINC01112, lncRNA-N3 "	lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"Figure 7: Neuronal lncRNAs act via diverse mechanisms. (A) Quantification of relative expression of lncRNAs in nuclear and cytoplasmic cell fractions. (B) Quantification of changes in hosted miRNAs in response to lncRNA_N2 knockdown. MiRNAs were quantified using Taqman miRNA qPCR. (C-E) RIP of lncRNAs with SUZ12 and REST antibodies. The interaction of HOTAIR with SUZ12 is a known interaction that serves as a positive control (Gupta et al, 2010). * and ** indicate P-values of <0.05 and <0.01, respectively. Data are collected from Figure 7. "
RLID00022163	78230	5033405D04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78230		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022164	78232	Trappc6b	http://www.ncbi.nlm.nih.gov/gene/?term=78232	"5830498C14Rik, C79212 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022165	78244	Dnajc21	http://www.ncbi.nlm.nih.gov/gene/?term=78244	"4930461P20Rik, 9930116P15Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022166	78246	Phf23	http://www.ncbi.nlm.nih.gov/gene/?term=78246	42522	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022167	78251	Zfp712	http://www.ncbi.nlm.nih.gov/gene/?term=78251	"4921504N20Rik, mszf31, mszf89 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022168	78252	Nxpe2	http://www.ncbi.nlm.nih.gov/gene/?term=78252	"4432416J03Rik, AI323362, Fam55b "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022169	78255	Ralgps2	http://www.ncbi.nlm.nih.gov/gene/?term=78255	"1810020P17Rik, 2210408F11Rik, 4921528G01Rik, 9130014M22Rik, AU043409, AW046161 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022170	78265	4632418H02Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78265		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022171	78267	Klhdc8b	http://www.ncbi.nlm.nih.gov/gene/?term=78267	4931406O17Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022172	78276	5330433J24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78276		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022173	78283	Map7d2	http://www.ncbi.nlm.nih.gov/gene/?term=78283	"1600028E09Rik, 2900002G04Rik, 5330432J06Rik, C030036K04Rik, Mtap7d2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022174	78294	Rps27a	http://www.ncbi.nlm.nih.gov/gene/?term=78294	"0610006J14Rik, Uba52, Ubb, Ubc "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022175	78294	Rps27a	http://www.ncbi.nlm.nih.gov/gene/?term=78294	"0610006J14Rik, Uba52, Ubb, Ubc "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00022176	782	CACNB1	http://www.ncbi.nlm.nih.gov/gene/?term=782	"CAB1, CACNLB1, CCHLB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022177	78303	Hist3h2ba	http://www.ncbi.nlm.nih.gov/gene/?term=78303	"1500011O09Rik, AI413321 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022178	78332	2510010K19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78332		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022179	78372	Snrnp25	http://www.ncbi.nlm.nih.gov/gene/?term=78372	"3300001G02Rik, AL033324, C16ORF33 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022180	78376	Sapcd1	http://www.ncbi.nlm.nih.gov/gene/?term=78376	"2810436B06Rik, G7d, Ng23 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022181	7837	PXDN	http://www.ncbi.nlm.nih.gov/gene/?term=7837	"COPOA, D2S448, D2S448E, MG50, PRG2, PXN, VPO "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00022182	7837	PXDN	http://www.ncbi.nlm.nih.gov/gene/?term=7837	"COPOA, D2S448, D2S448E, MG50, PRG2, PXN, VPO "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022183	7837	PXDN	http://www.ncbi.nlm.nih.gov/gene/?term=7837	"COPOA, D2S448, D2S448E, MG50, PRG2, PXN, VPO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022184	78385	2310063J23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78385		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022185	78388	Mvp	http://www.ncbi.nlm.nih.gov/gene/?term=78388	"2310009M24Rik, LRP, VAULT1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022186	78396	2810028B13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78396		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022187	7840	ALMS1	http://www.ncbi.nlm.nih.gov/gene/?term=7840	ALSS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022188	7841	MOGS	http://www.ncbi.nlm.nih.gov/gene/?term=7841	"CDG2B, CWH41, DER7, GCS1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022189	7841	MOGS	http://www.ncbi.nlm.nih.gov/gene/?term=7841	"CDG2B, CWH41, DER7, GCS1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022190	78425	9530053H05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78425		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022191	78435	A930014E10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78435		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022192	7844	RNF103	http://www.ncbi.nlm.nih.gov/gene/?term=7844	"HKF-1, KF-1, KF1, ZFP-103, ZFP103 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022193	7844	RNF103	http://www.ncbi.nlm.nih.gov/gene/?term=7844	"HKF-1, KF-1, KF1, ZFP-103, ZFP103 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022194	78455	Helz	http://www.ncbi.nlm.nih.gov/gene/?term=78455	"3110078M01Rik, 9430093I07Rik, 9630002H22Rik, AI851979, DRHC "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022195	78456	C030002A05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78456		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022196	7846	TUBA1A	http://www.ncbi.nlm.nih.gov/gene/?term=7846	"B-ALPHA-1, LIS3, TUBA3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022197	7846	TUBA1A	http://www.ncbi.nlm.nih.gov/gene/?term=7846	"B-ALPHA-1, LIS3, TUBA3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022198	78477	1700121M21Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78477		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022199	7849	PAX8	http://www.ncbi.nlm.nih.gov/gene/?term=7849		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022200	784	CACNB3	http://www.ncbi.nlm.nih.gov/gene/?term=784	"CAB3, CACNLB3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022201	7850	IL1R2	http://www.ncbi.nlm.nih.gov/gene/?term=7850	"CD121b, CDw121b, IL-1R-2, IL-1RT-2, IL-1RT2, IL1R2c, IL1RB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022202	78514	Arhgap10	http://www.ncbi.nlm.nih.gov/gene/?term=78514	"A930033B01Rik, PSGAP-m, PSGAP-s "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022203	7851	MALL	http://www.ncbi.nlm.nih.gov/gene/?term=7851	BENE	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022204	7851	MALL	http://www.ncbi.nlm.nih.gov/gene/?term=7851	BENE	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022205	7851	MALL	http://www.ncbi.nlm.nih.gov/gene/?term=7851	BENE	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022206	78521	B230219D22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78521	"AA119856, D530037I19Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022207	78523	Mrpl9	http://www.ncbi.nlm.nih.gov/gene/?term=78523	"8030480E20Rik, AA409733, C330013D18Rik, L9mt "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022208	78526	Platr21	http://www.ncbi.nlm.nih.gov/gene/?term=78526	C330013F16Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022209	7852	CXCR4	http://www.ncbi.nlm.nih.gov/gene/?term=7852	"CD184, D2S201E, FB22, HM89, HSY3RR, LAP-3, LAP3, LCR1, LESTR, NPY3R, NPYR, NPYRL, NPYY3R, WHIM, WHIMS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022210	7852	CXCR4	http://www.ncbi.nlm.nih.gov/gene/?term=7852	"CD184, D2S201E, FB22, HM89, HSY3RR, LAP-3, LAP3, LCR1, LESTR, NPY3R, NPYR, NPYRL, NPYY3R, WHIM, WHIMS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022211	78551	5430407F15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78551		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022212	78558	Htra3	http://www.ncbi.nlm.nih.gov/gene/?term=78558	"2210021K23Rik, 9530081K03Rik, Prsp, Tasp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022213	7855	FZD5	http://www.ncbi.nlm.nih.gov/gene/?term=7855	"C2orf31, HFZ5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022214	7855	FZD5	http://www.ncbi.nlm.nih.gov/gene/?term=7855	"C2orf31, HFZ5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022215	78570	9630014C11Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78570		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022216	78573	D530037P16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78573		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022217	78575	B430319G15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78575	D530025C14Rik	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022218	78579	D530043N20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78579		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022219	7857	SCG2	http://www.ncbi.nlm.nih.gov/gene/?term=7857	"CHGC, EM66, SN, SgII "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022220	78618	Acap2	http://www.ncbi.nlm.nih.gov/gene/?term=78618	"4832442G16, 9530039J15Rik, CNT-B2, Centb2, mKIAA0041 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022221	7862	BRPF1	http://www.ncbi.nlm.nih.gov/gene/?term=7862	BR140	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022222	7862	BRPF1	http://www.ncbi.nlm.nih.gov/gene/?term=7862	BR140	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022223	78633	1700096C16Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78633		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022224	78634	Spaca7	http://www.ncbi.nlm.nih.gov/gene/?term=78634	1700094C09Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022225	78642	1700127F24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78642		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022226	78653	Bola3	http://www.ncbi.nlm.nih.gov/gene/?term=78653	1810056O20Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022227	78654	1700066C05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78654		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022228	78656	Brd8	http://www.ncbi.nlm.nih.gov/gene/?term=78656	"2610007E11Rik, 4432404P07Rik, SMAP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022229	78658	Ncapd3	http://www.ncbi.nlm.nih.gov/gene/?term=78658	"2810487N22Rik, 4632407J06Rik, AI195468, AU018739, B130055D15Rik, mKIAA0056 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022230	7866	IFRD2	http://www.ncbi.nlm.nih.gov/gene/?term=7866	"IFNRP, SKMc15, SM15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022231	7866	IFRD2	http://www.ncbi.nlm.nih.gov/gene/?term=7866	"IFNRP, SKMc15, SM15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022232	78672	9530057J20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78672		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022233	7867	MAPKAPK3	http://www.ncbi.nlm.nih.gov/gene/?term=7867	"3PK, MAPKAP-K3, MAPKAP3, MAPKAPK-3, MK-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022234	7867	MAPKAPK3	http://www.ncbi.nlm.nih.gov/gene/?term=7867	"3PK, MAPKAP-K3, MAPKAP3, MAPKAPK-3, MK-3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022235	7867	MAPKAPK3	http://www.ncbi.nlm.nih.gov/gene/?term=7867	"3PK, MAPKAP-K3, MAPKAP3, MAPKAPK-3, MK-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022236	78688	Nol3	http://www.ncbi.nlm.nih.gov/gene/?term=78688	"ARC, B430311C09Rik, MYC, NOP, Nop30 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022237	78689	Naa35	http://www.ncbi.nlm.nih.gov/gene/?term=78689	"A330021G12Rik, A330027C19Rik, AI158944, C030004C14Rik, Mak10 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022238	78693	C030004M13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78693		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022239	78697	Pus7	http://www.ncbi.nlm.nih.gov/gene/?term=78697	C330017I15Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022240	7871	SLMAP	http://www.ncbi.nlm.nih.gov/gene/?term=7871	SLAP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022241	7871	SLMAP	http://www.ncbi.nlm.nih.gov/gene/?term=7871	SLAP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022242	7871	SLMAP	http://www.ncbi.nlm.nih.gov/gene/?term=7871	SLAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022243	7873	MANF	http://www.ncbi.nlm.nih.gov/gene/?term=7873	"ARMET, ARP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022244	7873	MANF	http://www.ncbi.nlm.nih.gov/gene/?term=7873	"ARMET, ARP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022245	78745	9530097N15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78745		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022246	7874	USP7	http://www.ncbi.nlm.nih.gov/gene/?term=7874	"HAUSP, TEF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022247	7874	USP7	http://www.ncbi.nlm.nih.gov/gene/?term=7874	"HAUSP, TEF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022248	78790	4930414F18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78790		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022249	78792	4930432F04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78792		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022250	78794	4930402H05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78794		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022251	78796	Zcchc4	http://www.ncbi.nlm.nih.gov/gene/?term=78796	4930449I23Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022252	78797	Ndor1	http://www.ncbi.nlm.nih.gov/gene/?term=78797	"4930447P04Rik, NR1, Ndor "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022253	78798	Eml4	http://www.ncbi.nlm.nih.gov/gene/?term=78798	"4930443C24Rik, AI644019 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022254	7879	RAB7A	http://www.ncbi.nlm.nih.gov/gene/?term=7879	"PRO2706, RAB7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022255	7879	RAB7A	http://www.ncbi.nlm.nih.gov/gene/?term=7879	"PRO2706, RAB7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022256	7879	RAB7A	http://www.ncbi.nlm.nih.gov/gene/?term=7879	"PRO2706, RAB7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022257	78816	Gmip	http://www.ncbi.nlm.nih.gov/gene/?term=78816	5031419I10Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022258	78825	Desi2	http://www.ncbi.nlm.nih.gov/gene/?term=78825	"5830417C01Rik, DeSI-2, Fam152a, Pppde1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022259	78829	Tsc22d4	http://www.ncbi.nlm.nih.gov/gene/?term=78829	"0610009M14Rik, 1700023B23Rik, AI415410, Thg-1pit, Tilz2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022260	78829	Tsc22d4	http://www.ncbi.nlm.nih.gov/gene/?term=78829	"0610009M14Rik, 1700023B23Rik, AI415410, Thg-1pit, Tilz2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022261	78830	Slc25a12	http://www.ncbi.nlm.nih.gov/gene/?term=78830	"2610002D09Rik, AI839531, B230107K20Rik, BB129864 "	lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022262	78832	Cacul1	http://www.ncbi.nlm.nih.gov/gene/?term=78832	"2700078E11Rik, 2810417M16Rik, 9830127L17Rik, AI450346, D130033C15Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022263	78833	Gins3	http://www.ncbi.nlm.nih.gov/gene/?term=78833	"2700085M18Rik, AI616142 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022264	7884	SLBP	http://www.ncbi.nlm.nih.gov/gene/?term=7884	HBP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022265	7884	SLBP	http://www.ncbi.nlm.nih.gov/gene/?term=7884	HBP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022266	7884	SLBP	http://www.ncbi.nlm.nih.gov/gene/?term=7884	HBP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022267	78887	Sfi1	http://www.ncbi.nlm.nih.gov/gene/?term=78887		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022268	78887	Sfi1	http://www.ncbi.nlm.nih.gov/gene/?term=78887		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022269	78889	Wsb1	http://www.ncbi.nlm.nih.gov/gene/?term=78889	"1110056B13Rik, 2700038M07Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022270	78891	Scyl1	http://www.ncbi.nlm.nih.gov/gene/?term=78891	"2810011O19Rik, C85140, Ntkl, mdf, mfd, p105 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022271	78895	Pus7l	http://www.ncbi.nlm.nih.gov/gene/?term=78895	3000003F02Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022272	78902	4833447P13Rik	http://www.ncbi.nlm.nih.gov/gene/?term=78902		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022273	78908	Igsf3	http://www.ncbi.nlm.nih.gov/gene/?term=78908	"1700016K10Rik, 2810035F16Rik, 4833439O17Rik, mKIAA0466 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022274	78912	Sp2	http://www.ncbi.nlm.nih.gov/gene/?term=78912	"4930480I16Rik, mKIAA0048 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022275	78913	Ltn1	http://www.ncbi.nlm.nih.gov/gene/?term=78913	"4930528H02Rik, AV266914, C87237, Listerin, Rnf160, Zfp294 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022276	78926	Gas2l1	http://www.ncbi.nlm.nih.gov/gene/?term=78926	"4930500E24Rik, D0Jmb1, Gar22, TU-71.1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022277	78937	Avl9	http://www.ncbi.nlm.nih.gov/gene/?term=78937	"5830411G16Rik, D730049P16Rik, mKIAA0241 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022278	78943	Ern1	http://www.ncbi.nlm.nih.gov/gene/?term=78943	"9030414B18Rik, AI225830, C85377, Ire1a, Ire1alpha, Ire1p "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022279	78943	Ern1	http://www.ncbi.nlm.nih.gov/gene/?term=78943	"9030414B18Rik, AI225830, C85377, Ire1a, Ire1alpha, Ire1p "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022280	78988	MRPL57	http://www.ncbi.nlm.nih.gov/gene/?term=78988	"MRP63, bMRP63 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022281	78991	PCYOX1L	http://www.ncbi.nlm.nih.gov/gene/?term=78991		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022282	78992	YIPF2	http://www.ncbi.nlm.nih.gov/gene/?term=78992	FinGER2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022283	78994	PRR14	http://www.ncbi.nlm.nih.gov/gene/?term=78994		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022284	78996	C7orf49	http://www.ncbi.nlm.nih.gov/gene/?term=78996	MRI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022285	78996	C7orf49	http://www.ncbi.nlm.nih.gov/gene/?term=78996	MRI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022286	78999	LRFN4	http://www.ncbi.nlm.nih.gov/gene/?term=78999	"FIGLER6, SALM3, SALM3. "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022287	79000	AUNIP	http://www.ncbi.nlm.nih.gov/gene/?term=79000	"AIBP, C1orf135 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022288	79000	AUNIP	http://www.ncbi.nlm.nih.gov/gene/?term=79000	"AIBP, C1orf135 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022289	79001	VKORC1	http://www.ncbi.nlm.nih.gov/gene/?term=79001	"EDTP308, MST134, MST576, VKCFD2, VKOR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022290	79001	VKORC1	http://www.ncbi.nlm.nih.gov/gene/?term=79001	"EDTP308, MST134, MST576, VKCFD2, VKOR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022291	79002	C19orf43	http://www.ncbi.nlm.nih.gov/gene/?term=79002	fSAP18	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022292	79004	CUEDC2	http://www.ncbi.nlm.nih.gov/gene/?term=79004	"C10orf66, bA18I14.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022293	79004	CUEDC2	http://www.ncbi.nlm.nih.gov/gene/?term=79004	"C10orf66, bA18I14.5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022294	79004	CUEDC2	http://www.ncbi.nlm.nih.gov/gene/?term=79004	"C10orf66, bA18I14.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022295	79005	SCNM1	http://www.ncbi.nlm.nih.gov/gene/?term=79005		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022296	79006	METRN	http://www.ncbi.nlm.nih.gov/gene/?term=79006	"C16orf23, c380A1.2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022297	79007	DBNDD1	http://www.ncbi.nlm.nih.gov/gene/?term=79007		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022298	79007	DBNDD1	http://www.ncbi.nlm.nih.gov/gene/?term=79007		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022299	79012	CAMKV	http://www.ncbi.nlm.nih.gov/gene/?term=79012	"1G5, VACAMKL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022300	79016	DDA1	http://www.ncbi.nlm.nih.gov/gene/?term=79016	"C19orf58, PCIA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022301	79017	GGCT	http://www.ncbi.nlm.nih.gov/gene/?term=79017	"C7orf24, CRF21, GCTG, GGC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022302	79019	CENPM	http://www.ncbi.nlm.nih.gov/gene/?term=79019	"C22orf18, CENP-M, PANE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022303	79019	CENPM	http://www.ncbi.nlm.nih.gov/gene/?term=79019	"C22orf18, CENP-M, PANE1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022304	79019	CENPM	http://www.ncbi.nlm.nih.gov/gene/?term=79019	"C22orf18, CENP-M, PANE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022305	79022	TMEM106C	http://www.ncbi.nlm.nih.gov/gene/?term=79022		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022306	79022	TMEM106C	http://www.ncbi.nlm.nih.gov/gene/?term=79022		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022307	79022	TMEM106C	http://www.ncbi.nlm.nih.gov/gene/?term=79022		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022308	79023	NUP37	http://www.ncbi.nlm.nih.gov/gene/?term=79023	p37	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022309	79023	NUP37	http://www.ncbi.nlm.nih.gov/gene/?term=79023	p37	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022310	79026	AHNAK	http://www.ncbi.nlm.nih.gov/gene/?term=79026	AHNAKRS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022311	79026	AHNAK	http://www.ncbi.nlm.nih.gov/gene/?term=79026	AHNAKRS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022312	79027	ZNF655	http://www.ncbi.nlm.nih.gov/gene/?term=79027	"VIK, VIK-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022313	79033	ERI3	http://www.ncbi.nlm.nih.gov/gene/?term=79033	"PINT1, PRNPIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022314	79033	ERI3	http://www.ncbi.nlm.nih.gov/gene/?term=79033	"PINT1, PRNPIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022315	79035	NABP2	http://www.ncbi.nlm.nih.gov/gene/?term=79035	"OBFC2B, SOSS-B1, SSB1, hSSB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022316	79036	KXD1	http://www.ncbi.nlm.nih.gov/gene/?term=79036	"BORCS4, C19orf50, KXDL, MST096, MSTP096 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022317	79038	ZFYVE21	http://www.ncbi.nlm.nih.gov/gene/?term=79038	"HCVP7TP1, ZF21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022318	79039	DDX54	http://www.ncbi.nlm.nih.gov/gene/?term=79039	DP97	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022319	79039	DDX54	http://www.ncbi.nlm.nih.gov/gene/?term=79039	DP97	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022320	7903	ST8SIA4	http://www.ncbi.nlm.nih.gov/gene/?term=7903	"PST, PST1, SIAT8D, ST8SIA-IV "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022321	7903	ST8SIA4	http://www.ncbi.nlm.nih.gov/gene/?term=7903	"PST, PST1, SIAT8D, ST8SIA-IV "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022322	79041	TMEM38A	http://www.ncbi.nlm.nih.gov/gene/?term=79041	"TRIC-A, TRICA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022323	79042	TSEN34	http://www.ncbi.nlm.nih.gov/gene/?term=79042	"LENG5, PCH2C, SEN34, SEN34L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022324	79042	TSEN34	http://www.ncbi.nlm.nih.gov/gene/?term=79042	"LENG5, PCH2C, SEN34, SEN34L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022325	79043	Spsb3	http://www.ncbi.nlm.nih.gov/gene/?term=79043	"2310012N15Rik, 3300001M01Rik, SSB3, Tce1, mKIAA4204 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022326	79047	KCTD15	http://www.ncbi.nlm.nih.gov/gene/?term=79047		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022327	79048	SECISBP2	http://www.ncbi.nlm.nih.gov/gene/?term=79048	SBP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022328	79050	NOC4L	http://www.ncbi.nlm.nih.gov/gene/?term=79050	"NET49, NOC4, UTP19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022329	79053	ALG8	http://www.ncbi.nlm.nih.gov/gene/?term=79053	CDG1H	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022330	79053	ALG8	http://www.ncbi.nlm.nih.gov/gene/?term=79053	CDG1H	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022331	79053	ALG8	http://www.ncbi.nlm.nih.gov/gene/?term=79053	CDG1H	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022332	79056	PRRG4	http://www.ncbi.nlm.nih.gov/gene/?term=79056	"PRGP4, TMG4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022333	79058	ASPSCR1	http://www.ncbi.nlm.nih.gov/gene/?term=79058	"ASPCR1, ASPL, ASPS, RCC17, TUG, UBXD9, UBXN9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022334	79058	ASPSCR1	http://www.ncbi.nlm.nih.gov/gene/?term=79058	"ASPCR1, ASPL, ASPS, RCC17, TUG, UBXD9, UBXN9 "	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00022335	7905	REEP5	http://www.ncbi.nlm.nih.gov/gene/?term=7905	"C5orf18, D5S346, DP1, TB2, YOP1, Yip2e "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022336	7905	REEP5	http://www.ncbi.nlm.nih.gov/gene/?term=7905	"C5orf18, D5S346, DP1, TB2, YOP1, Yip2e "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022337	79064	TMEM223	http://www.ncbi.nlm.nih.gov/gene/?term=79064		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022338	79065	ATG9A	http://www.ncbi.nlm.nih.gov/gene/?term=79065	"APG9L1, MGD3208, mATG9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022339	79065	ATG9A	http://www.ncbi.nlm.nih.gov/gene/?term=79065	"APG9L1, MGD3208, mATG9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022340	79066	METTL16	http://www.ncbi.nlm.nih.gov/gene/?term=79066	METT10D	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022341	79068	FTO	http://www.ncbi.nlm.nih.gov/gene/?term=79068	"ALKBH9, BMIQ14, GDFD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022342	79068	FTO	http://www.ncbi.nlm.nih.gov/gene/?term=79068	"ALKBH9, BMIQ14, GDFD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022343	79070	KDELC1	http://www.ncbi.nlm.nih.gov/gene/?term=79070	"EP58, ERp58, KDEL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022344	79070	KDELC1	http://www.ncbi.nlm.nih.gov/gene/?term=79070	"EP58, ERp58, KDEL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022345	79071	ELOVL6	http://www.ncbi.nlm.nih.gov/gene/?term=79071	"FACE, FAE, LCE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022346	79071	ELOVL6	http://www.ncbi.nlm.nih.gov/gene/?term=79071	"FACE, FAE, LCE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022347	79072	FASTKD3	http://www.ncbi.nlm.nih.gov/gene/?term=79072		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022348	79073	TMEM109	http://www.ncbi.nlm.nih.gov/gene/?term=79073		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022349	79074	C2orf49	http://www.ncbi.nlm.nih.gov/gene/?term=79074	asw	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022350	79075	DSCC1	http://www.ncbi.nlm.nih.gov/gene/?term=79075	DCC1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022351	79077	DCTPP1	http://www.ncbi.nlm.nih.gov/gene/?term=79077	"CDA03, RS21C6, XTP3TPA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022352	79077	DCTPP1	http://www.ncbi.nlm.nih.gov/gene/?term=79077	"CDA03, RS21C6, XTP3TPA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022353	79078	C1orf50	http://www.ncbi.nlm.nih.gov/gene/?term=79078		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022354	79080	CCDC86	http://www.ncbi.nlm.nih.gov/gene/?term=79080		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022355	79080	CCDC86	http://www.ncbi.nlm.nih.gov/gene/?term=79080		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022356	79081	LBHD1	http://www.ncbi.nlm.nih.gov/gene/?term=79081	C11orf48	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022357	79084	WDR77	http://www.ncbi.nlm.nih.gov/gene/?term=79084	"HKMT1069, MEP-50, MEP50, Nbla10071, p44, p44/Mep50 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022358	79085	SLC25A23	http://www.ncbi.nlm.nih.gov/gene/?term=79085	"APC2, MCSC2, SCaMC-3 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022359	79086	SMIM7	http://www.ncbi.nlm.nih.gov/gene/?term=79086	C19orf42	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022360	79086	SMIM7	http://www.ncbi.nlm.nih.gov/gene/?term=79086	C19orf42	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022361	79087	ALG12	http://www.ncbi.nlm.nih.gov/gene/?term=79087	"CDG1G, ECM39, PP14673, hALG12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022362	79089	TMUB2	http://www.ncbi.nlm.nih.gov/gene/?term=79089	FP2653	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022363	79090	TRAPPC6A	http://www.ncbi.nlm.nih.gov/gene/?term=79090	TRS33	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022364	79091	METTL22	http://www.ncbi.nlm.nih.gov/gene/?term=79091	C16orf68	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022365	790955	UQCC3	http://www.ncbi.nlm.nih.gov/gene/?term=790955	"C11orf83, CCDS41658.1, MC3DN9, UNQ655 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022366	790955	UQCC3	http://www.ncbi.nlm.nih.gov/gene/?term=790955	"C11orf83, CCDS41658.1, MC3DN9, UNQ655 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022367	79095	C9orf16	http://www.ncbi.nlm.nih.gov/gene/?term=79095	EST00098	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022368	790	CAD	http://www.ncbi.nlm.nih.gov/gene/?term=790	CDG1Z	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00022369	790	CAD	http://www.ncbi.nlm.nih.gov/gene/?term=790	CDG1Z	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022370	790	CAD	http://www.ncbi.nlm.nih.gov/gene/?term=790	CDG1Z	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022371	790	CAD	http://www.ncbi.nlm.nih.gov/gene/?term=790	CDG1Z	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022372	79101	TAF1D	http://www.ncbi.nlm.nih.gov/gene/?term=79101	"JOSD3, RAFI41, TAF(I)41, TAFI41 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022373	79101	TAF1D	http://www.ncbi.nlm.nih.gov/gene/?term=79101	"JOSD3, RAFI41, TAF(I)41, TAFI41 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022374	79109	MAPKAP1	http://www.ncbi.nlm.nih.gov/gene/?term=79109	"JC310, MIP1, SIN1, SIN1b, SIN1g "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022375	791315	Gm9875	http://www.ncbi.nlm.nih.gov/gene/?term=791315	ENSMUSG00000052389	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022376	79132	DHX58	http://www.ncbi.nlm.nih.gov/gene/?term=79132	"D11LGP2, D11lgp2e, LGP2, RLR-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022377	791331	BC005705	http://www.ncbi.nlm.nih.gov/gene/?term=791331	ENSMUSG00000042973	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022378	79133	NDUFAF5	http://www.ncbi.nlm.nih.gov/gene/?term=79133	"C20orf7, bA526K24.2, dJ842G6.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022379	791342	Gm10097	http://www.ncbi.nlm.nih.gov/gene/?term=791342	ENSMUSG00000061261	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022380	79134	TMEM185B	http://www.ncbi.nlm.nih.gov/gene/?term=79134	FAM11B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022381	79134	TMEM185B	http://www.ncbi.nlm.nih.gov/gene/?term=79134	FAM11B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022382	79135	APOO	http://www.ncbi.nlm.nih.gov/gene/?term=79135	"FAM121B, MIC26, Mic23, My025 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022383	79135	APOO	http://www.ncbi.nlm.nih.gov/gene/?term=79135	"FAM121B, MIC26, Mic23, My025 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022384	79137	FAM134A	http://www.ncbi.nlm.nih.gov/gene/?term=79137	"C2orf17, MAG-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022385	79137	FAM134A	http://www.ncbi.nlm.nih.gov/gene/?term=79137	"C2orf17, MAG-2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022386	79137	FAM134A	http://www.ncbi.nlm.nih.gov/gene/?term=79137	"C2orf17, MAG-2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022387	79137	FAM134A	http://www.ncbi.nlm.nih.gov/gene/?term=79137	C2orf17	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022388	79139	DERL1	http://www.ncbi.nlm.nih.gov/gene/?term=79139	"DER-1, DER1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022389	79139	DERL1	http://www.ncbi.nlm.nih.gov/gene/?term=79139	"DER-1, DER1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022390	79139	DERL1	http://www.ncbi.nlm.nih.gov/gene/?term=79139	"DER-1, DER1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022391	7913	DEK	http://www.ncbi.nlm.nih.gov/gene/?term=7913	D6S231E	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022392	79140	CCDC28B	http://www.ncbi.nlm.nih.gov/gene/?term=79140		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022393	79142	PHF23	http://www.ncbi.nlm.nih.gov/gene/?term=79142	hJUNE-1b	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022394	79143	MBOAT7	http://www.ncbi.nlm.nih.gov/gene/?term=79143	"BB1, LENG4, LPIAT, LRC4, MBOA7, OACT7, hMBOA-7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022395	79143	MBOAT7	http://www.ncbi.nlm.nih.gov/gene/?term=79143	"BB1, LENG4, LPIAT, LRC4, MBOA7, OACT7, hMBOA-7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022396	79144	PPDPF	http://www.ncbi.nlm.nih.gov/gene/?term=79144	"C20orf149, dJ697K14.9, exdpf "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022397	79145	CHCHD7	http://www.ncbi.nlm.nih.gov/gene/?term=79145	COX23	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022398	79145	CHCHD7	http://www.ncbi.nlm.nih.gov/gene/?term=79145	COX23	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022399	79147	FKRP	http://www.ncbi.nlm.nih.gov/gene/?term=79147	"LGMD2I, MDC1C, MDDGA5, MDDGB5, MDDGC5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022400	79147	FKRP	http://www.ncbi.nlm.nih.gov/gene/?term=79147	"LGMD2I, MDC1C, MDDGA5, MDDGB5, MDDGC5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022401	79147	FKRP	http://www.ncbi.nlm.nih.gov/gene/?term=79147	"LGMD2I, MDC1C, MDDGA5, MDDGB5, MDDGC5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022402	79153	GDPD3	http://www.ncbi.nlm.nih.gov/gene/?term=79153	GDE7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022403	79154	DHRS11	http://www.ncbi.nlm.nih.gov/gene/?term=79154	"ARPG836, SDR24C1, spDHRS11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022404	79155	TNIP2	http://www.ncbi.nlm.nih.gov/gene/?term=79155	"ABIN2, FLIP1, KLIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022405	79156	PLEKHF1	http://www.ncbi.nlm.nih.gov/gene/?term=79156	"APPD, LAPF, PHAFIN1, ZFYVE15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022406	79157	MFSD11	http://www.ncbi.nlm.nih.gov/gene/?term=79157	ET	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022407	79158	GNPTAB	http://www.ncbi.nlm.nih.gov/gene/?term=79158	"GNPTA, ICD "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022408	79158	GNPTAB	http://www.ncbi.nlm.nih.gov/gene/?term=79158	"GNPTA, ICD "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022409	79158	GNPTAB	http://www.ncbi.nlm.nih.gov/gene/?term=79158	"GNPTA, ICD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022410	79159	NOL12	http://www.ncbi.nlm.nih.gov/gene/?term=79159	"Nop25, dJ37E16.7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022411	7915	ALDH5A1	http://www.ncbi.nlm.nih.gov/gene/?term=7915	"SSADH, SSDH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022412	7915	ALDH5A1	http://www.ncbi.nlm.nih.gov/gene/?term=7915	"SSADH, SSDH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022413	7915	ALDH5A1	http://www.ncbi.nlm.nih.gov/gene/?term=7915	"SSADH, SSDH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022414	79161	TMEM243	http://www.ncbi.nlm.nih.gov/gene/?term=79161	"C7orf23, MM-TRAG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022415	79161	TMEM243	http://www.ncbi.nlm.nih.gov/gene/?term=79161	"C7orf23, MM-TRAG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022416	79169	C1orf35	http://www.ncbi.nlm.nih.gov/gene/?term=79169	MMTAG2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022417	79169	C1orf35	http://www.ncbi.nlm.nih.gov/gene/?term=79169	MMTAG2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022418	7916	PRRC2A	http://www.ncbi.nlm.nih.gov/gene/?term=7916	"BAT2, D6S51, D6S51E, G2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022419	79170	PRR15L	http://www.ncbi.nlm.nih.gov/gene/?term=79170	ATAD4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022420	79171	RBM42	http://www.ncbi.nlm.nih.gov/gene/?term=79171		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022421	79171	RBM42	http://www.ncbi.nlm.nih.gov/gene/?term=79171		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022422	79172	CENPO	http://www.ncbi.nlm.nih.gov/gene/?term=79172	"CENP-O, ICEN-36, MCM21R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022423	79172	CENPO	http://www.ncbi.nlm.nih.gov/gene/?term=79172	"CENP-O, ICEN-36, MCM21R "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022424	79173	C19orf57	http://www.ncbi.nlm.nih.gov/gene/?term=79173		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022425	79174	CRELD2	http://www.ncbi.nlm.nih.gov/gene/?term=79174		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022426	79174	CRELD2	http://www.ncbi.nlm.nih.gov/gene/?term=79174		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022427	79176	FBXL15	http://www.ncbi.nlm.nih.gov/gene/?term=79176	"FBXO37, Fbl15, JET, PSD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022428	79176	FBXL15	http://www.ncbi.nlm.nih.gov/gene/?term=79176	"FBXO37, Fbl15, JET, PSD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022429	79177	ZNF576	http://www.ncbi.nlm.nih.gov/gene/?term=79177		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022430	79177	ZNF576	http://www.ncbi.nlm.nih.gov/gene/?term=79177		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022431	79178	THTPA	http://www.ncbi.nlm.nih.gov/gene/?term=79178	"THTP, THTPASE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022432	7917	BAG6	http://www.ncbi.nlm.nih.gov/gene/?term=7917	"BAG-6, BAT3, D6S52E, G3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022433	79180	EFHD2	http://www.ncbi.nlm.nih.gov/gene/?term=79180	SWS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022434	79183	TTPAL	http://www.ncbi.nlm.nih.gov/gene/?term=79183	C20orf121	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022435	79183	TTPAL	http://www.ncbi.nlm.nih.gov/gene/?term=79183	C20orf121	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022436	79184	BRCC3	http://www.ncbi.nlm.nih.gov/gene/?term=79184	"BRCC36, C6.1A, CXorf53 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022437	79188	TMEM43	http://www.ncbi.nlm.nih.gov/gene/?term=79188	"ARVC5, ARVD5, EDMD7, LUMA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022438	7918	GPANK1	http://www.ncbi.nlm.nih.gov/gene/?term=7918	"ANKRD59, BAT4, D6S54E, G5, GPATCH10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022439	79191	IRX3	http://www.ncbi.nlm.nih.gov/gene/?term=79191	"IRX-1, IRXB1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022440	7919	DDX39B	http://www.ncbi.nlm.nih.gov/gene/?term=7919	"BAT1, D6S81E, UAP56 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022441	79202	Tnfrsf22	http://www.ncbi.nlm.nih.gov/gene/?term=79202	"2810028K06Rik, C130035G06Rik, SOBa, Tnfrh2, Tnfrsf1al2, mDcTrailr2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022442	79228	THOC6	http://www.ncbi.nlm.nih.gov/gene/?term=79228	"BBIS, WDR58, fSAP35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022443	7922	SLC39A7	http://www.ncbi.nlm.nih.gov/gene/?term=7922	"D6S115E, D6S2244E, H2-KE4, HKE4, KE4, RING5, ZIP7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022444	79230	ZNF557	http://www.ncbi.nlm.nih.gov/gene/?term=79230		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022445	7923	HSD17B8	http://www.ncbi.nlm.nih.gov/gene/?term=7923	"D6S2245E, FABG, FABGL, H2-KE6, HKE6, KE6, RING2, SDR30C1, dJ1033B10.9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022446	7923	HSD17B8	http://www.ncbi.nlm.nih.gov/gene/?term=7923	"D6S2245E, FABG, FABGL, H2-KE6, HKE6, KE6, RING2, SDR30C1, dJ1033B10.9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022447	79263	Trim39	http://www.ncbi.nlm.nih.gov/gene/?term=79263	"1100001D15Rik, E130103K13Rik, RBCC-B30.2, Rnf23, mKIAA4179, tfp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022448	79264	Krit1	http://www.ncbi.nlm.nih.gov/gene/?term=79264	"2010007K12Rik, A630036P20Rik, AA432855, AI450393, AI643869, BB155247, BB235701, Ccm1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022449	79269	DCAF10	http://www.ncbi.nlm.nih.gov/gene/?term=79269	WDR32	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022450	79269	DCAF10	http://www.ncbi.nlm.nih.gov/gene/?term=79269	WDR32	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022451	79364	ZXDC	http://www.ncbi.nlm.nih.gov/gene/?term=79364	ZXDL	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022452	79364	ZXDC	http://www.ncbi.nlm.nih.gov/gene/?term=79364	ZXDL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022453	7936	NELFE	http://www.ncbi.nlm.nih.gov/gene/?term=7936	"D6S45, NELF-E, RD, RDBP, RDP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022454	7936	NELFE	http://www.ncbi.nlm.nih.gov/gene/?term=7936	"D6S45, NELF-E, RD, RDBP, RDP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022455	793	CALB1	http://www.ncbi.nlm.nih.gov/gene/?term=793	"CALB, D-28K "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022456	79401	Spz1	http://www.ncbi.nlm.nih.gov/gene/?term=79401	"1700027M20Rik, AI429130 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022457	7940	LST1	http://www.ncbi.nlm.nih.gov/gene/?term=7940	"B144, D6S49E, LST-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022458	79441	HAUS3	http://www.ncbi.nlm.nih.gov/gene/?term=79441	"C4orf15, IT1, dgt3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022459	79441	HAUS3	http://www.ncbi.nlm.nih.gov/gene/?term=79441	"C4orf15, IT1, dgt3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022460	79441	HAUS3	http://www.ncbi.nlm.nih.gov/gene/?term=79441	"C4orf15, IT1, dgt3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022461	79443	FYCO1	http://www.ncbi.nlm.nih.gov/gene/?term=79443	"CATC2, CTRCT18, RUFY3, ZFYVE7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022462	79447	PAGR1	http://www.ncbi.nlm.nih.gov/gene/?term=79447	"C16orf53, GAS, PA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022463	79455	Pdcl2	http://www.ncbi.nlm.nih.gov/gene/?term=79455	"1700010B22Rik, 1700016K07Rik, Mgcphlp, Tphlp "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022464	79464	Lias	http://www.ncbi.nlm.nih.gov/gene/?term=79464	"2900022L22Rik, 4933425M12Rik, 7a5ex, C77512, LS, lip-syn "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022465	79469	DLEU2L	http://www.ncbi.nlm.nih.gov/gene/?term=79469	BCMSUNL	lncRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00022466	794	CALB2	http://www.ncbi.nlm.nih.gov/gene/?term=794	"CAB29, CAL2, CR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022467	79555	BC005537	http://www.ncbi.nlm.nih.gov/gene/?term=79555	"8030460C05Rik, C78201 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022468	79566	Sh3bp5l	http://www.ncbi.nlm.nih.gov/gene/?term=79566	"2310074E09Rik, BC003251, mKIAA1720 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022469	79567	FAM65A	http://www.ncbi.nlm.nih.gov/gene/?term=79567		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022470	79568	C2orf47	http://www.ncbi.nlm.nih.gov/gene/?term=79568		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022471	79571	GCC1	http://www.ncbi.nlm.nih.gov/gene/?term=79571	"GCC1P, GCC88 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022472	79571	GCC1	http://www.ncbi.nlm.nih.gov/gene/?term=79571	"GCC1P, GCC88 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022473	79572	ATP13A3	http://www.ncbi.nlm.nih.gov/gene/?term=79572	AFURS1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022474	79572	ATP13A3	http://www.ncbi.nlm.nih.gov/gene/?term=79572	AFURS1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022475	79574	EPS8L3	http://www.ncbi.nlm.nih.gov/gene/?term=79574	EPS8R3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022476	79577	CDC73	http://www.ncbi.nlm.nih.gov/gene/?term=79577	"C1orf28, FIHP, HPTJT, HRPT1, HRPT2, HYX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022477	79577	CDC73	http://www.ncbi.nlm.nih.gov/gene/?term=79577	"C1orf28, FIHP, HPTJT, HRPT1, HRPT2, HYX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022478	79581	SLC52A2	http://www.ncbi.nlm.nih.gov/gene/?term=79581	"BVVLS2, D15Ertd747e, GPCR41, GPR172A, PAR1, RFT3, RFVT2, hRFT3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022479	79582	SPAG16	http://www.ncbi.nlm.nih.gov/gene/?term=79582	"PF20, WDR29 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022480	79582	SPAG16	http://www.ncbi.nlm.nih.gov/gene/?term=79582	"PF20, WDR29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022481	79583	TMEM231	http://www.ncbi.nlm.nih.gov/gene/?term=79583	"ALYE870, JBTS20, MKS11, PRO1886 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022482	79585	CORO7	http://www.ncbi.nlm.nih.gov/gene/?term=79585	"0610011B16Rik, CRN7, POD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022483	79586	CHPF	http://www.ncbi.nlm.nih.gov/gene/?term=79586	"CHSY2, CSS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022484	79587	CARS2	http://www.ncbi.nlm.nih.gov/gene/?term=79587	"COXPD27, cysRS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022485	79590	MRPL24	http://www.ncbi.nlm.nih.gov/gene/?term=79590	"L24mt, MRP-L18, MRP-L24 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022486	79591	C10orf76	http://www.ncbi.nlm.nih.gov/gene/?term=79591		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022487	79591	C10orf76	http://www.ncbi.nlm.nih.gov/gene/?term=79591		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022488	79594	MUL1	http://www.ncbi.nlm.nih.gov/gene/?term=79594	"C1orf166, GIDE, MAPL, MULAN, RNF218 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022489	79594	MUL1	http://www.ncbi.nlm.nih.gov/gene/?term=79594	"C1orf166, GIDE, MAPL, MULAN, RNF218 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022490	79595	SAP130	http://www.ncbi.nlm.nih.gov/gene/?term=79595		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022491	79596	RNF219	http://www.ncbi.nlm.nih.gov/gene/?term=79596	C13orf7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022492	79598	CEP97	http://www.ncbi.nlm.nih.gov/gene/?term=79598	"2810403B08Rik, LRRIQ2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022493	79607	FAM118B	http://www.ncbi.nlm.nih.gov/gene/?term=79607		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022494	79609	VCPKMT	http://www.ncbi.nlm.nih.gov/gene/?term=79609	"C14orf138, METTL21D, VCP-KMT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022495	79613	TANGO6	http://www.ncbi.nlm.nih.gov/gene/?term=79613	TMCO7	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022496	79613	TANGO6	http://www.ncbi.nlm.nih.gov/gene/?term=79613	TMCO7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022497	79616	CCNJL	http://www.ncbi.nlm.nih.gov/gene/?term=79616		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022498	79621	RNASEH2B	http://www.ncbi.nlm.nih.gov/gene/?term=79621	"AGS2, DLEU8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022499	79622	SNRNP25	http://www.ncbi.nlm.nih.gov/gene/?term=79622	C16orf33	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022500	79622	SNRNP25	http://www.ncbi.nlm.nih.gov/gene/?term=79622	C16orf33	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022501	79624	ARMT1	http://www.ncbi.nlm.nih.gov/gene/?term=79624	C6orf211	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022502	79624	ARMT1	http://www.ncbi.nlm.nih.gov/gene/?term=79624	C6orf211	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022503	79626	TNFAIP8L2	http://www.ncbi.nlm.nih.gov/gene/?term=79626	TIPE2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022504	79628	SH3TC2	http://www.ncbi.nlm.nih.gov/gene/?term=79628	"CMT4C, MNMN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022505	79628	SH3TC2	http://www.ncbi.nlm.nih.gov/gene/?term=79628	"CMT4C, MNMN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022506	79633	FAT4	http://www.ncbi.nlm.nih.gov/gene/?term=79633	"CDHF14, CDHR11, FAT-J, FATJ, HKLLS2, NBLA00548, VMLDS2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022507	79637	ARMC7	http://www.ncbi.nlm.nih.gov/gene/?term=79637		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022508	79639	TMEM53	http://www.ncbi.nlm.nih.gov/gene/?term=79639	NET4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022509	79640	C22orf46	http://www.ncbi.nlm.nih.gov/gene/?term=79640		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022510	79641	ROGDI	http://www.ncbi.nlm.nih.gov/gene/?term=79641	KTZS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022511	79643	CHMP6	http://www.ncbi.nlm.nih.gov/gene/?term=79643	VPS20	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022512	79644	SRD5A3	http://www.ncbi.nlm.nih.gov/gene/?term=79644	"CDG1P, CDG1Q, KRIZI, SRD5A2L, SRD5A2L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022513	79644	SRD5A3	http://www.ncbi.nlm.nih.gov/gene/?term=79644	"CDG1P, CDG1Q, KRIZI, SRD5A2L, SRD5A2L1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022514	79646	PANK3	http://www.ncbi.nlm.nih.gov/gene/?term=79646		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022515	79646	PANK3	http://www.ncbi.nlm.nih.gov/gene/?term=79646		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022516	79647	AKIRIN1	http://www.ncbi.nlm.nih.gov/gene/?term=79647	"C1orf108, STRF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022517	79647	AKIRIN1	http://www.ncbi.nlm.nih.gov/gene/?term=79647	"C1orf108, STRF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022518	79648	MCPH1	http://www.ncbi.nlm.nih.gov/gene/?term=79648	"BRIT1, MCT "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022519	79648	MCPH1	http://www.ncbi.nlm.nih.gov/gene/?term=79648	"BRIT1, MCT "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022520	79648	MCPH1	http://www.ncbi.nlm.nih.gov/gene/?term=79648	"BRIT1, MCT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022521	79649	MAP7D3	http://www.ncbi.nlm.nih.gov/gene/?term=79649	MDP3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022522	79650	USB1	http://www.ncbi.nlm.nih.gov/gene/?term=79650	"C16orf57, HVSL1, Mpn1, PN, hUsb1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022523	79654	HECTD3	http://www.ncbi.nlm.nih.gov/gene/?term=79654		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022524	79656	BEND5	http://www.ncbi.nlm.nih.gov/gene/?term=79656	C1orf165	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022525	7965	AIMP2	http://www.ncbi.nlm.nih.gov/gene/?term=7965	"JTV-1, JTV1, P38, PRO0992 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022526	7965	AIMP2	http://www.ncbi.nlm.nih.gov/gene/?term=7965	"JTV-1, JTV1, P38, PRO0992 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022527	79660	PPP1R3B	http://www.ncbi.nlm.nih.gov/gene/?term=79660	"GL, PPP1R4, PTG "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022528	79660	PPP1R3B	http://www.ncbi.nlm.nih.gov/gene/?term=79660	"GL, PPP1R4, PTG "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022529	79660	PPP1R3B	http://www.ncbi.nlm.nih.gov/gene/?term=79660	"GL, PPP1R4, PTG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022530	79664	ICE2	http://www.ncbi.nlm.nih.gov/gene/?term=79664	"BRCC1, NARG2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022531	79664	ICE2	http://www.ncbi.nlm.nih.gov/gene/?term=79664	"BRCC1, NARG2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022532	79664	ICE2	http://www.ncbi.nlm.nih.gov/gene/?term=79664	"BRCC1, NARG2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022533	79664	ICE2	http://www.ncbi.nlm.nih.gov/gene/?term=79664	"BRCC1, NARG2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022534	79665	DHX40	http://www.ncbi.nlm.nih.gov/gene/?term=79665	"ARG147, DDX40, PAD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022535	79665	DHX40	http://www.ncbi.nlm.nih.gov/gene/?term=79665	"ARG147, DDX40, PAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022536	79666	PLEKHF2	http://www.ncbi.nlm.nih.gov/gene/?term=79666	"EAPF, PHAFIN2, ZFYVE18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022537	79669	C3orf52	http://www.ncbi.nlm.nih.gov/gene/?term=79669	TTMP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022538	79670	ZCCHC6	http://www.ncbi.nlm.nih.gov/gene/?term=79670	"PAPD6, TUT7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022539	79672	FN3KRP	http://www.ncbi.nlm.nih.gov/gene/?term=79672	FN3KL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022540	79672	FN3KRP	http://www.ncbi.nlm.nih.gov/gene/?term=79672	FN3KL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022541	79673	ZNF329	http://www.ncbi.nlm.nih.gov/gene/?term=79673		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022542	79673	ZNF329	http://www.ncbi.nlm.nih.gov/gene/?term=79673		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022543	79674	VEPH1	http://www.ncbi.nlm.nih.gov/gene/?term=79674	"MELT, VEPH "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022544	79675	FASTKD1	http://www.ncbi.nlm.nih.gov/gene/?term=79675		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022545	79676	OGFOD2	http://www.ncbi.nlm.nih.gov/gene/?term=79676		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022546	79677	SMC6	http://www.ncbi.nlm.nih.gov/gene/?term=79677	"SMC-6L1, hSMC6, SMC6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022547	79680	C22orf29	http://www.ncbi.nlm.nih.gov/gene/?term=79680	BOP	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022548	79682	CENPU	http://www.ncbi.nlm.nih.gov/gene/?term=79682	"CENP5050, KLIP1, MLF1IP, PBIP1, CENPU "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022549	79682	CENPU	http://www.ncbi.nlm.nih.gov/gene/?term=79682	"CENP5050, KLIP1, MLF1IP, PBIP1, CENPU "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022550	79682	CENPU	http://www.ncbi.nlm.nih.gov/gene/?term=79682	"CENP50, CENPU50, KLIP1, MLF1IP, PBIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022551	79685	SAP30L	http://www.ncbi.nlm.nih.gov/gene/?term=79685	NS4ATP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022552	79689	STEAP4	http://www.ncbi.nlm.nih.gov/gene/?term=79689	"STAMP2, TIARP, TNFAIP9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022553	79689	STEAP4	http://www.ncbi.nlm.nih.gov/gene/?term=79689	"STAMP2, TIARP, TNFAIP9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022554	79690	GAL3ST4	http://www.ncbi.nlm.nih.gov/gene/?term=79690	GAL3ST-4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022555	79690	GAL3ST4	http://www.ncbi.nlm.nih.gov/gene/?term=79690	GAL3ST-4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022556	79691	QTRT2	http://www.ncbi.nlm.nih.gov/gene/?term=79691	QTRTD1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022557	79691	QTRT2	http://www.ncbi.nlm.nih.gov/gene/?term=79691	QTRTD1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022558	79691	QTRT2	http://www.ncbi.nlm.nih.gov/gene/?term=79691	QTRTD1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022559	79693	YRDC	http://www.ncbi.nlm.nih.gov/gene/?term=79693	"DRIP3, IRIP, SUA5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022560	79693	YRDC	http://www.ncbi.nlm.nih.gov/gene/?term=79693	"DRIP3, IRIP, SUA5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022561	79694	MANEA	http://www.ncbi.nlm.nih.gov/gene/?term=79694	"ENDO, hEndo "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022562	79695	GALNT12	http://www.ncbi.nlm.nih.gov/gene/?term=79695	"CRCS1, GalNAc-T12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022563	79695	GALNT12	http://www.ncbi.nlm.nih.gov/gene/?term=79695	"CRCS1, GalNAc-T12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022564	79697	C14orf169	http://www.ncbi.nlm.nih.gov/gene/?term=79697	"MAPJD, NO66, ROX, URLC2, hsNO66 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022565	79699	ZYG11B	http://www.ncbi.nlm.nih.gov/gene/?term=79699	ZYG11	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022566	796	CALCA	http://www.ncbi.nlm.nih.gov/gene/?term=796	"CALC1, CGRP, CGRP-I, CGRP1, CT, KC, PCT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022567	79701	OGFOD3	http://www.ncbi.nlm.nih.gov/gene/?term=79701	C17orf101	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022568	79701	OGFOD3	http://www.ncbi.nlm.nih.gov/gene/?term=79701	C17orf101	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022569	79703	C11orf80	http://www.ncbi.nlm.nih.gov/gene/?term=79703		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022570	79707	NOL9	http://www.ncbi.nlm.nih.gov/gene/?term=79707	"Grc3, NET6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022571	79707	NOL9	http://www.ncbi.nlm.nih.gov/gene/?term=79707	"Grc3, NET6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022572	79709	COLGALT1	http://www.ncbi.nlm.nih.gov/gene/?term=79709	GLT25D1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022573	79709	COLGALT1	http://www.ncbi.nlm.nih.gov/gene/?term=79709	GLT25D1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022574	79709	COLGALT1	http://www.ncbi.nlm.nih.gov/gene/?term=79709	GLT25D1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022575	79710	MORC4	http://www.ncbi.nlm.nih.gov/gene/?term=79710	"ZCW4, ZCWCC2, dJ75H8.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022576	79710	MORC4	http://www.ncbi.nlm.nih.gov/gene/?term=79710	"ZCW4, ZCWCC2, dJ75H8.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022577	79714	CCDC51	http://www.ncbi.nlm.nih.gov/gene/?term=79714		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022578	79717	PPCS	http://www.ncbi.nlm.nih.gov/gene/?term=79717		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022579	79718	TBL1XR1	http://www.ncbi.nlm.nih.gov/gene/?term=79718	"C21, DC42, IRA1, TBLR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022580	79718	TBL1XR1	http://www.ncbi.nlm.nih.gov/gene/?term=79718	"C21, DC42, IRA1, TBLR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022581	79719	AAGAB	http://www.ncbi.nlm.nih.gov/gene/?term=79719	"KPPP1, PPKP1, PPKP1A, p34 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022582	79719	AAGAB	http://www.ncbi.nlm.nih.gov/gene/?term=79719	"KPPP1, PPKP1, PPKP1A, p34 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022583	79722	ANKRD55	http://www.ncbi.nlm.nih.gov/gene/?term=79722		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022584	79723	SUV39H2	http://www.ncbi.nlm.nih.gov/gene/?term=79723	KMT1B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022585	79727	LIN28A	http://www.ncbi.nlm.nih.gov/gene/?term=79727	"CSDD1, LIN-28, LIN28, ZCCHC1, lin-28A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022586	79727	LIN28A	http://www.ncbi.nlm.nih.gov/gene/?term=79727	"CSDD1, LIN-28, LIN28, ZCCHC1, lin-28A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022587	79728	PALB2	http://www.ncbi.nlm.nih.gov/gene/?term=79728	"FANCN, PNCA3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022588	79731	NARS2	http://www.ncbi.nlm.nih.gov/gene/?term=79731	"DFNB94, SLM5, asnRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022589	79733	E2F8	http://www.ncbi.nlm.nih.gov/gene/?term=79733	E2F-8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022590	79734	KCTD17	http://www.ncbi.nlm.nih.gov/gene/?term=79734		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022591	79736	TEFM	http://www.ncbi.nlm.nih.gov/gene/?term=79736	C17orf42	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022592	79741	CCDC7	http://www.ncbi.nlm.nih.gov/gene/?term=79741	"BIOT2, BioT2-A, BioT2-B, BioT2-C, C10orf68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022593	79746	ECHDC3	http://www.ncbi.nlm.nih.gov/gene/?term=79746		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022594	79748	LMAN1L	http://www.ncbi.nlm.nih.gov/gene/?term=79748	"ERGIC-53L, ERGL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022595	79751	SLC25A22	http://www.ncbi.nlm.nih.gov/gene/?term=79751	"EIEE3, GC-1, GC1, NET44 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022596	79751	SLC25A22	http://www.ncbi.nlm.nih.gov/gene/?term=79751	"EIEE3, GC1, NET44 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022597	79752	ZFAND1	http://www.ncbi.nlm.nih.gov/gene/?term=79752		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022598	79754	ASB13	http://www.ncbi.nlm.nih.gov/gene/?term=79754		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022599	79754	ASB13	http://www.ncbi.nlm.nih.gov/gene/?term=79754		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022600	79758	DHRS12	http://www.ncbi.nlm.nih.gov/gene/?term=79758	SDR40C1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022601	7975	MAFK	http://www.ncbi.nlm.nih.gov/gene/?term=7975	"NFE2U, P18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022602	79760	GEMIN7	http://www.ncbi.nlm.nih.gov/gene/?term=79760	SIP3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022603	79762	C1orf115	http://www.ncbi.nlm.nih.gov/gene/?term=79762		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022604	79763	ISOC2	http://www.ncbi.nlm.nih.gov/gene/?term=79763		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022605	79767	ELMO3	http://www.ncbi.nlm.nih.gov/gene/?term=79767	"CED-12, CED12, ELMO-3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022606	79768	KATNBL1	http://www.ncbi.nlm.nih.gov/gene/?term=79768	C15orf29	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022607	7976	FZD3	http://www.ncbi.nlm.nih.gov/gene/?term=7976	Fz-3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022608	79770	TXNDC15	http://www.ncbi.nlm.nih.gov/gene/?term=79770	"C5orf14, UNQ335 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022609	79770	TXNDC15	http://www.ncbi.nlm.nih.gov/gene/?term=79770	"C5orf14, UNQ335 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022610	79770	TXNDC15	http://www.ncbi.nlm.nih.gov/gene/?term=79770	"C5orf14, UNQ335 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022611	79774	GRTP1	http://www.ncbi.nlm.nih.gov/gene/?term=79774	TBC1D6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022612	79774	GRTP1	http://www.ncbi.nlm.nih.gov/gene/?term=79774	TBC1D6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022613	79776	ZFHX4	http://www.ncbi.nlm.nih.gov/gene/?term=79776	"ZFH4, ZHF4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022614	79776	ZFHX4	http://www.ncbi.nlm.nih.gov/gene/?term=79776	"ZFH4, ZHF4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022615	79777	ACBD4	http://www.ncbi.nlm.nih.gov/gene/?term=79777	HMFT0700	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022616	79778	MICALL2	http://www.ncbi.nlm.nih.gov/gene/?term=79778	"JRAB, MICAL-L2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022617	79778	MICALL2	http://www.ncbi.nlm.nih.gov/gene/?term=79778	"JRAB, MICAL-L2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022618	79782	LRRC31	http://www.ncbi.nlm.nih.gov/gene/?term=79782	HEL-S-293	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022619	7978	MTERF1	http://www.ncbi.nlm.nih.gov/gene/?term=7978	MTERF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022620	79791	FBXO31	http://www.ncbi.nlm.nih.gov/gene/?term=79791	"FBX14, FBXO14, Fbx31, MRT45, pp2386 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022621	79791	FBXO31	http://www.ncbi.nlm.nih.gov/gene/?term=79791	"FBX14, FBXO14, Fbx31, MRT45, pp2386 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022622	79792	GSDMD	http://www.ncbi.nlm.nih.gov/gene/?term=79792	"DF5L, DFNA5L, FKSG10C1, GSDMD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022623	79794	C12orf49	http://www.ncbi.nlm.nih.gov/gene/?term=79794		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022624	79794	C12orf49	http://www.ncbi.nlm.nih.gov/gene/?term=79794		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022625	7979	SHFM1	http://www.ncbi.nlm.nih.gov/gene/?term=7979	"DSS1, ECD, SEM1, SHFD1, SHSF1, Shfdg1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022626	7979	SHFM1	http://www.ncbi.nlm.nih.gov/gene/?term=7979	"DSS1, ECD, SEM1, SHFD1, SHSF1, Shfdg1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022627	797	CALCB	http://www.ncbi.nlm.nih.gov/gene/?term=797	"CALC2, CGRP-II, CGRP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022628	79801	SHCBP1	http://www.ncbi.nlm.nih.gov/gene/?term=79801	PAL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022629	79803	HPS6	http://www.ncbi.nlm.nih.gov/gene/?term=79803	BLOC2S3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022630	79807	GSTCD	http://www.ncbi.nlm.nih.gov/gene/?term=79807		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022631	79809	TTC21B	http://www.ncbi.nlm.nih.gov/gene/?term=79809	"ATD4, IFT139, IFT139B, JBTS11, NPHP12, Nbla10696, SRTD4, THM1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022632	79809	TTC21B	http://www.ncbi.nlm.nih.gov/gene/?term=79809	"ATD4, IFT139, IFT139B, JBTS11, NPHP12, Nbla10696, SRTD4, THM1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022633	7980	TFPI2	http://www.ncbi.nlm.nih.gov/gene/?term=7980	"PP5, REF1, TFPI-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022634	79811	SLTM	http://www.ncbi.nlm.nih.gov/gene/?term=79811	Met	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022635	79814	AGMAT	http://www.ncbi.nlm.nih.gov/gene/?term=79814		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022636	79817	MOB3B	http://www.ncbi.nlm.nih.gov/gene/?term=79817	"C9orf35, MOB1D, MOBKL2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022637	79817	MOB3B	http://www.ncbi.nlm.nih.gov/gene/?term=79817	"C9orf35, MOB1D, MOBKL2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022638	79818	ZNF552	http://www.ncbi.nlm.nih.gov/gene/?term=79818		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022639	79818	ZNF552	http://www.ncbi.nlm.nih.gov/gene/?term=79818		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022640	79818	ZNF552	http://www.ncbi.nlm.nih.gov/gene/?term=79818		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022641	79822	ARHGAP28	http://www.ncbi.nlm.nih.gov/gene/?term=79822		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022642	79828	METTL8	http://www.ncbi.nlm.nih.gov/gene/?term=79828	TIP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022643	79828	METTL8	http://www.ncbi.nlm.nih.gov/gene/?term=79828	TIP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022644	79828	METTL8	http://www.ncbi.nlm.nih.gov/gene/?term=79828	TIP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022645	79828	METTL8	http://www.ncbi.nlm.nih.gov/gene/?term=79828	TIP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022646	79828	METTL8	http://www.ncbi.nlm.nih.gov/gene/?term=79828	TIP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022647	79829	NAA40	http://www.ncbi.nlm.nih.gov/gene/?term=79829	"NAT11, PATT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022648	7982	ST7	http://www.ncbi.nlm.nih.gov/gene/?term=7982	"ETS7q, FAM4A, FAM4A1, HELG, RAY1, SEN4, TSG7 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022649	7982	ST7	http://www.ncbi.nlm.nih.gov/gene/?term=7982	"ETS7q, FAM4A, FAM4A1, HELG, RAY1, SEN4, TSG7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022650	79830	ZMYM1	http://www.ncbi.nlm.nih.gov/gene/?term=79830	MYM	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022651	79832	QSER1	http://www.ncbi.nlm.nih.gov/gene/?term=79832		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022652	79833	GEMIN6	http://www.ncbi.nlm.nih.gov/gene/?term=79833		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022653	79837	PIP4K2C	http://www.ncbi.nlm.nih.gov/gene/?term=79837	PIP5K2C	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022654	79842	ZBTB3	http://www.ncbi.nlm.nih.gov/gene/?term=79842		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022655	79842	ZBTB3	http://www.ncbi.nlm.nih.gov/gene/?term=79842		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022656	79847	MFSD13A	http://www.ncbi.nlm.nih.gov/gene/?term=79847	"C10orf77, TMEM180, bA18I14.8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022657	79847	MFSD13A	http://www.ncbi.nlm.nih.gov/gene/?term=79847	"C10orf77, TMEM180, bA18I14.8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022658	79848	CSPP1	http://www.ncbi.nlm.nih.gov/gene/?term=79848	"CSPP, JBTS21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022659	79850	FAM57A	http://www.ncbi.nlm.nih.gov/gene/?term=79850	CT120	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022660	79856	SNX22	http://www.ncbi.nlm.nih.gov/gene/?term=79856		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022661	79861	TUBAL3	http://www.ncbi.nlm.nih.gov/gene/?term=79861		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022662	79863	RBFA	http://www.ncbi.nlm.nih.gov/gene/?term=79863	"C18orf22, HsT169 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022663	79865	TREML2	http://www.ncbi.nlm.nih.gov/gene/?term=79865	"C6orf76, TLT-2, TLT2, dJ238O23.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022664	79866	BORA	http://www.ncbi.nlm.nih.gov/gene/?term=79866	C13orf34	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022665	79867	TCTN2	http://www.ncbi.nlm.nih.gov/gene/?term=79867	"C12orf38, JBTS24, MKS8, TECT2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022666	79867	TCTN2	http://www.ncbi.nlm.nih.gov/gene/?term=79867	"C12orf38, JBTS24, MKS8, TECT2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022667	79867	TCTN2	http://www.ncbi.nlm.nih.gov/gene/?term=79867	"C12orf38, JBTS24, MKS8, TECT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022668	79868	ALG13	http://www.ncbi.nlm.nih.gov/gene/?term=79868	"CDG1S, CXorf45, GLT28D1, MDS031, TDRD13, YGL047W "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022669	79869	CPSF7	http://www.ncbi.nlm.nih.gov/gene/?term=79869	CFIm59	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022670	79869	CPSF7	http://www.ncbi.nlm.nih.gov/gene/?term=79869	CFIm59	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022671	79871	RPAP2	http://www.ncbi.nlm.nih.gov/gene/?term=79871	"C1orf82, Rtr1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022672	79873	NUDT18	http://www.ncbi.nlm.nih.gov/gene/?term=79873	MTH3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022673	79874	RABEP2	http://www.ncbi.nlm.nih.gov/gene/?term=79874	FRA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022674	79876	UBA5	http://www.ncbi.nlm.nih.gov/gene/?term=79876	"THIFP1, UBE1DC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022675	79879	CCDC134	http://www.ncbi.nlm.nih.gov/gene/?term=79879		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022676	79882	ZC3H14	http://www.ncbi.nlm.nih.gov/gene/?term=79882	"MSUT-2, NY-REN-37, SUT2, UKp68 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022677	79885	HDAC11	http://www.ncbi.nlm.nih.gov/gene/?term=79885	HD11	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022678	79886	CAAP1	http://www.ncbi.nlm.nih.gov/gene/?term=79886	"C9orf82, CAAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022679	79886	CAAP1	http://www.ncbi.nlm.nih.gov/gene/?term=79886	"C9orf82, CAAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022680	79887	PLBD1	http://www.ncbi.nlm.nih.gov/gene/?term=79887		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022681	79888	LPCAT1	http://www.ncbi.nlm.nih.gov/gene/?term=79888	"AGPAT10, AGPAT9, AYTL2, PFAAP3, lpcat "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022682	79888	LPCAT1	http://www.ncbi.nlm.nih.gov/gene/?term=79888	"AGPAT10, AGPAT9, AYTL2, PFAAP3, lpcat "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022683	79888	LPCAT1	http://www.ncbi.nlm.nih.gov/gene/?term=79888	"AGPAT10, AGPAT9, AYTL2, PFAAP3, lpcat "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022684	7988	ZNF212	http://www.ncbi.nlm.nih.gov/gene/?term=7988	"C2H2-150, ZNF182, ZNFC150 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022685	79892	MCMBP	http://www.ncbi.nlm.nih.gov/gene/?term=79892	"C10orf119, MCM-BP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022686	79892	MCMBP	http://www.ncbi.nlm.nih.gov/gene/?term=79892	"C10orf119, MCM-BP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022687	79893	GGNBP2	http://www.ncbi.nlm.nih.gov/gene/?term=79893	"DIF-3, DIF3, LCRG1, LZK1, ZFP403, ZNF403 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022688	79893	GGNBP2	http://www.ncbi.nlm.nih.gov/gene/?term=79893	"DIF-3, DIF3, LCRG1, LZK1, ZFP403, ZNF403 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022689	79894	ZNF672	http://www.ncbi.nlm.nih.gov/gene/?term=79894		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022690	79896	THNSL1	http://www.ncbi.nlm.nih.gov/gene/?term=79896	TSH1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022691	79897	RPP21	http://www.ncbi.nlm.nih.gov/gene/?term=79897	"C6orf135, CAT60 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022692	79901	CYBRD1	http://www.ncbi.nlm.nih.gov/gene/?term=79901	"CYB561A2, DCYTB, FRRS3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022693	79902	NUP85	http://www.ncbi.nlm.nih.gov/gene/?term=79902	"FROUNT, Nup75 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022694	79902	NUP85	http://www.ncbi.nlm.nih.gov/gene/?term=79902	"FROUNT, Nup75 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022695	79902	NUP85	http://www.ncbi.nlm.nih.gov/gene/?term=79902	"FROUNT, Nup75 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022696	79906	MORN1	http://www.ncbi.nlm.nih.gov/gene/?term=79906		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022697	79912	PYROXD1	http://www.ncbi.nlm.nih.gov/gene/?term=79912		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022698	79918	SETD6	http://www.ncbi.nlm.nih.gov/gene/?term=79918		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022699	79918	SETD6	http://www.ncbi.nlm.nih.gov/gene/?term=79918		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022700	7991	TUSC3	http://www.ncbi.nlm.nih.gov/gene/?term=7991	"D8S1992, M33, MRT22, MRT7, N33, OST3A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022701	79921	TCEAL4	http://www.ncbi.nlm.nih.gov/gene/?term=79921	"NPD017, WEX7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022702	79921	TCEAL4	http://www.ncbi.nlm.nih.gov/gene/?term=79921	"NPD017, WEX7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022703	79923	NANOG	http://www.ncbi.nlm.nih.gov/gene/?term=79923		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022704	79923	NANOG	http://www.ncbi.nlm.nih.gov/gene/?term=79923		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022705	79925	SPEF2	http://www.ncbi.nlm.nih.gov/gene/?term=79925	"CT122, KPL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022706	79932	KIAA0319L	http://www.ncbi.nlm.nih.gov/gene/?term=79932	AAVR	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022707	79932	KIAA0319L	http://www.ncbi.nlm.nih.gov/gene/?term=79932	AAVR	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022708	79933	SYNPO2L	http://www.ncbi.nlm.nih.gov/gene/?term=79933		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022709	79933	SYNPO2L	http://www.ncbi.nlm.nih.gov/gene/?term=79933		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022710	79939	SLC35E1	http://www.ncbi.nlm.nih.gov/gene/?term=79939		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022711	79939	SLC35E1	http://www.ncbi.nlm.nih.gov/gene/?term=79939		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022712	79939	SLC35E1	http://www.ncbi.nlm.nih.gov/gene/?term=79939		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022713	7993	UBXN8	http://www.ncbi.nlm.nih.gov/gene/?term=7993	"D8S2298E, REP8, UBXD6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022714	79940	LINC00472	http://www.ncbi.nlm.nih.gov/gene/?term=79940	C6orf155	lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00022715	79940	LINC00472	http://www.ncbi.nlm.nih.gov/gene/?term=79940	C6orf155	lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00022716	7994	KAT6A	http://www.ncbi.nlm.nih.gov/gene/?term=7994	"MOZ, MRD32, MYST-3, MYST3, RUNXBP2, ZC2HC6A, ZNF220 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022717	7994	KAT6A	http://www.ncbi.nlm.nih.gov/gene/?term=7994	"MOZ, MRD32, MYST-3, MYST3, RUNXBP2, ZC2HC6A, ZNF220 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022718	79954	NOL10	http://www.ncbi.nlm.nih.gov/gene/?term=79954	PQBP5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022719	79954	NOL10	http://www.ncbi.nlm.nih.gov/gene/?term=79954	PQBP5	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022720	79954	NOL10	http://www.ncbi.nlm.nih.gov/gene/?term=79954	PQBP5	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022721	79956	ERMP1	http://www.ncbi.nlm.nih.gov/gene/?term=79956	"FXNA, KIAA1815, bA207C16.3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022722	79956	ERMP1	http://www.ncbi.nlm.nih.gov/gene/?term=79956	"FXNA, KIAA1815, bA207C16.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022723	79959	CEP76	http://www.ncbi.nlm.nih.gov/gene/?term=79959	"C18orf9, HsT1705 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022724	79960	JADE1	http://www.ncbi.nlm.nih.gov/gene/?term=79960	PHF17	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022725	79960	JADE1	http://www.ncbi.nlm.nih.gov/gene/?term=79960	PHF17	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022726	79960	JADE1	http://www.ncbi.nlm.nih.gov/gene/?term=79960	PHF17	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022727	79960	JADE1	http://www.ncbi.nlm.nih.gov/gene/?term=79960	PHF17	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022728	79960	JADE1	http://www.ncbi.nlm.nih.gov/gene/?term=79960	PHF17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022729	79962	DNAJC22	http://www.ncbi.nlm.nih.gov/gene/?term=79962	wus	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022730	79963	ABCA11P	http://www.ncbi.nlm.nih.gov/gene/?term=79963	"ABCA11, EST1133530 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022731	79966	SCD5	http://www.ncbi.nlm.nih.gov/gene/?term=79966	"ACOD4, FADS4, HSCD5, SCD2, SCD4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022732	79966	SCD5	http://www.ncbi.nlm.nih.gov/gene/?term=79966	"ACOD4, FADS4, HSCD5, SCD2, SCD4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022733	79966	SCD5	http://www.ncbi.nlm.nih.gov/gene/?term=79966	"ACOD4, FADS4, HSCD5, SCD2, SCD4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022734	79971	WLS	http://www.ncbi.nlm.nih.gov/gene/?term=79971	"C1orf139, EVI, GPR177, MRP, mig-14 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022735	79977	GRHL2	http://www.ncbi.nlm.nih.gov/gene/?term=79977	"BOM, DFNA28, ECTDS, TFCP2L3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022736	79979	TRMT2B	http://www.ncbi.nlm.nih.gov/gene/?term=79979	"CXorf34, dJ341D10.3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022737	79979	TRMT2B	http://www.ncbi.nlm.nih.gov/gene/?term=79979	"CXorf34, dJ341D10.3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022738	79979	TRMT2B	http://www.ncbi.nlm.nih.gov/gene/?term=79979	"CXorf34, dJ341D10.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022739	79980	DSN1	http://www.ncbi.nlm.nih.gov/gene/?term=79980	"C20orf172, KNL3, MIS13, dJ469A13.2, hKNL-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022740	79982	DNAJB14	http://www.ncbi.nlm.nih.gov/gene/?term=79982	"EGNR9427, PRO34683 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022741	79987	SVEP1	http://www.ncbi.nlm.nih.gov/gene/?term=79987	"C9orf13, CCP22, POLYDOM, SEL-OB, SELOB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022742	79990	PLEKHH3	http://www.ncbi.nlm.nih.gov/gene/?term=79990		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022743	79990	PLEKHH3	http://www.ncbi.nlm.nih.gov/gene/?term=79990		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022744	79991	OBFC1	http://www.ncbi.nlm.nih.gov/gene/?term=79991	"AAF-44, AAF44, RPA-32, STN1, bA541N10.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022745	79993	ELOVL7	http://www.ncbi.nlm.nih.gov/gene/?term=79993		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022746	79993	ELOVL7	http://www.ncbi.nlm.nih.gov/gene/?term=79993		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022747	80000	GREB1L	http://www.ncbi.nlm.nih.gov/gene/?term=80000	"C18orf6, KIAA1772 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022748	80003	PCNX2	http://www.ncbi.nlm.nih.gov/gene/?term=80003	PCNXL2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022749	80004	ESRP2	http://www.ncbi.nlm.nih.gov/gene/?term=80004	RBM35B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022750	80005	DOCK5	http://www.ncbi.nlm.nih.gov/gene/?term=80005		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022751	80006	TRAPPC13	http://www.ncbi.nlm.nih.gov/gene/?term=80006	C5orf44	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022752	80006	TRAPPC13	http://www.ncbi.nlm.nih.gov/gene/?term=80006	C5orf44	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022753	80007	C10orf88	http://www.ncbi.nlm.nih.gov/gene/?term=80007		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022754	80010	RMI1	http://www.ncbi.nlm.nih.gov/gene/?term=80010	"BLAP75, C9orf76, FAAP75 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022755	80011	FAM192A	http://www.ncbi.nlm.nih.gov/gene/?term=80011	"C16orf94, CDA018, CDA10, NIP30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022756	80011	FAM192A	http://www.ncbi.nlm.nih.gov/gene/?term=80011	"C16orf94, CDA018, CDA10, NIP30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022757	80014	WWC2	http://www.ncbi.nlm.nih.gov/gene/?term=80014	BOMB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022758	80018	NAA25	http://www.ncbi.nlm.nih.gov/gene/?term=80018	"C12orf30, MDM20, NAP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022759	80018	NAA25	http://www.ncbi.nlm.nih.gov/gene/?term=80018	"C12orf30, MDM20, NAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022760	80019	UBTD1	http://www.ncbi.nlm.nih.gov/gene/?term=80019		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022761	80020	FOXRED2	http://www.ncbi.nlm.nih.gov/gene/?term=80020	ERFAD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022762	80020	FOXRED2	http://www.ncbi.nlm.nih.gov/gene/?term=80020	ERFAD	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022763	80020	FOXRED2	http://www.ncbi.nlm.nih.gov/gene/?term=80020	ERFAD	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022764	80024	SLC8B1	http://www.ncbi.nlm.nih.gov/gene/?term=80024	"NCKX6, NCLX, SLC24A6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022765	80024	SLC8B1	http://www.ncbi.nlm.nih.gov/gene/?term=80024	"NCKX6, NCLX, SLC24A6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022766	80025	PANK2	http://www.ncbi.nlm.nih.gov/gene/?term=80025	"C20orf48, HARP, HSS, NBIA1, PKAN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022767	80025	PANK2	http://www.ncbi.nlm.nih.gov/gene/?term=80025	"C20orf48, HARP, HSS, NBIA1, PKAN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022768	80028	FBXL18	http://www.ncbi.nlm.nih.gov/gene/?term=80028	Fbl18	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022769	80028	FBXL18	http://www.ncbi.nlm.nih.gov/gene/?term=80028	Fbl18	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022770	80031	SEMA6D	http://www.ncbi.nlm.nih.gov/gene/?term=80031		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022771	80045	GPR157	http://www.ncbi.nlm.nih.gov/gene/?term=80045		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022772	80055	PGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=80055	"Bst1, ISPD3024, MRT42, SPG67 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022773	80055	PGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=80055	"Bst1, ISPD3024, MRT42, SPG67 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022774	80063	ATF7IP2	http://www.ncbi.nlm.nih.gov/gene/?term=80063	MCAF2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022775	80063	ATF7IP2	http://www.ncbi.nlm.nih.gov/gene/?term=80063	MCAF2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022776	80063	ATF7IP2	http://www.ncbi.nlm.nih.gov/gene/?term=80063	MCAF2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022777	80095	ZNF606	http://www.ncbi.nlm.nih.gov/gene/?term=80095	ZNF328	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022778	80097	MZT2B	http://www.ncbi.nlm.nih.gov/gene/?term=80097	"FAM128B, MOZART2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022779	800	CALD1	http://www.ncbi.nlm.nih.gov/gene/?term=800	"CDM, H-CAD, HCAD, L-CAD, LCAD, NAG22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022780	80115	BAIAP2L2	http://www.ncbi.nlm.nih.gov/gene/?term=80115		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022781	80124	VCPIP1	http://www.ncbi.nlm.nih.gov/gene/?term=80124	"DUBA3, VCIP135 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022782	80135	RPF1	http://www.ncbi.nlm.nih.gov/gene/?term=80135	BXDC5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022783	8013	NR4A3	http://www.ncbi.nlm.nih.gov/gene/?term=8013	"CHN, CSMF, MINOR, NOR1, TEC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022784	80142	PTGES2	http://www.ncbi.nlm.nih.gov/gene/?term=80142	"C9orf15, GBF-1, GBF1, PGES2, mPGES-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022785	80142	PTGES2	http://www.ncbi.nlm.nih.gov/gene/?term=80142	"C9orf15, GBF-1, GBF1, PGES2, mPGES-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022786	80143	SIKE1	http://www.ncbi.nlm.nih.gov/gene/?term=80143	SIKE	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022787	80143	SIKE1	http://www.ncbi.nlm.nih.gov/gene/?term=80143	SIKE	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022788	80143	SIKE1	http://www.ncbi.nlm.nih.gov/gene/?term=80143	SIKE	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022789	80143	SIKE1	http://www.ncbi.nlm.nih.gov/gene/?term=80143	SIKE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022790	80144	FRAS1	http://www.ncbi.nlm.nih.gov/gene/?term=80144		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022791	80145	THOC7	http://www.ncbi.nlm.nih.gov/gene/?term=80145	"NIF3L1BP1, fSAP24, hTREX30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022792	80146	UXS1	http://www.ncbi.nlm.nih.gov/gene/?term=80146	"SDR6E1, UGD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022793	80146	UXS1	http://www.ncbi.nlm.nih.gov/gene/?term=80146	"SDR6E1, UGD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022794	80148	PQLC1	http://www.ncbi.nlm.nih.gov/gene/?term=80148		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022795	80148	PQLC1	http://www.ncbi.nlm.nih.gov/gene/?term=80148		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022796	80150	ASRGL1	http://www.ncbi.nlm.nih.gov/gene/?term=80150	"ALP, ALP1, CRASH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022797	80153	EDC3	http://www.ncbi.nlm.nih.gov/gene/?term=80153	"LSM16, MRT50, YJDC, YJEFN2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022798	80153	EDC3	http://www.ncbi.nlm.nih.gov/gene/?term=80153	"LSM16, MRT50, YJDC, YJEFN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022799	80155	NAA15	http://www.ncbi.nlm.nih.gov/gene/?term=80155	"Ga19, NARG1, NAT1P, NATH, TBDN, TBDN100 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022800	80169	CTC1	http://www.ncbi.nlm.nih.gov/gene/?term=80169	"AAF-132, AAF132, C17orf68, CRMCC, tmp494178 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022801	80169	CTC1	http://www.ncbi.nlm.nih.gov/gene/?term=80169	"AAF-132, AAF132, C17orf68, CRMCC, tmp494178 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022802	80169	CTC1	http://www.ncbi.nlm.nih.gov/gene/?term=80169	"AAF-132, AAF132, C17orf68, CRMCC, tmp494178 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022803	80177	MYCT1	http://www.ncbi.nlm.nih.gov/gene/?term=80177	MTLC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022804	80178	C16orf59	http://www.ncbi.nlm.nih.gov/gene/?term=80178		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022805	80179	MYO19	http://www.ncbi.nlm.nih.gov/gene/?term=80179	MYOHD1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022806	80179	MYO19	http://www.ncbi.nlm.nih.gov/gene/?term=80179	MYOHD1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022807	80184	CEP290	http://www.ncbi.nlm.nih.gov/gene/?term=80184	"3H11Ag, BBS14, CT87, JBTS5, LCA10, MKS4, NPHP6, POC3, SLSN6, rd16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022808	80184	CEP290	http://www.ncbi.nlm.nih.gov/gene/?term=80184	"3H11Ag, BBS14, CT87, JBTS5, LCA10, MKS4, NPHP6, POC3, SLSN6, rd16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022809	80185	TTI2	http://www.ncbi.nlm.nih.gov/gene/?term=80185	"C8orf41, MRT39 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022810	80185	TTI2	http://www.ncbi.nlm.nih.gov/gene/?term=80185	"C8orf41, MRT39 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022811	80194	TMEM134	http://www.ncbi.nlm.nih.gov/gene/?term=80194		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022812	80194	TMEM134	http://www.ncbi.nlm.nih.gov/gene/?term=80194		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022813	80195	TMEM254	http://www.ncbi.nlm.nih.gov/gene/?term=80195	"C10orf57, bA369J21.6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022814	80198	MUS81	http://www.ncbi.nlm.nih.gov/gene/?term=80198	SLX3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022815	8019	BRD3	http://www.ncbi.nlm.nih.gov/gene/?term=8019	"ORFX, RING3L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022816	801	CALM1	http://www.ncbi.nlm.nih.gov/gene/?term=801	"CALML2, CAMI, CPVT4, DD132, LQT14, PHKD, caM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022817	80201	HKDC1	http://www.ncbi.nlm.nih.gov/gene/?term=80201		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022818	80204	FBXO11	http://www.ncbi.nlm.nih.gov/gene/?term=80204	"FBX11, PRMT9, UBR6, UG063H01, VIT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022819	80204	FBXO11	http://www.ncbi.nlm.nih.gov/gene/?term=80204	"FBX11, PRMT9, UBR6, UG063H01, VIT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022820	80205	CHD9	http://www.ncbi.nlm.nih.gov/gene/?term=80205	"AD013, CHD-9, CReMM, KISH2, PRIC320 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022821	80205	CHD9	http://www.ncbi.nlm.nih.gov/gene/?term=80205	"AD013, CHD-9, CReMM, KISH2, PRIC320 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022822	80207	OPA3	http://www.ncbi.nlm.nih.gov/gene/?term=80207	MGA3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022823	80207	OPA3	http://www.ncbi.nlm.nih.gov/gene/?term=80207	MGA3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022824	80208	SPG11	http://www.ncbi.nlm.nih.gov/gene/?term=80208	"ALS5, CMT2X, KIAA1840 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022825	80218	NAA50	http://www.ncbi.nlm.nih.gov/gene/?term=80218	"MAK3, NAT13, NAT13P, NAT5, NAT5P, SAN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022826	80218	NAA50	http://www.ncbi.nlm.nih.gov/gene/?term=80218	"MAK3, NAT13, NAT13P, NAT5, NAT5P, SAN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022827	80219	COQ10B	http://www.ncbi.nlm.nih.gov/gene/?term=80219		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022828	80219	COQ10B	http://www.ncbi.nlm.nih.gov/gene/?term=80219		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022829	8021	NUP214	http://www.ncbi.nlm.nih.gov/gene/?term=8021	"CAIN, CAN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022830	80221	ACSF2	http://www.ncbi.nlm.nih.gov/gene/?term=80221	"ACSMW, AVYV493 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022831	80222	TARS2	http://www.ncbi.nlm.nih.gov/gene/?term=80222	"COXPD21, TARSL1, thrRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022832	80223	RAB11FIP1	http://www.ncbi.nlm.nih.gov/gene/?term=80223	"NOEL1A, RCP, rab11-FIP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022833	80223	RAB11FIP1	http://www.ncbi.nlm.nih.gov/gene/?term=80223	"NOEL1A, RCP, rab11-FIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022834	80227	PAAF1	http://www.ncbi.nlm.nih.gov/gene/?term=80227	"PAAF, Rpn14, WDR71 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022835	80227	PAAF1	http://www.ncbi.nlm.nih.gov/gene/?term=80227	"PAAF, Rpn14, WDR71 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022836	80228	ORAI2	http://www.ncbi.nlm.nih.gov/gene/?term=80228	"C7orf19, CBCIP2, MEM142B, TMEM142B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022837	80228	ORAI2	http://www.ncbi.nlm.nih.gov/gene/?term=80228	"C7orf19, CBCIP2, MEM142B, TMEM142B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022838	80230	RUFY1	http://www.ncbi.nlm.nih.gov/gene/?term=80230	"RABIP4, ZFYVE12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022839	80232	WDR26	http://www.ncbi.nlm.nih.gov/gene/?term=80232	"CDW2, GID7, MIP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022840	80232	WDR26	http://www.ncbi.nlm.nih.gov/gene/?term=80232	"CDW2, GID7, MIP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022841	80232	WDR26	http://www.ncbi.nlm.nih.gov/gene/?term=80232	"CDW2, GID7, MIP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022842	80237	ELL3	http://www.ncbi.nlm.nih.gov/gene/?term=80237		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022843	80243	PREX2	http://www.ncbi.nlm.nih.gov/gene/?term=80243	"6230420N16Rik, DEP.2, DEPDC2, P-REX2, PPP1R129 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022844	80255	SLC35F5	http://www.ncbi.nlm.nih.gov/gene/?term=80255		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022845	80255	SLC35F5	http://www.ncbi.nlm.nih.gov/gene/?term=80255		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022846	80256	FAM214B	http://www.ncbi.nlm.nih.gov/gene/?term=80256	KIAA1539	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022847	80262	C16orf70	http://www.ncbi.nlm.nih.gov/gene/?term=80262	"C16orf6, LIN10, lin-10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022848	80262	C16orf70	http://www.ncbi.nlm.nih.gov/gene/?term=80262	"C16orf6, LIN10, lin-10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022849	80263	TRIM45	http://www.ncbi.nlm.nih.gov/gene/?term=80263	RNF99	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022850	80263	TRIM45	http://www.ncbi.nlm.nih.gov/gene/?term=80263	RNF99	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022851	80267	EDEM3	http://www.ncbi.nlm.nih.gov/gene/?term=80267	C1orf22	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022852	80267	EDEM3	http://www.ncbi.nlm.nih.gov/gene/?term=80267	C1orf22	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022853	80270	HSD3B7	http://www.ncbi.nlm.nih.gov/gene/?term=80270	"CBAS1, PFIC4, SDR11E3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022854	80270	HSD3B7	http://www.ncbi.nlm.nih.gov/gene/?term=80270	"CBAS1, PFIC4, SDR11E3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022855	80270	HSD3B7	http://www.ncbi.nlm.nih.gov/gene/?term=80270	"CBAS1, PFIC4, SDR11E3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022856	80271	ITPKC	http://www.ncbi.nlm.nih.gov/gene/?term=80271	"IP3-3KC, IP3KC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022857	80273	GRPEL1	http://www.ncbi.nlm.nih.gov/gene/?term=80273	"GrpE, HMGE, mt-GrpE#1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022858	80273	GRPEL1	http://www.ncbi.nlm.nih.gov/gene/?term=80273	"GrpE, HMGE, mt-GrpE#1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022859	8027	STAM	http://www.ncbi.nlm.nih.gov/gene/?term=8027	"STAM-11, STAM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022860	8027	STAM	http://www.ncbi.nlm.nih.gov/gene/?term=8027	"STAM-1, STAM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022861	80281	Cttnbp2nl	http://www.ncbi.nlm.nih.gov/gene/?term=80281	"AA552995, AA589392, AU018624, BC003236, mKIAA1433 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022862	80284	Smim12	http://www.ncbi.nlm.nih.gov/gene/?term=80284	BC003266	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022863	80286	Tusc3	http://www.ncbi.nlm.nih.gov/gene/?term=80286	"AU022242, BC003311, N33 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022864	8028	MLLT10	http://www.ncbi.nlm.nih.gov/gene/?term=8028	AF10	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022865	8028	MLLT10	http://www.ncbi.nlm.nih.gov/gene/?term=8028	AF10	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022866	80291	Rilpl2	http://www.ncbi.nlm.nih.gov/gene/?term=80291		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022867	80297	Sptbn4	http://www.ncbi.nlm.nih.gov/gene/?term=80297	"1700022P15Rik, 5830426A08Rik, ROSA62, SpbIV, Spnb4, dyn, lnd, nmf261, nmf379, qv "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022868	80298	MTERF2	http://www.ncbi.nlm.nih.gov/gene/?term=80298	"MTERFD3, mTERFL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022869	8029	CUBN	http://www.ncbi.nlm.nih.gov/gene/?term=8029	"IFCR, MGA1, gp280 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022870	80304	C2orf44	http://www.ncbi.nlm.nih.gov/gene/?term=80304	"PP384, WDCP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022871	80304	WDCP	http://www.ncbi.nlm.nih.gov/gene/?term=80304	"PP384, WDCP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022872	80305	TRABD	http://www.ncbi.nlm.nih.gov/gene/?term=80305	"LP6054, PP2447 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022873	80305	TRABD	http://www.ncbi.nlm.nih.gov/gene/?term=80305	"LP6054, PP2447 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022874	80306	MED28	http://www.ncbi.nlm.nih.gov/gene/?term=80306	"1500003D12Rik, EG1, magicin "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022875	80306	MED28	http://www.ncbi.nlm.nih.gov/gene/?term=80306	"1500003D12Rik, EG1, magicin "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022876	80306	MED28	http://www.ncbi.nlm.nih.gov/gene/?term=80306	"1500003D12Rik, EG1, magicin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022877	80307	FER1L4	http://www.ncbi.nlm.nih.gov/gene/?term=80307	C20orf124	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022878	80308	FLAD1	http://www.ncbi.nlm.nih.gov/gene/?term=80308	"FAD1, FADS, PP591 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022879	8030	CCDC6	http://www.ncbi.nlm.nih.gov/gene/?term=8030	"D10S170, H4, PTC, TPC, TST1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022880	8030	CCDC6	http://www.ncbi.nlm.nih.gov/gene/?term=8030	"D10S170, H4, PTC, TPC, TST1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022881	8030	CCDC6	http://www.ncbi.nlm.nih.gov/gene/?term=8030	"D10S170, H4, PTC, TPC, TST1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022882	80313	LRRC27	http://www.ncbi.nlm.nih.gov/gene/?term=80313		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022883	80313	LRRC27	http://www.ncbi.nlm.nih.gov/gene/?term=80313		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022884	80314	EPC1	http://www.ncbi.nlm.nih.gov/gene/?term=80314	Epl1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022885	80314	EPC1	http://www.ncbi.nlm.nih.gov/gene/?term=80314	Epl1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022886	80315	CPEB4	http://www.ncbi.nlm.nih.gov/gene/?term=80315	"CPE-BP4, hCPEB-4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022887	80315	CPEB4	http://www.ncbi.nlm.nih.gov/gene/?term=80315	"CPE-BP4, hCPEB-4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022888	80319	CXXC4	http://www.ncbi.nlm.nih.gov/gene/?term=80319	IDAX	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022889	8031	NCOA4	http://www.ncbi.nlm.nih.gov/gene/?term=8031	"ARA70, ELE1, PTC3, RFG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022890	80321	CEP70	http://www.ncbi.nlm.nih.gov/gene/?term=80321	BITE	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022891	80321	CEP70	http://www.ncbi.nlm.nih.gov/gene/?term=80321	BITE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022892	80324	PUS1	http://www.ncbi.nlm.nih.gov/gene/?term=80324	MLASA1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022893	80328	ULBP2	http://www.ncbi.nlm.nih.gov/gene/?term=80328	"ALCAN-alpha, N2DL2, NKG2DL2, RAET1H "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022894	80329	ULBP1	http://www.ncbi.nlm.nih.gov/gene/?term=80329	"N2DL-1, NKG2DL1, RAET1I "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022895	80329	ULBP1	http://www.ncbi.nlm.nih.gov/gene/?term=80329	"N2DL-1, NKG2DL1, RAET1I "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022896	80331	DNAJC5	http://www.ncbi.nlm.nih.gov/gene/?term=80331	"CLN4, CLN4B, CSPA, NCL, mir-941-2, mir-941-3, mir-941-4, mir-941-5, DNAJC5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022897	80333	KCNIP4	http://www.ncbi.nlm.nih.gov/gene/?term=80333	"CALP, KCHIP4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022898	80335	WDR82	http://www.ncbi.nlm.nih.gov/gene/?term=80335	"MST107, MSTP107, PRO2730, PRO34047, SWD2, TMEM113A, WDR82 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022899	80344	DCAF11	http://www.ncbi.nlm.nih.gov/gene/?term=80344	"GL014, PRO2389, WDR23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022900	80346	REEP4	http://www.ncbi.nlm.nih.gov/gene/?term=80346	"C8orf20, PP432, Yip2c "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022901	80347	COASY	http://www.ncbi.nlm.nih.gov/gene/?term=80347	"DPCK, NBIA6, NBP, PPAT, UKR1, pOV-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022902	80347	COASY	http://www.ncbi.nlm.nih.gov/gene/?term=80347	"DPCK, NBIA6, NBP, PPAT, UKR1, pOV-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022903	80349	WDR61	http://www.ncbi.nlm.nih.gov/gene/?term=80349	"REC14, SKI8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022904	8034	SLC25A16	http://www.ncbi.nlm.nih.gov/gene/?term=8034	"D10S105E, GDA, GDC, HGT.1, ML7, hML7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022905	8034	SLC25A16	http://www.ncbi.nlm.nih.gov/gene/?term=8034	"D10S105E, GDA, GDC, HGT.1, ML7, hML7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022906	8034	SLC25A16	http://www.ncbi.nlm.nih.gov/gene/?term=8034	"D10S105E, GDA, GDC, HGT.1, ML7, hML7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022907	80351	TNKS2	http://www.ncbi.nlm.nih.gov/gene/?term=80351	"ARTD6, PARP-5b, PARP-5c, PARP5B, PARP5C, TANK2, TNKL, pART6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022908	80351	TNKS2	http://www.ncbi.nlm.nih.gov/gene/?term=80351	"ARTD6, PARP-5b, PARP-5c, PARP5B, PARP5C, TANK2, TNKL, pART6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022909	80351	TNKS2	http://www.ncbi.nlm.nih.gov/gene/?term=80351	"ARTD6, PARP-5b, PARP-5c, PARP5B, PARP5C, TANK2, TNKL, pART6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022910	80352	RNF39	http://www.ncbi.nlm.nih.gov/gene/?term=80352	"HZF, HZFW, LIRF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022911	80381	CD276	http://www.ncbi.nlm.nih.gov/gene/?term=80381	"4Ig-B7-H3, B7-H3, B7H3, B7RP-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022912	80384	Tex21	http://www.ncbi.nlm.nih.gov/gene/?term=80384	"4931406F04Rik, 4931412D23Rik, 4931421K24Rik, tsec-2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022913	80385	Tusc2	http://www.ncbi.nlm.nih.gov/gene/?term=80385	"1190001E22Rik, AA407686, Fus1, Lgcc, PAP, Pdap2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022914	8038	ADAM12	http://www.ncbi.nlm.nih.gov/gene/?term=8038	"ADAM12-OT1, CAR10, MCMP, MCMPMltna, MLTN, MLTNA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022915	804477	ND2	http://www.ncbi.nlm.nih.gov/gene/?term=804477		mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00022916	8050	PDHX	http://www.ncbi.nlm.nih.gov/gene/?term=8050	"DLDBP, E3BP, OPDX, PDX1, proX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022917	8050	PDHX	http://www.ncbi.nlm.nih.gov/gene/?term=8050	"DLDBP, E3BP, OPDX, PDX1, proX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022918	805	CALM2	http://www.ncbi.nlm.nih.gov/gene/?term=805	"CAMII, LQT15, PHKD, PHKD2, caM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022919	8061	FOSL1	http://www.ncbi.nlm.nih.gov/gene/?term=8061	"FRA, FRA1, fra-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022920	8065	CUL5	http://www.ncbi.nlm.nih.gov/gene/?term=8065	"VACM-1, VACM1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022921	8065	CUL5	http://www.ncbi.nlm.nih.gov/gene/?term=8065	"VACM-1, VACM1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022922	8065	CUL5	http://www.ncbi.nlm.nih.gov/gene/?term=8065	"VACM-1, VACM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022923	80700	UBXN6	http://www.ncbi.nlm.nih.gov/gene/?term=80700	"UBXD1, UBXDC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022924	80700	UBXN6	http://www.ncbi.nlm.nih.gov/gene/?term=80700	"UBXD1, UBXDC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022925	80707	Wwox	http://www.ncbi.nlm.nih.gov/gene/?term=80707	"5330426P09Rik, 9030416C10Rik, WOX1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022926	80719	Igsf6	http://www.ncbi.nlm.nih.gov/gene/?term=80719		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022927	80724	ACAD10	http://www.ncbi.nlm.nih.gov/gene/?term=80724		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022928	80727	TTYH3	http://www.ncbi.nlm.nih.gov/gene/?term=80727		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022929	80727	TTYH3	http://www.ncbi.nlm.nih.gov/gene/?term=80727		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022930	80728	ARHGAP39	http://www.ncbi.nlm.nih.gov/gene/?term=80728	"CrGAP, Vilse "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022931	80732	Mynn	http://www.ncbi.nlm.nih.gov/gene/?term=80732	"2810011C24Rik, AA415053, AI661031, AW049392, Mynr, SBBIZ1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022932	8073	PTP4A2	http://www.ncbi.nlm.nih.gov/gene/?term=8073	"HH13, HH7-2, HU-PP-1, OV-1, PRL-2, PRL2, PTP4A, PTPCAAX2, ptp-IV1a, ptp-IV1b "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022933	8073	PTP4A2	http://www.ncbi.nlm.nih.gov/gene/?term=8073	"HH13, HH7-2, HU-PP-1, OV-1, PRL-2, PRL2, PTP4A, PTPCAAX2, ptp-IV1a, ptp-IV1b "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022934	80742	PRR3	http://www.ncbi.nlm.nih.gov/gene/?term=80742	CAT56	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022935	80743	Vps16	http://www.ncbi.nlm.nih.gov/gene/?term=80743	1810074M16Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022936	80745	THUMPD2	http://www.ncbi.nlm.nih.gov/gene/?term=80745	C2orf8	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022937	80746	TSEN2	http://www.ncbi.nlm.nih.gov/gene/?term=80746	"PCH2B, SEN2, SEN2L "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022938	80746	TSEN2	http://www.ncbi.nlm.nih.gov/gene/?term=80746	"PCH2B, SEN2, SEN2L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022939	80750	N4bp1	http://www.ncbi.nlm.nih.gov/gene/?term=80750	"AI481586, C81621 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022940	80755	AARSD1	http://www.ncbi.nlm.nih.gov/gene/?term=80755		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022941	80758	PRR7	http://www.ncbi.nlm.nih.gov/gene/?term=80758		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022942	80759	KHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=80759	"C6orf147, C6orf148, Em:AC019205.8, NDG1, bA257K9.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022943	80762	NDFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=80762	N4WBP5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022944	80762	NDFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=80762	N4WBP5	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022945	80764	THAP7	http://www.ncbi.nlm.nih.gov/gene/?term=80764		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022946	8076	MFAP5	http://www.ncbi.nlm.nih.gov/gene/?term=8076	"AAT9, MAGP-2, MAGP2, MFAP-5, MP25 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022947	80772	CPTP	http://www.ncbi.nlm.nih.gov/gene/?term=80772	GLTPD1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022948	80775	TMEM177	http://www.ncbi.nlm.nih.gov/gene/?term=80775		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022949	80776	B9D2	http://www.ncbi.nlm.nih.gov/gene/?term=80776	"ICIS-1, MKS10, MKSR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022950	80777	CYB5B	http://www.ncbi.nlm.nih.gov/gene/?term=80777	"CYB5-M, CYPB5M, OMB5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022951	80777	CYB5B	http://www.ncbi.nlm.nih.gov/gene/?term=80777	"CYB5-M, CYPB5M, OMB5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022952	80781	COL18A1	http://www.ncbi.nlm.nih.gov/gene/?term=80781	"KNO, KNO1, KS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022953	80781	COL18A1	http://www.ncbi.nlm.nih.gov/gene/?term=80781	"KNO, KNO1, KS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022954	80789	INTS5	http://www.ncbi.nlm.nih.gov/gene/?term=80789	"INT5, KIAA1698 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022955	80789	INTS5	http://www.ncbi.nlm.nih.gov/gene/?term=80789	"INT5, KIAA1698 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022956	8078	USP5	http://www.ncbi.nlm.nih.gov/gene/?term=8078	ISOT	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022957	8078	USP5	http://www.ncbi.nlm.nih.gov/gene/?term=8078	ISOT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022958	8078	USP5	http://www.ncbi.nlm.nih.gov/gene/?term=8078	ISOT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022959	80790	CMIP	http://www.ncbi.nlm.nih.gov/gene/?term=80790	TCMIP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022960	8079	MLF2	http://www.ncbi.nlm.nih.gov/gene/?term=8079	NTN4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022961	8079	MLF2	http://www.ncbi.nlm.nih.gov/gene/?term=8079	NTN4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022962	80817	CEP44	http://www.ncbi.nlm.nih.gov/gene/?term=80817	"KIAA1712, PS1TP3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022963	80817	CEP44	http://www.ncbi.nlm.nih.gov/gene/?term=80817	"KIAA1712, PS1TP3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022964	80817	CEP44	http://www.ncbi.nlm.nih.gov/gene/?term=80817	"KIAA1712, PS1TP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022965	80818	ZNF436	http://www.ncbi.nlm.nih.gov/gene/?term=80818	"ZNF, Zfp46 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022966	80821	DDHD1	http://www.ncbi.nlm.nih.gov/gene/?term=80821	"PA-PLA1, PAPLA1, SPG28 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022967	80824	DUSP16	http://www.ncbi.nlm.nih.gov/gene/?term=80824	"MKP-7, MKP7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022968	80824	DUSP16	http://www.ncbi.nlm.nih.gov/gene/?term=80824	"MKP-7, MKP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022969	80830	APOL6	http://www.ncbi.nlm.nih.gov/gene/?term=80830	"APOL-VI, APOLVI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022970	80830	APOL6	http://www.ncbi.nlm.nih.gov/gene/?term=80830	"APOL-VI, APOLVI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00022971	80838	Hist1h1a	http://www.ncbi.nlm.nih.gov/gene/?term=80838	"H1.1, H1a, H1f1, H1var3 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022972	80843	Sec61a1	http://www.ncbi.nlm.nih.gov/gene/80843	Sec61a	mRNA	Rattus norvegicus	15485813	Mitochondrion	Hepatoma cell	qRT-PCR	"Real-time RT-PCR revealed that the sec61a transcript was found in the mitochondrial fraction, but unlike ucp2 and oxa1 mRNA, sec61α mRNA was not removed from this fraction when mitochondria were harvested without attached polysomes (Fig. 4) (25). "
RLID00022973	80851	SH3BP5L	http://www.ncbi.nlm.nih.gov/gene/?term=80851		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022974	80853	KDM7A	http://www.ncbi.nlm.nih.gov/gene/?term=80853	JHDM1D	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022975	80854	SETD7	http://www.ncbi.nlm.nih.gov/gene/?term=80854	"KMT7, SET7, SET7/9, SET9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022976	80856	KIAA1715	http://www.ncbi.nlm.nih.gov/gene/?term=80856	"LNP, LNP1, Ul, ulnaless "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022977	80859	Nfkbiz	http://www.ncbi.nlm.nih.gov/gene/?term=80859	"AA408868, INAP, Mail "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022978	8087	FXR1	http://www.ncbi.nlm.nih.gov/gene/?term=8087	FXR1P	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00022979	8087	FXR1	http://www.ncbi.nlm.nih.gov/gene/?term=8087	FXR1P	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022980	8087	FXR1	http://www.ncbi.nlm.nih.gov/gene/?term=8087	FXR1P	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022981	80886	Senp3	http://www.ncbi.nlm.nih.gov/gene/?term=80886	"AA408656, Smt3ip, Smt3ip1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022982	80890	Trim2	http://www.ncbi.nlm.nih.gov/gene/?term=80890	"mKIAA0517, narf "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00022983	80892	Zfhx4	http://www.ncbi.nlm.nih.gov/gene/?term=80892	"A930021B15, C130041O22Rik, Zfh-4, Zfh4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022984	80895	ILKAP	http://www.ncbi.nlm.nih.gov/gene/?term=80895	"ILKAP23, PP2C-DELTA, PPM1O, ILKAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022985	80896	NPL	http://www.ncbi.nlm.nih.gov/gene/?term=80896	"C112, C1orf13, NAL, NPL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022986	80898	Erap1	http://www.ncbi.nlm.nih.gov/gene/?term=80898	"Arts1, ERAAP, PILSA, PILSAP "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022987	8089	YEATS4	http://www.ncbi.nlm.nih.gov/gene/?term=8089	"4930573H17Rik, B230215M10Rik, GAS41, NUBI-1, YAF9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022988	8089	YEATS4	http://www.ncbi.nlm.nih.gov/gene/?term=8089	"4930573H17Rik, B230215M10Rik, GAS41, NUBI-1, YAF9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022989	808	CALM3	http://www.ncbi.nlm.nih.gov/gene/?term=808	"HEL-S-72, PHKD, PHKD3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022990	80902	Zfp202	http://www.ncbi.nlm.nih.gov/gene/?term=80902	"C130037E22Rik, Znf202 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022991	80905	Polh	http://www.ncbi.nlm.nih.gov/gene/?term=80905	"RAD30A, XPV "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022992	80912	Pum1	http://www.ncbi.nlm.nih.gov/gene/?term=80912	"AA517475, Pumm, mKIAA0099 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022993	80913	Pum2	http://www.ncbi.nlm.nih.gov/gene/?term=80913	"5730503J23Rik, Pumm2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022994	8091	HMGA2	http://www.ncbi.nlm.nih.gov/gene/?term=8091	"BABL, HMGI-C, HMGIC, LIPO, STQTL9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022995	80986	Ckap2	http://www.ncbi.nlm.nih.gov/gene/?term=80986	"AI461656, AW228814, LB1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00022996	8099	CDK2AP1	http://www.ncbi.nlm.nih.gov/gene/?term=8099	"DOC1, DORC1, ST19, doc-1, p12DOC-1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00022997	8099	CDK2AP1	http://www.ncbi.nlm.nih.gov/gene/?term=8099	"DOC1, DORC1, ST19, doc-1, p12DOC-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00022998	8099	CDK2AP1	http://www.ncbi.nlm.nih.gov/gene/?term=8099	"DOC1, DORC1, ST19, doc-1, p12DOC-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00022999	81000	Rad54l2	http://www.ncbi.nlm.nih.gov/gene/?term=81000	"Arip4, D130058C05, G630026H09Rik, Srisnf2l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023000	81003	Trim23	http://www.ncbi.nlm.nih.gov/gene/?term=81003	"6330516O20Rik, AI450195, Arfd1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023001	8100	IFT88	http://www.ncbi.nlm.nih.gov/gene/?term=8100	"D13S1056E, DAF19, TG737, TTC10, hTg737 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023002	81011	Vmn1r148	http://www.ncbi.nlm.nih.gov/gene/?term=81011	"V1rd14, V3R8 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023003	81012	Vmn1r171	http://www.ncbi.nlm.nih.gov/gene/?term=81012	"V1rd7, V3R7 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023004	81013	Vmn1r65	http://www.ncbi.nlm.nih.gov/gene/?term=81013	"V1rd6, V3R6 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023005	81027	TUBB1	http://www.ncbi.nlm.nih.gov/gene/?term=81027		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023006	81029	WNT5B	http://www.ncbi.nlm.nih.gov/gene/?term=81029		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023007	81031	SLC2A10	http://www.ncbi.nlm.nih.gov/gene/?term=81031	"ATS, GLUT10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023008	81031	SLC2A10	http://www.ncbi.nlm.nih.gov/gene/?term=81031	"ATS, GLUT10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023009	81031	SLC2A10	http://www.ncbi.nlm.nih.gov/gene/?term=81031	"ATS, GLUT10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023010	81034	SLC25A32	http://www.ncbi.nlm.nih.gov/gene/?term=81034	"MFT, MFTC, RREI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023011	81034	SLC25A32	http://www.ncbi.nlm.nih.gov/gene/?term=81034	"MFT, MFTC, RREI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023012	81034	SLC25A32	http://www.ncbi.nlm.nih.gov/gene/?term=81034	"MFT, MFTC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023013	81037	CLPTM1L	http://www.ncbi.nlm.nih.gov/gene/?term=81037	CRR9	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023014	8106	PABPN1	http://www.ncbi.nlm.nih.gov/gene/?term=8106	"OPMD, PAB2, PABII, PABP-2, PABP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023015	8106	PABPN1	http://www.ncbi.nlm.nih.gov/gene/?term=8106	"OPMD, PAB2, PABII, PABP-2, PABP2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023016	8106	PABPN1	http://www.ncbi.nlm.nih.gov/gene/?term=8106	"OPMD, PAB2, PABII, PABP-2, PABP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023017	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023018	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	12923260	Endoplasmic reticulum	T-cell line Jurkat	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00023019	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. mRNAs for resident proteins of the ER lumen, including BiP, calreticulin, and GRP94, were also highly enriched on membrane-bound polysomes. "
RLID00023020	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	21431749	Endoplasmic reticulum	HEK293 cell	Northern blot	"Similarly, Northern blot analysis of the mRNA composition of the cytosol and membrane fractions show that the cytosol fraction is enriched for mRNAs encoding histone (H3F3A) and GAPDH, whereas the membrane fraction is enriched in mRNAs encoding ER resident proteins, such as GRP94 and calreticulin (Fig. 2 B). "
RLID00023021	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	25063809	Ribosome	HeLa cell	qRT-PCR	Figure 1: Endoplasmic reticulum-associated mRNAs are partitioned between detergent-resistant and detergent-sensitive membrane domains. Data are collected from Figure 1.
RLID00023022	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023023	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00023024	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	22679391	Endoplasmic reticulum	U2OS cell	RT-PCR	"Figure 3B: The levels of several transcripts in the ER fraction were analyzed as in (A). Measured transcripts include those encoding ER luminal proteins (BiP, Calreticulin), ER membrane proteins (Inositol-3-phosphate Receptor (IP3 Receptor), Sec61α, Trapα, and Fatty Acid Desaturase 3 (FADS3)), a Golgi protein (Mannosidase 2A (Man2A)), plasma membrane proteins (Integrin β1, and Transferrin Receptor (Tf Receptor)), and a secreted protein (Interleukin 7 (IL7)). All measurements were standardized to the level of mRNA in the ER fraction from control cells. Data are collected from Figure 3B. "
RLID00023025	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	22679391	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"Figure 2: ALPP and CALR, but not t-ftz or INSL3, mRNA remain associated with the ER independently of ribosomes and translation. (A–E) COS-7 cells were transfected with plasmids containing either the t-ftz (A), INSL3 (A–B), ALPP (A, C), cyto-ALPP (a version of ALPP lacking signal sequence and transmembrane domain coding regions; A, D–E), or CALR (A) genes and allowed to express mRNA for 18�4 h. The cells were then treated with DMSO (Cont), puromycin, or HHT for 30 min, and then extracted with digitonin alone or with 20 mM EDTA. Cells were then fixed, stained for mRNA using specific FISH probes, and imaged (see panels B–D for examples). The fluorescence intensities of mRNA in the ER and nucleus in the micrographs were quantified (A). Each bar represents the average and standard error of three independent experiments, each consisting of the average integrated intensity of 30 cells over background. Note that although ribosome disruption caused INSL3 mRNA to dissociate from the ER, the nuclear mRNA was unaffected (B, nuclei are denoted by arrows). (E) A single field of view containing a single HHT-treated, digitonin-extracted, COS-7 cell expressing cyto-ALPP mRNA. cyto-ALPP mRNA was visualized by FISH and for Trapα protein by immunofluorescence. Note the extensive co-localization of cyto-ALPP mRNA (red) and Trapα (green) in the overlay. All scale bars?=?20 um. Data are collected from Figure 2. "
RLID00023026	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"CRT, HEL-S-99n, RO, SSA, cC1qR "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023027	811	CALR	http://www.ncbi.nlm.nih.gov/gene/?term=811	"RO, CRT, SSA, cC1qR, HEL-S-99n "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00023028	8120	AP3B2	http://www.ncbi.nlm.nih.gov/gene/?term=8120	NAPTB	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00023029	8120	AP3B2	http://www.ncbi.nlm.nih.gov/gene/?term=8120	NAPTB	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00023030	8120	AP3B2	http://www.ncbi.nlm.nih.gov/gene/?term=8120	NAPTB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023031	8123	PWAR5	http://www.ncbi.nlm.nih.gov/gene/?term=8123	"D15S226E, PAR-5, PAR5 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023032	8125	ANP32A	http://www.ncbi.nlm.nih.gov/gene/?term=8125	"C15orf1, HPPCn, I1PP2A, LANP, MAPM, PHAP1, PHAPI, PP32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023033	81285	OR51E2	http://www.ncbi.nlm.nih.gov/gene/?term=81285	"OR51E3P, OR52A2, PSGR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023034	81285	OR51E2	http://www.ncbi.nlm.nih.gov/gene/?term=81285	"OR51E3P, OR52A2, PSGR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023035	8131	NPRL3	http://www.ncbi.nlm.nih.gov/gene/?term=8131	"C16orf35, CGTHBA, HS-40, MARE, NPR3, RMD11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023036	8139	GAN	http://www.ncbi.nlm.nih.gov/gene/?term=8139	"GAN1, KLHL16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023037	8139	GAN	http://www.ncbi.nlm.nih.gov/gene/?term=8139	"GAN1, KLHL16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023038	813	CALU	http://www.ncbi.nlm.nih.gov/gene/?term=813		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023039	813	CALU	http://www.ncbi.nlm.nih.gov/gene/?term=813		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023040	813	CALU	http://www.ncbi.nlm.nih.gov/gene/?term=813		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023041	8140	SLC7A5	http://www.ncbi.nlm.nih.gov/gene/?term=8140	"4F2LC, CD98, D16S469E, E16, LAT1, MPE16, hLAT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023042	8140	SLC7A5	http://www.ncbi.nlm.nih.gov/gene/?term=8140	"4F2LC, CD98, D16S469E, E16, LAT1, MPE16, hLAT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023043	8140	SLC7A5	http://www.ncbi.nlm.nih.gov/gene/?term=8140	"4F2LC, CD98, D16S469E, E16, LAT1, MPE16, hLAT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023044	8140	SLC7A5	http://www.ncbi.nlm.nih.gov/gene/?term=8140	"4F2LC, CD98, D16S469E, E16, LAT1, MPE16, hLAT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023045	814596	nad4	http://www.ncbi.nlm.nih.gov/gene/?term=814596	ArthMp051	mRNA	Arabidopsis thaliana	21251101	Mitochondrion	Plant	Next-generation sequencing	A restorer of fertility-like PPR gene is required for 5-end processing of the nad4 mRNA in mitochondria of Arabidopsis thaliana.
RLID00023046	814686	RGA1	http://www.ncbi.nlm.nih.gov/gene/?term=814686	"AT2G01570, F2I9.19, F2I9_19, REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023047	81488	POLR2M	http://www.ncbi.nlm.nih.gov/gene/?term=81488	"GCOM1, GRINL1A, Gdown, Gdown1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023048	81488	POLR2M	http://www.ncbi.nlm.nih.gov/gene/?term=81488	"GCOM1, GRINL1A, Gdown, Gdown1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023049	81488	POLR2M	http://www.ncbi.nlm.nih.gov/gene/?term=81488	"GCOM1, GRINL1A, Gdown, Gdown1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023050	81489	Dnajb1	http://www.ncbi.nlm.nih.gov/gene/?term=81489	"0610007I11Rik, DjB1, HSPF1, Hdj1, Hsp40 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023051	8148	TAF15	http://www.ncbi.nlm.nih.gov/gene/?term=8148	"Npl3, RBP56, TAF2N, TAFII68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023052	81490	PTDSS2	http://www.ncbi.nlm.nih.gov/gene/?term=81490	PSS2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023053	81493	SYNC	http://www.ncbi.nlm.nih.gov/gene/?term=81493	"SYNC1, SYNCOILIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023054	81502	HM13	http://www.ncbi.nlm.nih.gov/gene/?term=81502	"H13, IMP1, IMPAS, IMPAS-1, MSTP086, PSENL3, PSL3, SPP, SPPL1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023055	81532	MOB2	http://www.ncbi.nlm.nih.gov/gene/?term=81532	HCCA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023056	81533	ITFG1	http://www.ncbi.nlm.nih.gov/gene/?term=81533	"2310047C21Rik, CDA08, LNKN-1, TIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023057	81533	ITFG1	http://www.ncbi.nlm.nih.gov/gene/?term=81533	"2310047C21Rik, CDA08, LNKN-1, TIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023058	81535	Sgpp1	http://www.ncbi.nlm.nih.gov/gene/?term=81535	"AI463453, SPP, SPP1, Spph1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023059	81537	SGPP1	http://www.ncbi.nlm.nih.gov/gene/?term=81537	SPPase1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023060	81537	SGPP1	http://www.ncbi.nlm.nih.gov/gene/?term=81537	SPPase1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023061	81537	SGPP1	http://www.ncbi.nlm.nih.gov/gene/?term=81537	SPPase1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023062	81539	SLC38A1	http://www.ncbi.nlm.nih.gov/gene/?term=81539	"ATA1, NAT2, SAT1, SNAT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023063	8153	RND2	http://www.ncbi.nlm.nih.gov/gene/?term=8153	"ARHN, RHO7, RhoN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023064	8153	RND2	http://www.ncbi.nlm.nih.gov/gene/?term=8153	"ARHN, RHO7, RhoN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023065	8153	RND2	http://www.ncbi.nlm.nih.gov/gene/?term=8153	"ARHN, RHO7, RhoN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023066	81542	TMX1	http://www.ncbi.nlm.nih.gov/gene/?term=81542	"PDIA11, TMX, TXNDC, TXNDC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023067	81542	TMX1	http://www.ncbi.nlm.nih.gov/gene/?term=81542	"PDIA11, TMX, TXNDC, TXNDC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023068	81542	TMX1	http://www.ncbi.nlm.nih.gov/gene/?term=81542	"PDIA11, TMX, TXNDC, TXNDC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023069	81542	TMX1	http://www.ncbi.nlm.nih.gov/gene/?term=81542	"PDIA11, TMX, TXNDC, TXNDC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023070	81545	FBXO38	http://www.ncbi.nlm.nih.gov/gene/?term=81545	"Fbx38, HMN2D, MOKA, SP329 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023071	81545	FBXO38	http://www.ncbi.nlm.nih.gov/gene/?term=81545	"Fbx38, HMN2D, MOKA, SP329 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023072	81550	TDRD3	http://www.ncbi.nlm.nih.gov/gene/?term=81550		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023073	81550	TDRD3	http://www.ncbi.nlm.nih.gov/gene/?term=81550		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023074	81550	TDRD3	http://www.ncbi.nlm.nih.gov/gene/?term=81550		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023075	81553	FAM49A	http://www.ncbi.nlm.nih.gov/gene/?term=81553		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023076	81555	YIPF5	http://www.ncbi.nlm.nih.gov/gene/?term=81555	"FinGER5, SB140, SMAP-5, SMAP5, YIP1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023077	81555	YIPF5	http://www.ncbi.nlm.nih.gov/gene/?term=81555	"FinGER5, SB140, SMAP-5, SMAP5, YIP1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023078	81555	YIPF5	http://www.ncbi.nlm.nih.gov/gene/?term=81555	"FinGER5, SB140, SMAP-5, SMAP5, YIP1A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023079	81556	VWA9	http://www.ncbi.nlm.nih.gov/gene/?term=81556	C15orf44	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023080	81557	MAGED4B	http://www.ncbi.nlm.nih.gov/gene/?term=81557		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023081	81559	TRIM11	http://www.ncbi.nlm.nih.gov/gene/?term=81559	"BIA1, RNF92 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023082	81559	TRIM11	http://www.ncbi.nlm.nih.gov/gene/?term=81559	"BIA1, RNF92 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023083	81562	LMAN2L	http://www.ncbi.nlm.nih.gov/gene/?term=81562	"MRT52, VIPL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023084	81562	LMAN2L	http://www.ncbi.nlm.nih.gov/gene/?term=81562	VIPL	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023085	81565	NDEL1	http://www.ncbi.nlm.nih.gov/gene/?term=81565	"EOPA, MITAP1, NDE1L1, NDE2, NUDEL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023086	81565	NDEL1	http://www.ncbi.nlm.nih.gov/gene/?term=81565	"EOPA, MITAP1, NDE1L1, NDE2, NUDEL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023087	81566	CSRNP2	http://www.ncbi.nlm.nih.gov/gene/?term=81566	"C12orf2, C12orf22, FAM130A1, PPP1R72, TAIP-12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023088	81567	TXNDC5	http://www.ncbi.nlm.nih.gov/gene/?term=81567	"ENDOPDI, ERP46, HCC-2, HCC2, PDIA15, STRF8, UNQ364 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023089	81567	TXNDC5	http://www.ncbi.nlm.nih.gov/gene/?term=81567	"ENDOPDI, ERP46, HCC-2, HCC2, PDIA15, STRF8, UNQ364 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023090	81567	TXNDC5	http://www.ncbi.nlm.nih.gov/gene/?term=81567	"ENDOPDI, ERP46, HCC-2, HCC2, PDIA15, STRF8, UNQ364 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023091	81570	CLPB	http://www.ncbi.nlm.nih.gov/gene/?term=81570	"ANKCLB, HSP78, MEGCANN, MGCA7, SKD3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023092	81570	CLPB	http://www.ncbi.nlm.nih.gov/gene/?term=81570	"ANKCLB, HSP78, MEGCANN, MGCA7, SKD3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023093	81572	PDRG1	http://www.ncbi.nlm.nih.gov/gene/?term=81572	"C20orf126, PDRG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023094	81573	ANKRD13C	http://www.ncbi.nlm.nih.gov/gene/?term=81573	dJ677H15.3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023095	81575	APOLD1	http://www.ncbi.nlm.nih.gov/gene/?term=81575	VERGE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023096	81576	CCDC130	http://www.ncbi.nlm.nih.gov/gene/?term=81576		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023097	81577	GFOD2	http://www.ncbi.nlm.nih.gov/gene/?term=81577		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023098	81579	PLA2G12A	http://www.ncbi.nlm.nih.gov/gene/?term=81579	"GXII, PLA2G12, ROSSY "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023099	81579	PLA2G12A	http://www.ncbi.nlm.nih.gov/gene/?term=81579	"GXII, PLA2G12, ROSSY "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023100	81579	PLA2G12A	http://www.ncbi.nlm.nih.gov/gene/?term=81579	"GXII, PLA2G12, ROSSY "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023101	815	CAMK2A	http://www.ncbi.nlm.nih.gov/gene/?term=815	CAMKA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023102	81602	CDADC1	http://www.ncbi.nlm.nih.gov/gene/?term=81602	"NYD-SP15, bA103J18.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023103	81603	TRIM8	http://www.ncbi.nlm.nih.gov/gene/?term=81603	"GERP, RNF27 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023104	81605	URM1	http://www.ncbi.nlm.nih.gov/gene/?term=81605	C9orf74	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023105	81605	URM1	http://www.ncbi.nlm.nih.gov/gene/?term=81605	C9orf74	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023106	81605	URM1	http://www.ncbi.nlm.nih.gov/gene/?term=81605	C9orf74	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023107	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023108	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023109	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023110	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023111	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023112	81610	FAM83D	http://www.ncbi.nlm.nih.gov/gene/?term=81610	"C20orf129, CHICA, dJ616B8.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023113	81610	FAM83D	http://www.ncbi.nlm.nih.gov/gene/?term=81610	"C20orf129, CHICA, dJ616B8.3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023114	81610	FAM83D	http://www.ncbi.nlm.nih.gov/gene/?term=81610	"C20orf129, CHICA, dJ616B8.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023115	81611	ANP32E	http://www.ncbi.nlm.nih.gov/gene/?term=81611	"LANP-L, LANPL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023116	81611	ANP32E	http://www.ncbi.nlm.nih.gov/gene/?term=81611	"LANP-L, LANPL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023117	81611	ANP32E	http://www.ncbi.nlm.nih.gov/gene/?term=81611	"LANP-L, LANPL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023118	81614	NIPA2	http://www.ncbi.nlm.nih.gov/gene/?term=81614		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023119	81614	NIPA2	http://www.ncbi.nlm.nih.gov/gene/?term=81614		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023120	81618	ITM2C	http://www.ncbi.nlm.nih.gov/gene/?term=81618	"BRI3, BRICD2C, E25, E25C, ITM3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023121	81618	ITM2C	http://www.ncbi.nlm.nih.gov/gene/?term=81618	"BRI3, BRICD2C, E25, E25C, ITM3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023122	81619	TSPAN14	http://www.ncbi.nlm.nih.gov/gene/?term=81619	"DC-TM4F2, TM4SF14 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023123	8161	COIL	http://www.ncbi.nlm.nih.gov/gene/?term=8161	"CLN80, p80-coilin "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023124	81620	CDT1	http://www.ncbi.nlm.nih.gov/gene/?term=81620	"DUP, RIS2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023125	81622	UNC93B1	http://www.ncbi.nlm.nih.gov/gene/?term=81622	"IIAE1, UNC93, UNC93B, Unc-93B1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023126	81627	TRMT1L	http://www.ncbi.nlm.nih.gov/gene/?term=81627	"C1orf25, MST070, MSTP070, TRM1L, bG120K12.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023127	81628	TSC22D4	http://www.ncbi.nlm.nih.gov/gene/?term=81628	"THG-1, THG1, TILZ2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023128	81628	TSC22D4	http://www.ncbi.nlm.nih.gov/gene/?term=81628	"THG-1, THG1, TILZ2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023129	81631	MAP1LC3B	http://www.ncbi.nlm.nih.gov/gene/?term=81631	"ATG8F, LC3B, MAP1A/1BLC3-a, MAP1LC3B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023130	81631	MAP1LC3B	http://www.ncbi.nlm.nih.gov/gene/?term=81631	"ATG8F, LC3B, MAP1A/1BLC3-a, MAP1LC3B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023131	81631	MAP1LC3B	http://www.ncbi.nlm.nih.gov/gene/?term=81631	"ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023132	81657	Gabbr1	http://www.ncbi.nlm.nih.gov/gene/?term=81657	"MRG15, Tex189, TEG-189, MORFRG15, mKIAA4002 "	mRNA	Rattus norvegicus	12081654	Dendrite	Spinal neuron	In situ hybridization	"On spinal neurons both r1 and r2 mRNAs showed somatodendritic localization, extending out for >100 mm with punctate appearance especially in adult cells. Interestingly, a dendritic localization of the r1 and r2 mRNAs (Fig. 4C, arrows) was observed. However, in several neuronsthe mRNAs for r1 or r2 could be found more than 100 mm away from the cell soma, indicating localization to distal dendrites (Table 1). "
RLID00023133	8165	AKAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8165	"AKAP, AKAP121, AKAP149, AKAP84, D-AKAP1, PPP1R43, PRKA1, SAKAP84, TDRD17 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023134	81669	CCNL2	http://www.ncbi.nlm.nih.gov/gene/?term=81669	"ANIA-6B, CCNM, CCNS, HCLA-ISO, HLA-ISO, PCEE, SB138 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023135	81671	VMP1	http://www.ncbi.nlm.nih.gov/gene/?term=81671	"EPG3, TANGO5, TMEM49 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023136	81671	VMP1	http://www.ncbi.nlm.nih.gov/gene/?term=81671	"EPG3, TANGO5, TMEM49 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023137	81687	Mmp9	http://www.ncbi.nlm.nih.gov/gene/?term=81687		mRNA	Rattus norvegicus	23077039	Dendrite	Hippocampus	Fluorescence in situ hybridization	"In aggregate, our findings show that MMP-9 mRNA is transported to dendrites and locally translated and that the protein is released in an activity-dependent manner. "
RLID00023138	81688	C6orf62	http://www.ncbi.nlm.nih.gov/gene/?term=81688	"Nbla00237, XTP12, dJ30M3.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023139	81688	C6orf62	http://www.ncbi.nlm.nih.gov/gene/?term=81688	"Nbla00237, XTP12, dJ30M3.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023140	81688	C6orf62	http://www.ncbi.nlm.nih.gov/gene/?term=81688	"Nbla00237, XTP12, dJ30M3.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023141	81689	ISCA1	http://www.ncbi.nlm.nih.gov/gene/?term=81689	"HBLD2, ISA1, hIscA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023142	81689	ISCA1	http://www.ncbi.nlm.nih.gov/gene/?term=81689	"HBLD2, ISA1, hIscA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023143	81691	LOC81691	http://www.ncbi.nlm.nih.gov/gene/?term=81691		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023144	81693	AMN	http://www.ncbi.nlm.nih.gov/gene/?term=81693	"PRO1028, amnionless "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023145	81702	Ankrd17	http://www.ncbi.nlm.nih.gov/gene/?term=81702	"4933425K22Rik, A130069E23Rik, A930008M01, AA407558, AA516750, AU040470, Foe, Gtar, Mask, mKIAA0697 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023146	81704	DOCK8	http://www.ncbi.nlm.nih.gov/gene/?term=81704	"HEL-205, MRD2, ZIR8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023147	81706	PPP1R14C	http://www.ncbi.nlm.nih.gov/gene/?term=81706	"CPI17-like, KEPI, NY-BR-81 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023148	81706	PPP1R14C	http://www.ncbi.nlm.nih.gov/gene/?term=81706	"CPI17-like, KEPI, NY-BR-81 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023149	8170	SLC14A2	http://www.ncbi.nlm.nih.gov/gene/?term=8170	"HUT2, UT-A2, UT2, UTA, UTR, hUT-A6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023150	8170	SLC14A2	http://www.ncbi.nlm.nih.gov/gene/?term=8170	"HUT2, UT-A2, UT2, UTA, UTR, hUT-A6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023151	817365	CSD2	http://www.ncbi.nlm.nih.gov/gene/?term=817365	"AT2G28190, COPPER/ZINC SUPEROXIDE DISMUTASE, COPPER/ZINC SUPEROXIDE DISMUTASE 2, CZSOD2, F24D13.2, F24D13_2, copper/zinc superoxide dismutase 2 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023152	8175	SF3A2	http://www.ncbi.nlm.nih.gov/gene/?term=8175	"PRP11, PRPF11, SAP62, SF3a66 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023153	81768	Rpl22	http://www.ncbi.nlm.nih.gov/gene/?term=81768		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023154	81770	Rpl37	http://www.ncbi.nlm.nih.gov/gene/?term=81770		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023155	81786	TRIM7	http://www.ncbi.nlm.nih.gov/gene/?term=81786	"GNIP, RNF90 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023156	81788	NUAK2	http://www.ncbi.nlm.nih.gov/gene/?term=81788	SNARK	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023157	81788	NUAK2	http://www.ncbi.nlm.nih.gov/gene/?term=81788	SNARK	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023158	81789	TIGD6	http://www.ncbi.nlm.nih.gov/gene/?term=81789		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023159	8178	ELL	http://www.ncbi.nlm.nih.gov/gene/?term=8178	"C19orf17, ELL1, MEN, PPP1R68 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023160	81790	RNF170	http://www.ncbi.nlm.nih.gov/gene/?term=81790	"ADSA, SNAX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023161	81790	RNF170	http://www.ncbi.nlm.nih.gov/gene/?term=81790	"ADSA, SNAX1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023162	817948	SPL3	http://www.ncbi.nlm.nih.gov/gene/?term=817948	"AT2G33810, T1B8.11, T1B8_11, squamosa promoter binding protein-like 3 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023163	817	CAMK2D	http://www.ncbi.nlm.nih.gov/gene/?term=817	CAMKD	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023164	817	CAMK2D	http://www.ncbi.nlm.nih.gov/gene/?term=817	CAMKD	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023165	817	CAMK2D	http://www.ncbi.nlm.nih.gov/gene/?term=817	CAMKD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023166	818036	PHB	http://www.ncbi.nlm.nih.gov/gene/?term=818036	"AT2G34710, ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 14, ATHB-14, ATHB14, PHABULOSA, PHABULOSA 1D, PHB-1D, T29F13.8, T29F13_8 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023167	81814	Tmsb4x	http://www.ncbi.nlm.nih.gov/gene/?term=81814		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023168	81818	Vim	http://www.ncbi.nlm.nih.gov/gene/?term=81818		mRNA	Rattus norvegicus	15673657	Axon	Dorsal root ganglia	RT-PCR	"By RT-PCR, we were able to detect peripherin, vimentin, and cofilin mRNAs in DRG axonal preparations (Fig. 4A). By RT-PCR, rTpm3 mRNA was detected in axonal preparations from the cultured DRGs (Fig. 4A). alpha-B crystallin and HSP70 mRNAs appeared more concentrated in the axonal than in the cellbody RNA preparations. HSP60 and HSP90 mRNAs show relatively equal levels in the axonal and cell-body RNAs, whereas HSP27 and grp75 appear more concentrated in the cell-body than in the axonal RNAs. Resident-ER proteins and encoding mRNAs in DRG axons. A, RT-PCR for rat grp78/BiP, calreticulin, and ERp29 mRNAs shows that these transcripts extend into the DRG axons. Ubiquitin C-terminal hydrolase L1 (Uch-L1), SP22, r-synuclein, and dismutase (SOD1) were detected by the MS analyses, and RT-PCR confirmed that the mRNAs encoding each of these extends into the DRG axons (Fig. 7A). "
RLID00023169	81818	Vim	http://www.ncbi.nlm.nih.gov/gene/?term=81818		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023170	81822	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=81822	Actx	mRNA	Rattus norvegicus	20118926	Axon	Sensory neuron	RT-PCR	"Few 3’UTRs that direct the transport of mRNAs to dendrites have been identified. beta-actin mRNA (Actb) transport in axons, for example, is regulated by the interaction of the 3’zipcode element with the zipcode binding protein (ZBP), and a localization motif within the 3’UTR of the Ran GTPase RanBP1 mRNA (Ranbp1) contributes to the axonal targeting of this transcript in adult sensory neurons. "
RLID00023171	81822	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=81822	Actx	mRNA	Rattus norvegicus	20308067	Axon	Neuron	Fluorescence in situ hybridization	"Beta-Actin and gamma-actin mRNAs show characteristic localization, with beta-actin mRNA extending into the distal axons and gamma-actin mRNA being restricted to the proximal segment of the axon. "
RLID00023172	81822	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=81822	Actx	mRNA	Rattus norvegicus	21471362	Dendrite	Hippocampus|Cortical cell	Fluorescence in situ hybridization	Zipcode binding protein 1 (ZBP1) controls β-actin mRNA transport and translation in dendrites.  Fluorescence in situ hybridization with probes specific to β-actin mRNA revealed its presence in puncta in cell soma and in dendrites of control cells transfected with pSuper on DIV7 (Fig. 8A). 
RLID00023173	81822	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=81822	Actx	mRNA	Rattus norvegicus	22355657	Dendrite	Cortical neuron	Fluorescence in situ hybridization	"Here we report that Htt and the huntingtin-associated protein 1 (HAP1) are co-localized with the microtubule motor proteins, the KIF5A kinesin and dynein, during dendritic transport of β-actin mRNA. "
RLID00023174	81822	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=81822	Actx	mRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"By quantitative fluorescent in situ hybridization combined with immunofluorescence to unambiguously distinguish intra-axonal mRNAs, we show that regenerating spinal cord axons contain β-actin, GAP-43, Neuritin, Reg3a, Hamp, and Importin β1 mRNAs.  "
RLID00023175	81822	Actb	http://www.ncbi.nlm.nih.gov/gene/?term=81822	Actx	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023176	81839	VANGL1	http://www.ncbi.nlm.nih.gov/gene/?term=81839	"KITENIN, LPP2, STB2, STBM2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023177	81839	VANGL1	http://www.ncbi.nlm.nih.gov/gene/?term=81839	"KITENIN, LPP2, STB2, STBM2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023178	81846	SBF2	http://www.ncbi.nlm.nih.gov/gene/?term=81846	"CMT4B2, DENND7B, MTMR13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023179	81846	SBF2	http://www.ncbi.nlm.nih.gov/gene/?term=81846	"CMT4B2, DENND7B, MTMR13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023180	81846	SBF2	http://www.ncbi.nlm.nih.gov/gene/?term=81846	"CMT4B2, DENND7B, MTMR13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023181	81848	SPRY4	http://www.ncbi.nlm.nih.gov/gene/?term=81848	HH17	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023182	81853	TMEM14B	http://www.ncbi.nlm.nih.gov/gene/?term=81853		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023183	81853	TMEM14B	http://www.ncbi.nlm.nih.gov/gene/?term=81853		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023184	81855	SFXN3	http://www.ncbi.nlm.nih.gov/gene/?term=81855	"BA108L7.2, SFX3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023185	81858	SHARPIN	http://www.ncbi.nlm.nih.gov/gene/?term=81858	SIPL1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023186	81858	SHARPIN	http://www.ncbi.nlm.nih.gov/gene/?term=81858	SIPL1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023187	81873	ARPC5L	http://www.ncbi.nlm.nih.gov/gene/?term=81873	ARC16-2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023188	81876	RAB1B	http://www.ncbi.nlm.nih.gov/gene/?term=81876		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023189	81876	RAB1B	http://www.ncbi.nlm.nih.gov/gene/?term=81876		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023190	81876	RAB1B	http://www.ncbi.nlm.nih.gov/gene/?term=81876		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023191	81888	HYI	http://www.ncbi.nlm.nih.gov/gene/?term=81888	HT036	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023192	81889	FAHD1	http://www.ncbi.nlm.nih.gov/gene/?term=81889	"C16orf36, YISKL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023193	81890	QTRT1	http://www.ncbi.nlm.nih.gov/gene/?term=81890	"FP3235, TGT, TGUT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023194	81892	SLIRP	http://www.ncbi.nlm.nih.gov/gene/?term=81892	"C14orf156, DC50, PD04872 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023195	81898	Sf3b1	http://www.ncbi.nlm.nih.gov/gene/?term=81898	"155kDa, 2810001M05Rik, AA409119, Prp10, SAP155, SF3b155, TA-8, Targ4 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023196	8189	SYMPK	http://www.ncbi.nlm.nih.gov/gene/?term=8189	"SPK, SYM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023197	8189	SYMPK	http://www.ncbi.nlm.nih.gov/gene/?term=8189	"SPK, SYM "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023198	8189	SYMPK	http://www.ncbi.nlm.nih.gov/gene/?term=8189	"SPK, SYM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023199	818	CAMK2G	http://www.ncbi.nlm.nih.gov/gene/?term=818	"CAMK, CAMK-II, CAMKG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023200	818	CAMK2G	http://www.ncbi.nlm.nih.gov/gene/?term=818	"CAMK, CAMK-II, CAMKG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023201	81909	Zfpl1	http://www.ncbi.nlm.nih.gov/gene/?term=81909	1500015B20Rik	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023202	81910	Rrbp1	http://www.ncbi.nlm.nih.gov/gene/?term=81910	"1700087N07Rik, 5730465C04Rik, ES/130, mKIAA1398, mRRp0, mRRp1.8, mRRp10, mRRp15a, mRRp15b, mRRp16.8, mRRp2, mRRp41, mRRp47, mRRp5.4, p180 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023203	81918	Pard3	http://www.ncbi.nlm.nih.gov/gene/?term=81918	Par3	mRNA	Rattus norvegicus	19620967	Axon	Neuron	Fluorescence in situ hybridization	"Par3 mRNA is localized to developing axons, and NGF and netrin-1 trigger its local translation. "
RLID00023204	81926	ABHD17A	http://www.ncbi.nlm.nih.gov/gene/?term=81926	"C19orf27, FAM108A1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023205	81926	ABHD17A	http://www.ncbi.nlm.nih.gov/gene/?term=81926	"C19orf27, FAM108A1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023206	81928	CABLES2	http://www.ncbi.nlm.nih.gov/gene/?term=81928	"C20orf150, dJ908M14.2, ik3-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023207	81929	SEH1L	http://www.ncbi.nlm.nih.gov/gene/?term=81929	"SEC13L, SEH1A, SEH1B, Seh1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023208	81929	SEH1L	http://www.ncbi.nlm.nih.gov/gene/?term=81929	"SEC13L, SEH1A, SEH1B, Seh1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023209	8192	CLPP	http://www.ncbi.nlm.nih.gov/gene/?term=8192	"DFNB81, PRLTS3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023210	81931	ZNF93	http://www.ncbi.nlm.nih.gov/gene/?term=81931	"HPF34, HTF34, TF34, ZNF505 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023211	81932	HDHD3	http://www.ncbi.nlm.nih.gov/gene/?term=81932	"2810435D12Rik, C9orf158 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023212	81932	HDHD3	http://www.ncbi.nlm.nih.gov/gene/?term=81932	"2810435D12Rik, C9orf158 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023213	8195	MKKS	http://www.ncbi.nlm.nih.gov/gene/?term=8195	"BBS6, HMCS, KMS, MKS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023214	819	CAMLG	http://www.ncbi.nlm.nih.gov/gene/?term=819	"CAML, GET2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023215	819	CAMLG	http://www.ncbi.nlm.nih.gov/gene/?term=819	"CAML, GET2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023216	819	CAMLG	http://www.ncbi.nlm.nih.gov/gene/?term=819	"CAML, GET2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023217	81	ACTN4	http://www.ncbi.nlm.nih.gov/gene/?term=81	"ACTININ-4, FSGS, FSGS1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023218	81	ACTN4	http://www.ncbi.nlm.nih.gov/gene/?term=81	"ACTININ-4, FSGS, FSGS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023219	81	ACTN4	http://www.ncbi.nlm.nih.gov/gene/?term=81	"ACTININ-4, FSGS, FSGS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023220	8202	NCOA3	http://www.ncbi.nlm.nih.gov/gene/?term=8202	"ACTR, AIB-1, AIB1, CAGH16, CTG26, KAT13B, RAC3, SRC-3, SRC3, TNRC14, TNRC16, TRAM-1, bHLHe42, pCIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023221	8202	NCOA3	http://www.ncbi.nlm.nih.gov/gene/?term=8202	"ACTR, AIB-1, AIB1, CAGH16, CTG26, KAT13B, RAC3, SRC-3, SRC3, TNRC14, TNRC16, TRAM-1, bHLHe42, pCIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023222	8204	NRIP1	http://www.ncbi.nlm.nih.gov/gene/?term=8204	RIP140	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023223	8204	NRIP1	http://www.ncbi.nlm.nih.gov/gene/?term=8204	RIP140	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023224	820605	EIF4A1	http://www.ncbi.nlm.nih.gov/gene/?term=820605	"AT3G13920, RH4, TIF4A1, eukaryotic translation initiation factor 4A1 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023225	820732	TCP4	http://www.ncbi.nlm.nih.gov/gene/?term=820732	"AT3G15030, MEE35, TCP family transcription factor 4, maternal effect embryo arrest 35 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023226	8208	CHAF1B	http://www.ncbi.nlm.nih.gov/gene/?term=8208	"CAF-1, CAF-IP60, CAF1, CAF1A, CAF1P60, MPHOSPH7, MPP7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023227	8208	CHAF1B	http://www.ncbi.nlm.nih.gov/gene/?term=8208	"CAF-1, CAF-IP60, CAF1, CAF1A, CAF1P60, MPHOSPH7, MPP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023228	8209	C21orf33	http://www.ncbi.nlm.nih.gov/gene/?term=8209	"ES1, GT335, HES1, KNPH, KNPI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023229	8209	C21orf33	http://www.ncbi.nlm.nih.gov/gene/?term=8209	"ES1, GT335, HES1, KNPH, KNPI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023230	8214	DGCR6	http://www.ncbi.nlm.nih.gov/gene/?term=8214		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023231	8216	LZTR1	http://www.ncbi.nlm.nih.gov/gene/?term=8216	"BTBD29, LZTR-1, NS10, SWNTS2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023232	8216	LZTR1	http://www.ncbi.nlm.nih.gov/gene/?term=8216	"BTBD29, LZTR-1, NS10, SWNTS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023233	8218	CLTCL1	http://www.ncbi.nlm.nih.gov/gene/?term=8218	"CHC22, CLH22, CLTCL, CLTD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023234	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, IP90, P90 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023235	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, IP90, P90 "	mRNA	Homo sapiens	12923260	Endoplasmic reticulum	T-cell line Jurkat	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00023236	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, IP90, P90 "	mRNA	Homo sapiens	12923260	Ribosome	T-cell line Jurkat	S1 nuclease protection assays	"Using the procedures described above, the subcellular distribution of individual mRNAs in the cytosol and rough ER polysome fractions of Jurkat and J558 cells was determined. As depicted in Figure 4, Sec61a and calnexin were highly enriched in the membrane-bound fraction, as may be predicted for those mRNAs encoding signal sequences. "
RLID00023237	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, IP90, P90 "	mRNA	Homo sapiens	20453113	Ribosome	NCI/ADR-RES cell	qRT-PCR	"The relative partitioning of both cytosolic (ACTB, H3.3) and ER-bound (MDR1, CANX) transcripts between both fractions was marked, despite the small carryover of cytosol in the ER fraction (Fig. 2B). Polysome profile analyses from the isolated fractions indicated that these transcripts migrated in polyribosome-containing fractions (Fig. 2C). Notably, the distribution of ER-bound transcripts between the ER and cytosol did not change on arsenite treatment of NCI/ADR-RES cells (Fig. 2D). Data are collected from Figure 2. "
RLID00023238	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, IP90, P90 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023239	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, IP90, P90 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023240	821	CANX	http://www.ncbi.nlm.nih.gov/gene/?term=821	"CNX, P90, IP90 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Northern blot	"FIGURE 4. Steady-state mRNA partitioning between cytosolic and ER-bound polysomes. Total RNA was isolated from cytosol and ER membrane fractions of Jurkat and J558 cells, as indicated in Figure 1A. For each reaction, 10 ug of RNA was incubated with one of eight [32P]-labeled oligonucleotide probes representing three different classes of genes, based on the type of protein encoded: cytosolic, ER membrane, and ER lumenal. The nuclease-protected RNA fragments from parallel reactions with cytosol and ER-derived RNA were purified and separated by denaturing acrylamide gel electrophoresis. Quantification was performed by phosphorimager analysis; photostimulated luminescence output (PSL) values are indicated. Digital images of the phosphorimager output are depicted. The data are collected from Figure 4. "
RLID00023241	8220	DGCR14	http://www.ncbi.nlm.nih.gov/gene/?term=8220	"DGCR13, DGS-H, DGS-I, DGSH, DGSI, ES2, Es2el "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023242	8225	GTPBP6	http://www.ncbi.nlm.nih.gov/gene/?term=8225	PGPL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023243	8226	PUDP	http://www.ncbi.nlm.nih.gov/gene/?term=8226	"DXF68S1E, FAM16AX, GS1, HDHD1, HDHD1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023244	8226	PUDP	http://www.ncbi.nlm.nih.gov/gene/?term=8226	"DXF68S1E, FAM16AX, GS1, HDHD1, HDHD1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023245	8228	PNPLA4	http://www.ncbi.nlm.nih.gov/gene/?term=8228	"DXS1283E, GS2, iPLA2eta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023246	8228	PNPLA4	http://www.ncbi.nlm.nih.gov/gene/?term=8228	"DXS1283E, GS2, iPLA2eta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023247	822	CAPG	http://www.ncbi.nlm.nih.gov/gene/?term=822	"AFCP, HEL-S-66, MCP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023248	8233	ZRSR2	http://www.ncbi.nlm.nih.gov/gene/?term=8233	"U2AF1-RS2, U2AF1L2, U2AF1RS2, URP, ZC3H22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023249	8239	USP9X	http://www.ncbi.nlm.nih.gov/gene/?term=8239	"DFFRX, FAF, FAM, MRX99, MRXS99F "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023250	8239	USP9X	http://www.ncbi.nlm.nih.gov/gene/?term=8239	"DFFRX, FAF, FAM, MRX99, MRXS99F "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023251	8239	USP9X	http://www.ncbi.nlm.nih.gov/gene/?term=8239	"DFFRX, FAF, FAM, MRX99, MRXS99F "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023252	8239	USP9X	http://www.ncbi.nlm.nih.gov/gene/?term=8239	"DFFRX, FAF, FAM, MRX99, MRXS99F "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023253	8239	USP9X	http://www.ncbi.nlm.nih.gov/gene/?term=8239	"DFFRX, FAF, FAM, MRX99 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023254	823	CAPN1	http://www.ncbi.nlm.nih.gov/gene/?term=823	"CANP, CANP1, CANPL1, muCANP, muCL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023255	823	CAPN1	http://www.ncbi.nlm.nih.gov/gene/?term=823	"CANP, CANP1, CANPL1, muCANP, muCL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023256	8241	RBM10	http://www.ncbi.nlm.nih.gov/gene/?term=8241	"DXS8237E, GPATC9, GPATCH9, S1-1, TARPS, ZRANB5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023257	8241	RBM10	http://www.ncbi.nlm.nih.gov/gene/?term=8241	"DXS8237E, GPATC9, GPATCH9, S1-1, TARPS, ZRANB5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023258	8242	KDM5C	http://www.ncbi.nlm.nih.gov/gene/?term=8242	"DXS1272E, JARID1C, MRX13, MRXJ, MRXSCJ, MRXSJ, SMCX, XE169 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023259	8242	KDM5C	http://www.ncbi.nlm.nih.gov/gene/?term=8242	"DXS1272E, JARID1C, MRX13, MRXJ, MRXSCJ, MRXSJ, SMCX, XE169 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023260	8243	SMC1A	http://www.ncbi.nlm.nih.gov/gene/?term=8243	"CDLS2, DXS423E, SB1.8, SMC1, SMC1L1, SMC1alpha, SMCB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023261	8243	SMC1A	http://www.ncbi.nlm.nih.gov/gene/?term=8243	"CDLS2, DXS423E, SB1.8, SMC1, SMC1L1, SMC1alpha, SMCB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023262	8243	SMC1A	http://www.ncbi.nlm.nih.gov/gene/?term=8243	"CDLS2, DXS423E, SB1.8, SMC1, SMC1L1, SMC1alpha, SMCB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023263	824	CAPN2	http://www.ncbi.nlm.nih.gov/gene/?term=824	"CANP2, CANPL2, CANPml, mCANP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023264	824	CAPN2	http://www.ncbi.nlm.nih.gov/gene/?term=824	"CANP2, CANPL2, CANPml, mCANP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023265	824	CAPN2	http://www.ncbi.nlm.nih.gov/gene/?term=824	"CANP2, CANPL2, CANPml, mCANP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023266	825398	UBQ5	http://www.ncbi.nlm.nih.gov/gene/?term=825398	"AT3G62250, ubiquitin 5 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023267	825	CAPN3	http://www.ncbi.nlm.nih.gov/gene/?term=825	"CANP3, CANPL3, LGMD2, LGMD2A, nCL-1, p94 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023268	8260	NAA10	http://www.ncbi.nlm.nih.gov/gene/?term=8260	"ARD1, ARD1A, ARD1P, DXS707, MCOPS1, NATD, OGDNS, TE2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023269	8260	NAA10	http://www.ncbi.nlm.nih.gov/gene/?term=8260	"ARD1, ARD1A, ARD1P, DXS707, MCOPS1, NATD, OGDNS, TE2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023270	8266	UBL4A	http://www.ncbi.nlm.nih.gov/gene/?term=8266	"DX254E, DXS254E, G6PD, GDX, GET5, MDY2, TMA24, UBL4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023271	8266	UBL4A	http://www.ncbi.nlm.nih.gov/gene/?term=8266	"DX254E, DXS254E, G6PD, GDX, GET5, MDY2, TMA24, UBL4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023272	8266	UBL4A	http://www.ncbi.nlm.nih.gov/gene/?term=8266	"DX254E, DXS254E, G6PD, GDX, GET5, MDY2, TMA24, UBL4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023273	8269	TMEM187	http://www.ncbi.nlm.nih.gov/gene/?term=8269	"CXorf12, DXS9878E, ITBA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023274	826	CAPNS1	http://www.ncbi.nlm.nih.gov/gene/?term=826	"CALPAIN4, CANP, CANPS, CAPN4, CDPS, CSS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023275	826	CAPNS1	http://www.ncbi.nlm.nih.gov/gene/?term=826	"CALPAIN4, CANP, CANPS, CAPN4, CDPS, CSS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023276	826	CAPNS1	http://www.ncbi.nlm.nih.gov/gene/?term=826	"CALPAIN4, CANP, CANPS, CAPN4, CDPS, CSS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023277	8270	LAGE3	http://www.ncbi.nlm.nih.gov/gene/?term=8270	"CVG5, DXS9879E, DXS9951E, ESO3, ITBA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023278	8270	LAGE3	http://www.ncbi.nlm.nih.gov/gene/?term=8270	"CVG5, DXS9879E, DXS9951E, ESO3, ITBA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023279	8273	SLC10A3	http://www.ncbi.nlm.nih.gov/gene/?term=8273	"DXS253E, P3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023280	8287	USP9Y	http://www.ncbi.nlm.nih.gov/gene/?term=8287	"DFFRY, SPGFY2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023281	8290	HIST3H3	http://www.ncbi.nlm.nih.gov/gene/?term=8290	"H3.4, H3/g, H3FT, H3t "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023282	8290	HIST3H3	http://www.ncbi.nlm.nih.gov/gene/?term=8290	"H3.4, H3/g, H3FT, H3t "	mRNA	Homo sapiens	20453113	Cytosol	NCI/ADR-RES cell	qRT-PCR	"The relative partitioning of both cytosolic (ACTB, H3.3) and ER-bound (MDR1, CANX) transcripts between both fractions was marked, despite the small carryover of cytosol in the ER fraction (Fig. 2B). Polysome profile analyses from the isolated fractions indicated that these transcripts migrated in polyribosome-containing fractions (Fig. 2C). Notably, the distribution of ER-bound transcripts between the ER and cytosol did not change on arsenite treatment of NCI/ADR-RES cells (Fig. 2D). Data are collected from Figure 2. "
RLID00023283	8293	SERF1A	http://www.ncbi.nlm.nih.gov/gene/?term=8293	"4F5, FAM2A, H4F5, SERF1, SMAM1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023284	8293	SERF1A	http://www.ncbi.nlm.nih.gov/gene/?term=8293	"4F5, FAM2A, H4F5, SERF1, SMAM1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023285	8293	SERF1A	http://www.ncbi.nlm.nih.gov/gene/?term=8293	"4F5, FAM2A, H4F5, SERF1, SMAM1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023286	8294	HIST1H4I	http://www.ncbi.nlm.nih.gov/gene/?term=8294	"H4/m, H4FM, H4M "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023287	8294	HIST1H4I	http://www.ncbi.nlm.nih.gov/gene/?term=8294	"H4/m, H4FM, H4M "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023288	8295	TRRAP	http://www.ncbi.nlm.nih.gov/gene/?term=8295	"PAF350/400, PAF400, STAF40, TR-AP, Tra1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023289	829	CAPZA1	http://www.ncbi.nlm.nih.gov/gene/?term=829	"CAPPA1, CAPZ, CAZ1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023290	829	CAPZA1	http://www.ncbi.nlm.nih.gov/gene/?term=829	"CAPPA1, CAPZ, CAZ1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023291	8301	PICALM	http://www.ncbi.nlm.nih.gov/gene/?term=8301	"CALM, CLTH, LAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023292	8301	PICALM	http://www.ncbi.nlm.nih.gov/gene/?term=8301	"CALM, CLTH, LAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023293	8303	SNN	http://www.ncbi.nlm.nih.gov/gene/?term=8303		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023294	830	CAPZA2	http://www.ncbi.nlm.nih.gov/gene/?term=830	"CAPPA2, CAPZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023295	830	CAPZA2	http://www.ncbi.nlm.nih.gov/gene/?term=830	"CAPPA2, CAPZ "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023296	8310	ACOX3	http://www.ncbi.nlm.nih.gov/gene/?term=8310		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023297	8313	AXIN2	http://www.ncbi.nlm.nih.gov/gene/?term=8313	"AXIL, ODCRCS "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023298	8314	BAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8314	"HUCEP-13, UCHL2, hucep-6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023299	8314	BAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8314	"HUCEP-13, UCHL2, hucep-6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023300	8317	CDC7	http://www.ncbi.nlm.nih.gov/gene/?term=8317	"CDC7L1, HsCDC7, Hsk1, huCDC7 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023301	8317	CDC7	http://www.ncbi.nlm.nih.gov/gene/?term=8317	"CDC7L1, HsCDC7, Hsk1, huCDC7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023302	8317	CDC7	http://www.ncbi.nlm.nih.gov/gene/?term=8317	"CDC7L1, HsCDC7, Hsk1, huCDC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023303	8318	CDC45	http://www.ncbi.nlm.nih.gov/gene/?term=8318	"CDC45LL2, PORC-PI-1, CDC45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023304	8318	CDC45	http://www.ncbi.nlm.nih.gov/gene/?term=8318	"CDC45L, CDC45L2, PORC-PI-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023305	831	CAST	http://www.ncbi.nlm.nih.gov/gene/?term=831	"BS-17, PLACK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023306	831	CAST	http://www.ncbi.nlm.nih.gov/gene/?term=831	"BS-17, PLACK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023307	8321	FZD1	http://www.ncbi.nlm.nih.gov/gene/?term=8321		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023308	8322	FZD4	http://www.ncbi.nlm.nih.gov/gene/?term=8322	"CD344, EVR1, FEVRS, Fz-4, Fz4, FzE4, GPCR, hFz4, FZD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023309	8322	FZD4	http://www.ncbi.nlm.nih.gov/gene/?term=8322	"CD344, EVR1, FEVRS, Fz-4, Fz4, FzE4, GPCR, hFz4, FZD4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023310	8322	FZD4	http://www.ncbi.nlm.nih.gov/gene/?term=8322	"CD344, EVR1, FEVRS, Fz-4, Fz4, FzE4, GPCR, hFz4, FZD4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023311	8323	FZD6	http://www.ncbi.nlm.nih.gov/gene/?term=8323	"FZ-6, FZ6, HFZ6, NDNC10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023312	8323	FZD6	http://www.ncbi.nlm.nih.gov/gene/?term=8323	"FZ-6, FZ6, HFZ6, NDNC10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023313	8323	FZD6	http://www.ncbi.nlm.nih.gov/gene/?term=8323	"FZ-6, FZ6, HFZ6, NDNC10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023314	8324	FZD7	http://www.ncbi.nlm.nih.gov/gene/?term=8324	FzE3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023315	8325	FZD8	http://www.ncbi.nlm.nih.gov/gene/?term=8325	"FZ-8, hFZ8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023316	832990	BZO2H3	http://www.ncbi.nlm.nih.gov/gene/?term=832990	"AT5G28770, Arabidopsis thaliana basic leucine zipper 63, AtbZIP63, T32B20.4, T32B20_4 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023317	8329	HIST1H2AI	http://www.ncbi.nlm.nih.gov/gene/?term=8329	"H2A/c, H2AFC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023318	832	CAPZB	http://www.ncbi.nlm.nih.gov/gene/?term=832	"CAPB, CAPPB, CAPZ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023319	832	CAPZB	http://www.ncbi.nlm.nih.gov/gene/?term=832	"CAPB, CAPPB, CAPZ "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023320	832	CAPZB	http://www.ncbi.nlm.nih.gov/gene/?term=832	"CAPB, CAPPB, CAPZ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023321	8334	HIST1H2AC	http://www.ncbi.nlm.nih.gov/gene/?term=8334	"H2A/l, H2AFL, dJ221C16.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023322	8334	HIST1H2AC	http://www.ncbi.nlm.nih.gov/gene/?term=8334	"H2A/l, H2AFL, dJ221C16.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023323	83379	Klb	http://www.ncbi.nlm.nih.gov/gene/?term=83379	"AV071179, betaKlotho "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023324	8337	HIST2H2AA3	http://www.ncbi.nlm.nih.gov/gene/?term=8337	"H2A, H2A.2, H2A/O, H2A/q, H2AFO, H2a-615, HIST2H2AA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023325	83383	Tfap4	http://www.ncbi.nlm.nih.gov/gene/?term=83383	"AI642933, AP-4, D930048N17Rik, Tcfap4, bHLHc41 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023326	8338	HIST2H2AC	http://www.ncbi.nlm.nih.gov/gene/?term=8338	"H2A, H2A-GL101, H2A/q, H2AFQ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023327	833	CARS	http://www.ncbi.nlm.nih.gov/gene/?term=833	"CARS1, CYSRS, MGC:11246 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023328	833	CARS	http://www.ncbi.nlm.nih.gov/gene/?term=833	"CARS1, CYSRS, MGC:11246 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023329	8340	HIST1H2BL	http://www.ncbi.nlm.nih.gov/gene/?term=8340	"H2B/c, H2BFC, dJ97D16.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023330	8341	HIST1H2BN	http://www.ncbi.nlm.nih.gov/gene/?term=8341	"H2B/d, H2BFD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023331	83435	Plekha3	http://www.ncbi.nlm.nih.gov/gene/?term=83435	FAPP1	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023332	83439	TCF7L1	http://www.ncbi.nlm.nih.gov/gene/?term=83439	"TCF-3, TCF3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023333	83440	ADPGK	http://www.ncbi.nlm.nih.gov/gene/?term=83440	"2610017G09Rik, ADP-GK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023334	83442	SH3BGRL3	http://www.ncbi.nlm.nih.gov/gene/?term=83442	"HEL-S-297, SH3BP-1, TIP-B1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023335	83442	SH3BGRL3	http://www.ncbi.nlm.nih.gov/gene/?term=83442	"HEL-S-297, SH3BP-1, TIP-B1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023336	83442	SH3BGRL3	http://www.ncbi.nlm.nih.gov/gene/?term=83442	"HEL-S-297, SH3BP-1, TIP-B1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023337	83443	SF3B5	http://www.ncbi.nlm.nih.gov/gene/?term=83443	"SF3b10, Ysf3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023338	83443	SF3B5	http://www.ncbi.nlm.nih.gov/gene/?term=83443	"SF3b10, Ysf3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023339	83444	INO80B	http://www.ncbi.nlm.nih.gov/gene/?term=83444	"HMGA1L4, HMGIYL4, IES2, PAP-1BP, PAPA-1, PAPA1, ZNHIT4, hIes2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023340	83448	PUS7L	http://www.ncbi.nlm.nih.gov/gene/?term=83448		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023341	83450	DRC3	http://www.ncbi.nlm.nih.gov/gene/?term=83450	"CFAP134, LRRC48 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023342	83451	ABHD11	http://www.ncbi.nlm.nih.gov/gene/?term=83451	"PP1226, WBSCR21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023343	83451	ABHD11	http://www.ncbi.nlm.nih.gov/gene/?term=83451	"PP1226, WBSCR21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023344	83452	RAB33B	http://www.ncbi.nlm.nih.gov/gene/?term=83452	SMC2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023345	83452	RAB33B	http://www.ncbi.nlm.nih.gov/gene/?term=83452	SMC2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023346	8345	HIST1H2BH	http://www.ncbi.nlm.nih.gov/gene/?term=8345	"H2B/j, H2BFJ "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023347	8345	HIST1H2BH	http://www.ncbi.nlm.nih.gov/gene/?term=8345	"H2B/j, H2BFJ "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023348	83460	EMC6	http://www.ncbi.nlm.nih.gov/gene/?term=83460	TMEM93	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023349	83460	EMC6	http://www.ncbi.nlm.nih.gov/gene/?term=83460	TMEM93	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023350	83461	CDCA3	http://www.ncbi.nlm.nih.gov/gene/?term=83461	"GRCC8, TOME-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023351	83463	MXD3	http://www.ncbi.nlm.nih.gov/gene/?term=83463	"BHLHC13, MAD3, MYX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023352	83464	APH1B	http://www.ncbi.nlm.nih.gov/gene/?term=83464	"APH-1B, PRO1328, PSFL, TAAV688 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023353	83478	ARHGAP24	http://www.ncbi.nlm.nih.gov/gene/?term=83478	"FILGAP, RC-GAP72, RCGAP72, p73, p73RhoGAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023354	83479	DDX59	http://www.ncbi.nlm.nih.gov/gene/?term=83479	"OFD5, ZNHIT5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023355	8347	HIST1H2BC	http://www.ncbi.nlm.nih.gov/gene/?term=8347	"H2B.1, H2B/l, H2BFL, dJ221C16.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023356	8347	HIST1H2BC	http://www.ncbi.nlm.nih.gov/gene/?term=8347	"H2B.1, H2B/l, H2BFL, dJ221C16.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023357	83480	PUS3	http://www.ncbi.nlm.nih.gov/gene/?term=83480	"2610020J05Rik, FKSG32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023358	83486	Rbm5	http://www.ncbi.nlm.nih.gov/gene/?term=83486	D030069N10Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023359	83486	Rbm5	http://www.ncbi.nlm.nih.gov/gene/?term=83486	D030069N10Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023360	83493	Sacm1l	http://www.ncbi.nlm.nih.gov/gene/?term=83493	"SAC1, Sac1p, mKIAA0851 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023361	8349	HIST2H2BE	http://www.ncbi.nlm.nih.gov/gene/?term=8349	"GL105, H2B, H2B.1, H2BFQ, H2BGL105, H2BQ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023362	8349	HIST2H2BE	http://www.ncbi.nlm.nih.gov/gene/?term=8349	"GL105, H2B, H2B.1, H2BFQ, H2BGL105, H2BQ "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023363	83523	Impa1	http://www.ncbi.nlm.nih.gov/gene/?term=83523	Impa1-L	mRNA	Rattus norvegicus	20118926	Axon	Neuron	Fluorescence in situ hybridization	"Although MyrdEGFP-Impa1-S mRNA was visible in the cell bodies and proximal axonal segments, the signal was much lower in distal axons. These data indicate that the 120-nt element within the 3�UTR of Impa1-L transcript is sufficient to target MyrdEGFP mRNA to distal axons. "
RLID00023364	83523	Impa1	http://www.ncbi.nlm.nih.gov/gene/?term=83523	Impa1-L	mRNA	Rattus norvegicus	20118926	Cell body	Neuron	Fluorescence in situ hybridization	"Although MyrdEGFP-Impa1-S mRNA was visible in the cell bodies and proximal axonal segments, the signal was much lower in distal axons. These data indicate that the 120-nt element within the 3�UTR of Impa1-L transcript is sufficient to target MyrdEGFP mRNA to distal axons. "
RLID00023365	83532	Vdac3	http://www.ncbi.nlm.nih.gov/gene/?term=83532		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023366	83540	NUF2	http://www.ncbi.nlm.nih.gov/gene/?term=83540	"CDCA1, CT106, NUF2R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023367	83541	FAM110A	http://www.ncbi.nlm.nih.gov/gene/?term=83541	"C20orf55, F10, bA371L19.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023368	83543	AIF1L	http://www.ncbi.nlm.nih.gov/gene/?term=83543	"C9orf58, IBA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023369	83544	DNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=83544	"C14orf168, CILD16 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023370	83544	DNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=83544	"C14orf168, CILD16 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023371	835478	CUC2	http://www.ncbi.nlm.nih.gov/gene/?term=835478	"AT5G53950, ANAC098, ATCUC2, Arabidopsis NAC domain containing protein 98, CUP-SHAPED COTYLEDON 2, K19P17.12, K19P17_12 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023372	83547	RILP	http://www.ncbi.nlm.nih.gov/gene/?term=83547	PP10141	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023373	83547	RILP	http://www.ncbi.nlm.nih.gov/gene/?term=83547	PP10141	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023374	83548	COG3	http://www.ncbi.nlm.nih.gov/gene/?term=83548	SEC34	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023375	83548	COG3	http://www.ncbi.nlm.nih.gov/gene/?term=83548	SEC34	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023376	83549	UCK1	http://www.ncbi.nlm.nih.gov/gene/?term=83549	URK1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023377	83549	UCK1	http://www.ncbi.nlm.nih.gov/gene/?term=83549	URK1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023378	83555	Tex13	http://www.ncbi.nlm.nih.gov/gene/?term=83555	"4933403J23Rikb, Tex13 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023379	83555	Tex13	http://www.ncbi.nlm.nih.gov/gene/?term=83555	"4933403J23Rikb, Tex13 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023380	83564	Nlrp4c	http://www.ncbi.nlm.nih.gov/gene/?term=83564	"Nalp-alpha, Nalp4c, Rnh2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023381	8356	HIST1H3J	http://www.ncbi.nlm.nih.gov/gene/?term=8356	"H3/j, H3FJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023382	83590	TMUB1	http://www.ncbi.nlm.nih.gov/gene/?term=83590	"C7orf21, DULP, SB144 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023383	83591	THAP2	http://www.ncbi.nlm.nih.gov/gene/?term=83591		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023384	83591	THAP2	http://www.ncbi.nlm.nih.gov/gene/?term=83591		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023385	83596	BCL2L12	http://www.ncbi.nlm.nih.gov/gene/?term=83596		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023386	835	CASP2	http://www.ncbi.nlm.nih.gov/gene/?term=835	"CASP-2, ICH1, NEDD-2, NEDD2, PPP1R57 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023387	835	CASP2	http://www.ncbi.nlm.nih.gov/gene/?term=835	"CASP-2, ICH1, NEDD-2, NEDD2, PPP1R57 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023388	83603	Elovl4	http://www.ncbi.nlm.nih.gov/gene/?term=83603		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023389	83604	TMEM47	http://www.ncbi.nlm.nih.gov/gene/?term=83604	"BCMP1, TM4SF10 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023390	83605	CCM2	http://www.ncbi.nlm.nih.gov/gene/?term=83605	"C7orf22, OSM, PP10187 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023391	83606	GUCD1	http://www.ncbi.nlm.nih.gov/gene/?term=83606	"C22orf13, LLN4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023392	83606	GUCD1	http://www.ncbi.nlm.nih.gov/gene/?term=83606	"C22orf13, LLN4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023393	83606	GUCD1	http://www.ncbi.nlm.nih.gov/gene/?term=83606	"C22orf13, LLN4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023394	83607	AMMECR1L	http://www.ncbi.nlm.nih.gov/gene/?term=83607		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023395	83608	C18orf21	http://www.ncbi.nlm.nih.gov/gene/?term=83608	"HsT3108, PNAS-124, PNAS-131, XTP13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023396	83613	Nefl	http://www.ncbi.nlm.nih.gov/gene/?term=83613	"NF-L, Nfl "	mRNA	Rattus norvegicus	9322162	Cell body	Hippocampus	In situ hybridization	"The mRNAs for b-tubulin, neurofilament 68, and F1/GAP43 were restricted to the region of the cell body and very proximal dendrites in most neurons.  "
RLID00023397	83613	Nefl	http://www.ncbi.nlm.nih.gov/gene/?term=83613	"NF-L, Nfl "	mRNA	Rattus norvegicus	9322162	Dendrite	Hippocampus	In situ hybridization	"The mRNAs for b-tubulin, neurofilament 68, and F1/GAP43 were restricted to the region of the cell body and very proximal dendrites in most neurons.  "
RLID00023398	8362	HIST1H4K	http://www.ncbi.nlm.nih.gov/gene/?term=8362	"H4/d, H4F2iii, H4FD, dJ160A22.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023399	8362	HIST1H4K	http://www.ncbi.nlm.nih.gov/gene/?term=8362	"H4/d, H4F2iii, H4FD, dJ160A22.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023400	83633	Gabbr2	http://www.ncbi.nlm.nih.gov/gene/?term=83633	Gpr51	mRNA	Rattus norvegicus	12081654	Dendrite	Spinal neuron	In situ hybridization	"On spinal neurons both r1 and r2 mRNAs showed somatodendritic localization, extending out for >100 mm with punctate appearance especially in adult cells. Interestingly, a dendritic localization of the r1 and r2 mRNAs (Fig. 4C?, arrows) was observed. However, in several neuronsthe mRNAs for r1 or r2 could be found more than 100 mm away from the cell soma, indicating localization to distal dendrites (Table 1). "
RLID00023401	83636	C19orf12	http://www.ncbi.nlm.nih.gov/gene/?term=83636	"NBIA3, NBIA4, SPG43 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023402	83636	C19orf12	http://www.ncbi.nlm.nih.gov/gene/?term=83636	"NBIA3, NBIA4, SPG43 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023403	83636	C19orf12	http://www.ncbi.nlm.nih.gov/gene/?term=83636	"NBIA3, NBIA4, SPG43 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023404	83636	C19orf12	http://www.ncbi.nlm.nih.gov/gene/?term=83636	"NBIA3, NBIA4, SPG43 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023405	83637	ZMIZ2	http://www.ncbi.nlm.nih.gov/gene/?term=83637	"NET27, TRAFIP20, ZIMP7, hZIMP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023406	83638	C11orf68	http://www.ncbi.nlm.nih.gov/gene/?term=83638	"BLES03, P5326 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023407	83638	C11orf68	http://www.ncbi.nlm.nih.gov/gene/?term=83638	"BLES03, P5326 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023408	8363	HIST1H4J	http://www.ncbi.nlm.nih.gov/gene/?term=8363	"H4/e, H4F2iv, H4FE, dJ160A22.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023409	8363	HIST1H4J	http://www.ncbi.nlm.nih.gov/gene/?term=8363	"H4/e, H4F2iv, H4FE, dJ160A22.2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023410	8363	HIST1H4J	http://www.ncbi.nlm.nih.gov/gene/?term=8363	"H4/e, H4F2iv, H4FE, dJ160A22.2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023411	83640	FAM103A1	http://www.ncbi.nlm.nih.gov/gene/?term=83640	"C15orf18, HsT19360, RAM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023412	83640	FAM103A1	http://www.ncbi.nlm.nih.gov/gene/?term=83640	"C15orf18, HsT19360, RAM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023413	8364	HIST1H4C	http://www.ncbi.nlm.nih.gov/gene/?term=8364	"H4/g, H4FG, dJ221C16.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023414	8364	HIST1H4C	http://www.ncbi.nlm.nih.gov/gene/?term=8364	"H4/g, H4FG, dJ221C16.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023415	8364	HIST1H4C	http://www.ncbi.nlm.nih.gov/gene/?term=8364	"H4/g, H4FG, dJ221C16.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023416	8364	HIST1H4C	http://www.ncbi.nlm.nih.gov/gene/?term=8364	"H4/g, H4FG, dJ221C16.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023417	83658	DYNLRB1	http://www.ncbi.nlm.nih.gov/gene/?term=83658	"BITH, BLP, DNCL2A, DNLC2A, ROBLD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023418	8365	HIST1H4H	http://www.ncbi.nlm.nih.gov/gene/?term=8365	"H4/h, H4FH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023419	83660	TLN2	http://www.ncbi.nlm.nih.gov/gene/?term=83660	ILWEQ	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023420	83660	TLN2	http://www.ncbi.nlm.nih.gov/gene/?term=83660	ILWEQ	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023421	83661	MS4A8	http://www.ncbi.nlm.nih.gov/gene/?term=83661	"4SPAN4, CD20L5, MS4A4, MS4A8B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023422	83666	PARP9	http://www.ncbi.nlm.nih.gov/gene/?term=83666	"ARTD9, BAL, BAL1, MGC:7868 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023423	83667	SESN2	http://www.ncbi.nlm.nih.gov/gene/?term=83667	"HI95, SES2, SEST2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023424	83667	SESN2	http://www.ncbi.nlm.nih.gov/gene/?term=83667	"HI95, SES2, SEST2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023425	8366	HIST1H4B	http://www.ncbi.nlm.nih.gov/gene/?term=8366	"H4/I, H4FI "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023426	8366	HIST1H4B	http://www.ncbi.nlm.nih.gov/gene/?term=8366	"H4/I, H4FI "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023427	83673	Snhg1	http://www.ncbi.nlm.nih.gov/gene/?term=83673		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023428	83675	Bicc1	http://www.ncbi.nlm.nih.gov/gene/?term=83675	"Bic-C, bpk, jcpk "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023429	8367	HIST1H4E	http://www.ncbi.nlm.nih.gov/gene/?term=8367	"H4/j, H4FJ "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023430	836810	AT5G66770	http://www.ncbi.nlm.nih.gov/gene/?term=836810	"AT5G66770, MUD21.1, MUD21_1 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023431	83690	CRISPLD1	http://www.ncbi.nlm.nih.gov/gene/?term=83690	"CRISP-10, CRISP10, LCRISP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023432	83690	CRISPLD1	http://www.ncbi.nlm.nih.gov/gene/?term=83690	"CRISP-10, CRISP10, LCRISP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023433	83690	CRISPLD1	http://www.ncbi.nlm.nih.gov/gene/?term=83690	"CRISP-10, CRISP10, LCRISP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023434	83692	CD99L2	http://www.ncbi.nlm.nih.gov/gene/?term=83692	"CD99B, MIC2L1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023435	83693	HSDL1	http://www.ncbi.nlm.nih.gov/gene/?term=83693	SDR12C3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023436	83693	HSDL1	http://www.ncbi.nlm.nih.gov/gene/?term=83693	SDR12C3	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023437	83693	HSDL1	http://www.ncbi.nlm.nih.gov/gene/?term=83693	SDR12C3	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023438	83694	RPS6KL1	http://www.ncbi.nlm.nih.gov/gene/?term=83694	RSKL2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023439	83695	RHNO1	http://www.ncbi.nlm.nih.gov/gene/?term=83695	"C12orf32, HKMT1188, RHINO "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023440	83695	RHNO1	http://www.ncbi.nlm.nih.gov/gene/?term=83695	"C12orf32, HKMT1188, RHINO "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023441	83695	RHNO1	http://www.ncbi.nlm.nih.gov/gene/?term=83695	"C12orf32, HKMT1188, RHINO "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023442	83695	RHNO1	http://www.ncbi.nlm.nih.gov/gene/?term=83695	"C12orf32, HKMT1188, RHINO "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023443	83699	SH3BGRL2	http://www.ncbi.nlm.nih.gov/gene/?term=83699		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023444	836	CASP3	http://www.ncbi.nlm.nih.gov/gene/?term=836	"CPP32, CPP32B, SCA-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023445	836	CASP3	http://www.ncbi.nlm.nih.gov/gene/?term=836	"CPP32, CPP32B, SCA-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023446	83701	Srrt	http://www.ncbi.nlm.nih.gov/gene/?term=83701	"2810019G02Rik, ASR2A, ASR2B, ASR2C, ASR2D, Ars2, Asr2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023447	83706	FERMT3	http://www.ncbi.nlm.nih.gov/gene/?term=83706	"KIND3, MIG-2, MIG2B, UNC112C, URP2, URP2SF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023448	83707	TRPT1	http://www.ncbi.nlm.nih.gov/gene/?term=83707		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023449	83715	ESPN	http://www.ncbi.nlm.nih.gov/gene/?term=83715	"DFNB36, LP2654 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023450	83719	YPEL3	http://www.ncbi.nlm.nih.gov/gene/?term=83719		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023451	8372	HYAL3	http://www.ncbi.nlm.nih.gov/gene/?term=8372	"HYAL-3, LUCA-3, LUCA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023452	8372	HYAL3	http://www.ncbi.nlm.nih.gov/gene/?term=8372	"HYAL-3, LUCA-3, LUCA3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023453	83732	RIOK1	http://www.ncbi.nlm.nih.gov/gene/?term=83732	"AD034, RRP10, bA288G3.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023454	83734	ATG10	http://www.ncbi.nlm.nih.gov/gene/?term=83734	"APG10, APG10L, pp12616 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023455	83734	ATG10	http://www.ncbi.nlm.nih.gov/gene/?term=83734	"APG10, APG10L, pp12616 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023456	83737	ITCH	http://www.ncbi.nlm.nih.gov/gene/?term=83737	"ADMFD, AIF4, AIP4, NAPP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023457	83742	MARVELD1	http://www.ncbi.nlm.nih.gov/gene/?term=83742	"GB14, MARVD1, MRVLDC1, bA548K23.8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023458	83743	GRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=83743	"CDW4, GRWD, RRB1, WDR28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023459	83743	GRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=83743	"CDW4, GRWD, RRB1, WDR28 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023460	83743	GRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=83743	"CDW4, GRWD, RRB1, WDR28 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023461	83743	GRWD1	http://www.ncbi.nlm.nih.gov/gene/?term=83743	"CDW4, GRWD, RRB1, WDR28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023462	83746	L3MBTL2	http://www.ncbi.nlm.nih.gov/gene/?term=83746	"H-l(3)mbt-l, L3MBT "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023463	83752	LONP2	http://www.ncbi.nlm.nih.gov/gene/?term=83752	"LONP, LONPL "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023464	83752	LONP2	http://www.ncbi.nlm.nih.gov/gene/?term=83752	"LONP, LONPL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023465	83752	LONP2	http://www.ncbi.nlm.nih.gov/gene/?term=83752	"LONP, LONPL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023466	83786	FRMD8	http://www.ncbi.nlm.nih.gov/gene/?term=83786	FKSG44	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023467	83786	FRMD8	http://www.ncbi.nlm.nih.gov/gene/?term=83786	FKSG44	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023468	83786	FRMD8	http://www.ncbi.nlm.nih.gov/gene/?term=83786	FKSG44	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023469	83786	FRMD8	http://www.ncbi.nlm.nih.gov/gene/?term=83786	FKSG44	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023470	83787	ARMC10	http://www.ncbi.nlm.nih.gov/gene/?term=83787	"PNAS-112, PNAS112, PSEC0198, SVH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023471	83787	ARMC10	http://www.ncbi.nlm.nih.gov/gene/?term=83787	"PNAS-112, PNAS112, PSEC0198, SVH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023472	83796	Smarcd2	http://www.ncbi.nlm.nih.gov/gene/?term=83796	"AW322457, Baf60b "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023473	83797	Smarcd1	http://www.ncbi.nlm.nih.gov/gene/?term=83797	"AA407987, Baf60a, D15Kz1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023474	8379	MAD1L1	http://www.ncbi.nlm.nih.gov/gene/?term=8379	"MAD1, PIG9, TP53I9, TXBP181 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023475	837	CASP4	http://www.ncbi.nlm.nih.gov/gene/?term=837	"ICE(rel)II, ICEREL-II, ICH-2, Mih1/TX, TX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023476	83813	Tnk1	http://www.ncbi.nlm.nih.gov/gene/?term=83813	"Kos1a, Tnk1b, Tnk1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023477	83815	Cenpq	http://www.ncbi.nlm.nih.gov/gene/?term=83815	2610528M18Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023478	8382	NME5	http://www.ncbi.nlm.nih.gov/gene/?term=8382	"NM23-H5, NM23H5, RSPH23 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023479	83834	Nrn1	http://www.ncbi.nlm.nih.gov/gene/?term=83834	Nrn	mRNA	Rattus norvegicus	23966695	Axon	Sensory neuron	RT-PCR	"Neuritin mRNA shifts from cell body to axon predominantly after nerve crush injury, suggesting that it encodes a growth-associated protein. Consistent with this, overexpression of neuritin increases axon growth but only when its mRNA localizes into the axons. "
RLID00023480	83834	Nrn1	http://www.ncbi.nlm.nih.gov/gene/?term=83834	Nrn	mRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"By quantitative fluorescent in situ hybridization combined with immunofluorescence to unambiguously distinguish intra-axonal mRNAs, we show that regenerating spinal cord axons contain β-actin, GAP-43, Neuritin, Reg3a, Hamp, and Importin β1 mRNAs.  "
RLID00023481	83834	Nrn1	http://www.ncbi.nlm.nih.gov/gene/?term=83834	Nrn	mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00023482	83849	SYT15	http://www.ncbi.nlm.nih.gov/gene/?term=83849	"CHR10SYT, sytXV "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023483	83849	SYT15	http://www.ncbi.nlm.nih.gov/gene/?term=83849	"CHR10SYT, sytXV "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023484	83852	SETDB2	http://www.ncbi.nlm.nih.gov/gene/?term=83852	"C13orf4, CLLD8, CLLL8, KMT1F "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023485	83855	KLF16	http://www.ncbi.nlm.nih.gov/gene/?term=83855	"BTEB4, DRRF, NSLP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023486	83857	TMTC1	http://www.ncbi.nlm.nih.gov/gene/?term=83857	"ARG99, OLF, TMTC1A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023487	83858	ATAD3B	http://www.ncbi.nlm.nih.gov/gene/?term=83858	"AAA-TOB3, TOB3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023488	83860	TAF3	http://www.ncbi.nlm.nih.gov/gene/?term=83860	"TAF140, TAFII-140, TAFII140 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023489	83862	TMEM120A	http://www.ncbi.nlm.nih.gov/gene/?term=83862	"NET29, TMPIT "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023490	83874	TBC1D10A	http://www.ncbi.nlm.nih.gov/gene/?term=83874	"EPI64, TBC1D10, dJ130H16.1, dJ130H16.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023491	83876	MRO	http://www.ncbi.nlm.nih.gov/gene/?term=83876	"B29, C18orf3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023492	83876	MRO	http://www.ncbi.nlm.nih.gov/gene/?term=83876	"B29, C18orf3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023493	83877	TM2D2	http://www.ncbi.nlm.nih.gov/gene/?term=83877	BLP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023494	83878	USHBP1	http://www.ncbi.nlm.nih.gov/gene/?term=83878	"AIEBP, MCC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023495	83879	CDCA7	http://www.ncbi.nlm.nih.gov/gene/?term=83879	JPO1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023496	83879	CDCA7	http://www.ncbi.nlm.nih.gov/gene/?term=83879	JPO1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023497	83887	TTLL2	http://www.ncbi.nlm.nih.gov/gene/?term=83887	"C6orf104, NYD-TSPG, dJ366N23.3 "	mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00023498	83890	SPATA9	http://www.ncbi.nlm.nih.gov/gene/?term=83890	NYD-SP16	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023499	83891	SNX25	http://www.ncbi.nlm.nih.gov/gene/?term=83891	"MSTP043, SBBI31 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023500	83892	KCTD10	http://www.ncbi.nlm.nih.gov/gene/?term=83892	"BTBD28, MSTP028, ULRO61, hBACURD3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023501	83892	KCTD10	http://www.ncbi.nlm.nih.gov/gene/?term=83892	"BTBD28, MSTP028, ULRO61, hBACURD3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023502	83892	KCTD10	http://www.ncbi.nlm.nih.gov/gene/?term=83892	"BTBD28, MSTP028, ULRO61, hBACURD3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023503	83892	KCTD10	http://www.ncbi.nlm.nih.gov/gene/?term=83892	"BTBD28, MSTP028, ULRO61, hBACURD3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023504	83903	GSG2	http://www.ncbi.nlm.nih.gov/gene/?term=83903	HASPIN	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023505	83921	Tmem2	http://www.ncbi.nlm.nih.gov/gene/?term=83921		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023506	83925	Trps1	http://www.ncbi.nlm.nih.gov/gene/?term=83925	"AI115454, AI447310, D15Ertd586e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023507	83925	Trps1	http://www.ncbi.nlm.nih.gov/gene/?term=83925	"AI115454, AI447310, D15Ertd586e "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023508	83931	STK40	http://www.ncbi.nlm.nih.gov/gene/?term=83931	"SHIK, SgK495 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023509	83931	STK40	http://www.ncbi.nlm.nih.gov/gene/?term=83931	"SHIK, SgK495 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023510	83933	HDAC10	http://www.ncbi.nlm.nih.gov/gene/?term=83933	HD10	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023511	83937	RASSF4	http://www.ncbi.nlm.nih.gov/gene/?term=83937	AD037	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023512	83939	EIF2A	http://www.ncbi.nlm.nih.gov/gene/?term=83939	"CDA02, EIF-2A, MST089, MSTP004, MSTP089 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023513	83939	EIF2A	http://www.ncbi.nlm.nih.gov/gene/?term=83939	"CDA02, EIF-2A, MST089, MSTP004, MSTP089 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023514	83939	EIF2A	http://www.ncbi.nlm.nih.gov/gene/?term=83939	"CDA02, EIF-2A, MST089, MSTP004, MSTP089 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023515	83941	TM2D1	http://www.ncbi.nlm.nih.gov/gene/?term=83941	BBP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023516	83941	TM2D1	http://www.ncbi.nlm.nih.gov/gene/?term=83941	BBP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023517	83943	IMMP2L	http://www.ncbi.nlm.nih.gov/gene/?term=83943	"IMMP2L-IT1, IMP2, IMP2-LIKE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023518	83946	Phip	http://www.ncbi.nlm.nih.gov/gene/?term=83946	"2810004D21Rik, 4632404O06Rik, Ndrp, Wdr11 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023519	8394	PIP5K1A	http://www.ncbi.nlm.nih.gov/gene/?term=8394		mRNA	Homo sapiens	23452202	Ribosome	Lung fibroblast	qRT-PCR	"Cell spreading is also associated with an increase in the association of PIP5K1a mRNA with ribosomes (Table 1), suggesting that localized protein synthesis could modulate PtdIns(3,4,5)P3 levels, facilitating mTOR activation and WAVE complex clustering. "
RLID00023520	8394	PIP5K1A	http://www.ncbi.nlm.nih.gov/gene/?term=8394		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023521	8395	PIP5K1B	http://www.ncbi.nlm.nih.gov/gene/?term=8395	"MSS4, STM7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023522	83962	Btbd1	http://www.ncbi.nlm.nih.gov/gene/?term=83962	1190005H08Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023523	83964	Jam3	http://www.ncbi.nlm.nih.gov/gene/?term=83964	"1110002N23Rik, JAM-3, JAM-C, Jcam3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023524	83982	IFI27L2	http://www.ncbi.nlm.nih.gov/gene/?term=83982	"FAM14A, ISG12B, TLH29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023525	83983	TSSK6	http://www.ncbi.nlm.nih.gov/gene/?term=83983	"CT72, FKSG82, SSTK, TSSK4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023526	83986	FAM234A	http://www.ncbi.nlm.nih.gov/gene/?term=83986	"C16orf9, ITFG3, gs19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023527	83987	CCDC8	http://www.ncbi.nlm.nih.gov/gene/?term=83987	"3M3, PPP1R20, p90 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023528	83987	CCDC8	http://www.ncbi.nlm.nih.gov/gene/?term=83987	"3M3, PPP1R20, p90 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023529	83987	CCDC8	http://www.ncbi.nlm.nih.gov/gene/?term=83987	"3M3, PPP1R20, p90 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023530	83988	NCALD	http://www.ncbi.nlm.nih.gov/gene/?term=83988		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023531	83989	FAM172A	http://www.ncbi.nlm.nih.gov/gene/?term=83989	C5orf21	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023532	83989	FAM172A	http://www.ncbi.nlm.nih.gov/gene/?term=83989	C5orf21	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023533	83990	BRIP1	http://www.ncbi.nlm.nih.gov/gene/?term=83990	"BACH1, FANCJ, OF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023534	83998	REG4	http://www.ncbi.nlm.nih.gov/gene/?term=83998	"GISP, REG-IV, RELP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023535	83998	REG4	http://www.ncbi.nlm.nih.gov/gene/?term=83998	"GISP, REG-IV, RELP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023536	83999	KREMEN1	http://www.ncbi.nlm.nih.gov/gene/?term=83999	"KREMEN, KRM1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023537	8399	PLA2G10	http://www.ncbi.nlm.nih.gov/gene/?term=8399	"GXPLA2, GXSPLA2, SPLA2, sPLA2-X "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023538	8399	PLA2G10	http://www.ncbi.nlm.nih.gov/gene/?term=8399	"GXPLA2, GXSPLA2, SPLA2, sPLA2-X "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023539	839	CASP6	http://www.ncbi.nlm.nih.gov/gene/?term=839	MCH2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023540	839	CASP6	http://www.ncbi.nlm.nih.gov/gene/?term=839	MCH2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023541	839	CASP6	http://www.ncbi.nlm.nih.gov/gene/?term=839	MCH2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023542	84000	TMPRSS13	http://www.ncbi.nlm.nih.gov/gene/?term=84000	"MSP, MSPL, MSPS, TMPRSS11 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023543	84002	B3GNT5	http://www.ncbi.nlm.nih.gov/gene/?term=84002	"B3GN-T5, beta3Gn-T5 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023544	84002	B3GNT5	http://www.ncbi.nlm.nih.gov/gene/?term=84002	"B3GN-T5, beta3Gn-T5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023545	84027	Gsk3b	http://www.ncbi.nlm.nih.gov/gene/?term=84027		mRNA	Rattus norvegicus	24898526	Axon	Spinal motoneuron 	In situ hybridization|qRT-PCR	"In cultured cortical neurons which do not store glycogen but nevertheless express glycogen synthase, the GS mRNA is also subject to axonal and dendritic localization. In spinal motoneurons and trigeminal neurons in situ, however, the mRNAs could only be demonstrated in the neuronal somata but not in the nerves. "
RLID00023546	84027	Gsk3b	http://www.ncbi.nlm.nih.gov/gene/?term=84027		mRNA	Rattus norvegicus	24898526	Dendrite	Spinal motoneuron 	In situ hybridization|qRT-PCR	"In cultured cortical neurons which do not store glycogen but nevertheless express glycogen synthase, the GS mRNA is also subject to axonal and dendritic localization. In spinal motoneurons and trigeminal neurons in situ, however, the mRNAs could only be demonstrated in the neuronal somata but not in the nerves. "
RLID00023547	8402	SLC25A11	http://www.ncbi.nlm.nih.gov/gene/?term=8402	"OGC, SLC20A4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023548	8402	SLC25A11	http://www.ncbi.nlm.nih.gov/gene/?term=8402	"OGC, SLC20A4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023549	84033	OBSCN	http://www.ncbi.nlm.nih.gov/gene/?term=84033	"ARHGEF30, UNC89 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023550	84034	EMILIN2	http://www.ncbi.nlm.nih.gov/gene/?term=84034	"EMILIN-2, FOAP-10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023551	8404	SPARCL1	http://www.ncbi.nlm.nih.gov/gene/?term=8404	"MAST 9, MAST9, PIG33, SC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023552	84056	KATNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=84056		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023553	84056	KATNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=84056		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023554	84056	KATNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=84056		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023555	84059	ADGRV1	http://www.ncbi.nlm.nih.gov/gene/?term=84059	"FEB4, GPR98, MASS1, USH2B, USH2C, VLGR1, VLGR1b "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023556	8405	SPOP	http://www.ncbi.nlm.nih.gov/gene/?term=8405	"BTBD32, TEF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023557	8405	SPOP	http://www.ncbi.nlm.nih.gov/gene/?term=8405	"BTBD32, TEF2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023558	8405	SPOP	http://www.ncbi.nlm.nih.gov/gene/?term=8405	"BTBD32, TEF2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023559	8405	SPOP	http://www.ncbi.nlm.nih.gov/gene/?term=8405	"BTBD32, TEF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023560	84060	RBM48	http://www.ncbi.nlm.nih.gov/gene/?term=84060	"C7orf64, HSPC304, MGC16142 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023561	84060	RBM48	http://www.ncbi.nlm.nih.gov/gene/?term=84060	"C7orf64, HSPC304, MGC16142 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023562	84061	MAGT1	http://www.ncbi.nlm.nih.gov/gene/?term=84061	"IAP, MRX95, OST3B, PRO0756, XMEN, bA217H1.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023563	84061	MAGT1	http://www.ncbi.nlm.nih.gov/gene/?term=84061	"IAP, MRX95, OST3B, PRO0756, XMEN, bA217H1.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023564	84061	MAGT1	http://www.ncbi.nlm.nih.gov/gene/?term=84061	"IAP, MRX95, OST3B, PRO0756, XMEN, bA217H1.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023565	84061	MAGT1	http://www.ncbi.nlm.nih.gov/gene/?term=84061	"IAP, MRX95, OST3B, PRO0756, XMEN, bA217H1.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023566	84064	HDHD2	http://www.ncbi.nlm.nih.gov/gene/?term=84064	"3110052N05Rik, HEL-S-301 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023567	84065	TMEM222	http://www.ncbi.nlm.nih.gov/gene/?term=84065	C1orf160	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023568	84067	FAM160A2	http://www.ncbi.nlm.nih.gov/gene/?term=84067	C11orf56	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023569	84068	SLC10A7	http://www.ncbi.nlm.nih.gov/gene/?term=84068	"C4orf13, P7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023570	84078	KBTBD7	http://www.ncbi.nlm.nih.gov/gene/?term=84078		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023571	84079	ANKRD27	http://www.ncbi.nlm.nih.gov/gene/?term=84079	"PP12899, VARP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023572	84079	ANKRD27	http://www.ncbi.nlm.nih.gov/gene/?term=84079	"PP12899, VARP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023573	84079	ANKRD27	http://www.ncbi.nlm.nih.gov/gene/?term=84079	"PP12899, VARP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023574	8407	TAGLN2	http://www.ncbi.nlm.nih.gov/gene/?term=8407	HA1756	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023575	8407	TAGLN2	http://www.ncbi.nlm.nih.gov/gene/?term=8407	HA1756	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023576	84080	ENKD1	http://www.ncbi.nlm.nih.gov/gene/?term=84080	"C16orf48, DAKV6410 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023577	84081	NSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=84081	"CCDC55, HSPC095, NSrp70 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023578	8408	ULK1	http://www.ncbi.nlm.nih.gov/gene/?term=8408	"ATG1, ATG1A, UNC51, Unc51.1, hATG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023579	84092	Usp8	http://www.ncbi.nlm.nih.gov/gene/?term=84092	"AI574262, AW557536, Ubpy, mKIAA0055 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023580	8409	UXT	http://www.ncbi.nlm.nih.gov/gene/?term=8409	"ART-27, STAP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023581	8409	UXT	http://www.ncbi.nlm.nih.gov/gene/?term=8409	"ART-27, STAP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023582	8409	UXT	http://www.ncbi.nlm.nih.gov/gene/?term=8409	"ART-27, STAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023583	840	CASP7	http://www.ncbi.nlm.nih.gov/gene/?term=840	"CASP-7, CMH-1, ICE-LAP3, LICE2, MCH3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023584	840	CASP7	http://www.ncbi.nlm.nih.gov/gene/?term=840	"CASP-7, CMH-1, ICE-LAP3, LICE2, MCH3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023585	840	CASP7	http://www.ncbi.nlm.nih.gov/gene/?term=840	"CASP-7, CMH-1, ICE-LAP3, LICE2, MCH3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023586	84101	USP44	http://www.ncbi.nlm.nih.gov/gene/?term=84101		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023587	84105	PCBD2	http://www.ncbi.nlm.nih.gov/gene/?term=84105	"DCOH2, DCOHM, PHS2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023588	84105	PCBD2	http://www.ncbi.nlm.nih.gov/gene/?term=84105	"DCOH2, DCOHM, PHS2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023589	84109	QRFPR	http://www.ncbi.nlm.nih.gov/gene/?term=84109	"AQ27, GPR103, SP9155 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00023590	8411	EEA1	http://www.ncbi.nlm.nih.gov/gene/?term=8411	"MST105, MSTP105, ZFYVE2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023591	841262	AGO1	http://www.ncbi.nlm.nih.gov/gene/?term=841262	"AT1G48410, ARGONAUTE 1, T1N15.2, T1N15_2 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023592	84128	WDR75	http://www.ncbi.nlm.nih.gov/gene/?term=84128	"NET16, UTP17 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023593	84131	CEP78	http://www.ncbi.nlm.nih.gov/gene/?term=84131	"C9orf81, IP63 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023594	84132	USP42	http://www.ncbi.nlm.nih.gov/gene/?term=84132		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023595	84132	USP42	http://www.ncbi.nlm.nih.gov/gene/?term=84132		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023596	84133	ZNRF3	http://www.ncbi.nlm.nih.gov/gene/?term=84133	"BK747E2.3, RNF203 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023597	84133	ZNRF3	http://www.ncbi.nlm.nih.gov/gene/?term=84133	"BK747E2.3, RNF203 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023598	84133	ZNRF3	http://www.ncbi.nlm.nih.gov/gene/?term=84133	"BK747E2.3, RNF203 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023599	84133	ZNRF3	http://www.ncbi.nlm.nih.gov/gene/?term=84133	"BK747E2.3, RNF203 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023600	841347	ACT8	http://www.ncbi.nlm.nih.gov/gene/?term=841347	"AT1G49240, F27J15.1, F27J15_1, actin 8 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023601	84134	TOMM40L	http://www.ncbi.nlm.nih.gov/gene/?term=84134	TOMM40B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023602	84134	TOMM40L	http://www.ncbi.nlm.nih.gov/gene/?term=84134	TOMM40B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023603	84135	UTP15	http://www.ncbi.nlm.nih.gov/gene/?term=84135	NET21	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023604	84135	UTP15	http://www.ncbi.nlm.nih.gov/gene/?term=84135	NET21	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023605	84138	SLC7A6OS	http://www.ncbi.nlm.nih.gov/gene/?term=84138		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023606	84138	SLC7A6OS	http://www.ncbi.nlm.nih.gov/gene/?term=84138		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023607	84140	FAM161A	http://www.ncbi.nlm.nih.gov/gene/?term=84140	RP28	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023608	84140	FAM161A	http://www.ncbi.nlm.nih.gov/gene/?term=84140	RP28	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023609	84144	SYDE2	http://www.ncbi.nlm.nih.gov/gene/?term=84144		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023610	84144	SYDE2	http://www.ncbi.nlm.nih.gov/gene/?term=84144		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023611	84146	ZNF644	http://www.ncbi.nlm.nih.gov/gene/?term=84146	"BM-005, MYP21, NatF, ZEP-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023612	84148	KAT8	http://www.ncbi.nlm.nih.gov/gene/?term=84148	"MOF, MYST1, ZC2HC8, hMOF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023613	84148	KAT8	http://www.ncbi.nlm.nih.gov/gene/?term=84148	"MOF, MYST1, ZC2HC8, hMOF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023614	84152	PPP1R1B	http://www.ncbi.nlm.nih.gov/gene/?term=84152	"DARPP-32, DARPP32 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023615	84153	RNASEH2C	http://www.ncbi.nlm.nih.gov/gene/?term=84153	"AGS3, AYP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023616	84154	RPF2	http://www.ncbi.nlm.nih.gov/gene/?term=84154	"BXDC1, bA397G5.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023617	84159	ARID5B	http://www.ncbi.nlm.nih.gov/gene/?term=84159	"DESRT, MRF-2, MRF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023618	84162	KIAA1109	http://www.ncbi.nlm.nih.gov/gene/?term=84162	"FSA, Tweek "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023619	84162	KIAA1109	http://www.ncbi.nlm.nih.gov/gene/?term=84162	"FSA, Tweek "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023620	84163	GTF2IRD2	http://www.ncbi.nlm.nih.gov/gene/?term=84163	"FP630 alpha, GTF2IRD2A, GTF2IRD2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023621	84163	GTF2IRD2	http://www.ncbi.nlm.nih.gov/gene/?term=84163	"FP630 alpha, GTF2IRD2A, GTF2IRD2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023622	84164	ASCC2	http://www.ncbi.nlm.nih.gov/gene/?term=84164	"ASC1p100, p100 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023623	84164	ASCC2	http://www.ncbi.nlm.nih.gov/gene/?term=84164	"ASC1p100, p100 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023624	84166	NLRC5	http://www.ncbi.nlm.nih.gov/gene/?term=84166	"CLR16.1, NOD27, NOD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023625	84167	C19orf44	http://www.ncbi.nlm.nih.gov/gene/?term=84167		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023626	84168	ANTXR1	http://www.ncbi.nlm.nih.gov/gene/?term=84168	"ATR, GAPO, TEM8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023627	84172	POLR1B	http://www.ncbi.nlm.nih.gov/gene/?term=84172	"RPA135, RPA2, Rpo1-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023628	84173	ELMOD3	http://www.ncbi.nlm.nih.gov/gene/?term=84173	"DFNB88, LST3, RBED1, RBM29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023629	84174	SLA2	http://www.ncbi.nlm.nih.gov/gene/?term=84174	"C20orf156, MARS, SLAP-2, SLAP2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023630	84174	SLA2	http://www.ncbi.nlm.nih.gov/gene/?term=84174	"C20orf156, MARS, SLAP-2, SLAP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023631	84179	MFSD7	http://www.ncbi.nlm.nih.gov/gene/?term=84179	LP2561	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023632	8417	STX7	http://www.ncbi.nlm.nih.gov/gene/?term=8417		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023633	84181	CHD6	http://www.ncbi.nlm.nih.gov/gene/?term=84181	"CHD-6, CHD5, RIGB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023634	84181	CHD6	http://www.ncbi.nlm.nih.gov/gene/?term=84181	"CHD-6, CHD5, RIGB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023635	84181	CHD6	http://www.ncbi.nlm.nih.gov/gene/?term=84181	"CHD-6, CHD5, RIGB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023636	841868	EIF4A-2	http://www.ncbi.nlm.nih.gov/gene/?term=841868	"AT1G54270, F20D21.9, F20D21_9, eif4a-2 "	mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00023637	84186	ZCCHC7	http://www.ncbi.nlm.nih.gov/gene/?term=84186	"AIR1, HSPC086 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023638	84187	TMEM164	http://www.ncbi.nlm.nih.gov/gene/?term=84187	bB360B22.3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023639	84188	FAR1	http://www.ncbi.nlm.nih.gov/gene/?term=84188	"MLSTD2, PFCRD, SDR10E1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023640	84189	SLITRK6	http://www.ncbi.nlm.nih.gov/gene/?term=84189	DFNMYP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023641	84191	FAM96A	http://www.ncbi.nlm.nih.gov/gene/?term=84191		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023642	84191	FAM96A	http://www.ncbi.nlm.nih.gov/gene/?term=84191		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023643	84193	SETD3	http://www.ncbi.nlm.nih.gov/gene/?term=84193	C14orf154	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023644	84193	SETD3	http://www.ncbi.nlm.nih.gov/gene/?term=84193	C14orf154	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023645	84196	USP48	http://www.ncbi.nlm.nih.gov/gene/?term=84196	"RAP1GA1, USP31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023646	84196	USP48	http://www.ncbi.nlm.nih.gov/gene/?term=84196	"RAP1GA1, USP31 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023647	84197	POMK	http://www.ncbi.nlm.nih.gov/gene/?term=84197	"MDDGA12, MDDGC12, SGK196 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023648	841	CASP8	http://www.ncbi.nlm.nih.gov/gene/?term=841	"ALPS2B, CAP4, Casp-8, FLICE, MACH, MCH5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023649	841	CASP8	http://www.ncbi.nlm.nih.gov/gene/?term=841	"ALPS2B, CAP4, Casp-8, FLICE, MACH, MCH5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023650	841	CASP8	http://www.ncbi.nlm.nih.gov/gene/?term=841	"ALPS2B, CAP4, Casp-8, FLICE, MACH, MCH5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023651	8420	SNHG3	http://www.ncbi.nlm.nih.gov/gene/?term=8420	"NCRNA00014, RNU17C, RNU17D, U17HG, U17HG-A, U17HG-AB "	lncRNA	Homo sapiens	9671460	Cytoplasm	HeLa cell	Northern blot	"We investigated the cellular localization of the U17HG RNA. Cell fractionation experiments indicated that U17HG RNA is enriched in the cytoplasm (Fig.5A), similar to UHG RNA, another noncoding snoRNA host having no protein-coding potential (Fig.5B). As expected, U17 snoRNA, used as a control, was found mainly in the nuclear fraction (Fig.5C). "
RLID00023652	84219	WDR24	http://www.ncbi.nlm.nih.gov/gene/?term=84219	"C16orf21, JFP7 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00023653	84219	WDR24	http://www.ncbi.nlm.nih.gov/gene/?term=84219	"C16orf21, JFP7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023654	84219	WDR24	http://www.ncbi.nlm.nih.gov/gene/?term=84219	"C16orf21, JFP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023655	84220	RGPD5	http://www.ncbi.nlm.nih.gov/gene/?term=84220	"BS-63, BS63, HEL161, RGP5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023656	84220	RGPD5	http://www.ncbi.nlm.nih.gov/gene/?term=84220	"BS-63, BS63, HEL161, RGP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023657	84221	SPATC1L	http://www.ncbi.nlm.nih.gov/gene/?term=84221	C21orf56	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023658	84222	TMEM191A	http://www.ncbi.nlm.nih.gov/gene/?term=84222	TMEM191AP	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023659	84225	ZMYND15	http://www.ncbi.nlm.nih.gov/gene/?term=84225	SPGF14	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023660	84230	LRRC8C	http://www.ncbi.nlm.nih.gov/gene/?term=84230	"AD158, FAD158 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023661	84231	TRAF7	http://www.ncbi.nlm.nih.gov/gene/?term=84231	"RFWD1, RNF119 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023662	84232	MAF1	http://www.ncbi.nlm.nih.gov/gene/?term=84232		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023663	84232	MAF1	http://www.ncbi.nlm.nih.gov/gene/?term=84232		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023664	84233	TMEM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84233	OPA7	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023665	84233	TMEM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84233	OPA7	mRNA	Homo sapiens	23500070	Mitochondrion	SH-SY5Y cell	Fluorescence in situ hybridization	"TMEM126A mRNAs are strongly enriched in the vicinity of mitochondria and encode an inner mitochondrial membrane associated cristae protein. TMEM126A is a mitochondrial located mRNA (MLR) that may be translated in the mitochondrial surface and the protein is subsequently imported to the inner membrane. These results demonstrate that TMEM126A mRNA is an MLR, with asymmetric localization to the mitochondrial surface similar to UQCRC1 mRNA, which is known to encode a mitochondrial protein of the IM.  "
RLID00023666	84233	TMEM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84233	OPA7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023667	84236	RHBDD1	http://www.ncbi.nlm.nih.gov/gene/?term=84236	RRP4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023668	84240	ZCCHC9	http://www.ncbi.nlm.nih.gov/gene/?term=84240	PPP1R41	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023669	84243	ZDHHC18	http://www.ncbi.nlm.nih.gov/gene/?term=84243	"DHHC-18, DHHC18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023670	84243	ZDHHC18	http://www.ncbi.nlm.nih.gov/gene/?term=84243	"DHHC-18, DHHC18 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023671	84245	MRI1	http://www.ncbi.nlm.nih.gov/gene/?term=84245	"MRDI, MTNA, Ypr118w "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023672	84245	MRI1	http://www.ncbi.nlm.nih.gov/gene/?term=84245	"MRDI, MTNA, Ypr118w "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023673	84245	MRI1	http://www.ncbi.nlm.nih.gov/gene/?term=84245	"MRDI, MTNA, Ypr118w "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023674	84246	MED10	http://www.ncbi.nlm.nih.gov/gene/?term=84246	"L6, NUT2, TRG20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023675	84246	MED10	http://www.ncbi.nlm.nih.gov/gene/?term=84246	"L6, NUT2, TRG20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023676	84247	LDOC1L	http://www.ncbi.nlm.nih.gov/gene/?term=84247	"Mar6, Mart6, dJ1033E15.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023677	84247	LDOC1L	http://www.ncbi.nlm.nih.gov/gene/?term=84247	"Mar6, Mart6, dJ1033E15.2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023678	84247	LDOC1L	http://www.ncbi.nlm.nih.gov/gene/?term=84247	"Mar6, Mart6, dJ1033E15.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023679	84248	FYTTD1	http://www.ncbi.nlm.nih.gov/gene/?term=84248	UIF	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023680	84250	SLF1	http://www.ncbi.nlm.nih.gov/gene/?term=84250	"ANKRD32, BRCTD1, BRCTx "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023681	84251	SGIP1	http://www.ncbi.nlm.nih.gov/gene/?term=84251		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023682	84254	CAMKK1	http://www.ncbi.nlm.nih.gov/gene/?term=84254	CAMKKA	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023683	84255	SLC37A3	http://www.ncbi.nlm.nih.gov/gene/?term=84255		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023684	84255	SLC37A3	http://www.ncbi.nlm.nih.gov/gene/?term=84255		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023685	84259	DCUN1D5	http://www.ncbi.nlm.nih.gov/gene/?term=84259	SCCRO5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023686	84259	DCUN1D5	http://www.ncbi.nlm.nih.gov/gene/?term=84259	SCCRO5	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023687	8425	LTBP4	http://www.ncbi.nlm.nih.gov/gene/?term=8425	"ARCL1C, LTBP-4, LTBP4L, LTBP4S "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023688	84260	TCHP	http://www.ncbi.nlm.nih.gov/gene/?term=84260	TpMs	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023689	84261	FBXW9	http://www.ncbi.nlm.nih.gov/gene/?term=84261	Fbw9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023690	84262	PSMG3	http://www.ncbi.nlm.nih.gov/gene/?term=84262	"C7orf48, PAC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023691	84262	PSMG3	http://www.ncbi.nlm.nih.gov/gene/?term=84262	"C7orf48, PAC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023692	84263	HSDL2	http://www.ncbi.nlm.nih.gov/gene/?term=84263	"C9orf99, SDR13C1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023693	84263	HSDL2	http://www.ncbi.nlm.nih.gov/gene/?term=84263	"C9orf99, SDR13C1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023694	84264	HAGHL	http://www.ncbi.nlm.nih.gov/gene/?term=84264		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023695	84265	POLR3GL	http://www.ncbi.nlm.nih.gov/gene/?term=84265	"RPC32HOM, flj32422 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023696	84266	ALKBH7	http://www.ncbi.nlm.nih.gov/gene/?term=84266	"ABH7, SPATA11, UNQ6002 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023697	84266	ALKBH7	http://www.ncbi.nlm.nih.gov/gene/?term=84266	"ABH7, SPATA11, UNQ6002 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023698	84268	RPAIN	http://www.ncbi.nlm.nih.gov/gene/?term=84268	"HRIP, RIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023699	84268	RPAIN	http://www.ncbi.nlm.nih.gov/gene/?term=84268	"HRIP, RIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023700	84269	CHCHD5	http://www.ncbi.nlm.nih.gov/gene/?term=84269	"C2orf9, MIC14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023701	84270	CARD19	http://www.ncbi.nlm.nih.gov/gene/?term=84270	"BinCARD, C9orf89 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023702	84271	POLDIP3	http://www.ncbi.nlm.nih.gov/gene/?term=84271	"PDIP46, SKAR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023703	84271	POLDIP3	http://www.ncbi.nlm.nih.gov/gene/?term=84271	"PDIP46, SKAR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023704	84272	YIPF4	http://www.ncbi.nlm.nih.gov/gene/?term=84272	"FinGER4, Nbla11189 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023705	84272	YIPF4	http://www.ncbi.nlm.nih.gov/gene/?term=84272	"FinGER4, Nbla11189 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023706	84274	COQ5	http://www.ncbi.nlm.nih.gov/gene/?term=84274		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023707	84275	SLC25A33	http://www.ncbi.nlm.nih.gov/gene/?term=84275	"BMSC-MCP, PNC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023708	84275	SLC25A33	http://www.ncbi.nlm.nih.gov/gene/?term=84275	"BMSC-MCP, PNC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023709	84277	DNAJC30	http://www.ncbi.nlm.nih.gov/gene/?term=84277	WBSCR18	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023710	84277	DNAJC30	http://www.ncbi.nlm.nih.gov/gene/?term=84277	WBSCR18	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023711	84279	PRADC1	http://www.ncbi.nlm.nih.gov/gene/?term=84279	"C2orf7, PAP21 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023712	8427	ZNF282	http://www.ncbi.nlm.nih.gov/gene/?term=8427	HUB1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023713	84280	BTBD10	http://www.ncbi.nlm.nih.gov/gene/?term=84280	"GMRP-1, GMRP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023714	84280	BTBD10	http://www.ncbi.nlm.nih.gov/gene/?term=84280	"GMRP-1, GMRP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023715	84282	RNF135	http://www.ncbi.nlm.nih.gov/gene/?term=84282	"L13, MMFD, REUL, Riplet "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023716	84284	NTPCR	http://www.ncbi.nlm.nih.gov/gene/?term=84284	"C1orf57, HCR-NTPase "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023717	84285	EIF1AD	http://www.ncbi.nlm.nih.gov/gene/?term=84285	haponin	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023718	84285	EIF1AD	http://www.ncbi.nlm.nih.gov/gene/?term=84285	haponin	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023719	84285	EIF1AD	http://www.ncbi.nlm.nih.gov/gene/?term=84285	haponin	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023720	84287	ZDHHC16	http://www.ncbi.nlm.nih.gov/gene/?term=84287	"APH2, DHHC-16 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023721	84288	EFCAB2	http://www.ncbi.nlm.nih.gov/gene/?term=84288	"CFAP200, DRC8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023722	84289	ING5	http://www.ncbi.nlm.nih.gov/gene/?term=84289	p28ING5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023723	84289	ING5	http://www.ncbi.nlm.nih.gov/gene/?term=84289	p28ING5	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023724	84289	ING5	http://www.ncbi.nlm.nih.gov/gene/?term=84289	p28ING5	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023725	8428	STK24	http://www.ncbi.nlm.nih.gov/gene/?term=8428	"HEL-S-95, MST3, MST3B, STE20, STK3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023726	8428	STK24	http://www.ncbi.nlm.nih.gov/gene/?term=8428	"HEL-S-95, MST3, MST3B, STE20, STK3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023727	8428	STK24	http://www.ncbi.nlm.nih.gov/gene/?term=8428	"HEL-S-95, MST3, MST3B, STE20, STK3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023728	84293	FAM213A	http://www.ncbi.nlm.nih.gov/gene/?term=84293	"C10orf58, PAMM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023729	84295	PHF6	http://www.ncbi.nlm.nih.gov/gene/?term=84295	"BFLS, BORJ, CENP-31 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023730	84298	LLPH	http://www.ncbi.nlm.nih.gov/gene/?term=84298	"C12orf31, hLLP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023731	84299	MIEN1	http://www.ncbi.nlm.nih.gov/gene/?term=84299	"C17orf37, C35, ORB3, RDX12, XTP4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023732	842	CASP9	http://www.ncbi.nlm.nih.gov/gene/?term=842	"APAF-3, APAF3, ICE-LAP6, MCH6, PPP1R56 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023733	842	CASP9	http://www.ncbi.nlm.nih.gov/gene/?term=842	"APAF-3, APAF3, ICE-LAP6, MCH6, PPP1R56 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023734	84300	UQCC2	http://www.ncbi.nlm.nih.gov/gene/?term=84300	"C6orf125, Cbp6, M19, MNF1, bA6B20.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023735	84301	DDI2	http://www.ncbi.nlm.nih.gov/gene/?term=84301		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023736	84302	TMEM246	http://www.ncbi.nlm.nih.gov/gene/?term=84302	C9orf125	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023737	84302	TMEM246	http://www.ncbi.nlm.nih.gov/gene/?term=84302	C9orf125	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023738	84303	CHCHD6	http://www.ncbi.nlm.nih.gov/gene/?term=84303	"CHCM1, Mic25, PPP1R23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023739	84304	NUDT22	http://www.ncbi.nlm.nih.gov/gene/?term=84304		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023740	84305	PYM1	http://www.ncbi.nlm.nih.gov/gene/?term=84305	"PYM, WIBG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023741	84305	PYM1	http://www.ncbi.nlm.nih.gov/gene/?term=84305	"PYM, WIBG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023742	84306	PDCD2L	http://www.ncbi.nlm.nih.gov/gene/?term=84306		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023743	84307	ZNF397	http://www.ncbi.nlm.nih.gov/gene/?term=84307	"ZNF47, ZSCAN15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023744	84307	ZNF397	http://www.ncbi.nlm.nih.gov/gene/?term=84307	"ZNF47, ZSCAN15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023745	84309	NUDT16L1	http://www.ncbi.nlm.nih.gov/gene/?term=84309	SDOS	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023746	84310	C7orf50	http://www.ncbi.nlm.nih.gov/gene/?term=84310	YCR016W	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023747	84310	C7orf50	http://www.ncbi.nlm.nih.gov/gene/?term=84310	YCR016W	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023748	84311	MRPL45	http://www.ncbi.nlm.nih.gov/gene/?term=84311	"L45mt, MRP-L45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023749	84313	VPS25	http://www.ncbi.nlm.nih.gov/gene/?term=84313	"DERP9, EAP20, FAP20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023750	84313	VPS25	http://www.ncbi.nlm.nih.gov/gene/?term=84313	"DERP9, EAP20, FAP20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023751	84313	VPS25	http://www.ncbi.nlm.nih.gov/gene/?term=84313	"DERP9, EAP20, FAP20 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023752	84314	TMEM107	http://www.ncbi.nlm.nih.gov/gene/?term=84314	"GRVS638, PRO1268 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023753	84314	TMEM107	http://www.ncbi.nlm.nih.gov/gene/?term=84314	"GRVS638, PRO1268 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023754	84314	TMEM107	http://www.ncbi.nlm.nih.gov/gene/?term=84314	"GRVS638, PRO1268 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023755	84314	TMEM107	http://www.ncbi.nlm.nih.gov/gene/?term=84314	"GRVS638, PRO1268 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023756	84315	MON1A	http://www.ncbi.nlm.nih.gov/gene/?term=84315	SAND1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023757	84315	MON1A	http://www.ncbi.nlm.nih.gov/gene/?term=84315	SAND1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023758	84316	NAA38	http://www.ncbi.nlm.nih.gov/gene/?term=84316	"LSMD1, PFAAP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023759	84317	CCDC115	http://www.ncbi.nlm.nih.gov/gene/?term=84317	"CDG2O, ccp1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023760	84317	CCDC115	http://www.ncbi.nlm.nih.gov/gene/?term=84317	ccp1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023761	84319	CMSS1	http://www.ncbi.nlm.nih.gov/gene/?term=84319	C3orf26	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023762	84319	CMSS1	http://www.ncbi.nlm.nih.gov/gene/?term=84319	C3orf26	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023763	84321	THOC3	http://www.ncbi.nlm.nih.gov/gene/?term=84321	"THO3, hTREX45 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023764	84324	SARNP	http://www.ncbi.nlm.nih.gov/gene/?term=84324	"CIP29, HCC1, HSPC316, THO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023765	84326	C16orf13	http://www.ncbi.nlm.nih.gov/gene/?term=84326	JFP2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023766	84326	C16orf13	http://www.ncbi.nlm.nih.gov/gene/?term=84326	JFP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023767	84331	FAM195A	http://www.ncbi.nlm.nih.gov/gene/?term=84331	"C16orf14, c349E10.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023768	84331	MCRIP2	http://www.ncbi.nlm.nih.gov/gene/?term=84331	"C16orf14, c349E10.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023769	84333	PCGF5	http://www.ncbi.nlm.nih.gov/gene/?term=84333	RNF159	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023770	84334	APOPT1	http://www.ncbi.nlm.nih.gov/gene/?term=84334	"APOP, APOP1, C14orf153 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023771	84335	AKT1S1	http://www.ncbi.nlm.nih.gov/gene/?term=84335	"Lobe, PRAS40 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023772	84335	AKT1S1	http://www.ncbi.nlm.nih.gov/gene/?term=84335	"Lobe, PRAS40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023773	84336	TMEM101	http://www.ncbi.nlm.nih.gov/gene/?term=84336		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023774	84336	TMEM101	http://www.ncbi.nlm.nih.gov/gene/?term=84336		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023775	84337	ELOF1	http://www.ncbi.nlm.nih.gov/gene/?term=84337	ELF1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023776	84337	ELOF1	http://www.ncbi.nlm.nih.gov/gene/?term=84337	ELF1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023777	84340	GFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84340	"EF-G2mt, EFG2, MRRF2, MST027, MSTP027, RRF2, RRF2mt, hEFG2, mEF-G 2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023778	84340	GFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84340	"EF-G2mt, EFG2, MRRF2, MST027, MSTP027, RRF2, RRF2mt, hEFG2, mEF-G 2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023779	84343	HPS3	http://www.ncbi.nlm.nih.gov/gene/?term=84343	"BLOC2S1, SUTAL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023780	84364	ARFGAP2	http://www.ncbi.nlm.nih.gov/gene/?term=84364	"IRZ, NBLA10535, ZFP289, ZNF289 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023781	84365	NIFK	http://www.ncbi.nlm.nih.gov/gene/?term=84365	"MKI67IP, Nopp34 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023782	84365	NIFK	http://www.ncbi.nlm.nih.gov/gene/?term=84365	"MKI67IP, Nopp34 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023783	84365	NIFK	http://www.ncbi.nlm.nih.gov/gene/?term=84365	"MKI67IP, Nopp34 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023784	8436	SDPR	http://www.ncbi.nlm.nih.gov/gene/?term=8436	"CAVIN2, PS-p68, SDR, cavin-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023785	84376	HOOK3	http://www.ncbi.nlm.nih.gov/gene/?term=84376	HK3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023786	84376	HOOK3	http://www.ncbi.nlm.nih.gov/gene/?term=84376	HK3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023787	8438	RAD54L	http://www.ncbi.nlm.nih.gov/gene/?term=8438	"HR54, RAD54A, hHR54, hRAD54 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023788	8439	NSMAF	http://www.ncbi.nlm.nih.gov/gene/?term=8439	"FAN, GRAMD5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023789	8439	NSMAF	http://www.ncbi.nlm.nih.gov/gene/?term=8439	"FAN, GRAMD5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023790	843	CASP10	http://www.ncbi.nlm.nih.gov/gene/?term=843	"ALPS2, FLICE2, MCH4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023791	843	CASP10	http://www.ncbi.nlm.nih.gov/gene/?term=843	"ALPS2, FLICE2, MCH4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023792	843	CASP10	http://www.ncbi.nlm.nih.gov/gene/?term=843	"ALPS2, FLICE2, MCH4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023793	8440	NCK2	http://www.ncbi.nlm.nih.gov/gene/?term=8440	"GRB4, NCKbeta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023794	84418	CYSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=84418	"C5orf32, ORF1-FL49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023795	84418	CYSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=84418	"C5orf32, ORF1-FL49 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023796	84436	ZNF528	http://www.ncbi.nlm.nih.gov/gene/?term=84436		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023797	84436	ZNF528	http://www.ncbi.nlm.nih.gov/gene/?term=84436		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023798	84436	ZNF528	http://www.ncbi.nlm.nih.gov/gene/?term=84436		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023799	84437	MSANTD4	http://www.ncbi.nlm.nih.gov/gene/?term=84437	KIAA1826	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023800	8443	GNPAT	http://www.ncbi.nlm.nih.gov/gene/?term=8443	"DAP-AT, DAPAT, DHAPAT, RCDP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023801	84440	RAB11FIP4	http://www.ncbi.nlm.nih.gov/gene/?term=84440	RAB11-FIP4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023802	84440	RAB11FIP4	http://www.ncbi.nlm.nih.gov/gene/?term=84440	RAB11-FIP4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023803	84440	RAB11FIP4	http://www.ncbi.nlm.nih.gov/gene/?term=84440	RAB11-FIP4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023804	84444	DOT1L	http://www.ncbi.nlm.nih.gov/gene/?term=84444	"DOT1, KMT4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023805	84445	LZTS2	http://www.ncbi.nlm.nih.gov/gene/?term=84445	LAPSER1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023806	84445	LZTS2	http://www.ncbi.nlm.nih.gov/gene/?term=84445	LAPSER1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023807	84447	SYVN1	http://www.ncbi.nlm.nih.gov/gene/?term=84447	"DER3, HRD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023808	8444	DYRK3	http://www.ncbi.nlm.nih.gov/gene/?term=8444	"DYRK5, RED, REDK, hYAK3-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023809	84450	ZNF512	http://www.ncbi.nlm.nih.gov/gene/?term=84450		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023810	84455	EFCAB7	http://www.ncbi.nlm.nih.gov/gene/?term=84455		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023811	84458	LCOR	http://www.ncbi.nlm.nih.gov/gene/?term=84458	MLR2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023812	8445	DYRK2	http://www.ncbi.nlm.nih.gov/gene/?term=8445		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023813	8445	DYRK2	http://www.ncbi.nlm.nih.gov/gene/?term=8445		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023814	84460	ZMAT1	http://www.ncbi.nlm.nih.gov/gene/?term=84460		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023815	84460	ZMAT1	http://www.ncbi.nlm.nih.gov/gene/?term=84460		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023816	84461	NEURL4	http://www.ncbi.nlm.nih.gov/gene/?term=84461		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023817	84464	SLX4	http://www.ncbi.nlm.nih.gov/gene/?term=84464	"BTBD12, FANCP, MUS312 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023818	84464	SLX4	http://www.ncbi.nlm.nih.gov/gene/?term=84464	"BTBD12, FANCP, MUS312 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023819	8446	DUSP11	http://www.ncbi.nlm.nih.gov/gene/?term=8446	PIR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023820	8446	DUSP11	http://www.ncbi.nlm.nih.gov/gene/?term=8446	PIR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023821	84498	FAM120B	http://www.ncbi.nlm.nih.gov/gene/?term=84498	"CCPG, KIAA1838, PGCC1, dJ894D12.1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023822	8449	DHX16	http://www.ncbi.nlm.nih.gov/gene/?term=8449	"DBP2, DDX16, PRO2014, PRP8, PRPF2, Prp2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023823	84501	SPIRE2	http://www.ncbi.nlm.nih.gov/gene/?term=84501	Spir-2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023824	84502	JPH4	http://www.ncbi.nlm.nih.gov/gene/?term=84502	"JP4, JPHL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023825	84503	ZNF527	http://www.ncbi.nlm.nih.gov/gene/?term=84503		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023826	84503	ZNF527	http://www.ncbi.nlm.nih.gov/gene/?term=84503		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023827	84505	Setdb1	http://www.ncbi.nlm.nih.gov/gene/?term=84505	"AU022152, ESET, KMT1E, mKIAA0067 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00023828	84506	Hamp	http://www.ncbi.nlm.nih.gov/gene/?term=84506	"Hamp1, Hepc, Hepc1 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00023829	84513	PLPP5	http://www.ncbi.nlm.nih.gov/gene/?term=84513	"DPPL1, HTPAP, PPAPDC1B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023830	84514	GHDC	http://www.ncbi.nlm.nih.gov/gene/?term=84514	"D11LGP1, LGP1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023831	84514	GHDC	http://www.ncbi.nlm.nih.gov/gene/?term=84514	"D11LGP1, LGP1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023832	84515	MCM8	http://www.ncbi.nlm.nih.gov/gene/?term=84515	"C20orf154, POF10, dJ967N21.5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023833	84515	MCM8	http://www.ncbi.nlm.nih.gov/gene/?term=84515	"C20orf154, POF10, dJ967N21.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023834	84516	DCTN5	http://www.ncbi.nlm.nih.gov/gene/?term=84516		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023835	84516	DCTN5	http://www.ncbi.nlm.nih.gov/gene/?term=84516		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023836	84516	DCTN5	http://www.ncbi.nlm.nih.gov/gene/?term=84516		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023837	8451	CUL4A	http://www.ncbi.nlm.nih.gov/gene/?term=8451		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023838	84520	C14orf142	http://www.ncbi.nlm.nih.gov/gene/?term=84520	PNAS-127	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023839	84527	ZNF559	http://www.ncbi.nlm.nih.gov/gene/?term=84527	NBLA00121	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023840	84529	C15orf41	http://www.ncbi.nlm.nih.gov/gene/?term=84529	HH114	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023841	8452	CUL3	http://www.ncbi.nlm.nih.gov/gene/?term=8452	"CUL-3, PHA2E "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023842	8452	CUL3	http://www.ncbi.nlm.nih.gov/gene/?term=8452	"CUL-3, PHA2E "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023843	8452	CUL3	http://www.ncbi.nlm.nih.gov/gene/?term=8452	"CUL-3, PHA2E "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023844	8452	CUL3	http://www.ncbi.nlm.nih.gov/gene/?term=8452	"CUL-3, PHA2E "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023845	84530	SRRM4	http://www.ncbi.nlm.nih.gov/gene/?term=84530	"KIAA1853, MU-MB-2.76, nSR100 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023846	8453	CUL2	http://www.ncbi.nlm.nih.gov/gene/?term=8453		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023847	84545	MRPL43	http://www.ncbi.nlm.nih.gov/gene/?term=84545	"L43mt, MRP-L43, bMRP36a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023848	84545	MRPL43	http://www.ncbi.nlm.nih.gov/gene/?term=84545	"L43mt, MRP-L43, bMRP36a "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023849	84548	TMEM185A	http://www.ncbi.nlm.nih.gov/gene/?term=84548	"CXorf13, FAM11A, FRAXF, ee3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023850	84549	MAK16	http://www.ncbi.nlm.nih.gov/gene/?term=84549	"MAK16L, RBM13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023851	8454	CUL1	http://www.ncbi.nlm.nih.gov/gene/?term=8454		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023852	8454	CUL1	http://www.ncbi.nlm.nih.gov/gene/?term=8454		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023853	84552	PARD6G	http://www.ncbi.nlm.nih.gov/gene/?term=84552	"PAR-6G, PAR6gamma "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023854	84552	PARD6G	http://www.ncbi.nlm.nih.gov/gene/?term=84552	"PAR-6G, PAR6gamma "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023855	84557	MAP1LC3A	http://www.ncbi.nlm.nih.gov/gene/?term=84557	"ATG8E, LC3, LC3A, MAP1ALC3, MAP1BLC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023856	84557	MAP1LC3A	http://www.ncbi.nlm.nih.gov/gene/?term=84557	"ATG8E, LC3, LC3A, MAP1ALC3, MAP1BLC3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023857	8455	ATRN	http://www.ncbi.nlm.nih.gov/gene/?term=8455	"DPPT-L, MGCA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023858	8455	ATRN	http://www.ncbi.nlm.nih.gov/gene/?term=8455	"DPPT-L, MGCA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023859	84561	SLC12A8	http://www.ncbi.nlm.nih.gov/gene/?term=84561	CCC9	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023860	84572	GNPTG	http://www.ncbi.nlm.nih.gov/gene/?term=84572	"C16orf27, GNPTAG, LP2537, RJD9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023861	84572	GNPTG	http://www.ncbi.nlm.nih.gov/gene/?term=84572	"C16orf27, GNPTAG, LP2537, RJD9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023862	8458	TTF2	http://www.ncbi.nlm.nih.gov/gene/?term=8458	"HuF2, ZGRF6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023863	8459	TPST2	http://www.ncbi.nlm.nih.gov/gene/?term=8459	TANGO13B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023864	8459	TPST2	http://www.ncbi.nlm.nih.gov/gene/?term=8459	TANGO13B	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023865	84604	Hamp	http://www.ncbi.nlm.nih.gov/gene/?term=84604	Hepc	mRNA	Rattus norvegicus	26180210	Axon	Spinal cord	In situ hybridization	"By quantitative fluorescent in situ hybridization combined with immunofluorescence to unambiguously distinguish intra-axonal mRNAs, we show that regenerating spinal cord axons contain β-actin, GAP-43, Neuritin, Reg3a, Hamp, and Importin β1 mRNAs.  "
RLID00023866	84612	PARD6B	http://www.ncbi.nlm.nih.gov/gene/?term=84612	PAR6B	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023867	84612	PARD6B	http://www.ncbi.nlm.nih.gov/gene/?term=84612	PAR6B	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023868	84617	TUBB6	http://www.ncbi.nlm.nih.gov/gene/?term=84617	"HsT1601, TUBB-5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023869	84624	FNDC1	http://www.ncbi.nlm.nih.gov/gene/?term=84624	"AGS8, FNDC2, MEL4B3, bA243O10.1, dJ322A24.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023870	84626	KRBA1	http://www.ncbi.nlm.nih.gov/gene/?term=84626		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023871	84629	TNRC18	http://www.ncbi.nlm.nih.gov/gene/?term=84629	"CAGL79, TNRC18A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023872	84631	SLITRK2	http://www.ncbi.nlm.nih.gov/gene/?term=84631	"CXorf2, SLITL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023873	84632	AFAP1L2	http://www.ncbi.nlm.nih.gov/gene/?term=84632	"CTB-1144G6.4, KIAA1914, XB130 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023874	8463	TEAD2	http://www.ncbi.nlm.nih.gov/gene/?term=8463	"ETF, TEAD-2, TEF-4, TEF4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023875	84640	USP38	http://www.ncbi.nlm.nih.gov/gene/?term=84640	HP43.8KD	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023876	84640	USP38	http://www.ncbi.nlm.nih.gov/gene/?term=84640	HP43.8KD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023877	84641	MFSD14B	http://www.ncbi.nlm.nih.gov/gene/?term=84641	HIATL1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023878	84641	MFSD14B	http://www.ncbi.nlm.nih.gov/gene/?term=84641	HIATL1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023879	84649	DGAT2	http://www.ncbi.nlm.nih.gov/gene/?term=84649	"ARAT, GS1999FULL, HMFN1045 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023880	84649	DGAT2	http://www.ncbi.nlm.nih.gov/gene/?term=84649	"ARAT, GS1999FULL, HMFN1045 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023881	84650	EBPL	http://www.ncbi.nlm.nih.gov/gene/?term=84650	EBRP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023882	84650	EBPL	http://www.ncbi.nlm.nih.gov/gene/?term=84650	EBRP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023883	84661	DPY30	http://www.ncbi.nlm.nih.gov/gene/?term=84661	"Cps25, HDPY-30, Saf19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023884	84661	DPY30	http://www.ncbi.nlm.nih.gov/gene/?term=84661	"Cps25, HDPY-30, Saf19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023885	84662	GLIS2	http://www.ncbi.nlm.nih.gov/gene/?term=84662	"NKL, NPHP7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023886	84665	MYPN	http://www.ncbi.nlm.nih.gov/gene/?term=84665	"CMD1DD, CMH22, MYOP, RCM4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023887	84666	RETNLB	http://www.ncbi.nlm.nih.gov/gene/?term=84666	"FIZZ1, FIZZ2, HXCP2, RELM-beta, RELMb, RELMbeta, XCP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023888	84668	FAM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84668	"DRCTNNB1A, HCC, HLD5, HYCC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023889	84668	FAM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84668	"DRCTNNB1A, HCC, HLD5, HYCC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023890	84668	FAM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84668	"DRCTNNB1A, HCC, HLD5, HYCC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023891	84669	USP32	http://www.ncbi.nlm.nih.gov/gene/?term=84669	"NY-REN-60, USP10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023892	84678	KDM2B	http://www.ncbi.nlm.nih.gov/gene/?term=84678	"CXXC2, FBXL10, Fbl10, JHDM1B, PCCX2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023893	8467	SMARCA5	http://www.ncbi.nlm.nih.gov/gene/?term=8467	"ISWI, SNF2H, WCRF135, hISWI, hSNF2H "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023894	8467	SMARCA5	http://www.ncbi.nlm.nih.gov/gene/?term=8467	"ISWI, SNF2H, WCRF135, hISWI, hSNF2H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023895	84681	HINT2	http://www.ncbi.nlm.nih.gov/gene/?term=84681	HIT-17	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023896	84681	HINT2	http://www.ncbi.nlm.nih.gov/gene/?term=84681	HIT-17	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023897	84682	Cox4i2	http://www.ncbi.nlm.nih.gov/gene/?term=84682	"Cox4b, CoxIV-2 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	RT-PCR	Two mRNAs (Anxa2 and Cox4i2) colocalize with the SMN protein in axons from differentiated NSC-34 cells and that their axonal localization is dramatically reduced in SMN-deficient cells
RLID00023898	84695	LOXL3	http://www.ncbi.nlm.nih.gov/gene/?term=84695	LOXL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023899	84705	GTPBP3	http://www.ncbi.nlm.nih.gov/gene/?term=84705	"COXPD23, GTPBG3, MSS1, MTGP1, THDF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023900	84705	GTPBP3	http://www.ncbi.nlm.nih.gov/gene/?term=84705	"COXPD23, GTPBG3, MSS1, MTGP1, THDF1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023901	84705	GTPBP3	http://www.ncbi.nlm.nih.gov/gene/?term=84705	"COXPD23, GTPBG3, MSS1, MTGP1, THDF1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023902	84706	GPT2	http://www.ncbi.nlm.nih.gov/gene/?term=84706	"ALT2, GPT 2, MRT49 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023903	84720	PIGO	http://www.ncbi.nlm.nih.gov/gene/?term=84720	HPMRS2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023904	84720	PIGO	http://www.ncbi.nlm.nih.gov/gene/?term=84720	HPMRS2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023905	84722	PSRC1	http://www.ncbi.nlm.nih.gov/gene/?term=84722	"DDA3, FP3214 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023906	84725	PLEKHA8	http://www.ncbi.nlm.nih.gov/gene/?term=84725	FAPP2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023907	84725	PLEKHA8	http://www.ncbi.nlm.nih.gov/gene/?term=84725	FAPP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023908	84726	PRRC2B	http://www.ncbi.nlm.nih.gov/gene/?term=84726	"BAT2L, BAT2L1, KIAA0515, LQFBS-1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023909	8473	OGT	http://www.ncbi.nlm.nih.gov/gene/?term=8473	"HINCUT-1, HRNT1, O-GLCNAC "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023910	8473	OGT	http://www.ncbi.nlm.nih.gov/gene/?term=8473	"HINCUT-1, HRNT1, O-GLCNAC "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023911	8473	OGT	http://www.ncbi.nlm.nih.gov/gene/?term=8473	"HINCUT-1, HRNT1, O-GLCNAC "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023912	84740	AFAP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=84740	"AFAP1-AS, AFAP1AS "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023913	84747	UNC119B	http://www.ncbi.nlm.nih.gov/gene/?term=84747	POC7B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023914	84749	USP30	http://www.ncbi.nlm.nih.gov/gene/?term=84749		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023915	84752	B3GNT9	http://www.ncbi.nlm.nih.gov/gene/?term=84752		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023916	84769	MPV17L2	http://www.ncbi.nlm.nih.gov/gene/?term=84769	FKSG24	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023917	8476	CDC42BPA	http://www.ncbi.nlm.nih.gov/gene/?term=8476	"MRCK, MRCKA, PK428 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023918	8476	CDC42BPA	http://www.ncbi.nlm.nih.gov/gene/?term=8476	"MRCK, MRCKA, PK428 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023919	8476	CDC42BPA	http://www.ncbi.nlm.nih.gov/gene/?term=8476	"MRCK, MRCKA, PK428 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023920	84790	TUBA1C	http://www.ncbi.nlm.nih.gov/gene/?term=84790	"TUBA6, bcm948 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023921	84790	TUBA1C	http://www.ncbi.nlm.nih.gov/gene/?term=84790	"TUBA6, bcm948 "	mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00023922	84791	LINC00467	http://www.ncbi.nlm.nih.gov/gene/?term=84791	C1orf97	lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023923	84792	FAM220A	http://www.ncbi.nlm.nih.gov/gene/?term=84792	"ACPIN1, C7orf70, SIPAR "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023924	84798	C19orf48	http://www.ncbi.nlm.nih.gov/gene/?term=84798		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023925	8479	HIRIP3	http://www.ncbi.nlm.nih.gov/gene/?term=8479		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023926	847	CAT	http://www.ncbi.nlm.nih.gov/gene/?term=847		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023927	847	CAT	http://www.ncbi.nlm.nih.gov/gene/?term=847		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023928	84804	MFSD9	http://www.ncbi.nlm.nih.gov/gene/?term=84804		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023929	84809	CROCCP2	http://www.ncbi.nlm.nih.gov/gene/?term=84809	CROCCL1	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023930	8480	RAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8480	"MIG14, MRNP41, Mnrp41, dJ481F12.3, dJ800J21.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023931	8480	RAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8480	"MIG14, MRNP41, Mnrp41, dJ481F12.3, dJ800J21.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023932	8480	RAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8480	"MIG14, MRNP41, Mnrp41, dJ481F12.3, dJ800J21.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023933	84811	BUD13	http://www.ncbi.nlm.nih.gov/gene/?term=84811	"Cwc26, fSAP71 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023934	84811	BUD13	http://www.ncbi.nlm.nih.gov/gene/?term=84811	"Cwc26, fSAP71 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023935	84816	RTN4IP1	http://www.ncbi.nlm.nih.gov/gene/?term=84816	"NIMP, OPA10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023936	84816	RTN4IP1	http://www.ncbi.nlm.nih.gov/gene/?term=84816	"NIMP, OPA10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023937	84817	TXNDC17	http://www.ncbi.nlm.nih.gov/gene/?term=84817	"TRP14, TXNL5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023938	84817	TXNDC17	http://www.ncbi.nlm.nih.gov/gene/?term=84817	"TRP14, TXNL5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023939	84818	IL17RC	http://www.ncbi.nlm.nih.gov/gene/?term=84818	"CANDF9, IL17-RL, IL17RL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023940	8481	OFD1	http://www.ncbi.nlm.nih.gov/gene/?term=8481	"71-7A, CXorf5, JBTS10, RP23, SGBS2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023941	8481	OFD1	http://www.ncbi.nlm.nih.gov/gene/?term=8481	"71-7A, CXorf5, JBTS10, RP23, SGBS2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023942	84823	LMNB2	http://www.ncbi.nlm.nih.gov/gene/?term=84823	"EPM9, LAMB2, LMN2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023943	84823	LMNB2	http://www.ncbi.nlm.nih.gov/gene/?term=84823	"EPM9, LAMB2, LMN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023944	84824	FCRLA	http://www.ncbi.nlm.nih.gov/gene/?term=84824	"FCRL, FCRL1, FCRLM1, FCRLX, FCRLb, FCRLc1, FCRLc2, FCRLd, FCRLe, FCRX, FREB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023945	84826	SFT2D3	http://www.ncbi.nlm.nih.gov/gene/?term=84826		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023946	84826	SFT2D3	http://www.ncbi.nlm.nih.gov/gene/?term=84826		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023947	8482	SEMA7A	http://www.ncbi.nlm.nih.gov/gene/?term=8482	"CD108, CDw108, H-SEMA-K1, H-Sema-L, JMH, SEMAK1, SEMAL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023948	84830	ADTRP	http://www.ncbi.nlm.nih.gov/gene/?term=84830	"AIG1L, C6orf105, dJ413H6.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023949	84833	USMG5	http://www.ncbi.nlm.nih.gov/gene/?term=84833	"DAPIT, HCVFTP2, bA792D24.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023950	84838	ZNF496	http://www.ncbi.nlm.nih.gov/gene/?term=84838	"NIZP1, ZFP496, ZKSCAN17, ZSCAN49 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023951	84844	PHF5A	http://www.ncbi.nlm.nih.gov/gene/?term=84844	"INI, Rds3, SAP14b, SF3B7, SF3b14b, bK223H9.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023952	84844	PHF5A	http://www.ncbi.nlm.nih.gov/gene/?term=84844	"INI, Rds3, SAP14b, SF3B7, SF3b14b, bK223H9.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023953	84859	LRCH3	http://www.ncbi.nlm.nih.gov/gene/?term=84859		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023954	84864	MINA	http://www.ncbi.nlm.nih.gov/gene/?term=84864	"MDIG53, NO52, ROX, MINA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023955	84864	MINA	http://www.ncbi.nlm.nih.gov/gene/?term=84864	"MDIG53, NO52, ROX, MINA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023956	84864	MINA	http://www.ncbi.nlm.nih.gov/gene/?term=84864	"MDIG, MINA53, NO52, ROX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023957	84866	TMEM25	http://www.ncbi.nlm.nih.gov/gene/?term=84866		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023958	84868	HAVCR2	http://www.ncbi.nlm.nih.gov/gene/?term=84868	"CD366, HAVcr-2, KIM-3, TIM3, TIMD-3, TIMD3, Tim-3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023959	84868	HAVCR2	http://www.ncbi.nlm.nih.gov/gene/?term=84868	"CD366, HAVcr-2, KIM-3, TIM3, TIMD-3, TIMD3, Tim-3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023960	84869	CBR4	http://www.ncbi.nlm.nih.gov/gene/?term=84869	SDR45C1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023961	84869	CBR4	http://www.ncbi.nlm.nih.gov/gene/?term=84869	SDR45C1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023962	84869	CBR4	http://www.ncbi.nlm.nih.gov/gene/?term=84869	SDR45C1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023963	84872	ZC3H10	http://www.ncbi.nlm.nih.gov/gene/?term=84872	ZC3HDC10	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023964	84876	ORAI1	http://www.ncbi.nlm.nih.gov/gene/?term=84876	"CRACM1, IMD9, ORAT1, TAM2, TMEM142A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023965	84879	MFSD2A	http://www.ncbi.nlm.nih.gov/gene/?term=84879	"MCPH15, MFSD2, NLS1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023966	8487	GEMIN2	http://www.ncbi.nlm.nih.gov/gene/?term=8487	"SIP1, SIP1-delta "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023967	84881	RPUSD4	http://www.ncbi.nlm.nih.gov/gene/?term=84881		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023968	84881	RPUSD4	http://www.ncbi.nlm.nih.gov/gene/?term=84881		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023969	84883	AIFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84883	"AMID, PRG3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023970	84883	AIFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84883	"AMID, PRG3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023971	84883	AIFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84883	"AMID, PRG3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023972	84883	AIFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84883	"AMID, PRG3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023973	84885	ZDHHC12	http://www.ncbi.nlm.nih.gov/gene/?term=84885	"DHHC-12, ZNF400 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023974	84886	C1orf198	http://www.ncbi.nlm.nih.gov/gene/?term=84886		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023975	84886	C1orf198	http://www.ncbi.nlm.nih.gov/gene/?term=84886		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023976	84888	SPPL2A	http://www.ncbi.nlm.nih.gov/gene/?term=84888	"IMP3, PSL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023977	84888	SPPL2A	http://www.ncbi.nlm.nih.gov/gene/?term=84888	"IMP3, PSL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023978	84893	FBXO18	http://www.ncbi.nlm.nih.gov/gene/?term=84893	"FBH1, Fbx18, hFBH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023979	84893	FBXO18	http://www.ncbi.nlm.nih.gov/gene/?term=84893	"FBH1, Fbx18, hFBH1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023980	84895	FAM73B	http://www.ncbi.nlm.nih.gov/gene/?term=84895	C9orf54	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023981	84896	ATAD1	http://www.ncbi.nlm.nih.gov/gene/?term=84896	"AFDC1, FNP001, THORASE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023982	84896	ATAD1	http://www.ncbi.nlm.nih.gov/gene/?term=84896	"AFDC1, FNP001, THORASE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023983	84897	TBRG1	http://www.ncbi.nlm.nih.gov/gene/?term=84897	"NIAM, TB-5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023984	84897	TBRG1	http://www.ncbi.nlm.nih.gov/gene/?term=84897	"NIAM, TB-5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023985	84897	TBRG1	http://www.ncbi.nlm.nih.gov/gene/?term=84897	"NIAM, TB-5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023986	84897	TBRG1	http://www.ncbi.nlm.nih.gov/gene/?term=84897	"NIAM, TB-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023987	84900	RNFT2	http://www.ncbi.nlm.nih.gov/gene/?term=84900	TMEM118	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023988	84900	RNFT2	http://www.ncbi.nlm.nih.gov/gene/?term=84900	TMEM118	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023989	84901	NFATC2IP	http://www.ncbi.nlm.nih.gov/gene/?term=84901	"ESC2, NIP45, RAD60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023990	84904	ARHGEF39	http://www.ncbi.nlm.nih.gov/gene/?term=84904	C9orf100	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023991	84908	FAM136A	http://www.ncbi.nlm.nih.gov/gene/?term=84908		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023992	84908	FAM136A	http://www.ncbi.nlm.nih.gov/gene/?term=84908		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00023993	84908	FAM136A	http://www.ncbi.nlm.nih.gov/gene/?term=84908		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023994	84909	C9orf3	http://www.ncbi.nlm.nih.gov/gene/?term=84909	"AOPEP, AP-O, APO, C90RF3, ONPEP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023995	8490	RGS5	http://www.ncbi.nlm.nih.gov/gene/?term=8490	"MST092, MST106, MST129, MSTP032, MSTP092, MSTP106, MSTP129 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023996	84910	TMEM87B	http://www.ncbi.nlm.nih.gov/gene/?term=84910		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00023997	84914	ZNF587	http://www.ncbi.nlm.nih.gov/gene/?term=84914	ZF6	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00023998	84914	ZNF587	http://www.ncbi.nlm.nih.gov/gene/?term=84914	ZF6	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00023999	84914	ZNF587	http://www.ncbi.nlm.nih.gov/gene/?term=84914	ZF6	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024000	84916	UTP4	http://www.ncbi.nlm.nih.gov/gene/?term=84916	"CIRH1A, CIRHIN, NAIC, TEX292 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024001	84916	UTP4	http://www.ncbi.nlm.nih.gov/gene/?term=84916	"CIRH1A, CIRHIN, NAIC, TEX292 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024002	84918	LRP11	http://www.ncbi.nlm.nih.gov/gene/?term=84918	"MANSC3, bA350J20.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024003	84919	PPP1R15B	http://www.ncbi.nlm.nih.gov/gene/?term=84919	"CREP, MSSGM2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024004	84919	PPP1R15B	http://www.ncbi.nlm.nih.gov/gene/?term=84919	"CREP, MSSGM2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024005	84919	PPP1R15B	http://www.ncbi.nlm.nih.gov/gene/?term=84919	"CREP, MSSGM2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024006	84919	PPP1R15B	http://www.ncbi.nlm.nih.gov/gene/?term=84919	"CREP, MSSGM2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024007	8491	MAP4K3	http://www.ncbi.nlm.nih.gov/gene/?term=8491	"GLK, MAPKKKK3, MEKKK 3, MEKKK3, RAB8IPL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024008	84920	ALG10	http://www.ncbi.nlm.nih.gov/gene/?term=84920	"ALG10A, DIE2, KCR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024009	84920	ALG10	http://www.ncbi.nlm.nih.gov/gene/?term=84920	"ALG10A, DIE2, KCR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024010	84923	FAM104A	http://www.ncbi.nlm.nih.gov/gene/?term=84923		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024011	84923	FAM104A	http://www.ncbi.nlm.nih.gov/gene/?term=84923		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024012	84925	DIRC2	http://www.ncbi.nlm.nih.gov/gene/?term=84925	RCC4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024013	84926	SPRYD3	http://www.ncbi.nlm.nih.gov/gene/?term=84926		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024014	84929	FIBCD1	http://www.ncbi.nlm.nih.gov/gene/?term=84929		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024015	8492	PRSS12	http://www.ncbi.nlm.nih.gov/gene/?term=8492	"BSSP-3, BSSP3, MRT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024016	84930	MASTL	http://www.ncbi.nlm.nih.gov/gene/?term=84930	"GREATWALL, GW, GWL, MAST-L, THC2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024017	84933	C8orf76	http://www.ncbi.nlm.nih.gov/gene/?term=84933		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024018	84934	RITA1	http://www.ncbi.nlm.nih.gov/gene/?term=84934	"C12orf52, RITA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024019	84934	RITA1	http://www.ncbi.nlm.nih.gov/gene/?term=84934	"C12orf52, RITA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024020	84936	ZFYVE19	http://www.ncbi.nlm.nih.gov/gene/?term=84936	"ANCHR, MPFYVE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024021	84936	ZFYVE19	http://www.ncbi.nlm.nih.gov/gene/?term=84936	"ANCHR, MPFYVE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024022	84937	ZNRF1	http://www.ncbi.nlm.nih.gov/gene/?term=84937	NIN283	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024023	84937	ZNRF1	http://www.ncbi.nlm.nih.gov/gene/?term=84937	NIN283	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024024	84938	ATG4C	http://www.ncbi.nlm.nih.gov/gene/?term=84938	"APG4-C, APG4C, AUTL1, AUTL3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024025	84939	MUM1	http://www.ncbi.nlm.nih.gov/gene/?term=84939	"EXPAND1, HSPC211, MUM-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024026	8493	PPM1D	http://www.ncbi.nlm.nih.gov/gene/?term=8493	"PP2C-DELTA, WIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024027	84942	WDR73	http://www.ncbi.nlm.nih.gov/gene/?term=84942	"GAMOS, HSPC264 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024028	84945	ABHD13	http://www.ncbi.nlm.nih.gov/gene/?term=84945	"BEM46L1, C13orf6, bA153I24.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024029	84946	LTV1	http://www.ncbi.nlm.nih.gov/gene/?term=84946	"C6orf93, dJ468K18.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024030	84946	LTV1	http://www.ncbi.nlm.nih.gov/gene/?term=84946	"C6orf93, dJ468K18.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024031	84947	SERAC1	http://www.ncbi.nlm.nih.gov/gene/?term=84947		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024032	84948	TIGD5	http://www.ncbi.nlm.nih.gov/gene/?term=84948		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024033	84948	TIGD5	http://www.ncbi.nlm.nih.gov/gene/?term=84948		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024034	84950	PRPF38A	http://www.ncbi.nlm.nih.gov/gene/?term=84950	Prp38	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024035	84950	PRPF38A	http://www.ncbi.nlm.nih.gov/gene/?term=84950	Prp38	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024036	84954	MPND	http://www.ncbi.nlm.nih.gov/gene/?term=84954		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024037	84955	NUDCD1	http://www.ncbi.nlm.nih.gov/gene/?term=84955	"CML66, OVA66 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024038	84958	SYTL1	http://www.ncbi.nlm.nih.gov/gene/?term=84958	"JFC1, SLP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024039	84959	UBASH3B	http://www.ncbi.nlm.nih.gov/gene/?term=84959	"STS-1, STS1, TULA-2, TULA2, p70 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024040	84959	UBASH3B	http://www.ncbi.nlm.nih.gov/gene/?term=84959	"STS-1, STS1, TULA-2, TULA2, p70 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024041	84959	UBASH3B	http://www.ncbi.nlm.nih.gov/gene/?term=84959	"STS-1, STS1, TULA-2, TULA2, p70 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024042	8495	PPFIBP2	http://www.ncbi.nlm.nih.gov/gene/?term=8495	Cclp1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024043	84962	AJUBA	http://www.ncbi.nlm.nih.gov/gene/?term=84962	JUB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024044	84967	LSM10	http://www.ncbi.nlm.nih.gov/gene/?term=84967	"MST074, MSTP074 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024045	8496	PPFIBP1	http://www.ncbi.nlm.nih.gov/gene/?term=8496	"L2, SGT2, hSGT2, hSgt2p "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024046	8496	PPFIBP1	http://www.ncbi.nlm.nih.gov/gene/?term=8496	"L2, SGT2, hSGT2, hSgt2p "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024047	84971	ATG4D	http://www.ncbi.nlm.nih.gov/gene/?term=84971	"APG4-D, APG4D, AUTL4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024048	84973	SNHG7	http://www.ncbi.nlm.nih.gov/gene/?term=84973	NCRNA00061	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024049	84975	MFSD5	http://www.ncbi.nlm.nih.gov/gene/?term=84975	hsMOT2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024050	84976	DISP1	http://www.ncbi.nlm.nih.gov/gene/?term=84976	DISPA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024051	84981	MIR22HG	http://www.ncbi.nlm.nih.gov/gene/?term=84981	C17orf91	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024052	84984	CEP19	http://www.ncbi.nlm.nih.gov/gene/?term=84984	"C3orf34, MOSPGF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024053	84985	FAM83A	http://www.ncbi.nlm.nih.gov/gene/?term=84985	BJ-TSA-9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024054	84986	ARHGAP19	http://www.ncbi.nlm.nih.gov/gene/?term=84986		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024055	84987	COX14	http://www.ncbi.nlm.nih.gov/gene/?term=84987	C12orf62	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024056	84987	COX14	http://www.ncbi.nlm.nih.gov/gene/?term=84987	C12orf62	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024057	84988	PPP1R16A	http://www.ncbi.nlm.nih.gov/gene/?term=84988	MYPT3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024058	8498	RANBP3	http://www.ncbi.nlm.nih.gov/gene/?term=8498		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024059	84991	RBM17	http://www.ncbi.nlm.nih.gov/gene/?term=84991	SPF45	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024060	84991	RBM17	http://www.ncbi.nlm.nih.gov/gene/?term=84991	SPF45	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024061	84992	PIGY	http://www.ncbi.nlm.nih.gov/gene/?term=84992	"HPMRS6, PIG-Y "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024062	84996	URB1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=84996	"C21orf119, PRED84 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024063	8499	PPFIA2	http://www.ncbi.nlm.nih.gov/gene/?term=8499		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024064	8499	PPFIA2	http://www.ncbi.nlm.nih.gov/gene/?term=8499		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024065	8499	PPFIA2	http://www.ncbi.nlm.nih.gov/gene/?term=8499		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024066	85002	FAM86B1	http://www.ncbi.nlm.nih.gov/gene/?term=85002		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024067	85007	PHYKPL	http://www.ncbi.nlm.nih.gov/gene/?term=85007	"AGXT2L2, PHLU "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024068	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024069	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024070	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024071	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024072	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024073	85013	TMEM128	http://www.ncbi.nlm.nih.gov/gene/?term=85013		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024074	85014	TMEM141	http://www.ncbi.nlm.nih.gov/gene/?term=85014		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024075	85019	TMEM241	http://www.ncbi.nlm.nih.gov/gene/?term=85019	"C18orf45, hVVT "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024076	8501	SLC43A1	http://www.ncbi.nlm.nih.gov/gene/?term=8501	"LAT3, PB39, POV1, R00504 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024077	85021	REPS1	http://www.ncbi.nlm.nih.gov/gene/?term=85021	RALBP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024078	85026	ARRDC1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=85026	C9orf37	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024079	85028	SNHG12	http://www.ncbi.nlm.nih.gov/gene/?term=85028	"ASLNC04080, C1orf79, LINC00100, NCRNA00100 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024080	85028	SNHG12	http://www.ncbi.nlm.nih.gov/gene/?term=85028	"ASLNC04080, C1orf79, LINC00100, NCRNA00100 "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024081	850295	CHA1	http://www.ncbi.nlm.nih.gov/gene/?term=850295	YCL064C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024082	8502	PKP4	http://www.ncbi.nlm.nih.gov/gene/?term=8502	p0071	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024083	850305	PBN1	http://www.ncbi.nlm.nih.gov/gene/?term=850305	YCL052C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024084	850308	YCL049C	http://www.ncbi.nlm.nih.gov/gene/?term=850308	YCL049C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024085	850312	EMC1	http://www.ncbi.nlm.nih.gov/gene/?term=850312	YCL045C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024086	850314	PDI1	http://www.ncbi.nlm.nih.gov/gene/?term=850314	"YCL043C, MFP1, TRG1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024087	850319	ATG22	http://www.ncbi.nlm.nih.gov/gene/?term=850319	"YCL038C, AUT4 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024088	850343	NFS1	http://www.ncbi.nlm.nih.gov/gene/?term=850343	"YCL017C, SPL1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024089	850348	ILV6	http://www.ncbi.nlm.nih.gov/gene/?term=850348	YCL009C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024090	850361	CIT2	http://www.ncbi.nlm.nih.gov/gene/?term=850361	YCR005C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024091	850361	CIT2	http://www.ncbi.nlm.nih.gov/gene/?term=850361	YCR005C	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024092	850375	YCR016W	http://www.ncbi.nlm.nih.gov/gene/?term=850375	YCR016W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024093	850385	HSP30	http://www.ncbi.nlm.nih.gov/gene/?term=850385	"YCR021C, YRO1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024094	850389	PMP1	http://www.ncbi.nlm.nih.gov/gene/?term=850389	YCR024C-A	mRNA	Saccharomyces cerevisiae	18492794	Ribosome	Yeast	Fluorescence in situ hybridization	"By this method, the majority of PMP1 transcript, either expressed from its genomic loci (PMP1) or from a plasmid (pPMP1), appeared mostly in the fraction of membrane-bound polysomes (Fig. 5A). "
RLID00024095	8503	PIK3R3	http://www.ncbi.nlm.nih.gov/gene/?term=8503	"p55, p55-GAMMA, p55PIK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024096	8503	PIK3R3	http://www.ncbi.nlm.nih.gov/gene/?term=8503	"p55, p55-GAMMA, p55PIK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024097	850403	PHO87	http://www.ncbi.nlm.nih.gov/gene/?term=850403	YCR037C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024098	850432	ATG15	http://www.ncbi.nlm.nih.gov/gene/?term=850432	"YCR068W, AUT5, CVT17 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024099	850433	CPR4	http://www.ncbi.nlm.nih.gov/gene/?term=850433	"YCR069W, CYP4, SCC3, YCR070W "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024100	850456	CDC50	http://www.ncbi.nlm.nih.gov/gene/?term=850456	YCR094W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024101	850463	YCR099C	http://www.ncbi.nlm.nih.gov/gene/?term=850463	YCR099C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024102	850476	YFL068W	http://www.ncbi.nlm.nih.gov/gene/?term=850476	YFL068W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024103	850477	YFL067W	http://www.ncbi.nlm.nih.gov/gene/?term=850477	YFL067W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024104	850478	YFL066C	http://www.ncbi.nlm.nih.gov/gene/?term=850478	YFL066C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024105	850482	COS4	http://www.ncbi.nlm.nih.gov/gene/?term=850482	YFL062W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024106	850488	AAD6	http://www.ncbi.nlm.nih.gov/gene/?term=850488	"YFL056C, YFL057C "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024107	850502	FET5	http://www.ncbi.nlm.nih.gov/gene/?term=850502	YFL041W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024108	850505	YPT1	http://www.ncbi.nlm.nih.gov/gene/?term=850505	YFL038C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024109	850505	YPT1	http://www.ncbi.nlm.nih.gov/gene/?term=850505	YFL038C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024110	850505	YPT1	http://www.ncbi.nlm.nih.gov/gene/?term=850505	YFL038C	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024111	850518	STE2	http://www.ncbi.nlm.nih.gov/gene/?term=850518	YFL026W	mRNA	Saccharomyces cerevisiae	20457760	Cellular bud	Yeast	Fluorescence microscopy	"In addition, we found that adding a single U3 element to the 3'end of STE2 mRNA was sufficient to localize STE2 mRNA to the distal tip of buds (Fig. S1). "
RLID00024112	850527	LPD1	http://www.ncbi.nlm.nih.gov/gene/?term=850527	"YFL018C, HPD1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024113	850527	LPD1	http://www.ncbi.nlm.nih.gov/gene/?term=850527	"YFL018C, HPD1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024114	850530	MDJ1	http://www.ncbi.nlm.nih.gov/gene/?term=850530	YFL016C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024115	850530	MDJ1	http://www.ncbi.nlm.nih.gov/gene/?term=850530	YFL016C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024116	850536	HXT10	http://www.ncbi.nlm.nih.gov/gene/?term=850536	YFL011W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024117	850543	SEC4	http://www.ncbi.nlm.nih.gov/gene/?term=850543	"YFL005W, SRO6 "	mRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00024118	850543	SEC4	http://www.ncbi.nlm.nih.gov/gene/?term=850543	"YFL005W, SRO6 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024119	850543	SEC4	http://www.ncbi.nlm.nih.gov/gene/?term=850543	"YFL005W, SRO6 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. ?(Fig.1B).1B).  "
RLID00024120	850543	SEC4	http://www.ncbi.nlm.nih.gov/gene/?term=850543	"YFL005W, SRO6 "	mRNA	Saccharomyces cerevisiae	17339339	Nucleus	Yeast	Fluorescence in situ hybridization	"Cells in late G2/M also had SEC4 mRNA located in the nucleus of the mother cell. This may represent a maternal pool ofSEC4 mRNA yet to be exported. After mitosis, SEC4 mRNA was observed in both mother and daughter cells. "
RLID00024121	850543	SEC4	http://www.ncbi.nlm.nih.gov/gene/?term=850543	"YFL005W, SRO6 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As most POL proteins are enriched in the bud, we examined the localization of their mRNAs during cell division by FISH with specific digoxigenin-labeled antisense probes (Fig. 1). First, we examined the localization of endogenous mRNA encoding Sec4 (Fig. 1A), a bud-localized GTPase that mediates secretory vesicle fusion with the plasma membrane, in WT cells. FISH labeling of endogenous SEC4 mRNA yielded single punctate structures located near the cell surface prior to budding (G1?phase). These structures were distinct from the nucleus, which was revealed by propidium iodide staining (Fig. 1A). In cells undergoing division (early G2/M phase), nearly all SEC4 mRNA was found in the bud even though nuclear division and segregation had yet to occur. This pattern was observed in 85% of the cells examined. Cells in late G2/M also had SEC4 mRNA located in the nucleus of the mother cell. This may represent a maternal pool ofSEC4 mRNA yet to be exported. After mitosis, SEC4 mRNA was observed in both mother and daughter cells. "
RLID00024122	850543	SEC4	http://www.ncbi.nlm.nih.gov/gene/?term=850543	"YFL005W, SRO6 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024123	8505	PARG	http://www.ncbi.nlm.nih.gov/gene/?term=8505	PARG99	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024124	8505	PARG	http://www.ncbi.nlm.nih.gov/gene/?term=8505	PARG99	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024125	850602	ERJ5	http://www.ncbi.nlm.nih.gov/gene/?term=850602	YFR041C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024126	850605	DUG1	http://www.ncbi.nlm.nih.gov/gene/?term=850605	YFR044C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024127	850631	TPO1	http://www.ncbi.nlm.nih.gov/gene/?term=850631	YLL028W	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00024128	850637	POM33	http://www.ncbi.nlm.nih.gov/gene/?term=850637	YLL023C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024129	850659	YLL067C	http://www.ncbi.nlm.nih.gov/gene/?term=850659	YLL067C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024130	850660	YLL066C	http://www.ncbi.nlm.nih.gov/gene/?term=850660	YLL066C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024131	850685	SDH2	http://www.ncbi.nlm.nih.gov/gene/?term=850685	"YLL041C, ACN17 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024132	850685	SDH2	http://www.ncbi.nlm.nih.gov/gene/?term=850685	"YLL041C, ACN17 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024133	850686	DNM1	http://www.ncbi.nlm.nih.gov/gene/?term=850686	YLL001W	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024134	8506	CNTNAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8506	"CASPR, CNTNAP, NRXN4, P190 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024135	850704	MEU1	http://www.ncbi.nlm.nih.gov/gene/?term=850704	YLR017W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024136	850706	PSR2	http://www.ncbi.nlm.nih.gov/gene/?term=850706	YLR019W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024137	850710	IZH3	http://www.ncbi.nlm.nih.gov/gene/?term=850710	YLR023C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024138	850714	AAT2	http://www.ncbi.nlm.nih.gov/gene/?term=850714	"YLR027C, ASP5 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024139	850714	AAT2	http://www.ncbi.nlm.nih.gov/gene/?term=850714	"YLR027C, ASP5 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024140	850745	ERG3	http://www.ncbi.nlm.nih.gov/gene/?term=850745	"YLR056W, PSO6, SYR1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024141	850770	GAL2	http://www.ncbi.nlm.nih.gov/gene/?term=850770	YLR081W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024142	850778	ALT1	http://www.ncbi.nlm.nih.gov/gene/?term=850778	YLR089C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024143	850782	NYV1	http://www.ncbi.nlm.nih.gov/gene/?term=850782	"YLR093C, MAM2 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024144	850798	YLR108C	http://www.ncbi.nlm.nih.gov/gene/?term=850798	YLR108C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024145	8507	ENC1	http://www.ncbi.nlm.nih.gov/gene/?term=8507	"CCL28, ENC-1, KLHL35, KLHL37, NRPB, PIG10, TP53I10 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024146	850811	YPS1	http://www.ncbi.nlm.nih.gov/gene/?term=850811	"YLR120C, YAP3 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024147	850829	NHA1	http://www.ncbi.nlm.nih.gov/gene/?term=850829	YLR138W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024148	850841	YLR149C	http://www.ncbi.nlm.nih.gov/gene/?term=850841	YLR149C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024149	850844	PCD1	http://www.ncbi.nlm.nih.gov/gene/?term=850844	YLR151C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024150	850845	YLR152C	http://www.ncbi.nlm.nih.gov/gene/?term=850845	YLR152C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024151	850871	IDP2	http://www.ncbi.nlm.nih.gov/gene/?term=850871	YLR174W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024152	850888	PEX13	http://www.ncbi.nlm.nih.gov/gene/?term=850888	"YLR191W, PAS20 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024153	850888	PEX13	http://www.ncbi.nlm.nih.gov/gene/?term=850888	"YLR191W, PAS20 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024154	850893	PWP1	http://www.ncbi.nlm.nih.gov/gene/?term=850893	YLR196W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024155	8508	NIPSNAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8508		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024156	850900	MSS51	http://www.ncbi.nlm.nih.gov/gene/?term=850900	YLR203C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024157	850930	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=850930	YLR229C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024158	850930	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=850930	YLR229C	mRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00024159	850930	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=850930	YLR229C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024160	850942	CSC1	http://www.ncbi.nlm.nih.gov/gene/?term=850942	YLR241W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024161	850952	SSP120	http://www.ncbi.nlm.nih.gov/gene/?term=850952	YLR250W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024162	850953	SYM1	http://www.ncbi.nlm.nih.gov/gene/?term=850953	YLR251W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024163	850963	HSP60	http://www.ncbi.nlm.nih.gov/gene/?term=850963	"YLR259C, CPN60, MIF4, MNA2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024164	850973	SEC22	http://www.ncbi.nlm.nih.gov/gene/?term=850973	"YLR268W, SLY2, TS26, TSL26 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024165	850973	SEC22	http://www.ncbi.nlm.nih.gov/gene/?term=850973	"YLR268W, SLY2, TS26, TSL26 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024166	850990	ECI1	http://www.ncbi.nlm.nih.gov/gene/?term=850990	YLR284C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024167	8509	NDST2	http://www.ncbi.nlm.nih.gov/gene/?term=8509	"HSST2, NST2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024168	851007	EXG1	http://www.ncbi.nlm.nih.gov/gene/?term=851007	"YLR300W, BGL1, SCW6 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024169	851013	ACO1	http://www.ncbi.nlm.nih.gov/gene/?term=851013	"YLR304C, GLU1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024170	851013	ACO1	http://www.ncbi.nlm.nih.gov/gene/?term=851013	"YLR304C, GLU1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024171	851021	ATG39	http://www.ncbi.nlm.nih.gov/gene/?term=851021	YLR312C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024172	851042	MID2	http://www.ncbi.nlm.nih.gov/gene/?term=851042	"YLR332W, KAI1 "	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p colocalizes with a subset of mRNAs at the bud-tip of yeast cells.The U1A-GFP-tagged RNAs for ASH1, MID2, MTL1, and WSC2 colocalized with Khd1p, whereas BRO1 and TPO2 mRNAs did not colocalize. "
RLID00024173	851069	ILV5	http://www.ncbi.nlm.nih.gov/gene/?term=851069	YLR355C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024174	851070	ATG33	http://www.ncbi.nlm.nih.gov/gene/?term=851070	YLR356W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024175	851087	ELO3	http://www.ncbi.nlm.nih.gov/gene/?term=851087	"YLR372W, APA1, SRE1, SUR4, VBM1 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024176	851087	ELO3	http://www.ncbi.nlm.nih.gov/gene/?term=851087	"YLR372W, APA1, SRE1, SUR4, VBM1 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024177	851095	SEC61	http://www.ncbi.nlm.nih.gov/gene/?term=851095	YLR378C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024178	851095	SEC61	http://www.ncbi.nlm.nih.gov/gene/?term=851095	YLR378C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024179	851107	CCW14	http://www.ncbi.nlm.nih.gov/gene/?term=851107	"YLR390W-A, SSR1, YLR391W, YLR391W-A "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024180	851109	ATP10	http://www.ncbi.nlm.nih.gov/gene/?term=851109	YLR393W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024181	851109	ATP10	http://www.ncbi.nlm.nih.gov/gene/?term=851109	YLR393W	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	"Out of 24 tagged mMPs, we found that the ATM1, ATP2, ATP10, CYB2, COX10,MDM10, and OXA1 mRNA granules exhibited very high levels of colocalization with mitochondria (e.g., >80%), while the CBS1, CYC3, and FIS1 mRNAs demonstrated low levels of colocalization (i.e., �4%) on glucose-containing medium (Fig. 1A; Table 1). Taken together, the data suggest that the 3�UTR is necessary for ATP2 and OXA1 mRNA localization to mitochondria (Table 3). "
RLID00024182	851115	BDF1	http://www.ncbi.nlm.nih.gov/gene/?term=851115	YLR399C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024183	851132	PUN1	http://www.ncbi.nlm.nih.gov/gene/?term=851132	YLR414C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024184	851187	YRF1-4	http://www.ncbi.nlm.nih.gov/gene/?term=851187	"YLR466W, YRF1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024185	851192	CYC3	http://www.ncbi.nlm.nih.gov/gene/?term=851192	YAL039C	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024186	851203	SNC1	http://www.ncbi.nlm.nih.gov/gene/?term=851203	YAL030W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024187	851203	SNC1	http://www.ncbi.nlm.nih.gov/gene/?term=851203	YAL030W	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024188	851203	SNC1	http://www.ncbi.nlm.nih.gov/gene/?term=851203	YAL030W	mRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00024189	851203	SNC1	http://www.ncbi.nlm.nih.gov/gene/?term=851203	YAL030W	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024190	851203	SNC1	http://www.ncbi.nlm.nih.gov/gene/?term=851203	YAL030W	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024191	851210	PMT2	http://www.ncbi.nlm.nih.gov/gene/?term=851210	"YAL023C, FUN25 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024192	851210	PMT2	http://www.ncbi.nlm.nih.gov/gene/?term=851210	"YAL023C, FUN25 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024193	851210	PMT2	http://www.ncbi.nlm.nih.gov/gene/?term=851210	"YAL023C, FUN25 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024194	851211	FUN26	http://www.ncbi.nlm.nih.gov/gene/?term=851211	YAL022C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024195	851223	MDM10	http://www.ncbi.nlm.nih.gov/gene/?term=851223	"YAL010C, FUN37 "	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024196	851226	ERP2	http://www.ncbi.nlm.nih.gov/gene/?term=851226	YAL007C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024197	851238	BDH2	http://www.ncbi.nlm.nih.gov/gene/?term=851238	YAL061W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024198	851246	FLC2	http://www.ncbi.nlm.nih.gov/gene/?term=851246	YAL053W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024199	851256	ERV46	http://www.ncbi.nlm.nih.gov/gene/?term=851256	"YAL042W, FUN9 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024200	851279	UIP3	http://www.ncbi.nlm.nih.gov/gene/?term=851279	YAR027W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024201	851282	PRM9	http://www.ncbi.nlm.nih.gov/gene/?term=851282	YAR031W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024202	851292	YAR061W	http://www.ncbi.nlm.nih.gov/gene/?term=851292	"YAR061W, YAR062W "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024203	851304	FMP45	http://www.ncbi.nlm.nih.gov/gene/?term=851304	YDL222C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024204	851308	YDL218W	http://www.ncbi.nlm.nih.gov/gene/?term=851308	YDL218W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024205	851314	SHR3	http://www.ncbi.nlm.nih.gov/gene/?term=851314	"YDL212W, APF1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024206	851323	RTN2	http://www.ncbi.nlm.nih.gov/gene/?term=851323	YDL204W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024207	851348	COS7	http://www.ncbi.nlm.nih.gov/gene/?term=851348	YDL248W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024208	851352	HXT15	http://www.ncbi.nlm.nih.gov/gene/?term=851352	YDL245C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024209	851376	DLD2	http://www.ncbi.nlm.nih.gov/gene/?term=851376	"YDL178W, AIP2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024210	851380	DLD1	http://www.ncbi.nlm.nih.gov/gene/?term=851380	YDL174C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024211	851415	RPO21	http://www.ncbi.nlm.nih.gov/gene/?term=851415	"YDL140C, RPB1, RPB220, SUA8 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024212	851429	VCX1	http://www.ncbi.nlm.nih.gov/gene/?term=851429	"YDL128W, HUM1, MNR1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024213	851462	PMT1	http://www.ncbi.nlm.nih.gov/gene/?term=851462	YDL095W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024214	851481	MDH3	http://www.ncbi.nlm.nih.gov/gene/?term=851481	YDL078C	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024215	851487	YET3	http://www.ncbi.nlm.nih.gov/gene/?term=851487	YDL072C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024216	851488	BDF2	http://www.ncbi.nlm.nih.gov/gene/?term=851488	YDL070W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024217	851491	CBS1	http://www.ncbi.nlm.nih.gov/gene/?term=851491	YDL069C	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024218	851491	CBS1	http://www.ncbi.nlm.nih.gov/gene/?term=851491	YDL069C	mRNA	Saccharomyces cerevisiae	25971974	Mitochondrion	Ski2 cell	Northern blot	The tRNA splicing endonuclease complex cleaves the mitochondria-localized CBP1 mRNA.
RLID00024219	851493	IDP1	http://www.ncbi.nlm.nih.gov/gene/?term=851493	YDL066W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024220	8514	KCNAB2	http://www.ncbi.nlm.nih.gov/gene/?term=8514	"AKR6A5, HKvbeta2, HKvbeta2.1, HKvbeta2.2, KCNA2B, KV-BETA-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024221	851506	MCH1	http://www.ncbi.nlm.nih.gov/gene/?term=851506	YDL054C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024222	851514	NPC2	http://www.ncbi.nlm.nih.gov/gene/?term=851514	YDL046W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024223	851516	FAD1	http://www.ncbi.nlm.nih.gov/gene/?term=851516	YDL045C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024224	851527	GPR1	http://www.ncbi.nlm.nih.gov/gene/?term=851527	YDL035C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024225	851535	MRX9	http://www.ncbi.nlm.nih.gov/gene/?term=851535	YDL027C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024226	851537	DIA3	http://www.ncbi.nlm.nih.gov/gene/?term=851537	YDL024C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024227	851539	GPD1	http://www.ncbi.nlm.nih.gov/gene/?term=851539	"YDL022W, DAR1, HOR1, OSG1, OSR5 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024228	851539	GPD1	http://www.ncbi.nlm.nih.gov/gene/?term=851539	"YDL022W, DAR1, HOR1, OSG1, OSR5 "	mRNA	Saccharomyces cerevisiae	19903887	Endoplasmic reticulum	Yeast	RT-PCR	"To further analyze the specificity of mPP targeting, we examined the localization of the POX1 and GPD1 mRNAs in cells expressing Sec63-RFP (Fig. S1 B and C and Table S3). Interestingly, a high percentage of both RNAs colocalized with Sec63-RFP (59% and 71%, respectively; Table S3 and Fig. S1B and C). While mRNA localization to the ER could be due to the fact that ER fills much of the cell volume (see, e.g., Fig. S1B and C), we also demonstrated that peroxisomes decorate both nuclear and cortical ER (Fig. S1D). Thus, discerning whether mPP localization to the ER results from a direct association with ER membranes or is a consequence of binding to ER-associated peroxisomes is difficult. Alternatively, GPD1 mRNA, which encodes a glycerol-3-phosphate dehydrogenase found in the cytosol and peroxisomes, may preferentially localize to ER-like mRNAs encoding cytoplasmic proteins (13). This could allow for protein distribution to either compartment. Data are collected from Table S3: Localization of mPPs to ER. "
RLID00024229	851539	GPD1	http://www.ncbi.nlm.nih.gov/gene/?term=851539	"YDL022W, DAR1, HOR1, OSG1, OSR5 "	mRNA	Saccharomyces cerevisiae	19903887	Cell cortex	Yeast	RT-PCR	"To further analyze the specificity of mPP targeting, we examined the localization of the POX1 and GPD1 mRNAs in cells expressing Sec63-RFP (Fig. S1 B and C and Table S3). Interestingly, a high percentage of both RNAs colocalized with Sec63-RFP (59% and 71%, respectively; Table S3 and Fig. S1B and C). While mRNA localization to the ER could be due to the fact that ER fills much of the cell volume (see, e.g., Fig. S1B and C), we also demonstrated that peroxisomes decorate both nuclear and cortical ER (Fig. S1D). Thus, discerning whether mPP localization to the ER results from a direct association with ER membranes or is a consequence of binding to ER-associated peroxisomes is difficult. Alternatively, GPD1 mRNA, which encodes a glycerol-3-phosphate dehydrogenase found in the cytosol and peroxisomes, may preferentially localize to ER-like mRNAs encoding cytoplasmic proteins (13). This could allow for protein distribution to either compartment. Data are collected from Table S3: Localization of mPPs to ER. "
RLID00024230	851547	TSC13	http://www.ncbi.nlm.nih.gov/gene/?term=851547	YDL015C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024231	851551	GRX6	http://www.ncbi.nlm.nih.gov/gene/?term=851551	YDL010W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024232	851560	ATP16	http://www.ncbi.nlm.nih.gov/gene/?term=851560	YDL004W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024233	851566	RCR2	http://www.ncbi.nlm.nih.gov/gene/?term=851566	"YDR003W, SSH5 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024234	851570	TRP1	http://www.ncbi.nlm.nih.gov/gene/?term=851570	YDR007W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024235	851581	YDR018C	http://www.ncbi.nlm.nih.gov/gene/?term=851581	YDR018C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024236	851582	GCV1	http://www.ncbi.nlm.nih.gov/gene/?term=851582	"YDR019C, GSD1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024237	851597	MRH1	http://www.ncbi.nlm.nih.gov/gene/?term=851597	YDR033W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024238	851608	ENA5	http://www.ncbi.nlm.nih.gov/gene/?term=851608	YDR038C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024239	851609	ENA2	http://www.ncbi.nlm.nih.gov/gene/?term=851609	YDR039C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024240	851610	ENA1	http://www.ncbi.nlm.nih.gov/gene/?term=851610	"YDR040C, HOR6, PMR2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024241	851611	RSM10	http://www.ncbi.nlm.nih.gov/gene/?term=851611	YDR041W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024242	851616	BAP3	http://www.ncbi.nlm.nih.gov/gene/?term=851616	"YDR046C, PAP1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024243	851625	PST1	http://www.ncbi.nlm.nih.gov/gene/?term=851625	"YDR055W, HPF2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024244	851626	EMC10	http://www.ncbi.nlm.nih.gov/gene/?term=851626	YDR056C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024245	851627	YOS9	http://www.ncbi.nlm.nih.gov/gene/?term=851627	YDR057W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024246	851634	LCB2	http://www.ncbi.nlm.nih.gov/gene/?term=851634	"YDR062W, SCS1, TSC1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024247	851649	SED1	http://www.ncbi.nlm.nih.gov/gene/?term=851649	YDR077W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024248	851677	TVP15	http://www.ncbi.nlm.nih.gov/gene/?term=851677	YDR100W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024249	851687	YDR109C	http://www.ncbi.nlm.nih.gov/gene/?term=851687	YDR109C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024250	851694	MRPL1	http://www.ncbi.nlm.nih.gov/gene/?term=851694	YDR116C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024251	851701	INO2	http://www.ncbi.nlm.nih.gov/gene/?term=851701	"YDR123C, DIE1, SCS1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024252	851726	KGD2	http://www.ncbi.nlm.nih.gov/gene/?term=851726	YDR148C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024253	851726	KGD2	http://www.ncbi.nlm.nih.gov/gene/?term=851726	YDR148C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024254	851742	SEC1	http://www.ncbi.nlm.nih.gov/gene/?term=851742	YDR164C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024255	851742	SEC1	http://www.ncbi.nlm.nih.gov/gene/?term=851742	YDR164C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024256	851756	NGG1	http://www.ncbi.nlm.nih.gov/gene/?term=851756	"YDR176W, ADA3, SWI7 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024257	851763	CDC1	http://www.ncbi.nlm.nih.gov/gene/?term=851763	"YDR182W, DSC1, DSR1, ESP2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024258	851775	MSS116	http://www.ncbi.nlm.nih.gov/gene/?term=851775	YDR194C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024259	851785	COQ4	http://www.ncbi.nlm.nih.gov/gene/?term=851785	YDR204W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024260	851807	GTB1	http://www.ncbi.nlm.nih.gov/gene/?term=851807	YDR221W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024261	851819	RTN1	http://www.ncbi.nlm.nih.gov/gene/?term=851819	YDR233C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024262	851831	PEX5	http://www.ncbi.nlm.nih.gov/gene/?term=851831	"YDR244W, PAS10 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024263	851831	PEX5	http://www.ncbi.nlm.nih.gov/gene/?term=851831	"YDR244W, PAS10 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024264	851843	CTA1	http://www.ncbi.nlm.nih.gov/gene/?term=851843	YDR256C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024265	851843	CTA1	http://www.ncbi.nlm.nih.gov/gene/?term=851843	YDR256C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024266	851843	CTA1	http://www.ncbi.nlm.nih.gov/gene/?term=851843	YDR256C	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024267	851855	YDR262W	http://www.ncbi.nlm.nih.gov/gene/?term=851855	YDR262W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024268	851857	AKR1	http://www.ncbi.nlm.nih.gov/gene/?term=851857	YDR264C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024269	851858	PEX10	http://www.ncbi.nlm.nih.gov/gene/?term=851858	"YDR265W, PAS4 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024270	851866	DON1	http://www.ncbi.nlm.nih.gov/gene/?term=851866	YDR273W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024271	851868	BSC2	http://www.ncbi.nlm.nih.gov/gene/?term=851868	YDR275W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024272	851878	DPP1	http://www.ncbi.nlm.nih.gov/gene/?term=851878	"YDR284C, ZRG1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024273	851888	DPL1	http://www.ncbi.nlm.nih.gov/gene/?term=851888	"YDR294C, BST1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024274	8518	IKBKAP	http://www.ncbi.nlm.nih.gov/gene/?term=8518	"DYS, ELP1, FD, IKAP, IKI3, TOT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024275	8518	IKBKAP	http://www.ncbi.nlm.nih.gov/gene/?term=8518	"DYS, ELP1, FD, IKAP, IKI3, TOT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024276	8518	IKBKAP	http://www.ncbi.nlm.nih.gov/gene/?term=8518	"DYS, ELP1, FD, IKAP, IKI3, TOT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024277	851902	PMT7	http://www.ncbi.nlm.nih.gov/gene/?term=851902	YDR307W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024278	851929	PEX3	http://www.ncbi.nlm.nih.gov/gene/?term=851929	"YDR329C, PAS3 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024279	851929	PEX3	http://www.ncbi.nlm.nih.gov/gene/?term=851929	"YDR329C, PAS3 "	mRNA	Saccharomyces cerevisiae	17417645	Endoplasmic reticulum	Yeast	qRT-PCR	"We previously demonstrated that SRO7 mRNA undergoes polarized transport, along with cortical ER, to the bud tip11. Thus, PEX3 mRNA localizes to the endoplasmic reticulum, as seen previously11, and Pex3 is functional after MS2L integration into the PEX3 locus. We observed typical tubular-punctate mitochondrial morphology with Oxa1-RFP19.  "
RLID00024280	851929	PEX3	http://www.ncbi.nlm.nih.gov/gene/?term=851929	"YDR329C, PAS3 "	mRNA	Saccharomyces cerevisiae	19903887	Endoplasmic reticulum	Yeast	RT-PCR	"To further analyze the specificity of mPP targeting, we examined the localization of the POX1 and GPD1 mRNAs in cells expressing Sec63-RFP (Fig. S1 B and C and Table S3). Interestingly, a high percentage of both RNAs colocalized with Sec63-RFP (59% and 71%, respectively; Table S3 and Fig. S1B and C). While mRNA localization to the ER could be due to the fact that ER fills much of the cell volume (see, e.g., Fig. S1B and C), we also demonstrated that peroxisomes decorate both nuclear and cortical ER (Fig. S1D). Thus, discerning whether mPP localization to the ER results from a direct association with ER membranes or is a consequence of binding to ER-associated peroxisomes is difficult. Alternatively, GPD1 mRNA, which encodes a glycerol-3-phosphate dehydrogenase found in the cytosol and peroxisomes, may preferentially localize to ER-like mRNAs encoding cytoplasmic proteins (13). This could allow for protein distribution to either compartment. Data are collected from Table S3: Localization of mPPs to ER. "
RLID00024281	851929	PEX3	http://www.ncbi.nlm.nih.gov/gene/?term=851929	"YDR329C, PAS3 "	mRNA	Saccharomyces cerevisiae	19903887	Cell cortex	Yeast	RT-PCR	"To further analyze the specificity of mPP targeting, we examined the localization of the POX1 and GPD1 mRNAs in cells expressing Sec63-RFP (Fig. S1 B and C and Table S3). Interestingly, a high percentage of both RNAs colocalized with Sec63-RFP (59% and 71%, respectively; Table S3 and Fig. S1B and C). While mRNA localization to the ER could be due to the fact that ER fills much of the cell volume (see, e.g., Fig. S1B and C), we also demonstrated that peroxisomes decorate both nuclear and cortical ER (Fig. S1D). Thus, discerning whether mPP localization to the ER results from a direct association with ER membranes or is a consequence of binding to ER-associated peroxisomes is difficult. Alternatively, GPD1 mRNA, which encodes a glycerol-3-phosphate dehydrogenase found in the cytosol and peroxisomes, may preferentially localize to ER-like mRNAs encoding cytoplasmic proteins (13). This could allow for protein distribution to either compartment. Data are collected from Table S3: Localization of mPPs to ER. "
RLID00024282	851929	PEX3	http://www.ncbi.nlm.nih.gov/gene/?term=851929	"YDR329C, PAS3 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024283	851929	PEX3	http://www.ncbi.nlm.nih.gov/gene/?term=851929	"YDR329C, PAS3 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024284	851931	GPI8	http://www.ncbi.nlm.nih.gov/gene/?term=851931	YDR331W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024285	851943	HXT7	http://www.ncbi.nlm.nih.gov/gene/?term=851943	YDR342C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024286	851944	HXT6	http://www.ncbi.nlm.nih.gov/gene/?term=851944	YDR343C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024287	851946	HXT3	http://www.ncbi.nlm.nih.gov/gene/?term=851946	YDR345C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024288	8519	IFITM1	http://www.ncbi.nlm.nih.gov/gene/?term=8519	"9-27, CD225, DSPA2a, IFI17, LEU13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024289	8519	IFITM1	http://www.ncbi.nlm.nih.gov/gene/?term=8519	"9-27, CD225, DSPA2a, IFI17, LEU13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024290	852044	GPI17	http://www.ncbi.nlm.nih.gov/gene/?term=852044	YDR434W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024291	852063	PPN1	http://www.ncbi.nlm.nih.gov/gene/?term=852063	"YDR452W, PHM5 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024292	852066	NHX1	http://www.ncbi.nlm.nih.gov/gene/?term=852066	"YDR456W, NHA2, VPL27, VPS44 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024293	852090	PEX29	http://www.ncbi.nlm.nih.gov/gene/?term=852090	YDR479C	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024294	852092	PHO8	http://www.ncbi.nlm.nih.gov/gene/?term=852092	YDR481C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024295	852094	KRE2	http://www.ncbi.nlm.nih.gov/gene/?term=852094	"YDR483W, MNT1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024296	8520	HAT1	http://www.ncbi.nlm.nih.gov/gene/?term=8520	KAT1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024297	8520	HAT1	http://www.ncbi.nlm.nih.gov/gene/?term=8520	KAT1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024298	8520	HAT1	http://www.ncbi.nlm.nih.gov/gene/?term=8520	KAT1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024299	852108	ITR1	http://www.ncbi.nlm.nih.gov/gene/?term=852108	YDR497C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024300	852109	SEC20	http://www.ncbi.nlm.nih.gov/gene/?term=852109	YDR498C	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024301	852114	LPP1	http://www.ncbi.nlm.nih.gov/gene/?term=852114	YDR503C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024302	852121	GNP1	http://www.ncbi.nlm.nih.gov/gene/?term=852121	YDR508C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024303	852123	SDH7	http://www.ncbi.nlm.nih.gov/gene/?term=852123	"YDR511W, ACN9 "	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024304	852149	STL1	http://www.ncbi.nlm.nih.gov/gene/?term=852149	YDR536W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024305	852158	YRF1-1	http://www.ncbi.nlm.nih.gov/gene/?term=852158	"YDR545W, YRF1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024306	852159	YBL113C	http://www.ncbi.nlm.nih.gov/gene/?term=852159	YBL113C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024307	852160	YBL112C	http://www.ncbi.nlm.nih.gov/gene/?term=852160	YBL112C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024308	852161	YBL111C	http://www.ncbi.nlm.nih.gov/gene/?term=852161	YBL111C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024309	852168	SRO77	http://www.ncbi.nlm.nih.gov/gene/?term=852168	"YBL106C, SNI2, SOP2 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024310	852168	SRO77	http://www.ncbi.nlm.nih.gov/gene/?term=852168	"YBL106C, SNI2, SOP2 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024311	852173	ECM21	http://www.ncbi.nlm.nih.gov/gene/?term=852173	"YBL101C, ART2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024312	852177	ATP1	http://www.ncbi.nlm.nih.gov/gene/?term=852177	YBL099W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024313	852177	ATP1	http://www.ncbi.nlm.nih.gov/gene/?term=852177	YBL099W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024314	852179	BNA4	http://www.ncbi.nlm.nih.gov/gene/?term=852179	YBL098W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024315	8521	GCM1	http://www.ncbi.nlm.nih.gov/gene/?term=8521	"GCMA, hGCMa "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024316	8521	GCM1	http://www.ncbi.nlm.nih.gov/gene/?term=8521	"GCMA, hGCMa "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024317	852200	ATG8	http://www.ncbi.nlm.nih.gov/gene/?term=852200	"YBL078C, APG8, AUT7, CVT5 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024318	852215	PRX1	http://www.ncbi.nlm.nih.gov/gene/?term=852215	YBL064C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024319	852235	COR1	http://www.ncbi.nlm.nih.gov/gene/?term=852235	"YBL045C, QCR1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024320	852235	COR1	http://www.ncbi.nlm.nih.gov/gene/?term=852235	"YBL045C, QCR1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024321	852259	PIM1	http://www.ncbi.nlm.nih.gov/gene/?term=852259	YBL022C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024322	852264	PEP1	http://www.ncbi.nlm.nih.gov/gene/?term=852264	"YBL017C, VPS10, VPT1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024323	852266	ACH1	http://www.ncbi.nlm.nih.gov/gene/?term=852266	YBL015W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024324	852271	SCT1	http://www.ncbi.nlm.nih.gov/gene/?term=852271	"YBL011W, GAT2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024325	852292	DSF2	http://www.ncbi.nlm.nih.gov/gene/?term=852292	YBR007C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024326	8522	GAS7	http://www.ncbi.nlm.nih.gov/gene/?term=8522	MLL/GAS7	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024327	8522	GAS7	http://www.ncbi.nlm.nih.gov/gene/?term=8522	MLL/GAS7	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024328	8522	GAS7	http://www.ncbi.nlm.nih.gov/gene/?term=8522	MLL/GAS7	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024329	852302	GRX7	http://www.ncbi.nlm.nih.gov/gene/?term=852302	YBR014C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024330	852311	CHS3	http://www.ncbi.nlm.nih.gov/gene/?term=852311	"YBR023C, CAL1, CSD2, DIT101, KTI2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024331	852314	ETR1	http://www.ncbi.nlm.nih.gov/gene/?term=852314	"YBR026C, MRF1, MRF1' "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024332	852324	CSG2	http://www.ncbi.nlm.nih.gov/gene/?term=852324	"YBR036C, CLS2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024333	852325	SCO1	http://www.ncbi.nlm.nih.gov/gene/?term=852325	"YBR037C, PET161 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024334	852327	ATP3	http://www.ncbi.nlm.nih.gov/gene/?term=852327	YBR039W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024335	852327	ATP3	http://www.ncbi.nlm.nih.gov/gene/?term=852327	YBR039W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024336	852329	FAT1	http://www.ncbi.nlm.nih.gov/gene/?term=852329	YBR041W	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024337	852329	FAT1	http://www.ncbi.nlm.nih.gov/gene/?term=852329	YBR041W	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024338	852332	TCM62	http://www.ncbi.nlm.nih.gov/gene/?term=852332	YBR044C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024339	852335	ZTA1	http://www.ncbi.nlm.nih.gov/gene/?term=852335	YBR046C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024340	852343	YRO2	http://www.ncbi.nlm.nih.gov/gene/?term=852343	YBR054W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024341	852360	BAP2	http://www.ncbi.nlm.nih.gov/gene/?term=852360	YBR068C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024342	852366	PFF1	http://www.ncbi.nlm.nih.gov/gene/?term=852366	"YBR074W, YBR075W "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024343	85236	HIST1H2BK	http://www.ncbi.nlm.nih.gov/gene/?term=85236	"H2B/S, H2BFAiii, H2BFT, H2BK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024344	85236	HIST1H2BK	http://www.ncbi.nlm.nih.gov/gene/?term=85236	"H2B/S, H2BFAiii, H2BFT, H2BK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024345	852370	ECM33	http://www.ncbi.nlm.nih.gov/gene/?term=852370	YBR078W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024346	852382	IST2	http://www.ncbi.nlm.nih.gov/gene/?term=852382	YBR086C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024347	852382	IST2	http://www.ncbi.nlm.nih.gov/gene/?term=852382	YBR086C	mRNA	Saccharomyces cerevisiae	14691136	Cellular bud	Yeast	In situ hybridization	"We found that IST2 mRNA localized to the bud tip in wild-type cells and in an aux1Δ mutant, lacking the entire AUX1 gene (Fig. 8 A). Similar results were obtained when the localization of ASH1 mRNA was examined (not depicted).  "
RLID00024348	852382	IST2	http://www.ncbi.nlm.nih.gov/gene/?term=852382	YBR086C	mRNA	Saccharomyces cerevisiae	20713510	Cellular bud	Yeast	Chip-seq	"In yeast, the RNA-binding protein She2p binds several mRNAs and targets them for localization at the bud. Here we report that She2p is recruited cotranscriptionally to the nascent bud-localized ASH1, IST2, and EAR1 mRNA. "
RLID00024349	852382	IST2	http://www.ncbi.nlm.nih.gov/gene/?term=852382	YBR086C	mRNA	Saccharomyces cerevisiae	22994588	Cytoplasm	Yeast	qRT-PCR	"Figure 2. Deletion of AUX1 perturbs localization of WSC2, IST2, SRL1 and EAR1 mRNAs. Arrowheads indicate cytoplasmic mRNPs with tagged WSC2, IST2 or EAR1 mRNA.  "
RLID00024350	852389	PHO3	http://www.ncbi.nlm.nih.gov/gene/?term=852389	YBR092C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024351	852393	YBR096W	http://www.ncbi.nlm.nih.gov/gene/?term=852393	YBR096W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024352	852398	EXO84	http://www.ncbi.nlm.nih.gov/gene/?term=852398	"YBR102C, USA3 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024353	852398	EXO84	http://www.ncbi.nlm.nih.gov/gene/?term=852398	"YBR102C, USA3 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown.
RLID00024354	852398	EXO84	http://www.ncbi.nlm.nih.gov/gene/?term=852398	"YBR102C, USA3 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024355	852407	ALG1	http://www.ncbi.nlm.nih.gov/gene/?term=852407	YBR110W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024356	852407	ALG1	http://www.ncbi.nlm.nih.gov/gene/?term=852407	YBR110W	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024357	852429	AGP2	http://www.ncbi.nlm.nih.gov/gene/?term=852429	YBR132C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024358	852436	YBR139W	http://www.ncbi.nlm.nih.gov/gene/?term=852436	YBR139W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024359	852456	IFA38	http://www.ncbi.nlm.nih.gov/gene/?term=852456	YBR159W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024360	852463	UBS1	http://www.ncbi.nlm.nih.gov/gene/?term=852463	YBR165W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024361	852482	YBR184W	http://www.ncbi.nlm.nih.gov/gene/?term=852482	YBR184W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024362	852498	KTR4	http://www.ncbi.nlm.nih.gov/gene/?term=852498	YBR199W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024363	852504	KTR3	http://www.ncbi.nlm.nih.gov/gene/?term=852504	YBR205W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024364	852506	FTH1	http://www.ncbi.nlm.nih.gov/gene/?term=852506	YBR207W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024365	852521	YBR220C	http://www.ncbi.nlm.nih.gov/gene/?term=852521	YBR220C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024366	852522	PDB1	http://www.ncbi.nlm.nih.gov/gene/?term=852522	YBR221C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024367	852523	PCS60	http://www.ncbi.nlm.nih.gov/gene/?term=852523	"YBR222C, FAT2 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024368	852523	PCS60	http://www.ncbi.nlm.nih.gov/gene/?term=852523	"YBR222C, FAT2 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024369	852543	YBR241C	http://www.ncbi.nlm.nih.gov/gene/?term=852543	YBR241C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024370	852565	SHM1	http://www.ncbi.nlm.nih.gov/gene/?term=852565	"YBR263W, SHMT1, TMP3 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024371	852583	SAF1	http://www.ncbi.nlm.nih.gov/gene/?term=852583	YBR280C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024372	852586	SSH1	http://www.ncbi.nlm.nih.gov/gene/?term=852586	YBR283C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024373	852589	APE3	http://www.ncbi.nlm.nih.gov/gene/?term=852589	"YBR286W, APY1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024374	852590	YBR287W	http://www.ncbi.nlm.nih.gov/gene/?term=852590	YBR287W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024375	852599	PHO89	http://www.ncbi.nlm.nih.gov/gene/?term=852599	"YBR296C, ITN1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024376	8525	DGKZ	http://www.ncbi.nlm.nih.gov/gene/?term=8525	"DAGK5, DAGK6, DGK-ZETA, hDGKzeta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024377	8525	DGKZ	http://www.ncbi.nlm.nih.gov/gene/?term=8525	"DAGK5, DAGK6, DGK-ZETA, hDGKzeta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024378	852623	SHE10	http://www.ncbi.nlm.nih.gov/gene/?term=852623	YGL228W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024379	852637	ZRT1	http://www.ncbi.nlm.nih.gov/gene/?term=852637	YGL255W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024380	852654	MDM34	http://www.ncbi.nlm.nih.gov/gene/?term=852654	"YGL219C, MMM2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024381	852667	POX1	http://www.ncbi.nlm.nih.gov/gene/?term=852667	"YGL205W, FOX1 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024382	852667	POX1	http://www.ncbi.nlm.nih.gov/gene/?term=852667	"YGL205W, FOX1 "	mRNA	Saccharomyces cerevisiae	19903887	Mitochondrion	Yeast	RT-PCR	"We next examined the localization of POX1 mRNA in cells expressing Oxa1-RFP, a mitochondrial marker, and found that 44% of POX1 granules colocalized with mitochondria (Table S4). In contrast, 82% of OXA1 mRNA granules [which localize to mitochondria (13, 14)] colocalized with Oxa1-RFP. The large number of cells having POX1 mRNA localized to mitochondria might stem from the fact that Oxa1-RFP-labeled mitochondria fill a substantial volume of the cell. "
RLID00024383	852667	POX1	http://www.ncbi.nlm.nih.gov/gene/?term=852667	"YGL205W, FOX1 "	mRNA	Saccharomyces cerevisiae	19903887	Endoplasmic reticulum	Yeast	RT-PCR	"To further analyze the specificity of mPP targeting, we examined the localization of the POX1 and GPD1 mRNAs in cells expressing Sec63-RFP (Fig. S1 B and C and Table S3). Interestingly, a high percentage of both RNAs colocalized with Sec63-RFP (59% and 71%, respectively; Table S3 and Fig. S1B and C). While mRNA localization to the ER could be due to the fact that ER fills much of the cell volume (see, e.g., Fig. S1B and C), we also demonstrated that peroxisomes decorate both nuclear and cortical ER (Fig. S1D). Thus, discerning whether mPP localization to the ER results from a direct association with ER membranes or is a consequence of binding to ER-associated peroxisomes is difficult. Alternatively, GPD1 mRNA, which encodes a glycerol-3-phosphate dehydrogenase found in the cytosol and peroxisomes, may preferentially localize to ER-like mRNAs encoding cytoplasmic proteins (13). This could allow for protein distribution to either compartment. Data are collected from Table S3: Localization of mPPs to ER. "
RLID00024384	852667	POX1	http://www.ncbi.nlm.nih.gov/gene/?term=852667	"YGL205W, FOX1 "	mRNA	Saccharomyces cerevisiae	19903887	Cell cortex	Yeast	RT-PCR	"To further analyze the specificity of mPP targeting, we examined the localization of the POX1 and GPD1 mRNAs in cells expressing Sec63-RFP (Fig. S1 B and C and Table S3). Interestingly, a high percentage of both RNAs colocalized with Sec63-RFP (59% and 71%, respectively; Table S3 and Fig. S1B and C). While mRNA localization to the ER could be due to the fact that ER fills much of the cell volume (see, e.g., Fig. S1B and C), we also demonstrated that peroxisomes decorate both nuclear and cortical ER (Fig. S1D). Thus, discerning whether mPP localization to the ER results from a direct association with ER membranes or is a consequence of binding to ER-associated peroxisomes is difficult. Alternatively, GPD1 mRNA, which encodes a glycerol-3-phosphate dehydrogenase found in the cytosol and peroxisomes, may preferentially localize to ER-like mRNAs encoding cytoplasmic proteins (13). This could allow for protein distribution to either compartment. Data are collected from Table S3: Localization of mPPs to ER. "
RLID00024385	852667	POX1	http://www.ncbi.nlm.nih.gov/gene/?term=852667	"YGL205W, FOX1 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024386	852670	KEX1	http://www.ncbi.nlm.nih.gov/gene/?term=852670	YGL203C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024387	852675	EMP24	http://www.ncbi.nlm.nih.gov/gene/?term=852675	"YGL200C, BST2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024388	8526	DGKE	http://www.ncbi.nlm.nih.gov/gene/?term=8526	"AHUS7, DAGK5, DAGK6, DGK, NPHS7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024389	852708	HUR1	http://www.ncbi.nlm.nih.gov/gene/?term=852708	YGL168W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024390	852709	PMR1	http://www.ncbi.nlm.nih.gov/gene/?term=852709	"YGL167C, BSD1, LDB1, SSC1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024391	852716	AIM14	http://www.ncbi.nlm.nih.gov/gene/?term=852716	"YGL160W, YNO1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024392	852724	PEX14	http://www.ncbi.nlm.nih.gov/gene/?term=852724	YGL153W	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024393	852724	PEX14	http://www.ncbi.nlm.nih.gov/gene/?term=852724	YGL153W	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024394	852738	FLC3	http://www.ncbi.nlm.nih.gov/gene/?term=852738	YGL139W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024395	852764	YGL114W	http://www.ncbi.nlm.nih.gov/gene/?term=852764	YGL114W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024396	852775	RPL28	http://www.ncbi.nlm.nih.gov/gene/?term=852775	"YGL103W, CYH2 "	mRNA	Saccharomyces cerevisiae	8405926	Ribosome	Yeast	Northern blot	"Fig. 1. Segregation of secretory protein mRNA to membrane- bound ribosomes. Northern blot analysis with CYH2, PRC1 and PH05. DNA fragments from the genes CYH2, PRC1 and PH05 hybridized to a Northern blot of 1 ug poly(A)+-RNA from membrane-bound (MBP) and free polysomes (FP). Data are collected from Figure 1. "
RLID00024397	852780	USE1	http://www.ncbi.nlm.nih.gov/gene/?term=852780	"YGL098W, SLT1 "	mRNA	Saccharomyces cerevisiae	21705432	Nucleus	Yeast	Microarray|RT-PCR	"We found that the USE1 and YIP3 mRNAs localized primarily with ER peripheral to the nucleus (nuclear ER; nER) (i.e., 52% colocalization with nER and 26% colocalization with cER for USE1 [78% ER total]; and 40% colocalization with nER and 29% colocalization with cER for YIP3 [69% ER total]) (data not shown), but exhibited only low levels of colocalization with mitochondria (e.g., 28% and 32%) (Table 1). "
RLID00024398	852780	USE1	http://www.ncbi.nlm.nih.gov/gene/?term=852780	"YGL098W, SLT1 "	mRNA	Saccharomyces cerevisiae	21705432	Cell cortex	Yeast	Microarray|RT-PCR	"We found that the USE1 and YIP3 mRNAs localized primarily with ER peripheral to the nucleus (nuclear ER; nER) (i.e., 52% colocalization with nER and 26% colocalization with cER for USE1 [78% ER total]; and 40% colocalization with nER and 29% colocalization with cER for YIP3 [69% ER total]) (data not shown), but exhibited only low levels of colocalization with mitochondria (e.g., 28% and 32%) (Table 1). "
RLID00024399	852780	USE1	http://www.ncbi.nlm.nih.gov/gene/?term=852780	"YGL098W, SLT1 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024400	852780	USE1	http://www.ncbi.nlm.nih.gov/gene/?term=852780	"YGL098W, SLT1 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024401	8527	DGKD	http://www.ncbi.nlm.nih.gov/gene/?term=8527	"DGKdelta, dgkd-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024402	8527	DGKD	http://www.ncbi.nlm.nih.gov/gene/?term=8527	"DGKdelta, dgkd-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024403	852813	NPY1	http://www.ncbi.nlm.nih.gov/gene/?term=852813	YGL067W	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024404	852813	NPY1	http://www.ncbi.nlm.nih.gov/gene/?term=852813	YGL067W	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024405	852825	OLE1	http://www.ncbi.nlm.nih.gov/gene/?term=852825	"YGL055W, MDM2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024406	852830	MST27	http://www.ncbi.nlm.nih.gov/gene/?term=852830	YGL051W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024407	852844	YGL039W	http://www.ncbi.nlm.nih.gov/gene/?term=852844	YGL039W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024408	852857	CWH41	http://www.ncbi.nlm.nih.gov/gene/?term=852857	"YGL027C, DER7, GLS1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024409	852862	STT3	http://www.ncbi.nlm.nih.gov/gene/?term=852862	YGL022W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024410	852872	ERG4	http://www.ncbi.nlm.nih.gov/gene/?term=852872	YGL012W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024411	852874	MPO1	http://www.ncbi.nlm.nih.gov/gene/?term=852874	YGL010W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024412	852876	PMA1	http://www.ncbi.nlm.nih.gov/gene/?term=852876	"YGL008C, KTI10 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024413	852892	SEC9	http://www.ncbi.nlm.nih.gov/gene/?term=852892	"YGR009C, HSS7 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024414	852892	SEC9	http://www.ncbi.nlm.nih.gov/gene/?term=852892	"YGR009C, HSS7 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024415	852905	MTL1	http://www.ncbi.nlm.nih.gov/gene/?term=852905	YGR023W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024416	852905	MTL1	http://www.ncbi.nlm.nih.gov/gene/?term=852905	YGR023W	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p colocalizes with a subset of mRNAs at the bud-tip of yeast cells.The U1A-GFP-tagged RNAs for ASH1, MID2, MTL1, and WSC2 colocalized with Khd1p, whereas BRO1 and TPO3 mRNAs did not colocalize. "
RLID00024417	852910	YGR026W	http://www.ncbi.nlm.nih.gov/gene/?term=852910	YGR026W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024418	852919	IMO32	http://www.ncbi.nlm.nih.gov/gene/?term=852919	YGR031W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024419	852920	GSC2	http://www.ncbi.nlm.nih.gov/gene/?term=852920	"YGR032W, FKS2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024420	852921	TIM21	http://www.ncbi.nlm.nih.gov/gene/?term=852921	YGR033C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024421	852937	TAM41	http://www.ncbi.nlm.nih.gov/gene/?term=852937	"YGR046W, MMP37 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024422	852946	MUP1	http://www.ncbi.nlm.nih.gov/gene/?term=852946	YGR055W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024423	852968	PEX8	http://www.ncbi.nlm.nih.gov/gene/?term=852968	"YGR077C, PAS6 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024424	852968	PEX8	http://www.ncbi.nlm.nih.gov/gene/?term=852968	"YGR077C, PAS6 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024425	852980	NNF2	http://www.ncbi.nlm.nih.gov/gene/?term=852980	YGR089W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024426	852998	VOA1	http://www.ncbi.nlm.nih.gov/gene/?term=852998	YGR106C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024427	853009	SHY1	http://www.ncbi.nlm.nih.gov/gene/?term=853009	YGR112W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024428	853019	MEP1	http://www.ncbi.nlm.nih.gov/gene/?term=853019	"YGR121C, AMT1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024429	853026	YGR125W	http://www.ncbi.nlm.nih.gov/gene/?term=853026	YGR125W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024430	853039	TPO2	http://www.ncbi.nlm.nih.gov/gene/?term=853039	YGR138C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024431	853042	VPS62	http://www.ncbi.nlm.nih.gov/gene/?term=853042	YGR141W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024432	853045	SKN1	http://www.ncbi.nlm.nih.gov/gene/?term=853045	YGR143W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024433	853050	NAT2	http://www.ncbi.nlm.nih.gov/gene/?term=853050	YGR147C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024434	853052	YGR149W	http://www.ncbi.nlm.nih.gov/gene/?term=853052	YGR149W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024435	853053	CCM1	http://www.ncbi.nlm.nih.gov/gene/?term=853053	"YGR150C, DMR1, RRG2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024436	853061	CHO2	http://www.ncbi.nlm.nih.gov/gene/?term=853061	"YGR157W, PEM1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024437	85308	Emc9	http://www.ncbi.nlm.nih.gov/gene/?term=85308	"1500005A01Rik, Cgi112, Fam158a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00024438	853102	CRH1	http://www.ncbi.nlm.nih.gov/gene/?term=853102	YGR189C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024439	853104	HIP1	http://www.ncbi.nlm.nih.gov/gene/?term=853104	YGR191W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024440	853111	SNG1	http://www.ncbi.nlm.nih.gov/gene/?term=853111	YGR197C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024441	853139	AZR1	http://www.ncbi.nlm.nih.gov/gene/?term=853139	YGR224W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024442	853146	PHB2	http://www.ncbi.nlm.nih.gov/gene/?term=853146	YGR231C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024443	853151	SPG1	http://www.ncbi.nlm.nih.gov/gene/?term=853151	YGR236C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024444	853153	KEL2	http://www.ncbi.nlm.nih.gov/gene/?term=853153	YGR238C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024445	853154	PEX21	http://www.ncbi.nlm.nih.gov/gene/?term=853154	YGR239C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024446	853159	LSC2	http://www.ncbi.nlm.nih.gov/gene/?term=853159	YGR244C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024447	853159	LSC2	http://www.ncbi.nlm.nih.gov/gene/?term=853159	YGR244C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024448	85315	PAQR8	http://www.ncbi.nlm.nih.gov/gene/?term=85315	"C6orf33, LMPB1, MPRB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024449	85315	PAQR8	http://www.ncbi.nlm.nih.gov/gene/?term=85315	"C6orf33, LMPB1, MPRB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024450	85315	PAQR8	http://www.ncbi.nlm.nih.gov/gene/?term=85315	"C6orf33, LMPB1, MPRB "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024451	853196	SCW4	http://www.ncbi.nlm.nih.gov/gene/?term=853196	YGR279C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024452	853198	YOR1	http://www.ncbi.nlm.nih.gov/gene/?term=853198	"YGR281W, YRS1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024453	853199	BGL2	http://www.ncbi.nlm.nih.gov/gene/?term=853199	"YGR282C, SCW9 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024454	8531	YBX3	http://www.ncbi.nlm.nih.gov/gene/?term=8531	"CSDA, CSDA1, DBPA, ZONAB "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024455	8531	YBX3	http://www.ncbi.nlm.nih.gov/gene/?term=8531	"CSDA, CSDA1, DBPA, ZONAB "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024456	8531	YBX3	http://www.ncbi.nlm.nih.gov/gene/?term=8531	"CSDA, CSDA1, DBPA, ZONAB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024457	853201	ERV29	http://www.ncbi.nlm.nih.gov/gene/?term=853201	YGR284C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024458	853203	BIO2	http://www.ncbi.nlm.nih.gov/gene/?term=853203	YGR286C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024459	853212	COS6	http://www.ncbi.nlm.nih.gov/gene/?term=853212	YGR295C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024460	853213	YRF1-3	http://www.ncbi.nlm.nih.gov/gene/?term=853213	"YGR296W, YRF1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024461	853216	HXT8	http://www.ncbi.nlm.nih.gov/gene/?term=853216	YJL214W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024462	853231	YJL225C	http://www.ncbi.nlm.nih.gov/gene/?term=853231	YJL225C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024463	853233	VTH2	http://www.ncbi.nlm.nih.gov/gene/?term=853233	YJL222W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024464	853236	HXT9	http://www.ncbi.nlm.nih.gov/gene/?term=853236	YJL219W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024465	853265	KRE9	http://www.ncbi.nlm.nih.gov/gene/?term=853265	YJL174W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024466	853267	CPS1	http://www.ncbi.nlm.nih.gov/gene/?term=853267	YJL172W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024467	853276	YJL163C	http://www.ncbi.nlm.nih.gov/gene/?term=853276	YJL163C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024468	853280	PIR5	http://www.ncbi.nlm.nih.gov/gene/?term=853280	YJL160C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024469	853281	HSP150	http://www.ncbi.nlm.nih.gov/gene/?term=853281	"YJL159W, CCW7, ORE1, PIR2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024470	853282	CIS3	http://www.ncbi.nlm.nih.gov/gene/?term=853282	"YJL158C, CCW11, CCW5, PIR4, SCW8 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024471	853297	YJL144W	http://www.ncbi.nlm.nih.gov/gene/?term=853297	YJL144W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024472	8532	CPZ	http://www.ncbi.nlm.nih.gov/gene/?term=8532		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024473	853304	GLG2	http://www.ncbi.nlm.nih.gov/gene/?term=853304	YJL137C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024474	853307	LCB3	http://www.ncbi.nlm.nih.gov/gene/?term=853307	"YJL134W, LBP1, YSR2 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024475	853325	PHO86	http://www.ncbi.nlm.nih.gov/gene/?term=853325	YJL117W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024476	853356	SIP4	http://www.ncbi.nlm.nih.gov/gene/?term=853356	YJL089W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024477	853357	ARG3	http://www.ncbi.nlm.nih.gov/gene/?term=853357	YJL088W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024478	853366	PRY1	http://www.ncbi.nlm.nih.gov/gene/?term=853366	YJL079C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024479	853392	TIM54	http://www.ncbi.nlm.nih.gov/gene/?term=853392	YJL054W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024480	8533	COPS3	http://www.ncbi.nlm.nih.gov/gene/?term=8533	"CSN3, SGN3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024481	8533	COPS3	http://www.ncbi.nlm.nih.gov/gene/?term=8533	"CSN3, SGN3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024482	8533	COPS3	http://www.ncbi.nlm.nih.gov/gene/?term=8533	"CSN3, SGN3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024483	853405	YJL045W	http://www.ncbi.nlm.nih.gov/gene/?term=853405	YJL045W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024484	853418	KAR2	http://www.ncbi.nlm.nih.gov/gene/?term=853418	"YJL034W, GRP78 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024485	853455	OST1	http://www.ncbi.nlm.nih.gov/gene/?term=853455	"YJL002C, NLT1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024486	853464	MHO1	http://www.ncbi.nlm.nih.gov/gene/?term=853464	YJR008W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024487	853472	YJR015W	http://www.ncbi.nlm.nih.gov/gene/?term=853472	YJR015W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024488	853473	ILV3	http://www.ncbi.nlm.nih.gov/gene/?term=853473	YJR016C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024489	8534	CHST1	http://www.ncbi.nlm.nih.gov/gene/?term=8534	"C6ST, GST-1, KS6ST, KSGal6ST, KSST "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024490	853503	SSC1	http://www.ncbi.nlm.nih.gov/gene/?term=853503	"YJR045C, ENS1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024491	853503	SSC1	http://www.ncbi.nlm.nih.gov/gene/?term=853503	"YJR045C, ENS1 "	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024492	853510	OSM1	http://www.ncbi.nlm.nih.gov/gene/?term=853510	YJR051W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024493	853528	ARP3	http://www.ncbi.nlm.nih.gov/gene/?term=853528	"YJR065C, ACT4 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024494	853538	HOC1	http://www.ncbi.nlm.nih.gov/gene/?term=853538	YJR075W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024495	853540	MIR1	http://www.ncbi.nlm.nih.gov/gene/?term=853540	YJR077C	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"In contrast, mRNAs encoding Cox6p, Cox5a, Aac1p, and Mir1p are found enriched in free cytoplasmic polysome fractions. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The third family mRNAs were those predominantly associated with free cytoplasmic polysomes (Fig. ?(Fig.1A,1A, lanes F-P), such as COX6, COX5a, AAC1, and MIR1.  "
RLID00024496	853543	AIM24	http://www.ncbi.nlm.nih.gov/gene/?term=853543	"YJR080C, FMP26 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024497	853581	STE24	http://www.ncbi.nlm.nih.gov/gene/?term=853581	"YJR117W, AFC1, PIO2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024498	853584	YJR120W	http://www.ncbi.nlm.nih.gov/gene/?term=853584	YJR120W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024499	853585	ATP2	http://www.ncbi.nlm.nih.gov/gene/?term=853585	YJR121W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024500	853585	ATP2	http://www.ncbi.nlm.nih.gov/gene/?term=853585	YJR121W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024501	853585	ATP2	http://www.ncbi.nlm.nih.gov/gene/?term=853585	YJR121W	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"Some mRNAs exclusively localize to mitochondrion-bound polysomes, such as the ones coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The first family includes mRNAs exclusively localized to polysomes bound to mitochondria (Fig. ?(Fig.1A,1A, lanes M-P), such as ATM1, COX10, TIM44, ATP2, and COT1 mRNAs.  "
RLID00024502	853585	ATP2	http://www.ncbi.nlm.nih.gov/gene/?term=853585	YJR121W	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024503	853585	ATP2	http://www.ncbi.nlm.nih.gov/gene/?term=853585	YJR121W	mRNA	Saccharomyces cerevisiae	21705432	Endoplasmic reticulum	Yeast	Microarray|RT-PCR	TABLE 2. OXA1 and ATP2 mRNA localization to mitochondria and ER.
RLID00024504	85359	DGCR6L	http://www.ncbi.nlm.nih.gov/gene/?term=85359	DGCR6	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024505	85359	DGCR6L	http://www.ncbi.nlm.nih.gov/gene/?term=85359	DGCR6	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024506	8535	CBX4	http://www.ncbi.nlm.nih.gov/gene/?term=8535	"NBP16, PC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024507	853607	YJR142W	http://www.ncbi.nlm.nih.gov/gene/?term=853607	YJR142W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024508	853636	PEX1	http://www.ncbi.nlm.nih.gov/gene/?term=853636	"YKL197C, PAS1 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024509	853636	PEX1	http://www.ncbi.nlm.nih.gov/gene/?term=853636	"YKL197C, PAS1 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024510	853638	YKT6	http://www.ncbi.nlm.nih.gov/gene/?term=853638	YKL196C	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024511	853639	MIA40	http://www.ncbi.nlm.nih.gov/gene/?term=853639	"YKL195W, FMP15, TIM40 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024512	853639	MIA40	http://www.ncbi.nlm.nih.gov/gene/?term=853639	"YKL195W, FMP15, TIM40 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024513	85363	TRIM5	http://www.ncbi.nlm.nih.gov/gene/?term=85363	"RNF88alpha, TRIM5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024514	85363	TRIM5	http://www.ncbi.nlm.nih.gov/gene/?term=85363	"RNF88alpha, TRIM5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024515	853647	PXA2	http://www.ncbi.nlm.nih.gov/gene/?term=853647	"YKL188C, PAT1 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024516	85364	ZCCHC3	http://www.ncbi.nlm.nih.gov/gene/?term=85364	C20orf99	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024517	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	9809065	Cellular bud	Yeast	In situ hybridization	"ASH1 mRNA localizes to the bud tip in Saccharomyces cerevisiae to establish asymmetry of HO expression, important for mating type switching. "
RLID00024518	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	12504008	Cellular bud	Yeast	In situ hybridization	"ASH1 mRNA localizes at the bud tip of late-anaphase yeast, resulting in accumulation of Ash1p in the daughter nucleus. "
RLID00024519	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	14662358	Cellular bud	Yeast	Fluorescence in situ hybridization	Active transport and localized translation of the ASH1 mRNA at the bud tip of the budding yeast Saccharomyces cerevisiae is an essential process that is required for the regulation of the mating type switching.
RLID00024520	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	14691136	Cellular bud	Yeast	In situ hybridization	"We found that IST2 mRNA localized to the bud tip in wild-type cells and in an aux1Δ mutant, lacking the entire AUX1 gene (Fig. 8 A). Similar results were obtained when the localization of ASH1 mRNA was examined (not depicted).  "
RLID00024521	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	15328357	Cellular bud	Yeast	In situ hybridization	"In Saccharomyces cerevisiae, the localization of ASH1 mRNA to the distal tip of budding cells results in the asymmetric sorting of Ash1p to daughter cell nuclei. "
RLID00024522	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	15356266	Cellular bud	Yeast	Fluorescence in situ hybridization	"Figure 6. Arf1p and Pab1p are required for ASH1 mRNA localization to the bud tip. In the wild-type strain, >60% of cells showed the correct localization of ASH1 mRNA in the bud tip at 30 and 16°C. Our results indicate that restricting ASH1 mRNA to the bud tip requires functional ER-Golgi transport. "
RLID00024523	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	15601259	Cellular bud	Yeast	In situ hybridization	Figure 1: Intracellular distribution of ASH1 mRNA DNA oligonucleotide probes (red) complementary to ASH1 mRNA were used for in situ hybridization (left-hand panel). ASH1 mRNA is localized at distal tip of anaphase cells. Also shown (right-hand panel) is the corresponding DAPI (blue)/Nomarski merged image.
RLID00024524	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	15852043	Cellular bud	Yeast	-	"The best understood example of active transport of mRNA is the localization of ASH1 mRNA to the bud tip in S. cerevisiae, which results in the repression of MATING TYPE SWITCHING in the daughter cell (FIG. 1a,b). "
RLID00024525	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	16890529	Ribosome	She2 cell	Fluorescence in situ hybridization	"Here, a genome-wide analysis of translated mRNAs demonstrated that ASH1 is mainly translated on ER bound polysomes.  "
RLID00024526	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. (Fig.1B).1B).  "
RLID00024527	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00024528	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	17588515	Cellular bud	Yeast	Fluorescence in situ hybridization	"To determine if this defective sorting of Ash1p was caused by a decreased localization of the ASH1 mRNA at the bud tip in a khd1 strain, the localization of this transcript was assessed by FISH. "
RLID00024529	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	18413716	Cell cortex	Yeast	qRT-PCR	"In the wild-type strain, 80% of ASH1 mRNA was localized at the distal cortex of the bud. However, in the fun12 mutant, ASH1 mRNA was localized diffusely within the bud (62%), in the neck (16%), or in the mother and bud (12%) (Fig. 2G) "
RLID00024530	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00024531	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	19244342	Cellular bud	Yeast	Fluorescence in situ hybridization	"In yeast, the nucleocytoplasmic shuttling protein She2 binds the ASH1 mRNA and targets it for localization at the bud tip by recruiting the She3p-Myo4p complex. "
RLID00024532	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	20457760	Cellular bud	Yeast	Fluorescence microscopy	"Taken together, our data suggest that continuous transport of ASH1 mRNA to the bud tip is generated by recruiting multiple nonprocessive Myo4 motors to a localizatione element, possibly through interactions with the tetrameric She2. "
RLID00024533	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	20713510	Cytoplasm	Yeast	Fluorescence in situ hybridization	"Altogether, these results provide evidence that the cotranscriptional recruitment of She2p on the ASH1 gene via the Spt4-Spt5 elongation complex is important for cytoplasmic ASH1 mRNA localization. "
RLID00024534	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	20713510	Cellular bud	Yeast	Chip-seq	"In yeast, the RNA-binding protein She2p binds several mRNAs and targets them for localization at the bud. Here we report that She2p is recruited cotranscriptionally to the nascent bud-localized ASH1, IST2, and EAR1 mRNA. "
RLID00024535	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	21705432	Cellular bud	Yeast	Microarray|RT-PCR	"We found that tagged ASH1 and MYO2 mRNAs both localized to the bud tip and showed only a very low level of colocalization with mitochondria (e.g., 18% and 12%, respectively) (Table 1). "
RLID00024536	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	22994588	Endoplasmic reticulum	Yeast	qRT-PCR	Figure 1. Distribution of endogenous ASH1 mRNA is not impaired in a mutant that affects cER segregation. Figure S5. Localization of MS2-tagged ASH1 mRNA in ER segregation or morphology mutants.
RLID00024537	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	22994588	Cellular bud	Yeast	Microscopy	"Together with our previous observation that aux1 cells properly localize ASH1 mRNA, this indicates that ASH1 mRNA is transported to the bud tip independently of ER. Intriguingly, as has been described before, loss of Sec3p increases the number of mislocalizedASH1 mRNP particles, which suggests that Sec3p might have a more direct role in RNA localization at the bud tip (see Discussion). "
RLID00024538	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	24056370	Cellular bud	Yeast	-	"In budding yeast, mRNA localization has been studied mainly using ASH1 mRNA as a model RNA. ASH1 encodes a transcriptional repressor and cell fate determinant and is localized to the tip of the mature bud (the daughter cell).Besides ASH1, more than 30 additional mRNAs are localized in a Myo4p- and She2p-dependent way to the bud tip. "
RLID00024539	853650	ASH1	http://www.ncbi.nlm.nih.gov/gene/?term=853650	YKL185W	mRNA	Saccharomyces cerevisiae	10359695	Cellular bud	Yeast	Fluorescence in situ hybridization	Our live-cell studies reveal that ASH1 mRNA is anchored to cortical sites near the bud tip in vegetative cells as well as near the mating projection during karyogamy (fusion of haploid nuclei upon mating).
RLID00024540	85365	ALG2	http://www.ncbi.nlm.nih.gov/gene/?term=85365	"CDGIi, CMS14, CMSTA3, NET38, hALPG2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024541	85365	ALG2	http://www.ncbi.nlm.nih.gov/gene/?term=85365	"CDGIi, CMS14, CMSTA3, NET38, hALPG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024542	853663	JEN1	http://www.ncbi.nlm.nih.gov/gene/?term=853663	YKL217W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024543	853677	STE3	http://www.ncbi.nlm.nih.gov/gene/?term=853677	"YKL178C, DAF2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024544	853679	ZRT3	http://www.ncbi.nlm.nih.gov/gene/?term=853679	YKL175W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024545	853692	PIR1	http://www.ncbi.nlm.nih.gov/gene/?term=853692	"YKL164C, CCW6 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024546	853693	PIR3	http://www.ncbi.nlm.nih.gov/gene/?term=853693	"YKL163W, CCW8 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024547	85369	STRIP1	http://www.ncbi.nlm.nih.gov/gene/?term=85369	"FAM40A, FAR11A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024548	8536	CAMK1	http://www.ncbi.nlm.nih.gov/gene/?term=8536	CAMKI	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024549	8536	CAMK1	http://www.ncbi.nlm.nih.gov/gene/?term=8536	CAMKI	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024550	8536	CAMK1	http://www.ncbi.nlm.nih.gov/gene/?term=8536	CAMKI	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024551	853706	YKL151C	http://www.ncbi.nlm.nih.gov/gene/?term=853706	YKL151C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024552	853707	MCR1	http://www.ncbi.nlm.nih.gov/gene/?term=853707	YKL150W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024553	853707	MCR1	http://www.ncbi.nlm.nih.gov/gene/?term=853707	YKL150W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024554	853709	SDH1	http://www.ncbi.nlm.nih.gov/gene/?term=853709	YKL148C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024555	853709	SDH1	http://www.ncbi.nlm.nih.gov/gene/?term=853709	YKL148C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024556	853710	AVT3	http://www.ncbi.nlm.nih.gov/gene/?term=853710	YKL146W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024557	853716	SDH3	http://www.ncbi.nlm.nih.gov/gene/?term=853716	"YKL141W, CYB3, YKL4 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024558	853725	YKL133C	http://www.ncbi.nlm.nih.gov/gene/?term=853725	YKL133C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024559	853728	SHE2	http://www.ncbi.nlm.nih.gov/gene/?term=853728	YKL130C	mRNA	Saccharomyces cerevisiae	24056370	Endoplasmic reticulum	Yeast	Binding assay	"FIGURE 3: Recombinant She2p binds to ER microsomes but not to mitochondria. A, pelleting of purified microsomes with recombinant She2p and GST. She2p or GST were mixed with ER membranes or buffer before centrifugation through a 1.2 m sucrose cushion. Equivalent amounts of the pellet (Pel), supernatant (Sup), or input material were analyzed by Western blotting against She2p, GST, or Sec61p. She2p is detectable in the pellet only in the presence of membranes. Spurious amounts of GST can be seen in the pellet fraction. B, the indicated amounts of She2p were incubated with 40 μl of microsomes (corresponding to 40 μg of membrane-associated protein). Input and bound She2p were analyzed by quantitative Western blotting, and the ratio of bound She2p signal versus input was quantified. The mean ratio (in percent) and S.D. of three experiments is displayed. C, purified microsomes or yeast mitochondria were mixed with She2p and pelleted through a sucrose cushion. She2p copellets only with microsomes. Sec61p served as an ER marker, whereas Mcr1p indicated mitochondria. In the absence of membranes, She2p can only be detected in the supernatant. Inp, input. Data are collected from Figure 3. "
RLID00024560	853747	RAD27	http://www.ncbi.nlm.nih.gov/gene/?term=853747	"YKL113C, ERC11, FEN1, RTH1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024561	853753	YKL107W	http://www.ncbi.nlm.nih.gov/gene/?term=853753	YKL107W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024562	853763	MTC2	http://www.ncbi.nlm.nih.gov/gene/?term=853763	YKL098W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024563	853777	MDH1	http://www.ncbi.nlm.nih.gov/gene/?term=853777	YKL085W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024564	853777	MDH1	http://www.ncbi.nlm.nih.gov/gene/?term=853777	YKL085W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024565	85377	MICALL1	http://www.ncbi.nlm.nih.gov/gene/?term=85377	"MICAL-L1, MIRAB13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024566	85377	MICALL1	http://www.ncbi.nlm.nih.gov/gene/?term=85377	"MICAL-L1, MIRAB13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024567	853780	RRP14	http://www.ncbi.nlm.nih.gov/gene/?term=853780	YKL082C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024568	853785	YKL077W	http://www.ncbi.nlm.nih.gov/gene/?term=853785	YKL077W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024569	85379	KIAA1671	http://www.ncbi.nlm.nih.gov/gene/?term=85379		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024570	85379	KIAA1671	http://www.ncbi.nlm.nih.gov/gene/?term=85379		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024571	853801	MNR2	http://www.ncbi.nlm.nih.gov/gene/?term=853801	YKL064W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024572	853820	DCW1	http://www.ncbi.nlm.nih.gov/gene/?term=853820	YKL046C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024573	853832	TUL1	http://www.ncbi.nlm.nih.gov/gene/?term=853832	YKL034W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024574	853882	PRY2	http://www.ncbi.nlm.nih.gov/gene/?term=853882	"YKR013W, YFW12 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024575	85389	SNORD14C	http://www.ncbi.nlm.nih.gov/gene/?term=85389		snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00024576	853916	UTH1	http://www.ncbi.nlm.nih.gov/gene/?term=853916	YKR042W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024577	85391	SNORD14E	http://www.ncbi.nlm.nih.gov/gene/?term=85391		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024578	85391	SNORD14E	http://www.ncbi.nlm.nih.gov/gene/?term=85391		snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00024579	853940	CCP1	http://www.ncbi.nlm.nih.gov/gene/?term=853940	YKR066C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024580	853940	CCP1	http://www.ncbi.nlm.nih.gov/gene/?term=853940	YKR066C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024581	85395	FAM207A	http://www.ncbi.nlm.nih.gov/gene/?term=85395	"C21orf70, PRED56 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024582	85397	RGS8	http://www.ncbi.nlm.nih.gov/gene/?term=85397		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024583	853991	VPS68	http://www.ncbi.nlm.nih.gov/gene/?term=853991	YOL129W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024584	8539	API5	http://www.ncbi.nlm.nih.gov/gene/?term=8539	"AAC-11, AAC11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024585	8539	API5	http://www.ncbi.nlm.nih.gov/gene/?term=8539	"AAC-11, AAC11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024586	8539	API5	http://www.ncbi.nlm.nih.gov/gene/?term=8539	"AAC-11, AAC11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024587	854009	HXT11	http://www.ncbi.nlm.nih.gov/gene/?term=854009	"YOL156W, LGT3 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024588	854018	PEX11	http://www.ncbi.nlm.nih.gov/gene/?term=854018	"YOL147C, PMP24, PMP27 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024589	854018	PEX11	http://www.ncbi.nlm.nih.gov/gene/?term=854018	"YOL147C, PMP24, PMP27 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024590	854030	MCH4	http://www.ncbi.nlm.nih.gov/gene/?term=854030	YOL119C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024591	85403	EAF1	http://www.ncbi.nlm.nih.gov/gene/?term=85403		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024592	854057	COQ3	http://www.ncbi.nlm.nih.gov/gene/?term=854057	YOL096C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024593	85406	DNAJC14	http://www.ncbi.nlm.nih.gov/gene/?term=85406	"DNAJ, DRIP78, HDJ3, LIP6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024594	85406	DNAJC14	http://www.ncbi.nlm.nih.gov/gene/?term=85406	"DNAJ, DRIP78, HDJ3, LIP6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024595	85406	DNAJC14	http://www.ncbi.nlm.nih.gov/gene/?term=85406	"DNAJ, DRIP78, HDJ3, LIP6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024596	85406	DNAJC14	http://www.ncbi.nlm.nih.gov/gene/?term=85406	"DNAJ, DRIP78, HDJ3, LIP6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024597	854070	PHM7	http://www.ncbi.nlm.nih.gov/gene/?term=854070	YOL084W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024598	854071	ATG34	http://www.ncbi.nlm.nih.gov/gene/?term=854071	YOL083W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024599	854081	DSC2	http://www.ncbi.nlm.nih.gov/gene/?term=854081	YOL073C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024600	8540	AGPS	http://www.ncbi.nlm.nih.gov/gene/?term=8540	"ADAP-S, ADAS, ADHAPS, ADPS, ALDHPSY, RCDP3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024601	854109	RRT8	http://www.ncbi.nlm.nih.gov/gene/?term=854109	YOL048C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024602	854113	PEX15	http://www.ncbi.nlm.nih.gov/gene/?term=854113	"YOL044W, PAS21 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024603	854113	PEX15	http://www.ncbi.nlm.nih.gov/gene/?term=854113	"YOL044W, PAS21 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024604	854127	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=854127	YOL030W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024605	854130	MDM38	http://www.ncbi.nlm.nih.gov/gene/?term=854130	"YOL027C, MKH1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024606	854144	CMK2	http://www.ncbi.nlm.nih.gov/gene/?term=854144	YOL016C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024607	85414	SLC45A3	http://www.ncbi.nlm.nih.gov/gene/?term=85414	"IPCA-2, IPCA-6, IPCA-8, IPCA6, PCANAP2, PCANAP6, PCANAP8, PRST "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024608	85414	SLC45A3	http://www.ncbi.nlm.nih.gov/gene/?term=85414	"IPCA-2, IPCA-6, IPCA-8, IPCA6, PCANAP2, PCANAP6, PCANAP8, PRST "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024609	85415	RHPN2	http://www.ncbi.nlm.nih.gov/gene/?term=85415	"P76RBE, RHOBP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024610	85415	RHPN2	http://www.ncbi.nlm.nih.gov/gene/?term=85415	"P76RBE, RHOBP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024611	85415	RHPN2	http://www.ncbi.nlm.nih.gov/gene/?term=85415	"P76RBE, RHOBP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024612	85415	RHPN2	http://www.ncbi.nlm.nih.gov/gene/?term=85415	"P76RBE, RHOBP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024613	85415	RHPN2	http://www.ncbi.nlm.nih.gov/gene/?term=85415	"P76RBE, RHOBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024614	854170	SLG1	http://www.ncbi.nlm.nih.gov/gene/?term=854170	"YOR008C, HCS77, WSC1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024615	854188	AHC1	http://www.ncbi.nlm.nih.gov/gene/?term=854188	YOR023C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024616	8541	PPFIA3	http://www.ncbi.nlm.nih.gov/gene/?term=8541	LPNA3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024617	854201	PEP12	http://www.ncbi.nlm.nih.gov/gene/?term=854201	"YOR036W, VPL6, VPS6, VPT13 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024618	854201	PEP12	http://www.ncbi.nlm.nih.gov/gene/?term=854201	"YOR036W, VPL6, VPS6, VPT13 "	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024619	854231	CYT1	http://www.ncbi.nlm.nih.gov/gene/?term=854231	"YOR065W, CTC1, YOR29-16 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024620	854266	KTR1	http://www.ncbi.nlm.nih.gov/gene/?term=854266	YOR099W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024621	854275	LEU9	http://www.ncbi.nlm.nih.gov/gene/?term=854275	YOR108W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024622	8542	APOL1	http://www.ncbi.nlm.nih.gov/gene/?term=8542	"APO-L, APOL, APOL-I, FSGS4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024623	8542	APOL1	http://www.ncbi.nlm.nih.gov/gene/?term=8542	"APO-L, APOL, APOL-I, FSGS4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024624	854303	IDH2	http://www.ncbi.nlm.nih.gov/gene/?term=854303	YOR136W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024625	854303	IDH2	http://www.ncbi.nlm.nih.gov/gene/?term=854303	YOR136W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024626	854310	LSC1	http://www.ncbi.nlm.nih.gov/gene/?term=854310	YOR142W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024627	854332	PNS1	http://www.ncbi.nlm.nih.gov/gene/?term=854332	YOR161C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024628	854352	DCI1	http://www.ncbi.nlm.nih.gov/gene/?term=854352	"YOR180C, ECI2 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024629	854352	DCI1	http://www.ncbi.nlm.nih.gov/gene/?term=854352	"YOR180C, ECI2 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024630	854359	TUF1	http://www.ncbi.nlm.nih.gov/gene/?term=854359	YOR187W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024631	854368	PEX27	http://www.ncbi.nlm.nih.gov/gene/?term=854368	YOR193W	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024632	854371	LIP5	http://www.ncbi.nlm.nih.gov/gene/?term=854371	YOR196C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024633	85437	ZCRB1	http://www.ncbi.nlm.nih.gov/gene/?term=85437	"MADP-1, MADP1, RBM36, SNRNP31, ZCCHC19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024634	854386	MGM1	http://www.ncbi.nlm.nih.gov/gene/?term=854386	"YOR211C, MNA1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024635	854396	MCT1	http://www.ncbi.nlm.nih.gov/gene/?term=854396	YOR221C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024636	85439	STON2	http://www.ncbi.nlm.nih.gov/gene/?term=85439	"STN2, STNB, STNB2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024637	8543	LMO4	http://www.ncbi.nlm.nih.gov/gene/?term=8543		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024638	854407	MGE1	http://www.ncbi.nlm.nih.gov/gene/?term=854407	"YOR232W, YGE1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024639	85440	DOCK7	http://www.ncbi.nlm.nih.gov/gene/?term=85440	"EIEE23, ZIR2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024640	854419	DGA1	http://www.ncbi.nlm.nih.gov/gene/?term=854419	YOR245C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024641	85441	HELZ2	http://www.ncbi.nlm.nih.gov/gene/?term=85441	"PDIP-1, PRIC285 "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00024642	854421	SRL1	http://www.ncbi.nlm.nih.gov/gene/?term=854421	YOR247W	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00024643	854421	SRL1	http://www.ncbi.nlm.nih.gov/gene/?term=854421	YOR247W	mRNA	Saccharomyces cerevisiae	22994588	Cytoplasm	Yeast	qRT-PCR	"Figure 2. Deletion of AUX1 perturbs localization of WSC2, IST2, SRL1 and EAR1 mRNAs. Arrowheads indicate cytoplasmic mRNPs with tagged WSC2, IST2 or EAR1 mRNA.  "
RLID00024644	85442	KNDC1	http://www.ncbi.nlm.nih.gov/gene/?term=85442	"C10orf23, RASGEF2, bB439H18.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024645	854447	TPO4	http://www.ncbi.nlm.nih.gov/gene/?term=854447	YOR273C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024646	854454	FSH3	http://www.ncbi.nlm.nih.gov/gene/?term=854454	YOR280C	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024647	854494	COT1	http://www.ncbi.nlm.nih.gov/gene/?term=854494	YOR316C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024648	854494	COT1	http://www.ncbi.nlm.nih.gov/gene/?term=854494	YOR316C	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"Some mRNAs exclusively localize to mitochondrion-bound polysomes, such as the ones coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The first family includes mRNAs exclusively localized to polysomes bound to mitochondria (Fig. ?(Fig.1A,1A, lanes M-P), such as ATM1, COX10, TIM44, ATP2, and COT1 mRNAs.  "
RLID00024649	854495	FAA1	http://www.ncbi.nlm.nih.gov/gene/?term=854495	YOR317W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024650	85449	KIAA1755	http://www.ncbi.nlm.nih.gov/gene/?term=85449		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024651	85449	KIAA1755	http://www.ncbi.nlm.nih.gov/gene/?term=85449		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024652	8544	PIR	http://www.ncbi.nlm.nih.gov/gene/?term=8544		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024653	854504	MYO2	http://www.ncbi.nlm.nih.gov/gene/?term=854504	"YOR326W, CDC66 "	mRNA	Saccharomyces cerevisiae	21705432	Cellular bud	Yeast	Microarray|RT-PCR	"We found that tagged ASH1 and MYO2 mRNAs both localized to the bud tip and showed only a very low level of colocalization with mitochondria (e.g., 18% and 12%, respectively) (Table 1). "
RLID00024654	85450	ITPRIP	http://www.ncbi.nlm.nih.gov/gene/?term=85450	"DANGER, KIAA1754, bA127L20, bA127L20.2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024655	85451	UNK	http://www.ncbi.nlm.nih.gov/gene/?term=85451	"UNKEMPT, ZC3H5, ZC3HDC5 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024656	85452	CFAP74	http://www.ncbi.nlm.nih.gov/gene/?term=85452	"C1orf222, KIAA1751 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024657	85452	CFAP74	http://www.ncbi.nlm.nih.gov/gene/?term=85452	"C1orf222, KIAA1751 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024658	854538	CIR2	http://www.ncbi.nlm.nih.gov/gene/?term=854538	YOR356W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024659	854556	ALD4	http://www.ncbi.nlm.nih.gov/gene/?term=854556	"YOR374W, ALD7 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024660	85456	TNKS1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=85456	TAB182	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024661	85458	DIXDC1	http://www.ncbi.nlm.nih.gov/gene/?term=85458	CCD1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024662	85459	CEP295	http://www.ncbi.nlm.nih.gov/gene/?term=85459	KIAA1731	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024663	854622	COX2	http://www.ncbi.nlm.nih.gov/gene/?term=854622	"Q0250, OXI1, OXII "	mRNA	Pisum sativum	11788705	Mitochondrion	Pea	RT-PCR	RT-PCR analysis of 5' to 3'-end-ligated mRNAs identifies the extremities of cox2 transcripts in pea mitochondria.
RLID00024664	85462	FHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=85462		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024665	85462	FHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=85462		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024666	854636	HXT12	http://www.ncbi.nlm.nih.gov/gene/?term=854636	YIL170W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024667	85463	ZC3H12C	http://www.ncbi.nlm.nih.gov/gene/?term=85463	MCPIP3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024668	854642	NIT1	http://www.ncbi.nlm.nih.gov/gene/?term=854642	YIL164C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024669	854644	SUC2	http://www.ncbi.nlm.nih.gov/gene/?term=854644	YIL162W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024670	854644	SUC2	http://www.ncbi.nlm.nih.gov/gene/?term=854644	YIL162W	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024671	854644	SUC2	http://www.ncbi.nlm.nih.gov/gene/?term=854644	YIL162W	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024672	854651	GUT2	http://www.ncbi.nlm.nih.gov/gene/?term=854651	YIL155C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024673	85465	EPT1	http://www.ncbi.nlm.nih.gov/gene/?term=85465	"SELI, SEPI "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024674	854666	AXL2	http://www.ncbi.nlm.nih.gov/gene/?term=854666	"YIL140W, BUD10, SRO4 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024675	854668	TPM2	http://www.ncbi.nlm.nih.gov/gene/?term=854668	YIL138C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024676	854670	OM45	http://www.ncbi.nlm.nih.gov/gene/?term=854670	YIL136W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024677	854681	KGD1	http://www.ncbi.nlm.nih.gov/gene/?term=854681	"YIL125W, OGD1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024678	854681	KGD1	http://www.ncbi.nlm.nih.gov/gene/?term=854681	"YIL125W, OGD1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024679	854683	SIM1	http://www.ncbi.nlm.nih.gov/gene/?term=854683	YIL123W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024680	854685	QDR2	http://www.ncbi.nlm.nih.gov/gene/?term=854685	YIL121W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024681	854688	RHO3	http://www.ncbi.nlm.nih.gov/gene/?term=854688	YIL118W	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024682	854688	RHO3	http://www.ncbi.nlm.nih.gov/gene/?term=854688	YIL118W	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024683	854714	LYS12	http://www.ncbi.nlm.nih.gov/gene/?term=854714	"YIL094C, LYS10, LYS11 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024684	854718	ICE2	http://www.ncbi.nlm.nih.gov/gene/?term=854718	YIL090W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024685	854718	ICE2	http://www.ncbi.nlm.nih.gov/gene/?term=854718	YIL090W	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024686	854721	AVT7	http://www.ncbi.nlm.nih.gov/gene/?term=854721	YIL088C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024687	854764	SYG1	http://www.ncbi.nlm.nih.gov/gene/?term=854764	YIL047C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024688	854765	MET30	http://www.ncbi.nlm.nih.gov/gene/?term=854765	"YIL046W, ZRG11 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024689	854769	PKP1	http://www.ncbi.nlm.nih.gov/gene/?term=854769	YIL042C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024690	85476	GFM1	http://www.ncbi.nlm.nih.gov/gene/?term=85476	"COXPD1, EFG, EFG1, EFGM, EGF1, GFM, hEFG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024691	85476	GFM1	http://www.ncbi.nlm.nih.gov/gene/?term=85476	"COXPD1, EFG, EFG1, EFGM, EGF1, GFM, hEFG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024692	854771	APQ12	http://www.ncbi.nlm.nih.gov/gene/?term=854771	YIL040W	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024693	854772	TED1	http://www.ncbi.nlm.nih.gov/gene/?term=854772	YIL039W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024694	854781	SSM4	http://www.ncbi.nlm.nih.gov/gene/?term=854781	"YIL030C, DOA10, KIS3 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024695	854790	TIM44	http://www.ncbi.nlm.nih.gov/gene/?term=854790	"YIL022W, ISP45, MIM44, MPI1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024696	854790	TIM44	http://www.ncbi.nlm.nih.gov/gene/?term=854790	"YIL022W, ISP45, MIM44, MPI1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024697	854790	TIM44	http://www.ncbi.nlm.nih.gov/gene/?term=854790	"YIL022W, ISP45, MIM44, MPI1 "	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"Some mRNAs exclusively localize to mitochondrion-bound polysomes, such as the ones coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The first family includes mRNAs exclusively localized to polysomes bound to mitochondria (Fig. ?(Fig.1A,1A, lanes M-P), such as ATM1, COX10, TIM44, ATP2, and COT1 mRNAs.  "
RLID00024698	854841	DAL81	http://www.ncbi.nlm.nih.gov/gene/?term=854841	"YIR023W, UGA35 "	mRNA	Saccharomyces cerevisiae	17094940	Cellular bud	Yeast	Fluorescence in situ hybridization	"As described above, the long sequences of these mRNAs (3.4 kb ORF for CSR2 and 2.9 kb ORF for DAL81) might generate signals of the nucleus. To confirm that, 30 -tagged mRNAs, CSR2-U1A and DAL81-U1A, were constructed by insertion of the 4· U1A-tag between their ORF and 30-UTR. CSR2-U1A and DAL81-U1A were expressed from the GAL1 promoter and subjected to the U1A-tag-GFP system. They were detected at the bud-tip but not in the nucleus (Fig. 3A, c and g), whereas signals of both the 50-tagged and the 30-tagged mRNAs were detected in the nucleus and at the bud-tip by in situ hybridization (Fig. 3A, FISH column). These results suggested that CSR2 and DAL81 mRNAs were localized at the bud-tip after transcription. "
RLID00024699	854857	YPS6	http://www.ncbi.nlm.nih.gov/gene/?term=854857	YIR039C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024700	854861	YIR043C	http://www.ncbi.nlm.nih.gov/gene/?term=854861	"YIR043C, YIR044C "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024701	854872	TSL1	http://www.ncbi.nlm.nih.gov/gene/?term=854872	YML100W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024702	854883	RPM2	http://www.ncbi.nlm.nih.gov/gene/?term=854883	YML091C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024703	854886	UFO1	http://www.ncbi.nlm.nih.gov/gene/?term=854886	YML088W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024704	854889	TUB1	http://www.ncbi.nlm.nih.gov/gene/?term=854889	YML085C	mRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00024705	854889	TUB1	http://www.ncbi.nlm.nih.gov/gene/?term=854889	YML085C	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024706	854889	TUB1	http://www.ncbi.nlm.nih.gov/gene/?term=854889	YML085C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024707	8548	BLZF1	http://www.ncbi.nlm.nih.gov/gene/?term=8548	"GOLGIN-45, JEM-1, JEM-1s, JEM1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024708	8548	BLZF1	http://www.ncbi.nlm.nih.gov/gene/?term=8548	"GOLGIN-45, JEM-1, JEM-1s, JEM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024709	854907	COS3	http://www.ncbi.nlm.nih.gov/gene/?term=854907	YML132W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024710	854911	MSC1	http://www.ncbi.nlm.nih.gov/gene/?term=854911	YML128C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024711	854919	NDI1	http://www.ncbi.nlm.nih.gov/gene/?term=854919	YML120C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024712	854925	VAN1	http://www.ncbi.nlm.nih.gov/gene/?term=854925	"YML115C, LDB13, VRG7, VRG8 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024713	854930	COQ5	http://www.ncbi.nlm.nih.gov/gene/?term=854930	"YML110C, DBI56 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024714	854950	CYB2	http://www.ncbi.nlm.nih.gov/gene/?term=854950	"YML054C, FCB2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024715	854950	CYB2	http://www.ncbi.nlm.nih.gov/gene/?term=854950	"YML054C, FCB2 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024716	854950	CYB2	http://www.ncbi.nlm.nih.gov/gene/?term=854950	"YML054C, FCB2 "	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024717	854950	CYB2	http://www.ncbi.nlm.nih.gov/gene/?term=854950	"YML054C, FCB2 "	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	"Out of 24 tagged mMPs, we found that the ATM1, ATP2, ATP10, CYB2, COX10,MDM10, and OXA1 mRNA granules exhibited very high levels of colocalization with mitochondria (e.g., >80%), while the CBS1, CYC3, and FIS1 mRNAs demonstrated low levels of colocalization (i.e., �4%) on glucose-containing medium (Fig. 1A; Table 1). Taken together, the data suggest that the 3�UTR is necessary for ATP2 and OXA1 mRNA localization to mitochondria (Table 3). "
RLID00024718	85495	RPPH1	http://www.ncbi.nlm.nih.gov/gene/?term=85495	"H1RNA-1, RPPH1 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024719	85495	RPPH1	http://www.ncbi.nlm.nih.gov/gene/?term=85495	"H1RNA-1, RPPH1 "	tRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00024720	85495	RPPH1	http://www.ncbi.nlm.nih.gov/gene/?term=85495	"H1RNA-1, RPPH1 "	lncRNA	Homo sapiens	25690653	Cytoplasm	P493-6 cell	qRT-PCR	"To validate the isolation of nuclear and cytoplasmic fractions, the enrichment of 3 nuclear (ANRIL, MIAT, XIST) and 3 cytoplasmic (RPPH1, DANCR, tRNA-Lys) RNAs was analyzed by qRT-PCR. "
RLID00024721	854969	YML039W	http://www.ncbi.nlm.nih.gov/gene/?term=854969	YML039W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024722	8549	LGR5	http://www.ncbi.nlm.nih.gov/gene/?term=8549	"FEX, GPR49, GPR67, GRP49, HG38 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024723	8549	LGR5	http://www.ncbi.nlm.nih.gov/gene/?term=8549	"FEX, GPR49, GPR67, GRP49, HG38 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024724	8549	LGR5	http://www.ncbi.nlm.nih.gov/gene/?term=8549	"FEX, GPR49, GPR67, GRP49, HG38 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024725	855020	PLB1	http://www.ncbi.nlm.nih.gov/gene/?term=855020	YMR008C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024726	855023	HXT2	http://www.ncbi.nlm.nih.gov/gene/?term=855023	YMR011W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024727	855029	ERG5	http://www.ncbi.nlm.nih.gov/gene/?term=855029	"YMR015C, CYP61 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024728	855041	PEX12	http://www.ncbi.nlm.nih.gov/gene/?term=855041	"YMR026C, PAS11 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024729	855041	PEX12	http://www.ncbi.nlm.nih.gov/gene/?term=855041	"YMR026C, PAS11 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024730	855061	IOC4	http://www.ncbi.nlm.nih.gov/gene/?term=855061	YMR044W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024731	855070	YMR050C	http://www.ncbi.nlm.nih.gov/gene/?term=855070	YMR050C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024732	855078	AAC1	http://www.ncbi.nlm.nih.gov/gene/?term=855078	YMR056C	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"In contrast, mRNAs encoding Cox6p, Cox5a, Aac1p, and Mir1p are found enriched in free cytoplasmic polysome fractions. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The third family mRNAs were those predominantly associated with free cytoplasmic polysomes (Fig. ?(Fig.1A,1A, lanes F-P), such as COX6, COX5a, AAC1, and MIR1.  "
RLID00024733	855134	SPG4	http://www.ncbi.nlm.nih.gov/gene/?term=855134	YMR107W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024734	855176	NDE1	http://www.ncbi.nlm.nih.gov/gene/?term=855176	"YMR145C, NDH1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024735	855198	INP2	http://www.ncbi.nlm.nih.gov/gene/?term=855198	YMR163C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024736	855207	EAR1	http://www.ncbi.nlm.nih.gov/gene/?term=855207	YMR171C	mRNA	Saccharomyces cerevisiae	20713510	Cellular bud	Yeast	Chip-seq	"In yeast, the RNA-binding protein She2p binds several mRNAs and targets them for localization at the bud. Here we report that She2p is recruited cotranscriptionally to the nascent bud-localized ASH1, IST2, and EAR1 mRNA. "
RLID00024737	855207	EAR1	http://www.ncbi.nlm.nih.gov/gene/?term=855207	YMR171C	mRNA	Saccharomyces cerevisiae	22994588	Cytoplasm	Yeast	qRT-PCR	"Figure 2. Deletion of AUX1 perturbs localization of WSC2, IST2, SRL1 and EAR1 mRNAs. Arrowheads indicate cytoplasmic mRNPs with tagged WSC2, IST2 or EAR1 mRNA.  "
RLID00024738	855229	SPG5	http://www.ncbi.nlm.nih.gov/gene/?term=855229	YMR191W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024739	855231	MRPL24	http://www.ncbi.nlm.nih.gov/gene/?term=855231	YMR193W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024740	855240	ROT1	http://www.ncbi.nlm.nih.gov/gene/?term=855240	YMR200W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024741	855284	ZRC1	http://www.ncbi.nlm.nih.gov/gene/?term=855284	"YMR243C, OSR1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024742	855315	SCS7	http://www.ncbi.nlm.nih.gov/gene/?term=855315	"YMR272C, FAH1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024743	855335	HAS1	http://www.ncbi.nlm.nih.gov/gene/?term=855335	YMR290C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024744	855343	PRC1	http://www.ncbi.nlm.nih.gov/gene/?term=855343	"YMR297W, CPY1, LBC1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024745	855343	PRC1	http://www.ncbi.nlm.nih.gov/gene/?term=855343	"YMR297W, CPY1, LBC1 "	mRNA	Saccharomyces cerevisiae	8405926	Ribosome	Yeast	Northern blot	"Fig. 1. Segregation of secretory protein mRNA to membrane- bound ribosomes. Northern blot analysis with CYH2, PRC1 and PH05. DNA fragments from the genes CYH2, PRC1 and PH05 hybridized to a Northern blot of 1 ug poly(A)+-RNA from membrane-bound (MBP) and free polysomes (FP). Data are collected from Figure 1. "
RLID00024746	855347	ATM1	http://www.ncbi.nlm.nih.gov/gene/?term=855347	YMR301C	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"Some mRNAs exclusively localize to mitochondrion-bound polysomes, such as the ones coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The first family includes mRNAs exclusively localized to polysomes bound to mitochondria (Fig.(Fig.1A,1A, lanes M-P), such as ATM1, COX10, TIM44, ATP2, and COT1 mRNAs.  "
RLID00024747	855347	ATM1	http://www.ncbi.nlm.nih.gov/gene/?term=855347	YMR301C	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	"Out of 24 tagged mMPs, we found that the ATM1, ATP2, ATP10, CYB2, COX10,MDM10, and OXA1 mRNA granules exhibited very high levels of colocalization with mitochondria (e.g., >80%), while the CBS1, CYC3, and FIS1 mRNAs demonstrated low levels of colocalization (i.e., �4%) on glucose-containing medium (Fig. 1A; Table 1). Taken together, the data suggest that the 3�UTR is necessary for ATP2 and OXA1 mRNA localization to mitochondria (Table 3). "
RLID00024748	855348	YME2	http://www.ncbi.nlm.nih.gov/gene/?term=855348	"YMR302C, PRP12, RNA12 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024749	855355	GAS1	http://www.ncbi.nlm.nih.gov/gene/?term=855355	"YMR307W, CWH52, GGP1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024750	855369	FET4	http://www.ncbi.nlm.nih.gov/gene/?term=855369	YMR319C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024751	855380	COS1	http://www.ncbi.nlm.nih.gov/gene/?term=855380	YNL336W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024752	855383	SNZ2	http://www.ncbi.nlm.nih.gov/gene/?term=855383	YNL333W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024753	855387	PEX6	http://www.ncbi.nlm.nih.gov/gene/?term=855387	"YNL329C, PAS8 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024754	855389	EGT2	http://www.ncbi.nlm.nih.gov/gene/?term=855389	YNL327W	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00024755	855394	KRE1	http://www.ncbi.nlm.nih.gov/gene/?term=855394	YNL322C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024756	855411	BXI1	http://www.ncbi.nlm.nih.gov/gene/?term=855411	"YNL305C, YBH3 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024757	855422	RIM21	http://www.ncbi.nlm.nih.gov/gene/?term=855422	"YNL294C, PAL2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024758	855438	WSC2	http://www.ncbi.nlm.nih.gov/gene/?term=855438	"YNL283C, STA3 "	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p colocalizes with a subset of mRNAs at the bud-tip of yeast cells.The U1A-GFP-tagged RNAs for ASH1, MID2, MTL1, and WSC2 colocalized with Khd1p, whereas BRO1 and TPO4 mRNAs did not colocalize. "
RLID00024759	855438	WSC2	http://www.ncbi.nlm.nih.gov/gene/?term=855438	"YNL283C, STA3 "	mRNA	Saccharomyces cerevisiae	22994588	Endoplasmic reticulum	Yeast	qRT-PCR	Figure S4. Co-localization of WSC2-MS2 mRNA and ER in wild type and Δaux1 cells. WSC2-MS2 mRNA was imaged in wild type cells (RJY3786; left) or Δaux1 cells (RJY4168; right) expressing the ER marker protein Scs2-TMD-dsRed.
RLID00024760	855438	WSC2	http://www.ncbi.nlm.nih.gov/gene/?term=855438	"YNL283C, STA3 "	mRNA	Saccharomyces cerevisiae	22994588	Cytoplasm	Yeast	qRT-PCR	"Figure 2. Deletion of AUX1 perturbs localization of WSC2, IST2, SRL1 and EAR1 mRNAs. Arrowheads indicate cytoplasmic mRNPs with tagged WSC2, IST2 or EAR1 mRNA.  "
RLID00024761	855438	WSC2	http://www.ncbi.nlm.nih.gov/gene/?term=855438	"YNL283C, STA3 "	mRNA	Saccharomyces cerevisiae	24906800	Endoplasmic reticulum	Yeast	Flotation assay	"For colocalization studies, MS2L-tagged WSC2 mRNA was expressed in cells carrying Rtn1-mCherry as the ER marker. Wild-type cells showed a colocalization of WSC2-MS2L mRNPs and cortical ER at the bud tip, indicating that both are transported to the bud (Fig.3A, top row).  "
RLID00024762	855438	WSC2	http://www.ncbi.nlm.nih.gov/gene/?term=855438	"YNL283C, STA3 "	mRNA	Saccharomyces cerevisiae	24906800	Cellular bud	Yeast	Flotation assay	"For colocalization studies, MS2L-tagged WSC2 mRNA was expressed in cells carrying Rtn1-mCherry as the ER marker. Wild-type cells showed a colocalization of WSC2-MS2L mRNPs and cortical ER at the bud tip, indicating that both are transported to the bud (Fig.3A, top row).  "
RLID00024763	855441	ERG24	http://www.ncbi.nlm.nih.gov/gene/?term=855441	YNL280C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024764	855444	MET2	http://www.ncbi.nlm.nih.gov/gene/?term=855444	YNL277W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024765	855449	SEC2	http://www.ncbi.nlm.nih.gov/gene/?term=855449	YNL272C	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024766	8554	PIAS1	http://www.ncbi.nlm.nih.gov/gene/?term=8554	"DDXBP1, GBP, GU/RH-II, ZMIZ3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024767	855502	ALG9	http://www.ncbi.nlm.nih.gov/gene/?term=855502	YNL219C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024768	855526	YNL195C	http://www.ncbi.nlm.nih.gov/gene/?term=855526	YNL195C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024769	855527	YNL194C	http://www.ncbi.nlm.nih.gov/gene/?term=855527	YNL194C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024770	855529	CHS1	http://www.ncbi.nlm.nih.gov/gene/?term=855529	"YNL192W, USA4 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024771	855531	YNL190W	http://www.ncbi.nlm.nih.gov/gene/?term=855531	YNL190W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024772	855562	YGP1	http://www.ncbi.nlm.nih.gov/gene/?term=855562	YNL160W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024773	855593	CPT1	http://www.ncbi.nlm.nih.gov/gene/?term=855593	YNL130C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024774	8555	CDC14B	http://www.ncbi.nlm.nih.gov/gene/?term=8555	"CDC14B3, Cdc14B1, Cdc14B2, hCDC14B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024775	855602	TOM70	http://www.ncbi.nlm.nih.gov/gene/?term=855602	"YNL121C, MAS70, MOM72, OMP1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024776	855602	TOM70	http://www.ncbi.nlm.nih.gov/gene/?term=855602	"YNL121C, MAS70, MOM72, OMP1 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024777	855608	YNL115C	http://www.ncbi.nlm.nih.gov/gene/?term=855608	YNL115C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024778	855619	LEU4	http://www.ncbi.nlm.nih.gov/gene/?term=855619	YNL104C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024779	855630	APP1	http://www.ncbi.nlm.nih.gov/gene/?term=855630	YNL094W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024780	855653	LAT1	http://www.ncbi.nlm.nih.gov/gene/?term=855653	"YNL071W, ODP2, PDA2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024781	855675	COX5A	http://www.ncbi.nlm.nih.gov/gene/?term=855675	YNL052W	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"In contrast, mRNAs encoding Cox6p, Cox5a, Aac1p, and Mir1p are found enriched in free cytoplasmic polysome fractions. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The third family mRNAs were those predominantly associated with free cytoplasmic polysomes (Fig. ?(Fig.1A,1A, lanes F-P), such as COX6, COX5a, AAC1, and MIR1.  "
RLID00024782	855683	YIP3	http://www.ncbi.nlm.nih.gov/gene/?term=855683	YNL044W	mRNA	Saccharomyces cerevisiae	21705432	Cell cortex	Yeast	Microarray|RT-PCR	"We found that the USE1 and YIP3 mRNAs localized primarily with ER peripheral to the nucleus (nuclear ER; nER) (i.e., 52% colocalization with nER and 26% colocalization with cER for USE1 [78% ER total]; and 40% colocalization with nER and 29% colocalization with cER for YIP3 [69% ER total]) (data not shown), but exhibited only low levels of colocalization with mitochondria (e.g., 28% and 32%) (Table 1). "
RLID00024783	855683	YIP3	http://www.ncbi.nlm.nih.gov/gene/?term=855683	YNL044W	mRNA	Saccharomyces cerevisiae	21705432	Nucleus	Yeast	Microarray|RT-PCR	"We found that the USE1 and YIP3 mRNAs localized primarily with ER peripheral to the nucleus (nuclear ER; nER) (i.e., 52% colocalization with nER and 26% colocalization with cER for USE1 [78% ER total]; and 40% colocalization with nER and 29% colocalization with cER for YIP3 [69% ER total]) (data not shown), but exhibited only low levels of colocalization with mitochondria (e.g., 28% and 32%) (Table 1). "
RLID00024784	855683	YIP3	http://www.ncbi.nlm.nih.gov/gene/?term=855683	YNL044W	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024785	855683	YIP3	http://www.ncbi.nlm.nih.gov/gene/?term=855683	YNL044W	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024786	855691	IDH1	http://www.ncbi.nlm.nih.gov/gene/?term=855691	YNL037C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024787	8556	CDC14A	http://www.ncbi.nlm.nih.gov/gene/?term=8556	"cdc14, hCDC14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024788	855705	SAM50	http://www.ncbi.nlm.nih.gov/gene/?term=855705	"YNL026W, OMP85, TOB55 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024789	855723	IDP3	http://www.ncbi.nlm.nih.gov/gene/?term=855723	YNL009W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024790	855732	CIT1	http://www.ncbi.nlm.nih.gov/gene/?term=855732	"YNR001C, LYS6 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024791	855732	CIT1	http://www.ncbi.nlm.nih.gov/gene/?term=855732	"YNR001C, LYS6 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024792	855732	CIT1	http://www.ncbi.nlm.nih.gov/gene/?term=855732	"YNR001C, LYS6 "	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024793	855753	ARE2	http://www.ncbi.nlm.nih.gov/gene/?term=855753	"YNR019W, SAT1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024794	8557	TCAP	http://www.ncbi.nlm.nih.gov/gene/?term=8557	"CMD1N, CMH25, LGMD2G, T-cap, TELE, telethonin "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024795	855866	FUM1	http://www.ncbi.nlm.nih.gov/gene/?term=855866	YPL262W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024796	855866	FUM1	http://www.ncbi.nlm.nih.gov/gene/?term=855866	YPL262W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024797	855879	FMP40	http://www.ncbi.nlm.nih.gov/gene/?term=855879	YPL222W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024798	855883	SAR1	http://www.ncbi.nlm.nih.gov/gene/?term=855883	YPL218W	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024799	855886	CBP3	http://www.ncbi.nlm.nih.gov/gene/?term=855886	YPL215W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024800	855914	MF(ALPHA)1	http://www.ncbi.nlm.nih.gov/gene/?term=855914	YPL187W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024801	855927	TRE1	http://www.ncbi.nlm.nih.gov/gene/?term=855927	YPL176C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024802	855931	COX10	http://www.ncbi.nlm.nih.gov/gene/?term=855931	YPL172C	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024803	855931	COX10	http://www.ncbi.nlm.nih.gov/gene/?term=855931	YPL172C	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"Some mRNAs exclusively localize to mitochondrion-bound polysomes, such as the ones coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The first family includes mRNAs exclusively localized to polysomes bound to mitochondria (Fig. ?(Fig.1A,1A, lanes M-P), such as ATM1, COX10, TIM44, ATP2, and COT1 mRNAs.  "
RLID00024804	855931	COX10	http://www.ncbi.nlm.nih.gov/gene/?term=855931	YPL172C	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	TABLE 1: Localization of mRNAs encoding mitochondrial proteins in yeast. Data are collected from Table 1.
RLID00024805	855931	COX10	http://www.ncbi.nlm.nih.gov/gene/?term=855931	YPL172C	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	"Out of 24 tagged mMPs, we found that the ATM1, ATP2, ATP10, CYB2, COX10,MDM10, and OXA1 mRNA granules exhibited very high levels of colocalization with mitochondria (e.g., >80%), while the CBS1, CYC3, and FIS1 mRNAs demonstrated low levels of colocalization (i.e., �4%) on glucose-containing medium (Fig. 1A; Table 1). Taken together, the data suggest that the 3�UTR is necessary for ATP2 and OXA1 mRNA localization to mitochondria (Table 3). "
RLID00024806	855949	PEP4	http://www.ncbi.nlm.nih.gov/gene/?term=855949	"YPL154C, PHO9, PRA1, yscA "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024807	855956	PXA1	http://www.ncbi.nlm.nih.gov/gene/?term=855956	"YPL147W, LPI1, PAL1, PAT2, SSH2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024808	855956	PXA1	http://www.ncbi.nlm.nih.gov/gene/?term=855956	"YPL147W, LPI1, PAL1, PAT2, SSH2 "	mRNA	Saccharomyces cerevisiae	19903887	Peroxisome	Yeast	RT-PCR	"To examine endogenous mPP localization, we used m-TAG to create strains tagged with the MS2L sequence (Table S1). We first localized mRNAs encoding proteins involved in peroxisome biogenesis, called peroxins (PEX1-3, 5-8, 10-15, 17, 19, 21, 22, 27-30, and 32). On the expression of MS2-CP-GFP(x3) in cells bearing the tagged genes, we observed that few had fluorescent RNA granules when grown on glucose-containing medium. But when grown under conditions that induce peroxisome proliferation (i.e., media containing oleate), we saw a large increase in the number of cells bearing fluorescent granules. We then determined that between 56% and 80% of granules seen in the MS2L-tagged PEX1, 5, 8, 11, 12, 13, 14, or 15 strains colocalized with peroxisomes labeled with a peroxisomal matrix marker, RFP-PTS1 (68%, 56%, 66%, 80%, 58%, 78%, 60%, and 78% colocalization, respectively; Fig. 1A and Table S2). Thus, mPPs associate with peroxisomes, although we noted that the number of RFP-labeled peroxisomes observed per cell (2-6) was usually greater than the number of granules (1-3). This may indicate that mPPs are in transient/intermittent association with peroxisomes, or that there are distinct (i.e., mature) peroxisomes that do not associate with mRNA. Data are collected from Table S2. "
RLID00024809	855956	PXA1	http://www.ncbi.nlm.nih.gov/gene/?term=855956	"YPL147W, LPI1, PAL1, PAT2, SSH2 "	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024810	855969	ODC1	http://www.ncbi.nlm.nih.gov/gene/?term=855969	YPL134C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024811	855971	COX11	http://www.ncbi.nlm.nih.gov/gene/?term=855971	"YPL132W, LPI13, PSO7 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024812	8559	PRPF18	http://www.ncbi.nlm.nih.gov/gene/?term=8559	"PRP18, hPrp18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024813	856002	ELP4	http://www.ncbi.nlm.nih.gov/gene/?term=856002	"YPL101W, HAP1, KTI9, TOT7 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024814	856021	BRO1	http://www.ncbi.nlm.nih.gov/gene/?term=856021	"YPL084W, ASI6, LPF2, NPI3, VPS31 "	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00024815	856027	ATP4	http://www.ncbi.nlm.nih.gov/gene/?term=856027	"YPL078C, LPF7 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024816	856027	ATP4	http://www.ncbi.nlm.nih.gov/gene/?term=856027	"YPL078C, LPF7 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024817	856042	TIM50	http://www.ncbi.nlm.nih.gov/gene/?term=856042	YPL063W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024818	856042	TIM50	http://www.ncbi.nlm.nih.gov/gene/?term=856042	YPL063W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024819	856050	SUR1	http://www.ncbi.nlm.nih.gov/gene/?term=856050	"YPL057C, BCL21, CSG1, LPE15 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024820	856054	KTR6	http://www.ncbi.nlm.nih.gov/gene/?term=856054	"YPL053C, MNN6 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024821	856071	PMA2	http://www.ncbi.nlm.nih.gov/gene/?term=856071	YPL036W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024822	8560	DEGS1	http://www.ncbi.nlm.nih.gov/gene/?term=8560	"DEGS, DEGS-1, DES1, Des-1, FADS7, MIG15, MLD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024823	8560	DEGS1	http://www.ncbi.nlm.nih.gov/gene/?term=8560	"DEGS, DEGS-1, DES1, Des-1, FADS7, MIG15, MLD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024824	856107	CIT3	http://www.ncbi.nlm.nih.gov/gene/?term=856107	YPR001W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024825	856107	CIT3	http://www.ncbi.nlm.nih.gov/gene/?term=856107	YPR001W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024826	856137	ATH1	http://www.ncbi.nlm.nih.gov/gene/?term=856137	YPR026W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024827	856142	CSR2	http://www.ncbi.nlm.nih.gov/gene/?term=856142	"YPR030W, ART8, MRG19 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024828	856142	CSR2	http://www.ncbi.nlm.nih.gov/gene/?term=856142	"YPR030W, ART8, MRG19 "	mRNA	Saccharomyces cerevisiae	17094940	Cellular bud	Yeast	Fluorescence in situ hybridization	"As described above, the long sequences of these mRNAs (3.4 kb ORF for CSR2 and 2.9 kb ORF for DAL81) might generate signals of the nucleus. To confirm that, 30 -tagged mRNAs, CSR2-U1A and DAL81-U1A, were constructed by insertion of the 4· U1A-tag between their ORF and 30-UTR. CSR2-U1A and DAL81-U1A were expressed from the GAL1 promoter and subjected to the U1A-tag-GFP system. They were detected at the bud-tip but not in the nucleus (Fig. 3A, c and g), whereas signals of both the 50-tagged and the 30-tagged mRNAs were detected in the nucleus and at the bud-tip by in situ hybridization (Fig. 3A, FISH column). These results suggested that CSR2 and DAL81 mRNAs were localized at the bud-tip after transcription. "
RLID00024829	856144	SRO7	http://www.ncbi.nlm.nih.gov/gene/?term=856144	"YPR032W, SNI1, SOP1 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024830	856144	SRO7	http://www.ncbi.nlm.nih.gov/gene/?term=856144	"YPR032W, SNI1, SOP1 "	mRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00024831	856144	SRO7	http://www.ncbi.nlm.nih.gov/gene/?term=856144	"YPR032W, SNI1, SOP1 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024832	856144	SRO7	http://www.ncbi.nlm.nih.gov/gene/?term=856144	"YPR032W, SNI1, SOP1 "	mRNA	Saccharomyces cerevisiae	17417645	Endoplasmic reticulum	Yeast	qRT-PCR	"We previously demonstrated that SRO7 mRNA undergoes polarized transport, along with cortical ER, to the bud tip11. Thus, PEX3 mRNA localizes to the endoplasmic reticulum, as seen previously11, and Pex3 is functional after MS2L integration into the PEX3 locus. We observed typical tubular-punctate mitochondrial morphology with Oxa1-RFP19.  "
RLID00024833	856144	SRO7	http://www.ncbi.nlm.nih.gov/gene/?term=856144	"YPR032W, SNI1, SOP1 "	mRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00024834	856236	CLB2	http://www.ncbi.nlm.nih.gov/gene/?term=856236	YPR119W	mRNA	Saccharomyces cerevisiae	18805955	Cellular bud	Yeast	qRT-PCR	"Khd1p associates with a subset of bud-tip-localized mRNAs. ASH1, MID2, and MTL1 mRNAs, but not BRO1 mRNA, were detected by RT-PCR in RNAs isolated from total extracts (Input) and from Khd1p-TAP affinity isolations (Khd1p).overexpression inhibits ASH1 expression (Irie et al. 2002). Therefore, we systematically examined whether Khd1p modifies protein expression of other bud-tip-localized mRNAs that are bound by Khd1p (MID2, MTL1, WSC2, SRL1, EGT2, and CLB2).  "
RLID00024835	856243	YLH47	http://www.ncbi.nlm.nih.gov/gene/?term=856243	"YPR125W, MRS7 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024836	856271	YPR148C	http://www.ncbi.nlm.nih.gov/gene/?term=856271	YPR148C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024837	856272	NCE102	http://www.ncbi.nlm.nih.gov/gene/?term=856272	"YPR149W, NCE2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024838	856279	TPO3	http://www.ncbi.nlm.nih.gov/gene/?term=856279	YPR156C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024839	8562	DENR	http://www.ncbi.nlm.nih.gov/gene/?term=8562	"DRP, DRP1, SMAP-3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024840	8562	DENR	http://www.ncbi.nlm.nih.gov/gene/?term=8562	"DRP, DRP1, SMAP-3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024841	8562	DENR	http://www.ncbi.nlm.nih.gov/gene/?term=8562	"DRP, DRP1, SMAP-3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024842	856321	QCR2	http://www.ncbi.nlm.nih.gov/gene/?term=856321	"YPR191W, COR2, UCR2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024843	856321	QCR2	http://www.ncbi.nlm.nih.gov/gene/?term=856321	"YPR191W, COR2, UCR2 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024844	856334	YPR204W	http://www.ncbi.nlm.nih.gov/gene/?term=856334	YPR204W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024845	856335	YHL050C	http://www.ncbi.nlm.nih.gov/gene/?term=856335	YHL050C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024846	856337	COS8	http://www.ncbi.nlm.nih.gov/gene/?term=856337	YHL048W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024847	856353	GUT1	http://www.ncbi.nlm.nih.gov/gene/?term=856353	YHL032C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024848	856354	GOS1	http://www.ncbi.nlm.nih.gov/gene/?term=856354	YHL031C	mRNA	Saccharomyces cerevisiae	23904265	Endoplasmic reticulum	Yeast	Confocal microscopy	"We examined mRNA localization by confocal microscopy and found that 9 of 11 mSMPs tagged (ALG1, GOS1, ICE2, PEP12, PMT2, SUC2, SUR4, USE1, and YIP3) showed high levels of granule colocalization with ER (>70%; Figure 1 and Table 1), and 2 (NYV1 and SEC22) showed lower levels of ER localization (56%; Figure 1 and Table 1). A similar low level of ER localization was observed with two mRNAs that encode soluble SNAREs (SEC9 and SEC20) known to associate with the plasma and ER membranes (Figure 1 and Table 1). Of interest, some preference toward nER localization was observed with mSMPs such as PMT2, SUC2, SUR4, USE1, and YIP3, whereas in contrast, most of the mRNAs encoding SNAREs (e.g., GOS1, NYV1, PEP12, SEC9, and SEC22) demonstrated a preference for cER (Table 1).  Data are collected from Table 1. "
RLID00024849	856365	AIM17	http://www.ncbi.nlm.nih.gov/gene/?term=856365	"YHL021C, FMP12 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024850	856398	ERG11	http://www.ncbi.nlm.nih.gov/gene/?term=856398	"YHR007C, CYP51 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024851	8563	THOC5	http://www.ncbi.nlm.nih.gov/gene/?term=8563	"C22orf19, Fmip, PK1.3, fSAP79 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024852	8563	THOC5	http://www.ncbi.nlm.nih.gov/gene/?term=8563	"C22orf19, Fmip, PK1.3, fSAP79 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024853	856423	DAP2	http://www.ncbi.nlm.nih.gov/gene/?term=856423	"YHR028C, DPP2 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024854	856435	VMA10	http://www.ncbi.nlm.nih.gov/gene/?term=856435	"YHR039C-A, YHR039C-B "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024855	856438	NCP1	http://www.ncbi.nlm.nih.gov/gene/?term=856438	"YHR042W, CPR1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024856	856444	YHK8	http://www.ncbi.nlm.nih.gov/gene/?term=856444	YHR048W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024857	856448	COX6	http://www.ncbi.nlm.nih.gov/gene/?term=856448	YHR051W	mRNA	Saccharomyces cerevisiae	11027259	Ribosome	Yeast	Northern blot	"In contrast, mRNAs encoding Cox6p, Cox5a, Aac1p, and Mir1p are found enriched in free cytoplasmic polysome fractions. Transcripts coding for Atm1p, Cox10p, Tim44p, Atp2p, and Cot1p are exclusively localized to mitochondrion-bound polysomes, while mRNAs encoding Cox6p, Cox5ap, Aac1p, and Mir1p are enriched in free cytoplasmic polysomes. The third family mRNAs were those predominantly associated with free cytoplasmic polysomes (Fig. ?(Fig.1A,1A, lanes F-P), such as COX6, COX5a, AAC1, and MIR1.  "
RLID00024858	856451	YHR054C	http://www.ncbi.nlm.nih.gov/gene/?term=856451	YHR054C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024859	856475	PTC7	http://www.ncbi.nlm.nih.gov/gene/?term=856475	YHR076W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024860	856492	HXT4	http://www.ncbi.nlm.nih.gov/gene/?term=856492	"YHR092C, LGT1, RAG1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024861	856494	HXT1	http://www.ncbi.nlm.nih.gov/gene/?term=856494	"YHR094C, HOR4 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024862	856496	HXT5	http://www.ncbi.nlm.nih.gov/gene/?term=856496	YHR096C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024863	856499	TRA1	http://www.ncbi.nlm.nih.gov/gene/?term=856499	YHR099W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024864	8564	KMO	http://www.ncbi.nlm.nih.gov/gene/?term=8564	dJ317G22.1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024865	8564	KMO	http://www.ncbi.nlm.nih.gov/gene/?term=8564	dJ317G22.1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024866	856500	GEP4	http://www.ncbi.nlm.nih.gov/gene/?term=856500	YHR100C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024867	856517	TOM71	http://www.ncbi.nlm.nih.gov/gene/?term=856517	"YHR117W, TOM72 "	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024868	856533	ECM14	http://www.ncbi.nlm.nih.gov/gene/?term=856533	YHR132C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024869	856535	NSG1	http://www.ncbi.nlm.nih.gov/gene/?term=856535	YHR133C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024870	856541	SPS100	http://www.ncbi.nlm.nih.gov/gene/?term=856541	YHR139C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024871	856543	YHR140W	http://www.ncbi.nlm.nih.gov/gene/?term=856543	YHR140W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024872	856555	PEX28	http://www.ncbi.nlm.nih.gov/gene/?term=856555	YHR150W	mRNA	Saccharomyces cerevisiae	26367800	Peroxisome	Yeast	RT-PCR	Table 1: Predicted yeast mPP translation sites based on ER enrichment and imaging. A list of yeast peroxisomal genes was generated according to PeroxisomeDB 2.0. Data are collected from Table 1.
RLID00024873	8565	YARS	http://www.ncbi.nlm.nih.gov/gene/?term=8565	"CMTDIC, TYRRS, YRS, YTS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024874	8565	YARS	http://www.ncbi.nlm.nih.gov/gene/?term=8565	"CMTDIC, TYRRS, YRS, YTS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024875	8565	YARS	http://www.ncbi.nlm.nih.gov/gene/?term=8565	"CMTDIC, TYRRS, YRS, YTS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024876	856602	NVJ1	http://www.ncbi.nlm.nih.gov/gene/?term=856602	"YHR195W, VAB36 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024877	856606	AIM46	http://www.ncbi.nlm.nih.gov/gene/?term=856606	"YHR199C, FMP34 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024878	856628	YHR218W	http://www.ncbi.nlm.nih.gov/gene/?term=856628	YHR218W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024879	856629	YHR219W	http://www.ncbi.nlm.nih.gov/gene/?term=856629	YHR219W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024880	856630	YEL077C	http://www.ncbi.nlm.nih.gov/gene/?term=856630	YEL077C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024881	856638	DLD3	http://www.ncbi.nlm.nih.gov/gene/?term=856638	YEL071W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024882	856658	AFG1	http://www.ncbi.nlm.nih.gov/gene/?term=856658	YEL052W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024883	856660	RML2	http://www.ncbi.nlm.nih.gov/gene/?term=856660	YEL050C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024884	856668	YEL043W	http://www.ncbi.nlm.nih.gov/gene/?term=856668	YEL043W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024885	856669	GDA1	http://www.ncbi.nlm.nih.gov/gene/?term=856669	YEL042W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024886	856689	RIP1	http://www.ncbi.nlm.nih.gov/gene/?term=856689	YEL024W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024887	856690	YEL023C	http://www.ncbi.nlm.nih.gov/gene/?term=856690	YEL023C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024888	856692	URA3	http://www.ncbi.nlm.nih.gov/gene/?term=856692	YEL021W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024889	856694	YEL020C	http://www.ncbi.nlm.nih.gov/gene/?term=856694	YEL020C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024890	8566	PDXK	http://www.ncbi.nlm.nih.gov/gene/?term=8566	"C21orf124, C21orf97, HEL-S-1a, PKH, PNK, PRED79 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024891	8566	PDXK	http://www.ncbi.nlm.nih.gov/gene/?term=8566	"C21orf124, C21orf97, HEL-S-1a, PKH, PNK, PRED79 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024892	8566	PDXK	http://www.ncbi.nlm.nih.gov/gene/?term=8566	"C21orf124, C21orf97, HEL-S-1a, PKH, PNK, PRED79 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024893	856716	WBP1	http://www.ncbi.nlm.nih.gov/gene/?term=856716	YEL002C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024894	856717	IRC22	http://www.ncbi.nlm.nih.gov/gene/?term=856717	YEL001C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024895	856719	NOP16	http://www.ncbi.nlm.nih.gov/gene/?term=856719	YER002W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024896	856726	SEC3	http://www.ncbi.nlm.nih.gov/gene/?term=856726	"YER008C, PSL1 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	"As SEC4 mRNA is asymmetrically distributed to the bud prior to nuclear division, similar to ASH1 mRNA, we examined the localization of other POL mRNAs by FISH (Fig. 1B). Endogenous mRNAs encoding the Cdc42 and Rho3 GTPases (31); the Sec1, Sro7, and Sro77 SNARE regulators (23,25); the Sec3 and Exo84 exocyst components (27); and Ypt1, a GTPase involved in ER-Golgi transport, localized at least in part to the buds of G2/M phase cells prior to nuclear division. This pattern was discerned in �0% of cells for each mRNA examined (Fig. 1B), indicating that these mRNAs were also exported from mother cells. Asymmetric POL mRNA localization correlates with the bud-specific pattern of protein localization seen during cell division. "
RLID00024897	856726	SEC3	http://www.ncbi.nlm.nih.gov/gene/?term=856726	"YER008C, PSL1 "	mRNA	Saccharomyces cerevisiae	17339339	Cellular bud	Yeast	Fluorescence in situ hybridization	Figure 1B: Endogenous mRNAs encoding bud-localized proteins also localize to the bud tip prior to nuclear division. WT yeast cells were treated as above and hybridized in situ with specific digoxigenin-labeled RNA antisense probes for different POL genes (as labeled). Representative small-budded (early G2/M) cells are shown. Data are collected from Figure 1B.
RLID00024898	856733	HEM14	http://www.ncbi.nlm.nih.gov/gene/?term=856733	YER014W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024899	856745	YAT2	http://www.ncbi.nlm.nih.gov/gene/?term=856745	YER024W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024900	856788	FCY21	http://www.ncbi.nlm.nih.gov/gene/?term=856788	YER060W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024901	856789	FCY22	http://www.ncbi.nlm.nih.gov/gene/?term=856789	YER060W-A	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024902	8567	MADD	http://www.ncbi.nlm.nih.gov/gene/?term=8567	"DENN, IG20, RAB3GEP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024903	8567	MADD	http://www.ncbi.nlm.nih.gov/gene/?term=8567	"DENN, IG20, RAB3GEP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024904	856810	MRX1	http://www.ncbi.nlm.nih.gov/gene/?term=856810	YER077C	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024905	856813	AIM9	http://www.ncbi.nlm.nih.gov/gene/?term=856813	"YER080W, FMP29 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024906	856819	ILV1	http://www.ncbi.nlm.nih.gov/gene/?term=856819	"YER086W, ISO1 "	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024907	856884	COX15	http://www.ncbi.nlm.nih.gov/gene/?term=856884	YER141W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024908	856884	COX15	http://www.ncbi.nlm.nih.gov/gene/?term=856884	YER141W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024909	856893	SPI1	http://www.ncbi.nlm.nih.gov/gene/?term=856893	YER150W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024910	856898	OXA1	http://www.ncbi.nlm.nih.gov/gene/?term=856898	YER154W	mRNA	Saccharomyces cerevisiae	17108321	Mitochondrion	Yeast	RT-PCR	"MRNA from 112 genes was studied, and the percentage of each mRNA associated with mitochondria-bound polysomes was between 0 and 57% (Supplementary Table S1 and Supplementary Figure S1). Data are collected from Table S1 - Biochemical analysis of the mRNA localization of 107 mRNAs coding for the subunits of seven mitochondrial complexes.  "
RLID00024911	856898	OXA1	http://www.ncbi.nlm.nih.gov/gene/?term=856898	YER154W	mRNA	Saccharomyces cerevisiae	17417645	Mitochondrion	Yeast	qRT-PCR	"We previously demonstrated that SRO7 mRNA undergoes polarized transport, along with cortical ER, to the bud tip11. Thus, PEX3 mRNA localizes to the endoplasmic reticulum, as seen previously11, and Pex3 is functional after MS2L integration into the PEX3 locus. We observed typical tubular-punctate mitochondrial morphology with Oxa1-RFP19.  "
RLID00024912	856898	OXA1	http://www.ncbi.nlm.nih.gov/gene/?term=856898	YER154W	mRNA	Saccharomyces cerevisiae	19903887	Mitochondrion	Yeast	RT-PCR	"We next examined the localization of POX1 mRNA in cells expressing Oxa1-RFP, a mitochondrial marker, and found that 44% of POX1 granules colocalized with mitochondria (Table S4). In contrast, 82% of OXA1 mRNA granules [which localize to mitochondria (13, 14)] colocalized with Oxa1-RFP. The large number of cells having POX1 mRNA localized to mitochondria might stem from the fact that Oxa1-RFP-labeled mitochondria fill a substantial volume of the cell. "
RLID00024913	856898	OXA1	http://www.ncbi.nlm.nih.gov/gene/?term=856898	YER154W	mRNA	Saccharomyces cerevisiae	21705432	Mitochondrion	Yeast	Microarray|RT-PCR	"Out of 24 tagged mMPs, we found that the ATM1, ATP2, ATP10, CYB2, COX10,MDM10, and OXA1 mRNA granules exhibited very high levels of colocalization with mitochondria (e.g., >80%), while the CBS1, CYC3, and FIS1 mRNAs demonstrated low levels of colocalization (i.e., �4%) on glucose-containing medium (Fig. 1A; Table 1). Taken together, the data suggest that the 3�UTR is necessary for ATP2 and OXA1 mRNA localization to mitochondria (Table 3). "
RLID00024914	856898	OXA1	http://www.ncbi.nlm.nih.gov/gene/?term=856898	YER154W	mRNA	Saccharomyces cerevisiae	21705432	Endoplasmic reticulum	Yeast	Microarray|RT-PCR	TABLE 2. OXA1 and ATP2 mRNA localization to mitochondria and ER. Data are collected from Table 2.
RLID00024915	8568	RRP1	http://www.ncbi.nlm.nih.gov/gene/?term=8568	"D21S2056E, NNP-1, NOP52A, RRP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024916	856913	DNF1	http://www.ncbi.nlm.nih.gov/gene/?term=856913	YER166W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024917	856925	PDA1	http://www.ncbi.nlm.nih.gov/gene/?term=856925	YER178W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024918	856931	FMP10	http://www.ncbi.nlm.nih.gov/gene/?term=856931	YER182W	mRNA	Saccharomyces cerevisiae	11818335	Mitochondrion	Yeast	Microarray	Genome-wide analysis of mRNAs targeted to yeast mitochondria: all data have been shown in supplementary file : list of the 467 ORFs found to have a mitochondrial localization of mRNA (MLR) >80 in this study.
RLID00024919	8569	MKNK1	http://www.ncbi.nlm.nih.gov/gene/?term=8569	MNK1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024920	8569	MKNK1	http://www.ncbi.nlm.nih.gov/gene/?term=8569	MNK1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024921	8569	MKNK1	http://www.ncbi.nlm.nih.gov/gene/?term=8569	MNK1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024922	8570	KHSRP	http://www.ncbi.nlm.nih.gov/gene/?term=8570	"FBP2, FUBP2, KSRP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024923	8570	KHSRP	http://www.ncbi.nlm.nih.gov/gene/?term=8570	"FBP2, FUBP2, KSRP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024924	8570	KHSRP	http://www.ncbi.nlm.nih.gov/gene/?term=8570	"FBP2, FUBP2, KSRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024925	8573	CASK	http://www.ncbi.nlm.nih.gov/gene/?term=8573	"CAGH39, CAMGUK, CMG, FGS4, LIN2, MICPCH, MRXSNA, TNRC8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024926	8573	CASK	http://www.ncbi.nlm.nih.gov/gene/?term=8573	"CAGH39, CAMGUK, CMG, FGS4, LIN2, MICPCH, MRXSNA, TNRC8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024927	8574	AKR7A2	http://www.ncbi.nlm.nih.gov/gene/?term=8574	"AFAR, AFAR1, AFB1-AR1, AKR7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024928	8574	AKR7A2	http://www.ncbi.nlm.nih.gov/gene/?term=8574	"AFAR, AFAR1, AFB1-AR1, AKR7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024929	8576	STK16	http://www.ncbi.nlm.nih.gov/gene/?term=8576	"KRCT, MPSK, PKL12, TSF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024930	8577	TMEFF1	http://www.ncbi.nlm.nih.gov/gene/?term=8577	"C9orf2, CT120.1, H7365, TR-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024931	8578	SCARF1	http://www.ncbi.nlm.nih.gov/gene/?term=8578	"SREC, SREC-I, SREC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024932	8578	SCARF1	http://www.ncbi.nlm.nih.gov/gene/?term=8578	"SREC, SREC-I, SREC1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024933	857	CAV1	http://www.ncbi.nlm.nih.gov/gene/?term=857	"BSCL3, CGL3, LCCNS, MSTP085, PPH3, VIP21 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024934	858	CAV2	http://www.ncbi.nlm.nih.gov/gene/?term=858	CAV	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024935	858	CAV2	http://www.ncbi.nlm.nih.gov/gene/?term=858	CAV	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024936	8602	NOP14	http://www.ncbi.nlm.nih.gov/gene/?term=8602	"C4orf9, NOL14, RES4-25, RES425, UTP2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024937	8602	NOP14	http://www.ncbi.nlm.nih.gov/gene/?term=8602	"C4orf9, NOL14, RES4-25, RES425, UTP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024938	8603	FAM193A	http://www.ncbi.nlm.nih.gov/gene/?term=8603	"C4orf8, RES4-22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024939	8607	RUVBL1	http://www.ncbi.nlm.nih.gov/gene/?term=8607	"ECP-54, ECP54, INO80H, NMP 238, NMP238, PONTIN, Pontin52, RVB1, TIH1, TIP49, TIP49A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024940	8609	KLF7	http://www.ncbi.nlm.nih.gov/gene/?term=8609	UKLF	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024941	860	RUNX2	http://www.ncbi.nlm.nih.gov/gene/?term=860	"AML3, CBF-alpha-1, CBFA1, CCD, CCD1, CLCD, OSF-2, OSF2, PEA2aA, PEBP2aA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024942	8611	PLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=8611	"LLP1a, LPP1, PAP-2a, PAP2, PPAP2A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024943	8612	PLPP2	http://www.ncbi.nlm.nih.gov/gene/?term=8612	"LPP2, PAP-2c, PAP2-g, PPAP2C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024944	8614	STC2	http://www.ncbi.nlm.nih.gov/gene/?term=8614	"STC-2, STCRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024945	8614	STC2	http://www.ncbi.nlm.nih.gov/gene/?term=8614	"STC-2, STCRP "	mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00024946	8614	STC2	http://www.ncbi.nlm.nih.gov/gene/?term=8614	"STC-2, STCRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024947	8615	USO1	http://www.ncbi.nlm.nih.gov/gene/?term=8615	"P115, TAP, VDP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024948	8615	USO1	http://www.ncbi.nlm.nih.gov/gene/?term=8615	"P115, TAP, VDP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024949	8615	USO1	http://www.ncbi.nlm.nih.gov/gene/?term=8615	"P115, TAP, VDP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024950	861	RUNX1	http://www.ncbi.nlm.nih.gov/gene/?term=861	"AML1, AML1-EVI-1, AMLCR1, CBF2alpha, CBFA2, EVI-1, PEBP2aB, PEBP2alpha "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024951	8620	NPFF	http://www.ncbi.nlm.nih.gov/gene/?term=8620	FMRFAL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024952	8621	CDK13	http://www.ncbi.nlm.nih.gov/gene/?term=8621	"CDC2L, CDC2L5, CHED, hCDK13 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024953	8621	CDK13	http://www.ncbi.nlm.nih.gov/gene/?term=8621	"CDC2L, CDC2L5, CHED, hCDK13 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024954	8623	ASMTL	http://www.ncbi.nlm.nih.gov/gene/?term=8623	"ASMTLX, ASMTLY, ASTML "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024955	8624	PSMG1	http://www.ncbi.nlm.nih.gov/gene/?term=8624	"C21LRP, DSCR2, LRPC21, PAC-1, PAC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024956	8624	PSMG1	http://www.ncbi.nlm.nih.gov/gene/?term=8624	"C21LRP, DSCR2, LRPC21, PAC-1, PAC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024957	8624	PSMG1	http://www.ncbi.nlm.nih.gov/gene/?term=8624	"C21LRP, DSCR2, LRPC21, PAC-1, PAC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024958	8625	RFXANK	http://www.ncbi.nlm.nih.gov/gene/?term=8625	"ANKRA1, BLS, F14150_1, RFX-B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024959	8625	RFXANK	http://www.ncbi.nlm.nih.gov/gene/?term=8625	"ANKRA1, BLS, F14150_1, RFX-B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024960	8629	JRK	http://www.ncbi.nlm.nih.gov/gene/?term=8629	"JH8, jerky "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024961	8629	JRK	http://www.ncbi.nlm.nih.gov/gene/?term=8629	"JH8, jerky "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024962	862	RUNX1T1	http://www.ncbi.nlm.nih.gov/gene/?term=862	"AML1-MTG8, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024963	8630	HSD17B6	http://www.ncbi.nlm.nih.gov/gene/?term=8630	"HSE, RODH, SDR9C6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024964	8634	RTCA	http://www.ncbi.nlm.nih.gov/gene/?term=8634	"RPC, RTC1, RTCD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024965	8634	RTCA	http://www.ncbi.nlm.nih.gov/gene/?term=8634	"RPC, RTC1, RTCD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024966	8635	RNASET2	http://www.ncbi.nlm.nih.gov/gene/?term=8635	"RNASE6PL, bA514O12.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024967	8635	RNASET2	http://www.ncbi.nlm.nih.gov/gene/?term=8635	"RNASE6PL, bA514O12.3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024968	8635	RNASET2	http://www.ncbi.nlm.nih.gov/gene/?term=8635	"RNASE6PL, bA514O12.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024969	8636	SSNA1	http://www.ncbi.nlm.nih.gov/gene/?term=8636	"N14, NA-14, NA14 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024970	8639	AOC3	http://www.ncbi.nlm.nih.gov/gene/?term=8639	"HPAO, SSAO, VAP-1, VAP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024971	8644	AKR1C3	http://www.ncbi.nlm.nih.gov/gene/?term=8644	"DD3, DDX, HA1753, HAKRB, HAKRe, HSD17B5, PGFS, hluPGFS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024972	8644	AKR1C3	http://www.ncbi.nlm.nih.gov/gene/?term=8644	"DD3, DDX, HA1753, HAKRB, HAKRe, HSD17B5, PGFS, hluPGFS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024973	8648	NCOA1	http://www.ncbi.nlm.nih.gov/gene/?term=8648	"F-SRC-1, KAT13A, RIP160, SRC1, bHLHe42, bHLHe74 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024974	8649	LAMTOR3	http://www.ncbi.nlm.nih.gov/gene/?term=8649	"MAP2K1IP1, MAPBP, MAPKSP1, MP1, PRO0633, Ragulator3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024975	8649	LAMTOR3	http://www.ncbi.nlm.nih.gov/gene/?term=8649	"MAP2K1IP1, MAPBP, MAPKSP1, MP1, PRO0633, Ragulator3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024976	8649	LAMTOR3	http://www.ncbi.nlm.nih.gov/gene/?term=8649	"MAP2K1IP1, MAPBP, MAPKSP1, MP1, PRO0633, Ragulator3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024977	8650	NUMB	http://www.ncbi.nlm.nih.gov/gene/?term=8650	"C14orf41, S171, c14_5527 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024978	8650	NUMB	http://www.ncbi.nlm.nih.gov/gene/?term=8650	"C14orf41, S171, c14_5527 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024979	8651	SOCS1	http://www.ncbi.nlm.nih.gov/gene/?term=8651	"CIS1, CISH1, JAB, SOCS-1, SSI-1, SSI1, TIP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024980	8653	DDX3Y	http://www.ncbi.nlm.nih.gov/gene/?term=8653	DBY	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024981	8653	DDX3Y	http://www.ncbi.nlm.nih.gov/gene/?term=8653	DBY	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024982	8653	DDX3Y	http://www.ncbi.nlm.nih.gov/gene/?term=8653	DBY	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024983	8655	DYNLL1	http://www.ncbi.nlm.nih.gov/gene/?term=8655	"DLC1, DLC8, DNCL1, DNCLC1, LC8, LC8a, PIN, hdlc1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024984	8655	DYNLL1	http://www.ncbi.nlm.nih.gov/gene/?term=8655	"DLC1, DLC8, DNCL1, DNCLC1, LC8, LC8a, PIN, hdlc1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024985	8655	DYNLL1	http://www.ncbi.nlm.nih.gov/gene/?term=8655	"DLC1, DLC8, DNCL1, DNCLC1, LC8, LC8a, PIN, hdlc1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024986	865	CBFB	http://www.ncbi.nlm.nih.gov/gene/?term=865	PEBP2B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024987	865	CBFB	http://www.ncbi.nlm.nih.gov/gene/?term=865	PEBP2B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024988	8661	EIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=8661	"EIF3, EIF3S10, P167, TIF32, eIF3-p170, eIF3-theta, p180, p185 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024989	8661	EIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=8661	"EIF3, EIF3S10, P167, TIF32, eIF3-p170, eIF3-theta, p180, p185 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00024990	8662	EIF3B	http://www.ncbi.nlm.nih.gov/gene/?term=8662	"EIF3-ETA, EIF3-P110, EIF3-P116, EIF3S9, PRT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024991	8663	EIF3C	http://www.ncbi.nlm.nih.gov/gene/?term=8663	"EIF3CL, EIF3S8, eIF3-p110 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024992	8664	EIF3D	http://www.ncbi.nlm.nih.gov/gene/?term=8664	"EIF3S7, eIF3-p66, eIF3-zeta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024993	8666	EIF3G	http://www.ncbi.nlm.nih.gov/gene/?term=8666	"EIF3-P42, EIF3S4, eIF3-delta, eIF3-p44 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024994	8666	EIF3G	http://www.ncbi.nlm.nih.gov/gene/?term=8666	"EIF3-P42, EIF3S4, eIF3-delta, eIF3-p44 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024995	8666	EIF3G	http://www.ncbi.nlm.nih.gov/gene/?term=8666	"EIF3-P42, EIF3S4, eIF3-delta, eIF3-p44 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00024996	8667	EIF3H	http://www.ncbi.nlm.nih.gov/gene/?term=8667	"EIF3S3, eIF3-gamma, eIF3-p40 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024997	8668	EIF3I	http://www.ncbi.nlm.nih.gov/gene/?term=8668	"EIF3S2, PRO2242, TRIP-1, TRIP1, eIF3-beta, eIF3-p36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00024998	8668	EIF3I	http://www.ncbi.nlm.nih.gov/gene/?term=8668	"EIF3S2, PRO2242, TRIP-1, TRIP1, eIF3-beta, eIF3-p36 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00024999	8668	EIF3I	http://www.ncbi.nlm.nih.gov/gene/?term=8668	"EIF3S2, PRO2242, TRIP-1, TRIP1, eIF3-beta, eIF3-p36 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025000	8668	EIF3I	http://www.ncbi.nlm.nih.gov/gene/?term=8668	"EIF3S2, PRO2242, TRIP-1, TRIP1, eIF3-beta, eIF3-p36 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025001	8668	EIF3I	http://www.ncbi.nlm.nih.gov/gene/?term=8668	"EIF3S2, PRO2242, TRIP-1, TRIP1, eIF3-beta, eIF3-p36 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025002	8669	EIF3J	http://www.ncbi.nlm.nih.gov/gene/?term=8669	"EIF3S1, eIF3-alpha, eIF3-p35 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025003	8669	EIF3J	http://www.ncbi.nlm.nih.gov/gene/?term=8669	"EIF3S1, eIF3-alpha, eIF3-p35 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025004	8669	EIF3J	http://www.ncbi.nlm.nih.gov/gene/?term=8669	"EIF3S1, eIF3-alpha, eIF3-p35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025005	8672	EIF4G3	http://www.ncbi.nlm.nih.gov/gene/?term=8672	"eIF-4G 3, eIF4G 3, eIF4GII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025006	8673	VAMP8	http://www.ncbi.nlm.nih.gov/gene/?term=8673	"EDB, VAMP-8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025007	8674055	mgl	http://www.ncbi.nlm.nih.gov/gene/?term=8674055	"Dmel_CG42611, CG12139, CG12654, CG15316, CG34339, CG34352, CG42611, CT7830, Dm CG34352, Dmel\CG42611, Dmel_CG12139, Dmel_CG12654, Dmel_CG34339, Dmel_CG34352, LDLR, SOSIE, anon-WO0140519.108 "	mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00025008	8674	VAMP4	http://www.ncbi.nlm.nih.gov/gene/?term=8674	"VAMP-4, VAMP24 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025009	8675	STX16	http://www.ncbi.nlm.nih.gov/gene/?term=8675	SYN16	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025010	8676	STX11	http://www.ncbi.nlm.nih.gov/gene/?term=8676	"FHL4, HLH4, HPLH4 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025011	8676	STX11	http://www.ncbi.nlm.nih.gov/gene/?term=8676	"FHL4, HLH4, HPLH4 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025012	8677	STX10	http://www.ncbi.nlm.nih.gov/gene/?term=8677	"SYN10, hsyn10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025013	8678	BECN1	http://www.ncbi.nlm.nih.gov/gene/?term=8678	"ATG6, VPS30, beclin1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025014	867	CBL	http://www.ncbi.nlm.nih.gov/gene/?term=867	"C-CBL2, FRA11B, NSLL, RNF55, CBL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025015	867	CBL	http://www.ncbi.nlm.nih.gov/gene/?term=867	"C-CBL2, FRA11B, NSLL, RNF55, CBL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025016	867	CBL	http://www.ncbi.nlm.nih.gov/gene/?term=867	"C-CBL2, FRA11B, NSLL, RNF55, CBL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025017	867	CBL	http://www.ncbi.nlm.nih.gov/gene/?term=867	"C-CBL2, FRA11B, NSLL, RNF55, CBL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025018	867	CBL	http://www.ncbi.nlm.nih.gov/gene/?term=867	"C-CBL, CBL2, FRA11B, NSLL, RNF55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025019	8682	PEA15	http://www.ncbi.nlm.nih.gov/gene/?term=8682	"HMAT1, HUMMAT1H, MAT1, MAT1H, PEA-15, PED "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025020	8682	PEA15	http://www.ncbi.nlm.nih.gov/gene/?term=8682	"HMAT1, HUMMAT1H, MAT1, MAT1H, PEA-15, PED "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025021	8682	PEA15	http://www.ncbi.nlm.nih.gov/gene/?term=8682	"HMAT1, HUMMAT1H, MAT1, MAT1H, PEA-15, PED "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025022	8683	SRSF9	http://www.ncbi.nlm.nih.gov/gene/?term=8683	"SFRS9, SRp30c "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025023	8683	SRSF9	http://www.ncbi.nlm.nih.gov/gene/?term=8683	"SFRS9, SRp30c "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025024	868	CBLB	http://www.ncbi.nlm.nih.gov/gene/?term=868	"Cbl-b, Nbla00127, RNF56 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025025	8690	JRKL	http://www.ncbi.nlm.nih.gov/gene/?term=8690	HHMJG	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025026	8692	HYAL2	http://www.ncbi.nlm.nih.gov/gene/?term=8692	LUCA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025027	8694	DGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=8694	"ARAT, ARGP1, DGAT, DIAR7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025028	8694	DGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=8694	"ARAT, ARGP1, DGAT, DIAR7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025029	8697	CDC23	http://www.ncbi.nlm.nih.gov/gene/?term=8697	"ANAPC8, APC8, CUT23 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025030	86	ACTL6A	http://www.ncbi.nlm.nih.gov/gene/?term=86	"ACTL6, ARPN-BETA, Arp4, BAF53A, INO80K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025031	86	ACTL6A	http://www.ncbi.nlm.nih.gov/gene/?term=86	"ACTL6, ARPN-BETA, Arp4, BAF53A, INO80K "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025032	8702	B4GALT4	http://www.ncbi.nlm.nih.gov/gene/?term=8702	"B4Gal-T4, beta4Gal-T4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025033	8703	B4GALT3	http://www.ncbi.nlm.nih.gov/gene/?term=8703	beta4Gal-T3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025034	8704	B4GALT2	http://www.ncbi.nlm.nih.gov/gene/?term=8704	"B4Gal-T2, B4Gal-T3, beta4Gal-T2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025035	8705	B3GALT4	http://www.ncbi.nlm.nih.gov/gene/?term=8705	"BETA3GALT4, GALT2, GALT4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025036	8714	ABCC3	http://www.ncbi.nlm.nih.gov/gene/?term=8714	"ABC31, EST90757, MLP2, MOAT-D, MRP3, cMOAT2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025037	87178	PNPT1	http://www.ncbi.nlm.nih.gov/gene/?term=87178	"COXPD13, DFNB70, OLD35, PNPASE, old-35 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025038	87178	PNPT1	http://www.ncbi.nlm.nih.gov/gene/?term=87178	"COXPD13, DFNB70, OLD35, PNPASE, old-35 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025039	87178	PNPT1	http://www.ncbi.nlm.nih.gov/gene/?term=87178	"COXPD13, DFNB70, OLD35, PNPASE, old-35 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025040	8717	TRADD	http://www.ncbi.nlm.nih.gov/gene/?term=8717	Hs.89862	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025041	8717	TRADD	http://www.ncbi.nlm.nih.gov/gene/?term=8717	Hs.89862	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025042	8718	TNFRSF25	http://www.ncbi.nlm.nih.gov/gene/?term=8718	"APO-3, DDR3, DR3, LARD, TNFRSF12, TR3, TRAMP, WSL-1, WSL-LR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025043	871	SERPINH1	http://www.ncbi.nlm.nih.gov/gene/?term=871	"AsTP3, CBP1, CBP2, HSP47, OI10, PIG14, PPROM, RA-A47, SERPINH2, gp46 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025044	871	SERPINH1	http://www.ncbi.nlm.nih.gov/gene/?term=871	"AsTP3, CBP1, CBP2, HSP47, OI10, PIG14, PPROM, RA-A47, SERPINH2, gp46 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025045	8720	MBTPS1	http://www.ncbi.nlm.nih.gov/gene/?term=8720	"PCSK8, S1P, SKI-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025046	8720	MBTPS1	http://www.ncbi.nlm.nih.gov/gene/?term=8720	"PCSK8, S1P, SKI-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025047	8721	EDF1	http://www.ncbi.nlm.nih.gov/gene/?term=8721	"CFAP280, EDF-1, MBF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025048	8723	SNX4	http://www.ncbi.nlm.nih.gov/gene/?term=8723	ATG24B	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025049	8723	SNX4	http://www.ncbi.nlm.nih.gov/gene/?term=8723	ATG24B	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025050	8723	SNX4	http://www.ncbi.nlm.nih.gov/gene/?term=8723	ATG24B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025051	8724	SNX3	http://www.ncbi.nlm.nih.gov/gene/?term=8724	"Grd19, MCOPS8, SDP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025052	8725	URI1	http://www.ncbi.nlm.nih.gov/gene/?term=8725	"C19orf2, NNX3, PPP1R19, RMP, URI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025053	8726	EED	http://www.ncbi.nlm.nih.gov/gene/?term=8726	"HEED, WAIT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025054	8727	CTNNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=8727	"ACRP, CLLP, alpha-CATU "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025055	8727	CTNNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=8727	"ACRP, CLLP, alpha-CATU "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025056	8727	CTNNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=8727	"ACRP, CLLP, alpha-CATU "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025057	8729	GBF1	http://www.ncbi.nlm.nih.gov/gene/?term=8729	ARF1GEF	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025058	8729	GBF1	http://www.ncbi.nlm.nih.gov/gene/?term=8729	ARF1GEF	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025059	8731	RNMT	http://www.ncbi.nlm.nih.gov/gene/?term=8731	"CMT1, CMT1c, MET, Met, RG7MT1, cm1p, hCMT1, hMet "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025060	8731	RNMT	http://www.ncbi.nlm.nih.gov/gene/?term=8731	"CMT1, CMT1c, MET, Met, RG7MT1, cm1p, hCMT1, hMet "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025061	8733	GPAA1	http://www.ncbi.nlm.nih.gov/gene/?term=8733	"GAA1, hGAA1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025062	8737	RIPK1	http://www.ncbi.nlm.nih.gov/gene/?term=8737	"RIP, RIP-1, RIP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025063	8737	RIPK1	http://www.ncbi.nlm.nih.gov/gene/?term=8737	"RIP, RIP-1, RIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025064	8738	CRADD	http://www.ncbi.nlm.nih.gov/gene/?term=8738	"MRT34, RAIDD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025065	8738	CRADD	http://www.ncbi.nlm.nih.gov/gene/?term=8738	"MRT34, RAIDD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025066	873	CBR1	http://www.ncbi.nlm.nih.gov/gene/?term=873	"CBR, SDR21C1, hCBR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025067	873	CBR1	http://www.ncbi.nlm.nih.gov/gene/?term=873	"CBR, SDR21C1, hCBR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025068	873	CBR1	http://www.ncbi.nlm.nih.gov/gene/?term=873	"CBR, SDR21C1, hCBR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025069	8741	TNFSF13	http://www.ncbi.nlm.nih.gov/gene/?term=8741	"APRIL, CD256, TALL-2, TALL2, TNLG7B, TRDL-1, UNQ383/PRO715, ZTNF2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025070	8743	TNFSF10	http://www.ncbi.nlm.nih.gov/gene/?term=8743	"APO2L, Apo-2L, CD253, TL2, TNLG6A, TRAIL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025071	8744	TNFSF9	http://www.ncbi.nlm.nih.gov/gene/?term=8744	"4-1BB-L, CD137L, TNLG5A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025072	8745	ADAM23	http://www.ncbi.nlm.nih.gov/gene/?term=8745	"MDC-3, MDC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025073	8751	ADAM15	http://www.ncbi.nlm.nih.gov/gene/?term=8751	MDC15	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025074	8751	ADAM15	http://www.ncbi.nlm.nih.gov/gene/?term=8751	MDC15	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025075	8754	ADAM9	http://www.ncbi.nlm.nih.gov/gene/?term=8754	"CORD9, MCMP, MDC9, Mltng "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025076	8754	ADAM9	http://www.ncbi.nlm.nih.gov/gene/?term=8754	"CORD9, MCMP, MDC9, Mltng "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025077	8754	ADAM9	http://www.ncbi.nlm.nih.gov/gene/?term=8754	"CORD9, MCMP, MDC9, Mltng "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025078	875	CBS	http://www.ncbi.nlm.nih.gov/gene/?term=875	HIP4	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025079	875	CBS	http://www.ncbi.nlm.nih.gov/gene/?term=875	HIP4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025080	8761	PABPC4	http://www.ncbi.nlm.nih.gov/gene/?term=8761	"APP-1, APP1, PABP4, iPABP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025081	8763	CD164	http://www.ncbi.nlm.nih.gov/gene/?term=8763	"DFNA66, MGC-24, MUC-24, endolyn "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025082	8763	CD164	http://www.ncbi.nlm.nih.gov/gene/?term=8763	"DFNA66, MGC-24, MUC-24, endolyn "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025083	8764	TNFRSF14	http://www.ncbi.nlm.nih.gov/gene/?term=8764	"ATAR, CD270, HVEA, HVEM, LIGHTR, TR2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025084	8766	RAB11A	http://www.ncbi.nlm.nih.gov/gene/?term=8766	YL8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025085	8766	RAB11A	http://www.ncbi.nlm.nih.gov/gene/?term=8766	YL8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025086	8772	FADD	http://www.ncbi.nlm.nih.gov/gene/?term=8772	"GIG3, MORT1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025087	8772	FADD	http://www.ncbi.nlm.nih.gov/gene/?term=8772	"GIG3, MORT1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025088	8772	FADD	http://www.ncbi.nlm.nih.gov/gene/?term=8772	"GIG3, MORT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025089	8773	SNAP23	http://www.ncbi.nlm.nih.gov/gene/?term=8773	"HsT17016, SNAP-23A, SNAP23B, SNAP23 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025090	8773	SNAP23	http://www.ncbi.nlm.nih.gov/gene/?term=8773	"HsT17016, SNAP-23A, SNAP23B, SNAP23 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025091	8773	SNAP23	http://www.ncbi.nlm.nih.gov/gene/?term=8773	"HsT17016, SNAP-23, SNAP23A, SNAP23B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025092	8774	NAPG	http://www.ncbi.nlm.nih.gov/gene/?term=8774	GAMMASNAP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025093	8775	NAPA	http://www.ncbi.nlm.nih.gov/gene/?term=8775	SNAPA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025094	8775	NAPA	http://www.ncbi.nlm.nih.gov/gene/?term=8775	SNAPA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025095	8776	MTMR1	http://www.ncbi.nlm.nih.gov/gene/?term=8776		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025096	8780	RIOK3	http://www.ncbi.nlm.nih.gov/gene/?term=8780	SUDD	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025097	8780	RIOK3	http://www.ncbi.nlm.nih.gov/gene/?term=8780	SUDD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025098	8784	TNFRSF18	http://www.ncbi.nlm.nih.gov/gene/?term=8784	"AITR, CD357, GITR, GITR-D "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025099	8788	DLK1	http://www.ncbi.nlm.nih.gov/gene/?term=8788	"DLK, DLK-1, Delta1, FA1, PREF1, Pref-1, ZOG, pG2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025100	8790	FPGT	http://www.ncbi.nlm.nih.gov/gene/?term=8790	GFPP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025101	8790	FPGT	http://www.ncbi.nlm.nih.gov/gene/?term=8790	GFPP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025102	8793	TNFRSF10D	http://www.ncbi.nlm.nih.gov/gene/?term=8793	"CD264, DCR2, TRAIL-R4, TRAILR4, TRUNDD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025103	8793	TNFRSF10D	http://www.ncbi.nlm.nih.gov/gene/?term=8793	"CD264, DCR2, TRAIL-R4, TRAILR4, TRUNDD "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025104	8795	TNFRSF10B	http://www.ncbi.nlm.nih.gov/gene/?term=8795	"CD262, DR5, KILLER, KILLER/DR5, TRAIL-R2, TRAILR2, TRICK2, TRICK2A, TRICK2B, TRICKB, ZTNFR9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025105	8795	TNFRSF10B	http://www.ncbi.nlm.nih.gov/gene/?term=8795	"CD262, DR5, KILLER, KILLER/DR5, TRAIL-R2, TRAILR2, TRICK2, TRICK2A, TRICK2B, TRICKB, ZTNFR9 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025106	8795	TNFRSF10B	http://www.ncbi.nlm.nih.gov/gene/?term=8795	"CD262, DR5, KILLER, KILLER/DR5, TRAIL-R2, TRAILR2, TRICK2, TRICK2A, TRICK2B, TRICKB, ZTNFR9 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025107	8795	TNFRSF10B	http://www.ncbi.nlm.nih.gov/gene/?term=8795	"CD262, DR5, KILLER, KILLER/DR5, TRAIL-R2, TRAILR2, TRICK2, TRICK2A, TRICK2B, TRICKB, ZTNFR9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025108	8796	SCEL	http://www.ncbi.nlm.nih.gov/gene/?term=8796		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025109	8797	TNFRSF10A	http://www.ncbi.nlm.nih.gov/gene/?term=8797	"APO2, CD261, DR4, TRAILR-1, TRAILR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025110	8798	DYRK4	http://www.ncbi.nlm.nih.gov/gene/?term=8798		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025111	8798	DYRK4	http://www.ncbi.nlm.nih.gov/gene/?term=8798		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025112	8799	PEX11B	http://www.ncbi.nlm.nih.gov/gene/?term=8799	"PEX11-BETA, PEX14B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025113	87	ACTN1	http://www.ncbi.nlm.nih.gov/gene/?term=87	BDPLT15	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025114	8801	SUCLG2	http://www.ncbi.nlm.nih.gov/gene/?term=8801	GBETA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025115	8801	SUCLG2	http://www.ncbi.nlm.nih.gov/gene/?term=8801	GBETA	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025116	8802	SUCLG1	http://www.ncbi.nlm.nih.gov/gene/?term=8802	"GALPHA, MTDPS9, SUCLA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025117	8803	SUCLA2	http://www.ncbi.nlm.nih.gov/gene/?term=8803	"A-BETA, MTDPS5, SCS-betaA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025118	8804	CREG1	http://www.ncbi.nlm.nih.gov/gene/?term=8804	CREG	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025119	8804	CREG1	http://www.ncbi.nlm.nih.gov/gene/?term=8804	CREG	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025120	8804	CREG1	http://www.ncbi.nlm.nih.gov/gene/?term=8804	CREG	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025121	8805	TRIM24	http://www.ncbi.nlm.nih.gov/gene/?term=8805	"PTC6, RNF82, TF1A, TIF1, TIF1A, TIF1ALPHA, hTIF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025122	8809	IL18R1	http://www.ncbi.nlm.nih.gov/gene/?term=8809	"CD218a, CDw218a, IL-1Rrp, IL18RA, IL1RRP "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025123	8809	IL18R1	http://www.ncbi.nlm.nih.gov/gene/?term=8809	"CD218a, CDw218a, IL-1Rrp, IL18RA, IL1RRP "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025124	8809	IL18R1	http://www.ncbi.nlm.nih.gov/gene/?term=8809	"CD218a, CDw218a, IL-1Rrp, IL18RA, IL1RRP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025125	8813	DPM1	http://www.ncbi.nlm.nih.gov/gene/?term=8813	"CDGIE, MPDS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025126	8813	DPM1	http://www.ncbi.nlm.nih.gov/gene/?term=8813	"CDGIE, MPDS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025127	8815	BANF1	http://www.ncbi.nlm.nih.gov/gene/?term=8815	"BAF, BCRP1, D14S1460, NGPS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025128	8815	BANF1	http://www.ncbi.nlm.nih.gov/gene/?term=8815	"BAF, BCRP1, D14S1460, NGPS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025129	8815	BANF1	http://www.ncbi.nlm.nih.gov/gene/?term=8815	"BAF, BCRP1, D14S1460, NGPS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025130	8816	DCAF5	http://www.ncbi.nlm.nih.gov/gene/?term=8816	"BCRG2, BCRP2, D14S1461E, WDR22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025131	8818	DPM2	http://www.ncbi.nlm.nih.gov/gene/?term=8818	CDG1U	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025132	8818	DPM2	http://www.ncbi.nlm.nih.gov/gene/?term=8818	CDG1U	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025133	8818	DPM2	http://www.ncbi.nlm.nih.gov/gene/?term=8818	CDG1U	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025134	8819	SAP30	http://www.ncbi.nlm.nih.gov/gene/?term=8819		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025135	8824	CES2	http://www.ncbi.nlm.nih.gov/gene/?term=8824	"CE-2, CES2A1, PCE-2, iCE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025136	8826	IQGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8826	"HUMORFA01, SAR1, p195 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025137	8826	IQGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8826	"HUMORFA01, SAR1, p195 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025138	8826	IQGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=8826	"HUMORFA01, SAR1, p195 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025139	8829	NRP1	http://www.ncbi.nlm.nih.gov/gene/?term=8829	"BDCA4, CD304, NP1, NRP, VEGF165R "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025140	8833	GMPS	http://www.ncbi.nlm.nih.gov/gene/?term=8833		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025141	8833	GMPS	http://www.ncbi.nlm.nih.gov/gene/?term=8833		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025142	8833	GMPS	http://www.ncbi.nlm.nih.gov/gene/?term=8833		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025143	8834	TMEM11	http://www.ncbi.nlm.nih.gov/gene/?term=8834	"C17orf35, PM1, PMI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025144	8834	TMEM11	http://www.ncbi.nlm.nih.gov/gene/?term=8834	"C17orf35, PM1, PMI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025145	8835	SOCS2	http://www.ncbi.nlm.nih.gov/gene/?term=8835	"CIS2, Cish2, SOCS-2, SSI-2, SSI2, STATI2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025146	8836	GGH	http://www.ncbi.nlm.nih.gov/gene/?term=8836	GH	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025147	8836	GGH	http://www.ncbi.nlm.nih.gov/gene/?term=8836	GH	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025148	8836	GGH	http://www.ncbi.nlm.nih.gov/gene/?term=8836	GH	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025149	8837	CFLAR	http://www.ncbi.nlm.nih.gov/gene/?term=8837	"CASH, CASP8AP1, CLARP, Casper, FLAME, FLAME-1, FLAME1, FLIP, I-FLICE, MRIT, c-FLIP, c-FLIPL, c-FLIPR, c-FLIPS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025150	883	KYAT1	http://www.ncbi.nlm.nih.gov/gene/?term=883	"GTK, KAT1, KATI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025151	8841	HDAC3	http://www.ncbi.nlm.nih.gov/gene/?term=8841	"HD3, RPD3, RPD3-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025152	8841	HDAC3	http://www.ncbi.nlm.nih.gov/gene/?term=8841	"HD3, RPD3, RPD3-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025153	8841	HDAC3	http://www.ncbi.nlm.nih.gov/gene/?term=8841	"HD3, RPD3, RPD3-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025154	8841	HDAC3	http://www.ncbi.nlm.nih.gov/gene/?term=8841	"HD3, RPD3, RPD3-2 "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00025155	8842	PROM1	http://www.ncbi.nlm.nih.gov/gene/?term=8842	"AC133, CD133, CORD12, MCDR2, MSTP061, PROML1, RP41, STGD4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025156	8846	ALKBH1	http://www.ncbi.nlm.nih.gov/gene/?term=8846	"ABH, ABH1, ALKBH, alkB, hABH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025157	8846	ALKBH1	http://www.ncbi.nlm.nih.gov/gene/?term=8846	"ABH, ABH1, ALKBH, alkB, hABH "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025158	8847	DLEU2	http://www.ncbi.nlm.nih.gov/gene/?term=8847	"1B4, BCMSUN, DLB2, LEU2, LINC00022, MIR15AHG, NCRNA00022, RFP2OS, TRIM13OS "	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025159	8848	TSC22D1	http://www.ncbi.nlm.nih.gov/gene/?term=8848	"Ptg-2, TGFB1I4, TSC22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025160	8848	TSC22D1	http://www.ncbi.nlm.nih.gov/gene/?term=8848	"Ptg-2, TGFB1I4, TSC22 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025161	8848	TSC22D1	http://www.ncbi.nlm.nih.gov/gene/?term=8848	"Ptg-2, TGFB1I4, TSC22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025162	8850	KAT2B	http://www.ncbi.nlm.nih.gov/gene/?term=8850	"CAF, P/CAF, PCAF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025163	8853	ASAP2	http://www.ncbi.nlm.nih.gov/gene/?term=8853	"AMAP2, CENTB3, DDEF2, PAG3, PAP, Pap-alpha, SHAG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025164	8853	ASAP2	http://www.ncbi.nlm.nih.gov/gene/?term=8853	"AMAP2, CENTB3, DDEF2, PAG3, PAP, Pap-alpha, SHAG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025165	8854	ALDH1A2	http://www.ncbi.nlm.nih.gov/gene/?term=8854	"RALDH(II), RALDH2, RALDH2-T "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025166	8854	ALDH1A2	http://www.ncbi.nlm.nih.gov/gene/?term=8854	"RALDH(II), RALDH2, RALDH2-T "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025167	8857	FCGBP	http://www.ncbi.nlm.nih.gov/gene/?term=8857	FC(GAMMA)BP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025168	8861	LDB1	http://www.ncbi.nlm.nih.gov/gene/?term=8861	"CLIM-2, CLIM2, LDB-1, NLI "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025169	8864	PER2	http://www.ncbi.nlm.nih.gov/gene/?term=8864	"FASPS, FASPS1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025170	8864	PER2	http://www.ncbi.nlm.nih.gov/gene/?term=8864	"FASPS, FASPS1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025171	8867	SYNJ1	http://www.ncbi.nlm.nih.gov/gene/?term=8867	"INPP5G, PARK20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025172	8869	ST3GAL5	http://www.ncbi.nlm.nih.gov/gene/?term=8869	"SATI, SIAT9, SIATGM3S, ST3GalV "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025173	8869	ST3GAL5	http://www.ncbi.nlm.nih.gov/gene/?term=8869	"SATI, SIAT9, SIATGM3S, ST3GalV "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025174	8870	IER3	http://www.ncbi.nlm.nih.gov/gene/?term=8870	"DIF-2, DIF2, GLY96, IEX-1, IEX-1L, IEX1, PRG1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025175	8870	IER3	http://www.ncbi.nlm.nih.gov/gene/?term=8870	"DIF-2, DIF2, GLY96, IEX-1, IEX-1L, IEX1, PRG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025176	8871	SYNJ2	http://www.ncbi.nlm.nih.gov/gene/?term=8871	INPP5H	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025177	8872	CDC123	http://www.ncbi.nlm.nih.gov/gene/?term=8872	"C10orf7, D123 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025178	8872	CDC123	http://www.ncbi.nlm.nih.gov/gene/?term=8872	"C10orf7, D123 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025179	8872	CDC123	http://www.ncbi.nlm.nih.gov/gene/?term=8872	"C10orf7, D123 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025180	88745	RRP36	http://www.ncbi.nlm.nih.gov/gene/?term=88745	"C6orf153, dJ20C7.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025181	88745	RRP36	http://www.ncbi.nlm.nih.gov/gene/?term=88745	"C6orf153, dJ20C7.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025182	8874	ARHGEF7	http://www.ncbi.nlm.nih.gov/gene/?term=8874	"BETA-PIX, COOL-1, COOL1, Nbla10314, P50, P50BP, P85, P85COOL1, P85SPR, PAK3, PIXB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025183	8874	ARHGEF7	http://www.ncbi.nlm.nih.gov/gene/?term=8874	"BETA-PIX, COOL-1, COOL1, Nbla10314, P50, P50BP, P85, P85COOL1, P85SPR, PAK3, PIXB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025184	8876	VNN1	http://www.ncbi.nlm.nih.gov/gene/?term=8876	"HDLCQ8, Tiff66 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025185	8878	SQSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=8878	"A170, FTDALS3, OSIL, PDB3, ZIP3, p60, p62, p62B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025186	8879	SGPL1	http://www.ncbi.nlm.nih.gov/gene/?term=8879	"S1PL, SPL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025187	8879	SGPL1	http://www.ncbi.nlm.nih.gov/gene/?term=8879	"S1PL, SPL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025188	8879	SGPL1	http://www.ncbi.nlm.nih.gov/gene/?term=8879	"S1PL, SPL "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025189	8879	SGPL1	http://www.ncbi.nlm.nih.gov/gene/?term=8879	"S1PL, SPL "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025190	8879	SGPL1	http://www.ncbi.nlm.nih.gov/gene/?term=8879	"S1PL, SPL "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025191	8880	FUBP1	http://www.ncbi.nlm.nih.gov/gene/?term=8880	"FBP, FUBP, hDH V "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025192	8880	FUBP1	http://www.ncbi.nlm.nih.gov/gene/?term=8880	"FBP, FUBP, hDH V "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025193	8881	CDC16	http://www.ncbi.nlm.nih.gov/gene/?term=8881	"ANAPC6, APC6Hs, CUT9, CDC16 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025194	8881	CDC16	http://www.ncbi.nlm.nih.gov/gene/?term=8881	"ANAPC6, APC6, CDC16Hs, CUT9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025195	8882	ZPR1	http://www.ncbi.nlm.nih.gov/gene/?term=8882	ZNF259	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025196	8883	NAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8883	"A-116A10.1, APPBP1, HPP1, ula-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025197	8883	NAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8883	"A-116A10.1, APPBP1, HPP1, ula-1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025198	8883	NAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8883	"A-116A10.1, APPBP1, HPP1, ula-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025199	8884	SLC5A6	http://www.ncbi.nlm.nih.gov/gene/?term=8884	SMVT	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025200	8884	SLC5A6	http://www.ncbi.nlm.nih.gov/gene/?term=8884	SMVT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025201	8884	SLC5A6	http://www.ncbi.nlm.nih.gov/gene/?term=8884	SMVT	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025202	8886	DDX18	http://www.ncbi.nlm.nih.gov/gene/?term=8886	MrDb	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025203	8886	DDX18	http://www.ncbi.nlm.nih.gov/gene/?term=8886	MrDb	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025204	8887	TAX1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=8887	"CALCOCO3, T6BP, TXBP151 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025205	8887	TAX1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=8887	"CALCOCO3, T6BP, TXBP151 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025206	8888	MCM3AP	http://www.ncbi.nlm.nih.gov/gene/?term=8888	"GANP, MAP80, SAC3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025207	8888	MCM3AP	http://www.ncbi.nlm.nih.gov/gene/?term=8888	"GANP, MAP80, SAC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025208	8888	MCM3AP	http://www.ncbi.nlm.nih.gov/gene/?term=8888	"GANP, MAP80, SAC3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025209	8890	EIF2B4	http://www.ncbi.nlm.nih.gov/gene/?term=8890	"EIF-2B, EIF2B, EIF2Bdelta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025210	8890	EIF2B4	http://www.ncbi.nlm.nih.gov/gene/?term=8890	"EIF-2B, EIF2B, EIF2Bdelta "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025211	8890	EIF2B4	http://www.ncbi.nlm.nih.gov/gene/?term=8890	"EIF-2B, EIF2B, EIF2Bdelta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025212	8892	EIF2B2	http://www.ncbi.nlm.nih.gov/gene/?term=8892	"EIF-2Bbeta, EIF2B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025213	8892	EIF2B2	http://www.ncbi.nlm.nih.gov/gene/?term=8892	"EIF-2Bbeta, EIF2B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025214	8892	EIF2B2	http://www.ncbi.nlm.nih.gov/gene/?term=8892	"EIF-2Bbeta, EIF2B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025215	8893	EIF2B5	http://www.ncbi.nlm.nih.gov/gene/?term=8893	"CACH, CLE, EIF-2B, EIF2Bepsilon, LVWM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025216	8894	EIF2S2	http://www.ncbi.nlm.nih.gov/gene/?term=8894	"EIF2, EIF2B, EIF2beta, PPP1R67, eIF-2-beta "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025217	8894	EIF2S2	http://www.ncbi.nlm.nih.gov/gene/?term=8894	"EIF2, EIF2B, EIF2beta, PPP1R67, eIF-2-beta "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025218	8895	CPNE3	http://www.ncbi.nlm.nih.gov/gene/?term=8895	"CPN3, PRO1071 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025219	8896	BUD31	http://www.ncbi.nlm.nih.gov/gene/?term=8896	"Cwc14, EDG-2, EDG2, G10, YCR063W, fSAP17 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025220	8896	BUD31	http://www.ncbi.nlm.nih.gov/gene/?term=8896	"Cwc14, EDG-2, EDG2, G10, YCR063W, fSAP17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025221	8897	MTMR3	http://www.ncbi.nlm.nih.gov/gene/?term=8897	"FYVE-DSP1, ZFYVE10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025222	8898	MTMR2	http://www.ncbi.nlm.nih.gov/gene/?term=8898	"CMT4B, CMT4B1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025223	8898	MTMR2	http://www.ncbi.nlm.nih.gov/gene/?term=8898	"CMT4B, CMT4B1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025224	8898	MTMR2	http://www.ncbi.nlm.nih.gov/gene/?term=8898	"CMT4B, CMT4B1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025225	8899	PRPF4B	http://www.ncbi.nlm.nih.gov/gene/?term=8899	"PR4H, PRP4, PRP4H, PRP4K, dJ1013A10.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025226	8904	CPNE1	http://www.ncbi.nlm.nih.gov/gene/?term=8904	"COPN1, CPN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025227	8904	CPNE1	http://www.ncbi.nlm.nih.gov/gene/?term=8904	"COPN1, CPN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025228	8905	AP1S2	http://www.ncbi.nlm.nih.gov/gene/?term=8905	"DC22, MRX59, MRXS21, MRXS5, MRXSF, PGS, SIGMA1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025229	8906	AP1G2	http://www.ncbi.nlm.nih.gov/gene/?term=8906	G2AD	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025230	8906	AP1G2	http://www.ncbi.nlm.nih.gov/gene/?term=8906	G2AD	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025231	8907	AP1M1	http://www.ncbi.nlm.nih.gov/gene/?term=8907	"AP47, CLAPM2, CLTNM, MU-1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025232	8908	GYG2	http://www.ncbi.nlm.nih.gov/gene/?term=8908	"GN-2, GN2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025233	890	CCNA2	http://www.ncbi.nlm.nih.gov/gene/?term=890	"CCN1, CCNA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025234	890	CCNA2	http://www.ncbi.nlm.nih.gov/gene/?term=890	"CCN1, CCNA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025235	890	CCNA2	http://www.ncbi.nlm.nih.gov/gene/?term=890	"CCN1, CCNA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025236	8910	SGCE	http://www.ncbi.nlm.nih.gov/gene/?term=8910	"DYT11, ESG "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025237	8910	SGCE	http://www.ncbi.nlm.nih.gov/gene/?term=8910	"DYT11, ESG "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025238	8911	CACNA1I	http://www.ncbi.nlm.nih.gov/gene/?term=8911	"Cav3.3, ca(v)3.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025239	8914	TIMELESS	http://www.ncbi.nlm.nih.gov/gene/?term=8914	"TIM, TIM1, hTIM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025240	8915	BCL10	http://www.ncbi.nlm.nih.gov/gene/?term=8915	"CARMEN, CIPER, CLAP, IMD37, c-E10, mE10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025241	8915	BCL10	http://www.ncbi.nlm.nih.gov/gene/?term=8915	"CARMEN, CIPER, CLAP, IMD37, c-E10, mE10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025242	8916	HERC3	http://www.ncbi.nlm.nih.gov/gene/?term=8916		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025243	8916	HERC3	http://www.ncbi.nlm.nih.gov/gene/?term=8916		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025244	891	CCNB1	http://www.ncbi.nlm.nih.gov/gene/?term=891	CCNB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025245	8924	HERC2	http://www.ncbi.nlm.nih.gov/gene/?term=8924	"D15F37S1, MRT38, SHEP1, jdf2, p528 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025246	8924	HERC2	http://www.ncbi.nlm.nih.gov/gene/?term=8924	"D15F37S1, MRT38, SHEP1, jdf2, p528 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025247	8925	HERC1	http://www.ncbi.nlm.nih.gov/gene/?term=8925	"p532, p619 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025248	892	CCNC	http://www.ncbi.nlm.nih.gov/gene/?term=892	CycC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025249	892	CCNC	http://www.ncbi.nlm.nih.gov/gene/?term=892	CycC	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025250	8930	MBD4	http://www.ncbi.nlm.nih.gov/gene/?term=8930	MED1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025251	8930	MBD4	http://www.ncbi.nlm.nih.gov/gene/?term=8930	MED1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025252	8932	MBD2	http://www.ncbi.nlm.nih.gov/gene/?term=8932	"DMTase, NY-CO-41 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025253	8932	MBD2	http://www.ncbi.nlm.nih.gov/gene/?term=8932	"DMTase, NY-CO-41 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025254	8932	MBD2	http://www.ncbi.nlm.nih.gov/gene/?term=8932	"DMTase, NY-CO-41 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025255	8933	FAM127A	http://www.ncbi.nlm.nih.gov/gene/?term=8933	"CXX1, MAR8C, MART8C, Mar8, Mart8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025256	8933	FAM127A	http://www.ncbi.nlm.nih.gov/gene/?term=8933	"CXX1, MAR8C, MART8C, Mar8, Mart8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025257	8939	FUBP3	http://www.ncbi.nlm.nih.gov/gene/?term=8939	FBP3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025258	8939	FUBP3	http://www.ncbi.nlm.nih.gov/gene/?term=8939	FBP3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025259	8941	CDK5R2	http://www.ncbi.nlm.nih.gov/gene/?term=8941	"NCK5AI, P39, p39nck5ai "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025260	8943	AP3D1	http://www.ncbi.nlm.nih.gov/gene/?term=8943	"ADTD, hBLVR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025261	8943	AP3D1	http://www.ncbi.nlm.nih.gov/gene/?term=8943	"ADTD, hBLVR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025262	8944	SNORD73A	http://www.ncbi.nlm.nih.gov/gene/?term=8944	"RNU73, RNU73A, U73, U73a "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00025263	894	CCND2	http://www.ncbi.nlm.nih.gov/gene/?term=894	"KIAK0002, MPPH3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025264	894	CCND2	http://www.ncbi.nlm.nih.gov/gene/?term=894	"KIAK0002, MPPH3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025265	8969	HIST1H2AG	http://www.ncbi.nlm.nih.gov/gene/?term=8969	"H2A.1b, H2A/p, H2AFP, H2AG, pH2A/f "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025266	8969	HIST1H2AG	http://www.ncbi.nlm.nih.gov/gene/?term=8969	"H2A.1b, H2A/p, H2AFP, H2AG, pH2A/f "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025267	8969	HIST1H2AG	http://www.ncbi.nlm.nih.gov/gene/?term=8969	"H2A.1b, H2A/p, H2AFP, H2AG, pH2A/f "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025268	8970	HIST1H2BJ	http://www.ncbi.nlm.nih.gov/gene/?term=8970	"H2B/r, H2BFR, H2BJ "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025269	8971	H1FX	http://www.ncbi.nlm.nih.gov/gene/?term=8971	"H1.10, H1X "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025270	8971	H1FX	http://www.ncbi.nlm.nih.gov/gene/?term=8971	"H1.10, H1X "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025271	8972	MGAM	http://www.ncbi.nlm.nih.gov/gene/?term=8972	"MG, MGA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025272	8974	P4HA2	http://www.ncbi.nlm.nih.gov/gene/?term=8974		mRNA	Homo sapiens	25753659	Endoplasmic reticulum	HT1080 cell	Fluorescence in situ hybridization	Table 1. Motif enrichment in 5'- and 3'-UTRs of candidates that are increased in total mRNA level and being increasingly present at the ER during hypoxia in HT1080 cells. Data are collected from Table 1.
RLID00025273	8975	USP13	http://www.ncbi.nlm.nih.gov/gene/?term=8975	"ISOT3, IsoT-3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025274	8976	WASL	http://www.ncbi.nlm.nih.gov/gene/?term=8976	"N-WASP, NWASP, WASPB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025275	8976	WASL	http://www.ncbi.nlm.nih.gov/gene/?term=8976	"N-WASP, NWASP, WASPB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025276	8976	WASL	http://www.ncbi.nlm.nih.gov/gene/?term=8976	"N-WASP, NWASP, WASPB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025277	89781	HPS4	http://www.ncbi.nlm.nih.gov/gene/?term=89781	"BLOC3S2, LE "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025278	89781	HPS4	http://www.ncbi.nlm.nih.gov/gene/?term=89781	"BLOC3S2, LE "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025279	89781	HPS4	http://www.ncbi.nlm.nih.gov/gene/?term=89781	"BLOC3S2, LE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025280	89782	LMLN	http://www.ncbi.nlm.nih.gov/gene/?term=89782	"GP63, INV, IX14, MSP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025281	89795	NAV3	http://www.ncbi.nlm.nih.gov/gene/?term=89795	"POMFIL1, STEERIN3, unc53H3 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025282	89796	NAV1	http://www.ncbi.nlm.nih.gov/gene/?term=89796	"POMFIL3, STEERIN1, UNC53H1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025283	89796	NAV1	http://www.ncbi.nlm.nih.gov/gene/?term=89796	"POMFIL3, STEERIN1, UNC53H1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025284	89796	NAV1	http://www.ncbi.nlm.nih.gov/gene/?term=89796	"POMFIL3, STEERIN1, UNC53H1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025285	89797	NAV2	http://www.ncbi.nlm.nih.gov/gene/?term=89797	"HELAD1, POMFIL2, RAINB1, STEERIN2, UNC53H2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025286	89797	NAV2	http://www.ncbi.nlm.nih.gov/gene/?term=89797	"HELAD1, POMFIL2, RAINB1, STEERIN2, UNC53H2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025287	89801	PPP1R3F	http://www.ncbi.nlm.nih.gov/gene/?term=89801	"HB2E, R3F "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025288	89832	CHRFAM7A	http://www.ncbi.nlm.nih.gov/gene/?term=89832	"CHRNA7, CHRNA7-DR1, D-10 "	mRNA	Homo sapiens	26206074	Nucleus	Neocortex	In situ hybridization	"CHRNA7 and CHRFAM7A mRNAs were expressed in the same neuronal nuclei of the human neocortex. We demonstrated that CHRNA7 and CHRFAM7A mRNAs are colocalized in a subset of putative neuronal nuclei (large DAPI-stained nuclei), both in the dorsolateral prefrontal cortex and anterior cingulate cortex (Figure 3). "
RLID00025289	89848	FCHSD1	http://www.ncbi.nlm.nih.gov/gene/?term=89848	NWK2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025290	89849	ATG16L2	http://www.ncbi.nlm.nih.gov/gene/?term=89849	"ATG16B, WDR80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025291	89853	MVB12B	http://www.ncbi.nlm.nih.gov/gene/?term=89853	"C9orf28, FAM125B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025292	89857	KLHL6	http://www.ncbi.nlm.nih.gov/gene/?term=89857		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025293	89857	KLHL6	http://www.ncbi.nlm.nih.gov/gene/?term=89857		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025294	8985	PLOD3	http://www.ncbi.nlm.nih.gov/gene/?term=8985	LH3	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025295	8985	PLOD3	http://www.ncbi.nlm.nih.gov/gene/?term=8985	LH3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025296	89870	TRIM15	http://www.ncbi.nlm.nih.gov/gene/?term=89870	"RNF93, ZNF178, ZNFB7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025297	89872	AQP10	http://www.ncbi.nlm.nih.gov/gene/?term=89872	AQPA_HUMAN	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00025298	89874	SLC25A21	http://www.ncbi.nlm.nih.gov/gene/?term=89874	"ODC, ODC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025299	89885	FATE1	http://www.ncbi.nlm.nih.gov/gene/?term=89885	"CT43, FATE "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025300	89891	WDR34	http://www.ncbi.nlm.nih.gov/gene/?term=89891	"DIC5, FAP133, SRTD11, bA216B9.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025301	89891	WDR34	http://www.ncbi.nlm.nih.gov/gene/?term=89891	"DIC5, FAP133, SRTD11, bA216B9.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025302	89894	TMEM116	http://www.ncbi.nlm.nih.gov/gene/?term=89894		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025303	89894	TMEM116	http://www.ncbi.nlm.nih.gov/gene/?term=89894		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025304	89894	TMEM116	http://www.ncbi.nlm.nih.gov/gene/?term=89894		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025305	898	CCNE1	http://www.ncbi.nlm.nih.gov/gene/?term=898	"CCNE, pCCNE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025306	898	CCNE1	http://www.ncbi.nlm.nih.gov/gene/?term=898	"CCNE, pCCNE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025307	89910	UBE3B	http://www.ncbi.nlm.nih.gov/gene/?term=89910	"BPIDS, KOS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025308	8991	SELENBP1	http://www.ncbi.nlm.nih.gov/gene/?term=8991	"HEL-S-134P, LPSB, SBP56, SP56, hSBP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025309	8991	SELENBP1	http://www.ncbi.nlm.nih.gov/gene/?term=8991	"HEL-S-134P, LPSB, SBP56, SP56, hSBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025310	89927	C16orf45	http://www.ncbi.nlm.nih.gov/gene/?term=89927		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025311	8992	ATP6V0E1	http://www.ncbi.nlm.nih.gov/gene/?term=8992	"ATP6H, ATP6V0E, M9.2, Vma21, Vma21p "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025312	8992	ATP6V0E1	http://www.ncbi.nlm.nih.gov/gene/?term=8992	"ATP6H, ATP6V0E, M9.2, Vma21, Vma21p "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025313	89941	RHOT2	http://www.ncbi.nlm.nih.gov/gene/?term=89941	"ARHT2, C16orf39, MIRO-2, MIRO2, RASL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025314	89941	RHOT2	http://www.ncbi.nlm.nih.gov/gene/?term=89941	"ARHT2, C16orf39, MIRO-2, MIRO2, RASL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025315	89944	GLB1L2	http://www.ncbi.nlm.nih.gov/gene/?term=89944	"MST114, MSTP114 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025316	89944	GLB1L2	http://www.ncbi.nlm.nih.gov/gene/?term=89944	"MST114, MSTP114 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025317	8994	LIMD1	http://www.ncbi.nlm.nih.gov/gene/?term=8994		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025318	8994	LIMD1	http://www.ncbi.nlm.nih.gov/gene/?term=8994		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025319	8994	LIMD1	http://www.ncbi.nlm.nih.gov/gene/?term=8994		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025320	89953	KLC4	http://www.ncbi.nlm.nih.gov/gene/?term=89953	"KNSL8, bA387M24.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025321	89958	SAPCD2	http://www.ncbi.nlm.nih.gov/gene/?term=89958	"C9orf140, p42.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025322	89958	SAPCD2	http://www.ncbi.nlm.nih.gov/gene/?term=89958	"C9orf140, p42.3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025323	8996	NOL3	http://www.ncbi.nlm.nih.gov/gene/?term=8996	"ARC, FCM, MYP, NOP, NOP30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025324	89970	RSPRY1	http://www.ncbi.nlm.nih.gov/gene/?term=89970	SEMDFA	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025325	89970	RSPRY1	http://www.ncbi.nlm.nih.gov/gene/?term=89970	SEMDFA	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025326	89970	RSPRY1	http://www.ncbi.nlm.nih.gov/gene/?term=89970	SEMDFA	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025327	89978	DPH6	http://www.ncbi.nlm.nih.gov/gene/?term=89978	ATPBD4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025328	899	CCNF	http://www.ncbi.nlm.nih.gov/gene/?term=899	"FBX1, FBXO1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025329	89	ACTN3	http://www.ncbi.nlm.nih.gov/gene/?term=89		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025330	90011	KIR3DX1	http://www.ncbi.nlm.nih.gov/gene/?term=90011	"KIR3DL0, LENG12 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025331	90011	KIR3DX1	http://www.ncbi.nlm.nih.gov/gene/?term=90011	"KIR3DL0, LENG12 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025332	90024	FLJ20021	http://www.ncbi.nlm.nih.gov/gene/?term=90024		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025333	90025	UBE3D	http://www.ncbi.nlm.nih.gov/gene/?term=90025	"C6orf157, H10BH, UBE2CBP, YJR141W "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025334	90025	UBE3D	http://www.ncbi.nlm.nih.gov/gene/?term=90025	"C6orf157, H10BH, UBE2CBP, YJR141W "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025335	90075	ZNF30	http://www.ncbi.nlm.nih.gov/gene/?term=90075	KOX28	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025336	900	CCNG1	http://www.ncbi.nlm.nih.gov/gene/?term=900	CCNG	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025337	90120	C9orf69	http://www.ncbi.nlm.nih.gov/gene/?term=90120		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025338	90121	TSR2	http://www.ncbi.nlm.nih.gov/gene/?term=90121	"DBA14, DT1P1A10, WGG1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025339	90121	TSR2	http://www.ncbi.nlm.nih.gov/gene/?term=90121	"DBA14, DT1P1A10, WGG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025340	90133	KRT8P12	http://www.ncbi.nlm.nih.gov/gene/?term=90133	KRT8L2	lncRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025341	90134	KCNH7	http://www.ncbi.nlm.nih.gov/gene/?term=90134	"ERG3, HERG3, Kv11.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025342	90135	BTBD6	http://www.ncbi.nlm.nih.gov/gene/?term=90135	BDPL	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025343	90135	BTBD6	http://www.ncbi.nlm.nih.gov/gene/?term=90135	BDPL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025344	90139	TSPAN18	http://www.ncbi.nlm.nih.gov/gene/?term=90139	TSPAN	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025345	9013	TAF1C	http://www.ncbi.nlm.nih.gov/gene/?term=9013	"MGC:39976, SL1, TAFI110, TAFI95 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025346	90141	EFCAB11	http://www.ncbi.nlm.nih.gov/gene/?term=90141	C14orf143	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025347	90141	EFCAB11	http://www.ncbi.nlm.nih.gov/gene/?term=90141	C14orf143	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025348	9014	TAF1B	http://www.ncbi.nlm.nih.gov/gene/?term=9014	"MGC:9349, RAF1B, RAFI63, SL1, TAFI63 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025349	9016	SLC25A14	http://www.ncbi.nlm.nih.gov/gene/?term=9016	"BMCP1, UCP5 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025350	90196	SYS1	http://www.ncbi.nlm.nih.gov/gene/?term=90196	"C20orf169, dJ453C12.4, dJ453C12.4.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025351	90199	WFDC8	http://www.ncbi.nlm.nih.gov/gene/?term=90199	"C20orf170, HEL-S-292, WAP8, dJ461P17.1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025352	90199	WFDC8	http://www.ncbi.nlm.nih.gov/gene/?term=90199	"C20orf170, HEL-S-292, WAP8, dJ461P17.1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025353	9019	MPZL1	http://www.ncbi.nlm.nih.gov/gene/?term=9019	"MPZL1b, PZR, PZR1b, PZRa, PZRb "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025354	9019	MPZL1	http://www.ncbi.nlm.nih.gov/gene/?term=9019	"MPZL1b, PZR, PZR1b, PZRa, PZRb "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025355	901	CCNG2	http://www.ncbi.nlm.nih.gov/gene/?term=901		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025356	901	CCNG2	http://www.ncbi.nlm.nih.gov/gene/?term=901		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025357	90203	SNX21	http://www.ncbi.nlm.nih.gov/gene/?term=90203	"C20orf161, PP3993, SNX-L, dJ337O18.4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025358	9021	SOCS3	http://www.ncbi.nlm.nih.gov/gene/?term=9021	"ATOD4, CIS3, Cish3, SOCS-3, SSI-3, SSI3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025359	9022	CLIC3	http://www.ncbi.nlm.nih.gov/gene/?term=9022		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025360	90231	KIAA2013	http://www.ncbi.nlm.nih.gov/gene/?term=90231		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025361	90233	ZNF551	http://www.ncbi.nlm.nih.gov/gene/?term=90233		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025362	9025	RNF8	http://www.ncbi.nlm.nih.gov/gene/?term=9025	hRNF8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025363	9025	RNF8	http://www.ncbi.nlm.nih.gov/gene/?term=9025	hRNF8	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025364	9025	RNF8	http://www.ncbi.nlm.nih.gov/gene/?term=9025	hRNF8	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025365	9025	RNF8	http://www.ncbi.nlm.nih.gov/gene/?term=9025	hRNF8	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025366	90268	OTULIN	http://www.ncbi.nlm.nih.gov/gene/?term=90268	"FAM105B, GUM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025367	90268	OTULIN	http://www.ncbi.nlm.nih.gov/gene/?term=90268	"FAM105B, GUM "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025368	90268	OTULIN	http://www.ncbi.nlm.nih.gov/gene/?term=90268	"FAM105B, GUM "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025369	90268	OTULIN	http://www.ncbi.nlm.nih.gov/gene/?term=90268	"FAM105B, GUM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025370	9026	HIP1R	http://www.ncbi.nlm.nih.gov/gene/?term=9026	"HIP12, HIP3, ILWEQ "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025371	90293	KLHL13	http://www.ncbi.nlm.nih.gov/gene/?term=90293	BKLHD2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025372	902	CCNH	http://www.ncbi.nlm.nih.gov/gene/?term=902	"CAK, CycH, p34, p37 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025373	902	CCNH	http://www.ncbi.nlm.nih.gov/gene/?term=902	"CAK, CycH, p34, p37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025374	9031	BAZ1B	http://www.ncbi.nlm.nih.gov/gene/?term=9031	"WBSCR10, WBSCR9, WSTF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025375	9031	BAZ1B	http://www.ncbi.nlm.nih.gov/gene/?term=9031	"WBSCR10, WBSCR9, WSTF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025376	90326	THAP3	http://www.ncbi.nlm.nih.gov/gene/?term=90326		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025377	90362	FAM110B	http://www.ncbi.nlm.nih.gov/gene/?term=90362	C8orf72	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025378	90378	SAMD1	http://www.ncbi.nlm.nih.gov/gene/?term=90378		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025379	90379	DCAF15	http://www.ncbi.nlm.nih.gov/gene/?term=90379	C19orf72	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025380	9037	SEMA5A	http://www.ncbi.nlm.nih.gov/gene/?term=9037	"SEMAF, semF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025381	90390	MED30	http://www.ncbi.nlm.nih.gov/gene/?term=90390	"MED30S, THRAP6, TRAP25 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025382	9039	UBA3	http://www.ncbi.nlm.nih.gov/gene/?term=9039	"NAE2, UBE1C, hUBA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025383	90407	TMEM41A	http://www.ncbi.nlm.nih.gov/gene/?term=90407	2900010K02Rik	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025384	9040	UBE2M	http://www.ncbi.nlm.nih.gov/gene/?term=9040	"UBC-RS2, UBC12, hUbc12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025385	9040	UBE2M	http://www.ncbi.nlm.nih.gov/gene/?term=9040	"UBC-RS2, UBC12, hUbc12 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025386	90410	IFT20	http://www.ncbi.nlm.nih.gov/gene/?term=90410		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025387	90410	IFT20	http://www.ncbi.nlm.nih.gov/gene/?term=90410		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025388	90410	IFT20	http://www.ncbi.nlm.nih.gov/gene/?term=90410		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025389	90411	MCFD2	http://www.ncbi.nlm.nih.gov/gene/?term=90411	"F5F8D, F5F8D2, LMAN1IP, SDNSF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025390	90411	MCFD2	http://www.ncbi.nlm.nih.gov/gene/?term=90411	"F5F8D, F5F8D2, LMAN1IP, SDNSF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025391	90416	C15orf57	http://www.ncbi.nlm.nih.gov/gene/?term=90416	CCDC32	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025392	90416	C15orf57	http://www.ncbi.nlm.nih.gov/gene/?term=90416	CCDC32	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025393	90417	KNSTRN	http://www.ncbi.nlm.nih.gov/gene/?term=90417	"C15orf23, HSD11, SKAP, TRAF4AF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025394	90417	KNSTRN	http://www.ncbi.nlm.nih.gov/gene/?term=90417	"C15orf23, HSD11, SKAP, TRAF4AF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025395	9044	BTAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9044	"MOT1, TAF(II)170, TAF172, TAFII170 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025396	9044	BTAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9044	"MOT1, TAF(II)170, TAF172, TAFII170 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025397	90459	ERI1	http://www.ncbi.nlm.nih.gov/gene/?term=90459	"3'HEXO, HEXO, THEX1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025398	90459	ERI1	http://www.ncbi.nlm.nih.gov/gene/?term=90459	"3'HEXO, HEXO, THEX1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025399	9045	RPL14	http://www.ncbi.nlm.nih.gov/gene/?term=9045	"CAG-ISL-7, CTG-B33, L14, RL14, hRL14 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025400	9045	RPL14	http://www.ncbi.nlm.nih.gov/gene/?term=9045	"CAG-ISL-7, CTG-B33, L14, RL14, hRL14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025401	9047	SH2D2A	http://www.ncbi.nlm.nih.gov/gene/?term=9047	"F2771, SCAP, TSAD, VRAP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025402	90480	GADD45GIP1	http://www.ncbi.nlm.nih.gov/gene/?term=90480	"CKBBP2, CKbetaBP2, CRIF1, MRP-L59, PLINP, PLINP-1, PRG6, Plinp1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025403	90480	GADD45GIP1	http://www.ncbi.nlm.nih.gov/gene/?term=90480	"CKBBP2, CKbetaBP2, CRIF1, MRP-L59, PLINP, PLINP-1, PRG6, Plinp1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025404	90488	TMEM263	http://www.ncbi.nlm.nih.gov/gene/?term=90488	C12orf23	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025405	90488	TMEM263	http://www.ncbi.nlm.nih.gov/gene/?term=90488	C12orf23	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025406	9049	AIP	http://www.ncbi.nlm.nih.gov/gene/?term=9049	"ARA9, FKBP16, FKBP37, SMTPHN, XAP-2, XAP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025407	9049	AIP	http://www.ncbi.nlm.nih.gov/gene/?term=9049	"ARA9, FKBP16, FKBP37, SMTPHN, XAP-2, XAP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025408	904	CCNT1	http://www.ncbi.nlm.nih.gov/gene/?term=904	"CCNT, CYCT1, HIVE1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025409	904	CCNT1	http://www.ncbi.nlm.nih.gov/gene/?term=904	"CCNT, CYCT1, HIVE1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025410	9050	PSTPIP2	http://www.ncbi.nlm.nih.gov/gene/?term=9050	MAYP	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025411	9050	PSTPIP2	http://www.ncbi.nlm.nih.gov/gene/?term=9050	MAYP	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025412	90522	YIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=90522	FinGER8	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025413	90523	MLIP	http://www.ncbi.nlm.nih.gov/gene/?term=90523	C6orf142	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025414	90527	DUOXA1	http://www.ncbi.nlm.nih.gov/gene/?term=90527	"NIP, NUMBIP, mol "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025415	90527	DUOXA1	http://www.ncbi.nlm.nih.gov/gene/?term=90527	"NIP, NUMBIP, mol "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025416	9052	GPRC5A	http://www.ncbi.nlm.nih.gov/gene/?term=9052	"GPCR5A, PEIG-1, RAI3, RAIG1, TIG1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025417	9052	GPRC5A	http://www.ncbi.nlm.nih.gov/gene/?term=9052	"GPCR5A, PEIG-1, RAI3, RAIG1, TIG1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025418	9052	GPRC5A	http://www.ncbi.nlm.nih.gov/gene/?term=9052	"GPCR5A, PEIG-1, RAI3, RAIG1, TIG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025419	9053	MAP7	http://www.ncbi.nlm.nih.gov/gene/?term=9053	"E-MAP-115, EMAP115 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025420	9053	MAP7	http://www.ncbi.nlm.nih.gov/gene/?term=9053	"E-MAP-115, EMAP115 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025421	9054	NFS1	http://www.ncbi.nlm.nih.gov/gene/?term=9054	"HUSSY-08, IscS, NIFS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025422	9054	NFS1	http://www.ncbi.nlm.nih.gov/gene/?term=9054	"HUSSY-08, IscS, NIFS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025423	90550	MCU	http://www.ncbi.nlm.nih.gov/gene/?term=90550	"C10orf42, CCDC109A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025424	9055	PRC1	http://www.ncbi.nlm.nih.gov/gene/?term=9055	ASE1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025425	9055	PRC1	http://www.ncbi.nlm.nih.gov/gene/?term=9055	ASE1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025426	9055	PRC1	http://www.ncbi.nlm.nih.gov/gene/?term=9055	ASE1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025427	9056	SLC7A7	http://www.ncbi.nlm.nih.gov/gene/?term=9056	"LAT3, LPI, MOP-2, Y+LAT1, y+LAT-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025428	9057	SLC7A6	http://www.ncbi.nlm.nih.gov/gene/?term=9057	"LAT-2, LAT3, y+LAT-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025429	90580	C19orf52	http://www.ncbi.nlm.nih.gov/gene/?term=90580		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025430	905	CCNT2	http://www.ncbi.nlm.nih.gov/gene/?term=905	CYCT2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025431	905	CCNT2	http://www.ncbi.nlm.nih.gov/gene/?term=905	CYCT2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025432	905	CCNT2	http://www.ncbi.nlm.nih.gov/gene/?term=905	CYCT2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025433	9060	PAPSS2	http://www.ncbi.nlm.nih.gov/gene/?term=9060	"ATPSK2, BCYM4, SK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025434	9061	PAPSS1	http://www.ncbi.nlm.nih.gov/gene/?term=9061	"ATPSK1, PAPSS, SK1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025435	9061	PAPSS1	http://www.ncbi.nlm.nih.gov/gene/?term=9061	"ATPSK1, PAPSS, SK1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025436	90624	LYRM7	http://www.ncbi.nlm.nih.gov/gene/?term=90624	"C5orf31, MC3DN8, MZM1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025437	90624	LYRM7	http://www.ncbi.nlm.nih.gov/gene/?term=90624	"C5orf31, MC3DN8, MZM1L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025438	90624	LYRM7	http://www.ncbi.nlm.nih.gov/gene/?term=90624	"C5orf31, MC3DN8, MZM1L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025439	90624	LYRM7	http://www.ncbi.nlm.nih.gov/gene/?term=90624	"C5orf31, MC3DN8, MZM1L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025440	90627	STARD13	http://www.ncbi.nlm.nih.gov/gene/?term=90627	"ARHGAP37, DLC2, GT650, LINC00464 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025441	90639	COX19	http://www.ncbi.nlm.nih.gov/gene/?term=90639		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025442	90639	COX19	http://www.ncbi.nlm.nih.gov/gene/?term=90639		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025443	9063	PIAS2	http://www.ncbi.nlm.nih.gov/gene/?term=9063	"ARIP3, DIP, MIZ, MIZ1, PIASX, PIASX-ALPHA, PIASX-BETA, SIZ2, ZMIZ4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025444	9064	MAP3K6	http://www.ncbi.nlm.nih.gov/gene/?term=9064	"ASK2, MAPKKK6, MEKK6 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025445	90668	CARMIL3	http://www.ncbi.nlm.nih.gov/gene/?term=90668	"C14orf121, CARMIL3, crml-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025446	9068	ANGPTL1	http://www.ncbi.nlm.nih.gov/gene/?term=9068	"ANG3, ANGPT3, ARP1, AngY, UNQ162, dJ595C2.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025447	90693	CCDC126	http://www.ncbi.nlm.nih.gov/gene/?term=90693		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025448	9069	CLDN12	http://www.ncbi.nlm.nih.gov/gene/?term=9069		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025449	90701	SEC11C	http://www.ncbi.nlm.nih.gov/gene/?term=90701	"SEC11L3, SPC21, SPCS4C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025450	9071	CLDN10	http://www.ncbi.nlm.nih.gov/gene/?term=9071	"CPETRL3, OSP-L "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025451	9075	CLDN2	http://www.ncbi.nlm.nih.gov/gene/?term=9075		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025452	9076	CLDN1	http://www.ncbi.nlm.nih.gov/gene/?term=9076	"CLD1, ILVASC, SEMP1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025453	9077	DIRAS3	http://www.ncbi.nlm.nih.gov/gene/?term=9077	"ARHI, NOEY2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025454	90780	PYGO2	http://www.ncbi.nlm.nih.gov/gene/?term=90780	1190004M21Rik	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025455	90780	PYGO2	http://www.ncbi.nlm.nih.gov/gene/?term=90780	1190004M21Rik	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025456	90799	CEP95	http://www.ncbi.nlm.nih.gov/gene/?term=90799	CCDC45	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025457	90799	CEP95	http://www.ncbi.nlm.nih.gov/gene/?term=90799	CCDC45	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025458	90806	ANGEL2	http://www.ncbi.nlm.nih.gov/gene/?term=90806	"Ccr4d, KIAA0759L "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025459	90806	ANGEL2	http://www.ncbi.nlm.nih.gov/gene/?term=90806	"Ccr4d, KIAA0759L "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025460	90806	ANGEL2	http://www.ncbi.nlm.nih.gov/gene/?term=90806	"Ccr4d, KIAA0759L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025461	90809	TMEM55B	http://www.ncbi.nlm.nih.gov/gene/?term=90809	C14orf9	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025462	90809	TMEM55B	http://www.ncbi.nlm.nih.gov/gene/?term=90809	C14orf9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025463	90826	PRMT9	http://www.ncbi.nlm.nih.gov/gene/?term=90826	PRMT10	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025464	90843	TCEAL8	http://www.ncbi.nlm.nih.gov/gene/?term=90843	WEX3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025465	90850	ZNF598	http://www.ncbi.nlm.nih.gov/gene/?term=90850		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025466	90850	ZNF598	http://www.ncbi.nlm.nih.gov/gene/?term=90850		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025467	90861	HN1L	http://www.ncbi.nlm.nih.gov/gene/?term=90861	"C16orf34, L11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025468	90861	HN1L	http://www.ncbi.nlm.nih.gov/gene/?term=90861	"C16orf34, L11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025469	90861	HN1L	http://www.ncbi.nlm.nih.gov/gene/?term=90861	"C16orf34, L11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025470	9086	EIF1AY	http://www.ncbi.nlm.nih.gov/gene/?term=9086	eIF-4C	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025471	90871	TMEM261	http://www.ncbi.nlm.nih.gov/gene/?term=90871	C9orf123	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025472	90871	TMEM261	http://www.ncbi.nlm.nih.gov/gene/?term=90871	C9orf123	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025473	90874	ZNF697	http://www.ncbi.nlm.nih.gov/gene/?term=90874		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025474	9087	TMSB4Y	http://www.ncbi.nlm.nih.gov/gene/?term=9087	TB4Y	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025475	9088	PKMYT1	http://www.ncbi.nlm.nih.gov/gene/?term=9088	"MYT1, PPP1R126 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025476	9088	PKMYT1	http://www.ncbi.nlm.nih.gov/gene/?term=9088	"MYT1, PPP1R126 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025477	908	CCT6A	http://www.ncbi.nlm.nih.gov/gene/?term=908	"CCT-zeta, CCT-zeta-1, CCT6, Cctz, HTR3, MoDP-2, TCP-1-zeta, TCP20, TCPZ, TTCP20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025478	908	CCT6A	http://www.ncbi.nlm.nih.gov/gene/?term=908	"CCT-zeta, CCT-zeta-1, CCT6, Cctz, HTR3, MoDP-2, TCP-1-zeta, TCP20, TCPZ, TTCP20 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025479	908	CCT6A	http://www.ncbi.nlm.nih.gov/gene/?term=908	"CCT-zeta, CCT-zeta-1, CCT6, Cctz, HTR3, MoDP-2, TCP-1-zeta, TCP20, TCPZ, TTCP20 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025480	9091	PIGQ	http://www.ncbi.nlm.nih.gov/gene/?term=9091	"GPI1, c407A10.1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025481	9091	PIGQ	http://www.ncbi.nlm.nih.gov/gene/?term=9091	"GPI1, c407A10.1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025482	9092	SART1	http://www.ncbi.nlm.nih.gov/gene/?term=9092	"Ara1, HOMS1, SART1259, SNRNP110, Snu66 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025483	9093	DNAJA3	http://www.ncbi.nlm.nih.gov/gene/?term=9093	"HCA57, TID1, hTID-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025484	9094	UNC119	http://www.ncbi.nlm.nih.gov/gene/?term=9094	"HRG4, IMD13, POC7, POC7A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025485	9094	UNC119	http://www.ncbi.nlm.nih.gov/gene/?term=9094	"HRG4, IMD13, POC7, POC7A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025486	90956	ADCK2	http://www.ncbi.nlm.nih.gov/gene/?term=90956	AARF	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025487	90956	ADCK2	http://www.ncbi.nlm.nih.gov/gene/?term=90956	AARF	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025488	9097	USP14	http://www.ncbi.nlm.nih.gov/gene/?term=9097	TGT	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025489	9097	USP14	http://www.ncbi.nlm.nih.gov/gene/?term=9097	TGT	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025490	9097	USP14	http://www.ncbi.nlm.nih.gov/gene/?term=9097	TGT	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025491	90993	CREB3L1	http://www.ncbi.nlm.nih.gov/gene/?term=90993	OASIS	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025492	90	ACVR1	http://www.ncbi.nlm.nih.gov/gene/?term=90	"ACTRI, ACVR1A, ACVRLK2, ALK2, FOP, SKR1, TSRI "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025493	9100	USP10	http://www.ncbi.nlm.nih.gov/gene/?term=9100	UBPO	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025494	9100	USP10	http://www.ncbi.nlm.nih.gov/gene/?term=9100	UBPO	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025495	91010	FMNL3	http://www.ncbi.nlm.nih.gov/gene/?term=91010	"FHOD3, FRL2, WBP-3, WBP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025496	91012	CERS5	http://www.ncbi.nlm.nih.gov/gene/?term=91012	"LASS5, Trh4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025497	91012	CERS5	http://www.ncbi.nlm.nih.gov/gene/?term=91012	"LASS5, Trh4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025498	9101	USP8	http://www.ncbi.nlm.nih.gov/gene/?term=9101	"HumORF8, SPG59, UBPY "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025499	9101	USP8	http://www.ncbi.nlm.nih.gov/gene/?term=9101	"HumORF8, SPG59, UBPY "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025500	91039	DPP9	http://www.ncbi.nlm.nih.gov/gene/?term=91039	"DP9, DPLP9, DPRP-2, DPRP2 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025501	91039	DPP9	http://www.ncbi.nlm.nih.gov/gene/?term=91039	"DP9, DPLP9, DPRP-2, DPRP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025502	9104	RGN	http://www.ncbi.nlm.nih.gov/gene/?term=9104	"GNL, HEL-S-41, RC, SMP30 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025503	91050	CCDC149	http://www.ncbi.nlm.nih.gov/gene/?term=91050		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025504	91050	CCDC149	http://www.ncbi.nlm.nih.gov/gene/?term=91050		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025505	91056	AP5B1	http://www.ncbi.nlm.nih.gov/gene/?term=91056	"AP-5, PP1030 "	mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00025506	91056	AP5B1	http://www.ncbi.nlm.nih.gov/gene/?term=91056	"AP-5, PP1030 "	mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmid containing either full-length ALPP, t-ftz, AP1, AP2, AP3, AP4, or AP5 and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (C or Ctrl) or HHT (H) for 30 min and then extracted with digitonin. Cells were then fixed, stained for mRNAs using specific FISH probes (ftz probe was used to detect AP1-5), and imaged. Figure 3A, quantification of the fluorescence intensities of mRNA in the ER and nucleus. Data are collected from Figure 3. "
RLID00025507	91056	AP5B1	http://www.ncbi.nlm.nih.gov/gene/?term=91056	"AP-5, PP1030 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025508	91056	AP5B1	http://www.ncbi.nlm.nih.gov/gene/?term=91056	"AP-5, PP1030 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025509	9107	MTMR6	http://www.ncbi.nlm.nih.gov/gene/?term=9107		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025510	91107	TRIM47	http://www.ncbi.nlm.nih.gov/gene/?term=91107	"GOA, RNF100 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025511	9110	MTMR4	http://www.ncbi.nlm.nih.gov/gene/?term=9110	"FYVE-DSP2, ZFYVE11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025512	9110	MTMR4	http://www.ncbi.nlm.nih.gov/gene/?term=9110	"FYVE-DSP2, ZFYVE11 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025513	9110	MTMR4	http://www.ncbi.nlm.nih.gov/gene/?term=9110	"FYVE-DSP2, ZFYVE11 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025514	9111	NMI	http://www.ncbi.nlm.nih.gov/gene/?term=9111		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025515	9112	MTA1	http://www.ncbi.nlm.nih.gov/gene/?term=9112		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025516	9112	MTA1	http://www.ncbi.nlm.nih.gov/gene/?term=9112		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025517	9112	MTA1	http://www.ncbi.nlm.nih.gov/gene/?term=9112		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025518	91133	L3MBTL4	http://www.ncbi.nlm.nih.gov/gene/?term=91133	HsT1031	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025519	91137	SLC25A46	http://www.ncbi.nlm.nih.gov/gene/?term=91137	HMSN6B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025520	9114	ATP6V0D1	http://www.ncbi.nlm.nih.gov/gene/?term=9114	"ATP6D, ATP6DV, P39, VATX, VMA6, VPATPD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025521	9114	ATP6V0D1	http://www.ncbi.nlm.nih.gov/gene/?term=9114	"ATP6D, ATP6DV, P39, VATX, VMA6, VPATPD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025522	9117	SEC22C	http://www.ncbi.nlm.nih.gov/gene/?term=9117	SEC22L3	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025523	9117	SEC22C	http://www.ncbi.nlm.nih.gov/gene/?term=9117	SEC22L3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025524	9121	SLC16A5	http://www.ncbi.nlm.nih.gov/gene/?term=9121	"MCT5, MCT6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025525	91227	GGTLC2	http://www.ncbi.nlm.nih.gov/gene/?term=91227	GGTL4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025526	9122	SLC16A4	http://www.ncbi.nlm.nih.gov/gene/?term=9122	"MCT4, MCT5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025527	9122	SLC16A4	http://www.ncbi.nlm.nih.gov/gene/?term=9122	"MCT4, MCT5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025528	9123	SLC16A3	http://www.ncbi.nlm.nih.gov/gene/?term=9123	"MCT 3, MCT 4, MCT-3, MCT-4, MCT3, MCT4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025529	9123	SLC16A3	http://www.ncbi.nlm.nih.gov/gene/?term=9123	"MCT 3, MCT 4, MCT-3, MCT-4, MCT3, MCT4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025530	91252	SLC39A13	http://www.ncbi.nlm.nih.gov/gene/?term=91252	LZT-Hs9	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025531	9125	RQCD1	http://www.ncbi.nlm.nih.gov/gene/?term=9125	"CAF40, CNOT9, CT129, RCD-1, RCD1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025532	9125	CNOT9	http://www.ncbi.nlm.nih.gov/gene/?term=9125	"CAF40, CNOT9, CT129, RCD-1, RCD1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025533	9126	SMC3	http://www.ncbi.nlm.nih.gov/gene/?term=9126	"BAM, BMH, CDLS3, CSPG6, HCAPL1, SMC3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025534	9126	SMC3	http://www.ncbi.nlm.nih.gov/gene/?term=9126	"BAM, BMH, CDLS3, CSPG6, HCAP, SMC3L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025535	91272	BOD1	http://www.ncbi.nlm.nih.gov/gene/?term=91272	FAM44B	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025536	91283	MSANTD3	http://www.ncbi.nlm.nih.gov/gene/?term=91283	"C9orf30, L8 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025537	91289	LMF2	http://www.ncbi.nlm.nih.gov/gene/?term=91289	"TMEM112B, TMEM153 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025538	9128	PRPF4	http://www.ncbi.nlm.nih.gov/gene/?term=9128	"HPRP4, HPRP4P, PRP4, Prp4p, RP70, SNRNP60 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025539	9128	PRPF4	http://www.ncbi.nlm.nih.gov/gene/?term=9128	"HPRP4, HPRP4P, PRP4, Prp4p, RP70, SNRNP60 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025540	91298	C12orf29	http://www.ncbi.nlm.nih.gov/gene/?term=91298		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025541	912	CD1D	http://www.ncbi.nlm.nih.gov/gene/?term=912	"CD1A, R3, R3G1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025542	91304	TMEM259	http://www.ncbi.nlm.nih.gov/gene/?term=91304	"ASBABP1, C19orf6, MBRL, MEMBRALIN, R32184_3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025543	91304	TMEM259	http://www.ncbi.nlm.nih.gov/gene/?term=91304	"ASBABP1, C19orf6, MBRL, MEMBRALIN, R32184_3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025544	9130	FAM50A	http://www.ncbi.nlm.nih.gov/gene/?term=9130	"9F, DXS9928E, HXC-26, HXC26, XAP5 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025545	9131	AIFM1	http://www.ncbi.nlm.nih.gov/gene/?term=9131	"AIF, CMT2D, CMTX4, COWCK, COXPD6, DFNX5, NADMR, NAMSD, PDCD8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025546	9131	AIFM1	http://www.ncbi.nlm.nih.gov/gene/?term=9131	"AIF, CMT2D, CMTX4, COWCK, COXPD6, DFNX5, NADMR, NAMSD, PDCD8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025547	9133	CCNB2	http://www.ncbi.nlm.nih.gov/gene/?term=9133	HsT17299	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025548	9134	CCNE2	http://www.ncbi.nlm.nih.gov/gene/?term=9134	CYCE2	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00025549	9134	CCNE2	http://www.ncbi.nlm.nih.gov/gene/?term=9134	CYCE2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025550	9134	CCNE2	http://www.ncbi.nlm.nih.gov/gene/?term=9134	CYCE2	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00025551	91351	DDX60L	http://www.ncbi.nlm.nih.gov/gene/?term=91351		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025552	91351	DDX60L	http://www.ncbi.nlm.nih.gov/gene/?term=91351		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025553	9135	RABEP1	http://www.ncbi.nlm.nih.gov/gene/?term=9135	"RAB5EP, RABPT5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025554	9135	RABEP1	http://www.ncbi.nlm.nih.gov/gene/?term=9135	"RAB5EP, RABPT5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025555	91368	CDKN2AIPNL	http://www.ncbi.nlm.nih.gov/gene/?term=91368		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025556	91368	CDKN2AIPNL	http://www.ncbi.nlm.nih.gov/gene/?term=91368		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025557	91369	ANKRD40	http://www.ncbi.nlm.nih.gov/gene/?term=91369		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025558	91369	ANKRD40	http://www.ncbi.nlm.nih.gov/gene/?term=91369		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025559	9136	RRP9	http://www.ncbi.nlm.nih.gov/gene/?term=9136	"RNU3IP2, U3-55K "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025560	9136	RRP9	http://www.ncbi.nlm.nih.gov/gene/?term=9136	"RNU3IP2, U3-55K "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025561	91373	UAP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=91373		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025562	91373	UAP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=91373		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025563	91373	UAP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=91373		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025564	9138	ARHGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=9138	"GEF1, LBCL2, LSC, P115-RHOGEF, SUB1.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025565	9139	CBFA2T2	http://www.ncbi.nlm.nih.gov/gene/?term=9139	"EHT, MTGR1, ZMYND3, p85 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025566	9139	CBFA2T2	http://www.ncbi.nlm.nih.gov/gene/?term=9139	"EHT, MTGR1, ZMYND3, p85 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025567	9139	CBFA2T2	http://www.ncbi.nlm.nih.gov/gene/?term=9139	"EHT, MTGR1, ZMYND3, p85 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025568	91408	BTF3L4	http://www.ncbi.nlm.nih.gov/gene/?term=91408		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025569	9140	ATG12	http://www.ncbi.nlm.nih.gov/gene/?term=9140	"APG12, APG12L, FBR93, HAPG12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025570	91419	ATP23	http://www.ncbi.nlm.nih.gov/gene/?term=91419	"KUB3, XRCC6BP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025571	9141	PDCD5	http://www.ncbi.nlm.nih.gov/gene/?term=9141	TFAR19	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025572	9141	PDCD5	http://www.ncbi.nlm.nih.gov/gene/?term=9141	TFAR19	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025573	91433	RCCD1	http://www.ncbi.nlm.nih.gov/gene/?term=91433		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025574	91433	RCCD1	http://www.ncbi.nlm.nih.gov/gene/?term=91433		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025575	9143	SYNGR3	http://www.ncbi.nlm.nih.gov/gene/?term=9143		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025576	91445	RNF185	http://www.ncbi.nlm.nih.gov/gene/?term=91445		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025577	9144	SYNGR2	http://www.ncbi.nlm.nih.gov/gene/?term=9144		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025578	91452	ACBD5	http://www.ncbi.nlm.nih.gov/gene/?term=91452		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025579	9145	SYNGR1	http://www.ncbi.nlm.nih.gov/gene/?term=9145		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025580	9146	HGS	http://www.ncbi.nlm.nih.gov/gene/?term=9146	HRS	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025581	9146	HGS	http://www.ncbi.nlm.nih.gov/gene/?term=9146	HRS	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025582	9146	HGS	http://www.ncbi.nlm.nih.gov/gene/?term=9146	HRS	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025583	9147	NEMF	http://www.ncbi.nlm.nih.gov/gene/?term=9147	"NY-CO-1, SDCCAG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025584	9153	SLC28A2	http://www.ncbi.nlm.nih.gov/gene/?term=9153	"CNT2, HCNT2, HsT17153, SPNT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025585	9153	SLC28A2	http://www.ncbi.nlm.nih.gov/gene/?term=9153	"CNT2, HCNT2, HsT17153, SPNT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025586	91544	UBXN11	http://www.ncbi.nlm.nih.gov/gene/?term=91544	"COA-1, PP2243, SOC, SOCI, UBXD5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025587	9154	SLC28A1	http://www.ncbi.nlm.nih.gov/gene/?term=9154	"CNT1, HCNT1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025588	9156	EXO1	http://www.ncbi.nlm.nih.gov/gene/?term=9156	"HEX1, hExoI "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025589	91574	C12orf65	http://www.ncbi.nlm.nih.gov/gene/?term=91574	"COXPD7, SPG55 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025590	91582	RPS19BP1	http://www.ncbi.nlm.nih.gov/gene/?term=91582	"AROS, S19BP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025591	9158	FIBP	http://www.ncbi.nlm.nih.gov/gene/?term=9158	"FGFIBP-1, FIBP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025592	9158	FIBP	http://www.ncbi.nlm.nih.gov/gene/?term=9158	"FGFIBP, FIBP-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025593	9159	PCSK7	http://www.ncbi.nlm.nih.gov/gene/?term=9159	"LPC, PC7, PC8, SPC7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025594	9159	PCSK7	http://www.ncbi.nlm.nih.gov/gene/?term=9159	"LPC, PC7, PC8, SPC7 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025595	915	CD3D	http://www.ncbi.nlm.nih.gov/gene/?term=915	"CD3-DELTA, IMD19, T3D "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025596	91603	ZNF830	http://www.ncbi.nlm.nih.gov/gene/?term=91603	"CCDC16, OMCG1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025597	91607	SLFN11	http://www.ncbi.nlm.nih.gov/gene/?term=91607	SLFN8/9	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025598	91607	SLFN11	http://www.ncbi.nlm.nih.gov/gene/?term=91607	SLFN8/9	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025599	91612	CHURC1	http://www.ncbi.nlm.nih.gov/gene/?term=91612	"C14orf52, My015, chch "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025600	91614	DEPDC7	http://www.ncbi.nlm.nih.gov/gene/?term=91614	"TR2, dJ85M6.4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025601	91647	ATPAF2	http://www.ncbi.nlm.nih.gov/gene/?term=91647	"ATP12, ATP12p, LP3663, MC5DN1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025602	91647	ATPAF2	http://www.ncbi.nlm.nih.gov/gene/?term=91647	"ATP12, ATP12p, LP3663, MC5DN1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025603	9164923	RDN18-1	http://www.ncbi.nlm.nih.gov/gene/?term=9164923	RDN18-1	rRNA	Saccharomyces cerevisiae	17339339	Endoplasmic reticulum	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00025604	9164923	RDN18-1	http://www.ncbi.nlm.nih.gov/gene/?term=9164923	RDN18-1	rRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00025605	9164932	RDN18-2	http://www.ncbi.nlm.nih.gov/gene/?term=9164932	RDN18-2	rRNA	Saccharomyces cerevisiae	17339339	Cytosol	Yeast	RT-PCR	"Importantly, mRNAs encoding Sec4, Cdc42, Sro7, and Snc1 were specifically enriched in the ER fraction, along with ASH1 mRNA (Fig. 9B), which was shown to be enriched on the ER (18). mRNAs encoding RDN18, a ribosomal rRNA, and TUB1 were found in both the ER and cytosolic fractions (Fig. 9B).  "
RLID00025606	9164932	RDN18-2	http://www.ncbi.nlm.nih.gov/gene/?term=9164932	RDN18-2	rRNA	Saccharomyces cerevisiae	23904265	Cytosol	Yeast	RT-PCR	"Figure 2: mSMPs cofractionate with ER in WT cells. (A) Fractionation of lysates into ER (microsomal) and cytosolic fractions. WT yeast were lysed and subjected to sucrose density gradient centrifugation as described in Materials and Methods. Aliquots from the different fractions obtained through centrifugation were subjected to SDS–PAGE and detected in blots with antibodies against an ER marker, dolichol phosphate mannose (anti-Dpm1) synthase, or a cytosolic marker, phosphoglycerate kinase (anti-PGK1). Note lack of overlap between markers in the different fractions. (B) Distribution of mSMPs. Total mRNA isolated from the fractions (ER or cytosol [Cyt]) obtained using density gradient centrifugation was subjected to DNase I treatment and RT-PCR with oligonucleotide pairs specific to each mSMP. Genomic DNA served as a positive control for the PCR (Genomic), and RT without RNA template served as a negative control (�. PCR amplification of RNA from the ER and cytosolic fractions without reverse transcription (–RT) served as controls to detect DNA contamination. PCR amplification of RNA from the ER and cytosolic fractions with reverse transcription (+RT) is shown in duplicate. Samples were electrophoresed on agarose gels and documented by ethidium bromide labeling. (C) Distribution of an mRNA encoding a cytosolic protein. Same as in B except that an oligonucleotide pair specific to FSH3 was used. (D) Distribution of mRNAs not encoding mSMPs. Same as in B except that oligonucleotide pairs specific to mRNAs encoding proteins not translocated into the ER, but instead associated either with the cytosolic leaflet of the secretory pathway (SAR1, SEC9, SRO7, YKT6, YPT1) or ribosome (RDN18) were used. Data are collected from Figure 2. "
RLID00025607	91661	ZNF765	http://www.ncbi.nlm.nih.gov/gene/?term=91661		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025608	91661	ZNF765	http://www.ncbi.nlm.nih.gov/gene/?term=91661		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025609	91663	MYADM	http://www.ncbi.nlm.nih.gov/gene/?term=91663	SB135	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025610	91663	MYADM	http://www.ncbi.nlm.nih.gov/gene/?term=91663	SB135	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025611	91663	MYADM	http://www.ncbi.nlm.nih.gov/gene/?term=91663	SB135	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025612	9166	EBAG9	http://www.ncbi.nlm.nih.gov/gene/?term=9166	"EB9, PDAF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025613	9167	COX7A2L	http://www.ncbi.nlm.nih.gov/gene/?term=9167	"COX7AR, COX7RP, EB1, SIG81 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025614	9167	COX7A2L	http://www.ncbi.nlm.nih.gov/gene/?term=9167	"COX7AR, COX7RP, EB1, SIG81 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025615	91689	SMDT1	http://www.ncbi.nlm.nih.gov/gene/?term=91689	"C22orf32, DDDD, EMRE, dJ186O1.1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025616	91689	SMDT1	http://www.ncbi.nlm.nih.gov/gene/?term=91689	"C22orf32, DDDD, EMRE, dJ186O1.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025617	9168	TMSB10	http://www.ncbi.nlm.nih.gov/gene/?term=9168	"MIG12, TB10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025618	9168	TMSB10	http://www.ncbi.nlm.nih.gov/gene/?term=9168	"MIG12, TB10 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025619	9168	TMSB10	http://www.ncbi.nlm.nih.gov/gene/?term=9168	"MIG12, TB10 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025620	9168	TMSB10	http://www.ncbi.nlm.nih.gov/gene/?term=9168	"MIG12, TB10 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025621	9169	SCAF11	http://www.ncbi.nlm.nih.gov/gene/?term=9169	"CASP11, SFRS2IP, SIP1, SRRP129, SRSF2IP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025622	9169	SCAF11	http://www.ncbi.nlm.nih.gov/gene/?term=9169	"CASP11, SFRS2IP, SIP1, SRRP129, SRSF2IP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025623	91703	ACY3	http://www.ncbi.nlm.nih.gov/gene/?term=91703	"ACY-3, HCBP1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025624	9170	LPAR2	http://www.ncbi.nlm.nih.gov/gene/?term=9170	"EDG-4, EDG4, LPA-2, LPA2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025625	9170	LPAR2	http://www.ncbi.nlm.nih.gov/gene/?term=9170	"EDG-4, EDG4, LPA-2, LPA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025626	91734	IDI2	http://www.ncbi.nlm.nih.gov/gene/?term=91734	IPPI2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025627	9173	IL1RL1	http://www.ncbi.nlm.nih.gov/gene/?term=9173	"DER4, FIT-1, IL33R, ST2, ST2L, ST2V, T1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025628	91746	YTHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=91746	"YT521, YT521-B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025629	91746	YTHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=91746	"YT521, YT521-B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025630	91748	ELMSAN1	http://www.ncbi.nlm.nih.gov/gene/?term=91748	"C14orf117, C14orf43, LSR68, MIDEAS, c14_5541 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025631	91748	ELMSAN1	http://www.ncbi.nlm.nih.gov/gene/?term=91748	"C14orf117, C14orf43, LSR68, MIDEAS, c14_5541 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025632	91748	ELMSAN1	http://www.ncbi.nlm.nih.gov/gene/?term=91748	"C14orf117, C14orf43, LSR68, MIDEAS, c14_5541 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025633	91749	MFSD4B	http://www.ncbi.nlm.nih.gov/gene/?term=91749	"KIAA1919, NaGLT1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025634	91749	MFSD4B	http://www.ncbi.nlm.nih.gov/gene/?term=91749	"KIAA1919, NaGLT1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025635	91754	NEK9	http://www.ncbi.nlm.nih.gov/gene/?term=91754	"NERCC, NERCC1, Nek8 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025636	91754	NEK9	http://www.ncbi.nlm.nih.gov/gene/?term=91754	"NERCC, NERCC1, Nek8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025637	91754	NEK9	http://www.ncbi.nlm.nih.gov/gene/?term=91754	"NERCC, NERCC1, Nek8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025638	9175	MAP3K13	http://www.ncbi.nlm.nih.gov/gene/?term=9175	"LZK, MEKK13, MLK "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025639	9175	MAP3K13	http://www.ncbi.nlm.nih.gov/gene/?term=9175	"LZK, MEKK13, MLK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025640	91775	NXPE3	http://www.ncbi.nlm.nih.gov/gene/?term=91775	"FAM55C, MST115, MSTP115 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025641	91775	NXPE3	http://www.ncbi.nlm.nih.gov/gene/?term=91775	"FAM55C, MST115, MSTP115 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025642	91775	NXPE3	http://www.ncbi.nlm.nih.gov/gene/?term=91775	"FAM55C, MST115, MSTP115 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025643	91782	CHMP7	http://www.ncbi.nlm.nih.gov/gene/?term=91782		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025644	9179	AP4M1	http://www.ncbi.nlm.nih.gov/gene/?term=9179	"CPSQ3, MU-4, MU-ARP2, SPG50 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025645	917	CD3G	http://www.ncbi.nlm.nih.gov/gene/?term=917	"CD3-GAMMA, IMD17, T3G "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025646	91807	MYLK3	http://www.ncbi.nlm.nih.gov/gene/?term=91807	"MLCK, MLCK2, caMLCK "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025647	91807	MYLK3	http://www.ncbi.nlm.nih.gov/gene/?term=91807	"MLCK, MLCK2, caMLCK "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025648	9181	ARHGEF2	http://www.ncbi.nlm.nih.gov/gene/?term=9181	"GEF, GEF-H1, GEFH1, LFP40, P40 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025649	91833	WDR20	http://www.ncbi.nlm.nih.gov/gene/?term=91833	DMR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025650	9183	ZW10	http://www.ncbi.nlm.nih.gov/gene/?term=9183	"HZW10, KNTC1AP "	mRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00025651	9183	ZW10	http://www.ncbi.nlm.nih.gov/gene/?term=9183	"HZW10, KNTC1AP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025652	9183	ZW10	http://www.ncbi.nlm.nih.gov/gene/?term=9183	"HZW10, KNTC1AP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025653	9183	ZW10	http://www.ncbi.nlm.nih.gov/gene/?term=9183	"HZW10, KNTC1AP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025654	9184	BUB3	http://www.ncbi.nlm.nih.gov/gene/?term=9184	"BUB3L, hBUB3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025655	9184	BUB3	http://www.ncbi.nlm.nih.gov/gene/?term=9184	"BUB3L, hBUB3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025656	9185	REPS2	http://www.ncbi.nlm.nih.gov/gene/?term=9185	POB1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025657	9185	REPS2	http://www.ncbi.nlm.nih.gov/gene/?term=9185	POB1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025658	91862	MARVELD3	http://www.ncbi.nlm.nih.gov/gene/?term=91862	"MARVD3, MRVLDC3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025659	91875	TTC5	http://www.ncbi.nlm.nih.gov/gene/?term=91875	Strap	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025660	91875	TTC5	http://www.ncbi.nlm.nih.gov/gene/?term=91875	Strap	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025661	91875	TTC5	http://www.ncbi.nlm.nih.gov/gene/?term=91875	Strap	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025662	9187	SLC24A1	http://www.ncbi.nlm.nih.gov/gene/?term=9187	"CSNB1D, HsT17412, NCKX, NCKX1, RODX "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025663	9188	DDX21	http://www.ncbi.nlm.nih.gov/gene/?term=9188	"GUA, GURDB, RH-II/GU, RH-II/GuA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025664	9188	DDX21	http://www.ncbi.nlm.nih.gov/gene/?term=9188	"GUA, GURDB, RH-II/GU, RH-II/GuA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025665	91893	FDXACB1	http://www.ncbi.nlm.nih.gov/gene/?term=91893	hCG_2033039	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025666	91893	FDXACB1	http://www.ncbi.nlm.nih.gov/gene/?term=91893	hCG_2033039	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025667	91893	FDXACB1	http://www.ncbi.nlm.nih.gov/gene/?term=91893	hCG_2033039	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025668	9189	ZBED1	http://www.ncbi.nlm.nih.gov/gene/?term=9189	"ALTE, DREF, TRAMP, hDREF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025669	9191	DEDD	http://www.ncbi.nlm.nih.gov/gene/?term=9191	"CASP8IP11, DEFT, FLDED1, KE05, DEDD "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025670	9191	DEDD	http://www.ncbi.nlm.nih.gov/gene/?term=9191	"CASP8IP1, DEDD1, DEFT, FLDED1, KE05 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025671	91942	NDUFAF2	http://www.ncbi.nlm.nih.gov/gene/?term=91942	"B17.2L, MMTN, NDUFA12L, mimitin "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025672	91949	COG7	http://www.ncbi.nlm.nih.gov/gene/?term=91949	CDG2E	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025673	91966	CXorf40A	http://www.ncbi.nlm.nih.gov/gene/?term=91966	"CXorf40, EOLA1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025674	9197	SLC33A1	http://www.ncbi.nlm.nih.gov/gene/?term=9197	"ACATN, AT-1, AT1, CCHLND, SPG42 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025675	9197	SLC33A1	http://www.ncbi.nlm.nih.gov/gene/?term=9197	"ACATN, AT-1, AT1, CCHLND, SPG42 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025676	9197	SLC33A1	http://www.ncbi.nlm.nih.gov/gene/?term=9197	"ACATN, AT-1, AT1, CCHLND, SPG42 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025677	91	ACVR1B	http://www.ncbi.nlm.nih.gov/gene/?term=91	"ACTRIB, ACVRLK4, ALK4, SKR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025678	9200	HACD1	http://www.ncbi.nlm.nih.gov/gene/?term=9200	"CAP, PTPLA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025679	92014	SLC25A51	http://www.ncbi.nlm.nih.gov/gene/?term=92014	"CG7943, MCART1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025680	9201	DCLK1	http://www.ncbi.nlm.nih.gov/gene/?term=9201	"CL1, CLICK1, DCAMKL1, DCDC3A, DCLK "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025681	9202	ZMYM4	http://www.ncbi.nlm.nih.gov/gene/?term=9202	"CDIR, MYM, ZNF198L3, ZNF262 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025682	9203	ZMYM3	http://www.ncbi.nlm.nih.gov/gene/?term=9203	"DXS6673E, MYM, XFIM, ZNF198L2, ZNF261 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025683	9204	ZMYM6	http://www.ncbi.nlm.nih.gov/gene/?term=9204	"Buster2, MYM, ZBED7, ZNF198L4, ZNF258 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025684	9204	ZMYM6	http://www.ncbi.nlm.nih.gov/gene/?term=9204	"Buster2, MYM, ZBED7, ZNF198L4, ZNF258 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025685	9204	ZMYM6	http://www.ncbi.nlm.nih.gov/gene/?term=9204	"Buster2, MYM, ZBED7, ZNF198L4, ZNF258 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025686	92070	CTBP1-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=92070	"C4orf42, CTBP1-AS1 "	lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025687	9208	LRRFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=9208	"FLAP-1, FLAP1, FLIIAP1, GCF-2, GCF2, HUFI-1, TRIP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025688	9208	LRRFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=9208	"FLAP-1, FLAP1, FLIIAP1, GCF-2, GCF2, HUFI-1, TRIP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025689	92092	ZC3HAV1L	http://www.ncbi.nlm.nih.gov/gene/?term=92092	C7orf39	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025690	920	CD4	http://www.ncbi.nlm.nih.gov/gene/?term=920	CD4mut	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025691	92105	INTS4	http://www.ncbi.nlm.nih.gov/gene/?term=92105	"INT4, MST093 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025692	92106	OXNAD1	http://www.ncbi.nlm.nih.gov/gene/?term=92106		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025693	92126	DSEL	http://www.ncbi.nlm.nih.gov/gene/?term=92126	C18orf4	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025694	92126	DSEL	http://www.ncbi.nlm.nih.gov/gene/?term=92126	C18orf4	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025695	9212	AURKB	http://www.ncbi.nlm.nih.gov/gene/?term=9212	"AIK2, AIM-1, AIM1, ARK2, AurB, IPL1, PPP1R48, STK12, STK5, aurkb-sv1, aurkb-sv2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025696	9212	AURKB	http://www.ncbi.nlm.nih.gov/gene/?term=9212	"AIK2, AIM-1, AIM1, ARK2, AurB, IPL1, PPP1R48, STK12, STK5, aurkb-sv1, aurkb-sv2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025697	9213	XPR1	http://www.ncbi.nlm.nih.gov/gene/?term=9213	"IBGC6, SYG1, X3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025698	9213	XPR1	http://www.ncbi.nlm.nih.gov/gene/?term=9213	"IBGC6, SYG1, X3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025699	92140	MTDH	http://www.ncbi.nlm.nih.gov/gene/?term=92140	"3D3, AEG-1, AEG1, LYRIC, LYRIC/3D3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025700	92140	MTDH	http://www.ncbi.nlm.nih.gov/gene/?term=92140	"3D3, AEG-1, AEG1, LYRIC, LYRIC/3D3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025701	9215	LARGE	http://www.ncbi.nlm.nih.gov/gene/?term=9215	"MDC1D, MDDGA6, MDDGB6 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025702	92170	MTG1	http://www.ncbi.nlm.nih.gov/gene/?term=92170	"GTP, GTPBP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025703	9217	VAPB	http://www.ncbi.nlm.nih.gov/gene/?term=9217	"ALS8, VAMP-B, VAP-B "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025704	9217	VAPB	http://www.ncbi.nlm.nih.gov/gene/?term=9217	"ALS8, VAMP-B, VAP-B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025705	92181	UBTD2	http://www.ncbi.nlm.nih.gov/gene/?term=92181	DCUBP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025706	92181	UBTD2	http://www.ncbi.nlm.nih.gov/gene/?term=92181	DCUBP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025707	9218	VAPA	http://www.ncbi.nlm.nih.gov/gene/?term=9218	"VAP-33, VAP-A, VAP33, hVAP-33 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025708	9218	VAPA	http://www.ncbi.nlm.nih.gov/gene/?term=9218	"VAP-33, VAP-A, VAP33, hVAP-33 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025709	9218	VAPA	http://www.ncbi.nlm.nih.gov/gene/?term=9218	"VAP-33, VAP-A, VAP33, hVAP-33 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025710	9218	VAPA	http://www.ncbi.nlm.nih.gov/gene/?term=9218	"VAP-33, VAP-A, VAP33, hVAP-33 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025711	9219	MTA2	http://www.ncbi.nlm.nih.gov/gene/?term=9219	"MTA1L1, PID "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025712	9220	TIAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9220	"MAJN, SPR210 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025713	9221	NOLC1	http://www.ncbi.nlm.nih.gov/gene/?term=9221	"NOPP130, NOPP140, NS5ATP13, P130 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025714	92235	DUSP27	http://www.ncbi.nlm.nih.gov/gene/?term=92235		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025715	9223	MAGI1	http://www.ncbi.nlm.nih.gov/gene/?term=9223	"AIP-3, AIP3, BAIAP1, BAP-1, BAP1, MAGI-1, Magi1d, TNRC19, WWP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025716	92249	LINC01278	http://www.ncbi.nlm.nih.gov/gene/?term=92249		lncRNA	Homo sapiens	25630241	Cytoplasm	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00025717	92249	LINC01278	http://www.ncbi.nlm.nih.gov/gene/?term=92249		lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00025718	92249	LINC01278	http://www.ncbi.nlm.nih.gov/gene/?term=92249		lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00025719	92259	MRPS36	http://www.ncbi.nlm.nih.gov/gene/?term=92259	"DC47, MRP-S36 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025720	92270	ATP6AP1L	http://www.ncbi.nlm.nih.gov/gene/?term=92270		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025721	9227	LRAT	http://www.ncbi.nlm.nih.gov/gene/?term=9227	LCA14	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025722	9227	LRAT	http://www.ncbi.nlm.nih.gov/gene/?term=9227	LCA14	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025723	92283	ZNF461	http://www.ncbi.nlm.nih.gov/gene/?term=92283	"GIOT-1, GIOT1, HZF28 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025724	92283	ZNF461	http://www.ncbi.nlm.nih.gov/gene/?term=92283	"GIOT-1, GIOT1, HZF28 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025725	92305	TMEM129	http://www.ncbi.nlm.nih.gov/gene/?term=92305	D4S2561E	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025726	92305	TMEM129	http://www.ncbi.nlm.nih.gov/gene/?term=92305	D4S2561E	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025727	9230	RAB11B	http://www.ncbi.nlm.nih.gov/gene/?term=9230	H-YPT3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025728	9230	RAB11B	http://www.ncbi.nlm.nih.gov/gene/?term=9230	H-YPT3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025729	9231	DLG5	http://www.ncbi.nlm.nih.gov/gene/?term=9231	"LP-DLG, P-DLG5, PDLG "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025730	9231	DLG5	http://www.ncbi.nlm.nih.gov/gene/?term=9231	"LP-DLG, P-DLG5, PDLG "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025731	9231	DLG5	http://www.ncbi.nlm.nih.gov/gene/?term=9231	"LP-DLG, P-DLG5, PDLG "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025732	9231	DLG5	http://www.ncbi.nlm.nih.gov/gene/?term=9231	"LP-DLG, P-DLG5, PDLG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025733	9232	PTTG1	http://www.ncbi.nlm.nih.gov/gene/?term=9232	"EAP1, HPTTG, PTTG, TUTR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025734	9232	PTTG1	http://www.ncbi.nlm.nih.gov/gene/?term=9232	"EAP1, HPTTG, PTTG, TUTR1 "	mRNA	Homo sapiens	25627474	Cytoplasm	AGS cell|SGC7901 cell	qRT-PCR	"PTTG1 expression was nuclear and cytoplasmic, with higher cytoplasmic expression. PTTG1 was expressed in the nuclear and cytoplasmic fractions. These results suggest that PTTG1 exhibits nuclear and cytoplasmic expression, with slightly higher cytoplasmic expression.  "
RLID00025735	9232	PTTG1	http://www.ncbi.nlm.nih.gov/gene/?term=9232	"EAP1, HPTTG, PTTG, TUTR1 "	mRNA	Homo sapiens	25627474	Nucleus	AGS cell|SGC7901 cell	qRT-PCR	"PTTG1 expression was nuclear and cytoplasmic, with higher cytoplasmic expression. PTTG1 was expressed in the nuclear and cytoplasmic fractions. These results suggest that PTTG1 exhibits nuclear and cytoplasmic expression, with slightly higher cytoplasmic expression.  "
RLID00025736	9232	PTTG1	http://www.ncbi.nlm.nih.gov/gene/?term=9232	"EAP1, HPTTG, PTTG, TUTR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025737	9232	PTTG1	http://www.ncbi.nlm.nih.gov/gene/?term=9232	"EAP1, HPTTG, PTTG, TUTR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025738	92335	STRADA	http://www.ncbi.nlm.nih.gov/gene/?term=92335	"LYK5, NY-BR-96, PMSE, STRAD, Stlk "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025739	92342	METTL18	http://www.ncbi.nlm.nih.gov/gene/?term=92342	"AsTP2, C1orf156, HPM1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025740	92344	GORAB	http://www.ncbi.nlm.nih.gov/gene/?term=92344	"GO, NTKLBP1, SCYL1BP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025741	92359	CRB3	http://www.ncbi.nlm.nih.gov/gene/?term=92359		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025742	9235	IL32	http://www.ncbi.nlm.nih.gov/gene/?term=9235	"IL-32alpha, IL-32beta, IL-32delta, IL-32gamma, NK4, TAIF, TAIFa, TAIFb, TAIFc, TAIFd "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025743	9235	IL32	http://www.ncbi.nlm.nih.gov/gene/?term=9235	"IL-32alpha, IL-32beta, IL-32delta, IL-32gamma, NK4, TAIF, TAIFa, TAIFb, TAIFc, TAIFd "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025744	9236	CCPG1	http://www.ncbi.nlm.nih.gov/gene/?term=9236	CPR8	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025745	92370	PXYLP1	http://www.ncbi.nlm.nih.gov/gene/?term=92370	"ACPL2, HEL124, XYLP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025746	9238	TBRG4	http://www.ncbi.nlm.nih.gov/gene/?term=9238	"CPR2, FASTKD4 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025747	9238	TBRG4	http://www.ncbi.nlm.nih.gov/gene/?term=9238	"CPR2, FASTKD4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025748	92399	MRRF	http://www.ncbi.nlm.nih.gov/gene/?term=92399	"MRFF, MTRRF, RRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025749	92400	RBM18	http://www.ncbi.nlm.nih.gov/gene/?term=92400		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025750	92421	CHMP4C	http://www.ncbi.nlm.nih.gov/gene/?term=92421	"SNF7-3, Shax3, VPS32C "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025751	92421	CHMP4C	http://www.ncbi.nlm.nih.gov/gene/?term=92421	"SNF7-3, Shax3, VPS32C "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025752	92421	CHMP4C	http://www.ncbi.nlm.nih.gov/gene/?term=92421	"SNF7-3, Shax3, VPS32C "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025753	9246	UBE2L6	http://www.ncbi.nlm.nih.gov/gene/?term=9246	"RIG-B, UBCH8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025754	9246	UBE2L6	http://www.ncbi.nlm.nih.gov/gene/?term=9246	"RIG-B, UBCH8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025755	92482	BBIP1	http://www.ncbi.nlm.nih.gov/gene/?term=92482	"BBIP10, BBS18, NCRNA00081, bA348N5.3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025756	9249	DHRS3	http://www.ncbi.nlm.nih.gov/gene/?term=9249	"DD83.1, RDH17, Rsdr1, SDR1, SDR16C1, retSDR1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025757	92521	SPECC1	http://www.ncbi.nlm.nih.gov/gene/?term=92521	"CYTSB, HCMOGT-1, HCMOGT1, NSP "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025758	92521	SPECC1	http://www.ncbi.nlm.nih.gov/gene/?term=92521	"CYTSB, HCMOGT-1, HCMOGT1, NSP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025759	9252	RPS6KA5	http://www.ncbi.nlm.nih.gov/gene/?term=9252	"MSK1, MSPK1, RLPK "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025760	9252	RPS6KA5	http://www.ncbi.nlm.nih.gov/gene/?term=9252	"MSK1, MSPK1, RLPK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025761	9254	CACNA2D2	http://www.ncbi.nlm.nih.gov/gene/?term=9254	CACNA2D	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025762	9255	AIMP1	http://www.ncbi.nlm.nih.gov/gene/?term=9255	"EMAP2, EMAPII, HLD3, SCYE1, p43 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025763	9255	AIMP1	http://www.ncbi.nlm.nih.gov/gene/?term=9255	"EMAP2, EMAPII, HLD3, SCYE1, p43 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025764	92579	G6PC3	http://www.ncbi.nlm.nih.gov/gene/?term=92579	"SCN4, UGRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025765	9258	MFHAS1	http://www.ncbi.nlm.nih.gov/gene/?term=9258	"LRRC65, MASL1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025766	92591	ASB16	http://www.ncbi.nlm.nih.gov/gene/?term=92591		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025767	92591	ASB16	http://www.ncbi.nlm.nih.gov/gene/?term=92591		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025768	92595	ZNF764	http://www.ncbi.nlm.nih.gov/gene/?term=92595		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025769	92595	ZNF764	http://www.ncbi.nlm.nih.gov/gene/?term=92595		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025770	92595	ZNF764	http://www.ncbi.nlm.nih.gov/gene/?term=92595		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025771	92597	MOB1B	http://www.ncbi.nlm.nih.gov/gene/?term=92597	"MATS2, MOB4A, MOBKL1A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025772	92597	MOB1B	http://www.ncbi.nlm.nih.gov/gene/?term=92597	"MATS2, MOB4A, MOBKL1A "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025773	92597	MOB1B	http://www.ncbi.nlm.nih.gov/gene/?term=92597	"MATS2, MOB4A, MOBKL1A "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025774	92597	MOB1B	http://www.ncbi.nlm.nih.gov/gene/?term=92597	"MATS2, MOB4A, MOBKL1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025775	92609	TIMM50	http://www.ncbi.nlm.nih.gov/gene/?term=92609	"TIM50, TIM50L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025776	9260	PDLIM7	http://www.ncbi.nlm.nih.gov/gene/?term=9260	"LMP1, LMP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025777	9261	MAPKAPK2	http://www.ncbi.nlm.nih.gov/gene/?term=9261	"MAPKAP-K2, MK-2, MK2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025778	9261	MAPKAPK2	http://www.ncbi.nlm.nih.gov/gene/?term=9261	"MAPKAP-K2, MK-2, MK2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025779	9262	STK17B	http://www.ncbi.nlm.nih.gov/gene/?term=9262	DRAK2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025780	9263	STK17A	http://www.ncbi.nlm.nih.gov/gene/?term=9263	DRAK1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025781	9263	STK17A	http://www.ncbi.nlm.nih.gov/gene/?term=9263	DRAK1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025782	92659	MAFG-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=92659		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025783	9266	CYTH2	http://www.ncbi.nlm.nih.gov/gene/?term=9266	"ARNO, CTS18, CTS18.1, PSCD2, PSCD2L, SEC7L, Sec7p-L, Sec7p-like "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025784	9266	CYTH2	http://www.ncbi.nlm.nih.gov/gene/?term=9266	"ARNO, CTS18, CTS18.1, PSCD2, PSCD2L, SEC7L, Sec7p-L, Sec7p-like "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025785	9266	CYTH2	http://www.ncbi.nlm.nih.gov/gene/?term=9266	"ARNO, CTS18, CTS18.1, PSCD2, PSCD2L, SEC7L, Sec7p-L, Sec7p-like "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025786	9266	CYTH2	http://www.ncbi.nlm.nih.gov/gene/?term=9266	"ARNO, CTS18, CTS18.1, PSCD2, PSCD2L, SEC7L, Sec7p-L, Sec7p-like "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025787	92675	DTD1	http://www.ncbi.nlm.nih.gov/gene/?term=92675	"C20orf88, DUE-B, DUEB, HARS2, pqn-68 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025788	9267	CYTH1	http://www.ncbi.nlm.nih.gov/gene/?term=9267	"B2-1, CYTOHESIN-1, D17S811E, PSCD1, SEC7 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025789	9267	CYTH1	http://www.ncbi.nlm.nih.gov/gene/?term=9267	"B2-1, CYTOHESIN-1, D17S811E, PSCD1, SEC7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025790	92689	FAM114A1	http://www.ncbi.nlm.nih.gov/gene/?term=92689	Noxp20	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025791	92691	TMEM169	http://www.ncbi.nlm.nih.gov/gene/?term=92691		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025792	92691	TMEM169	http://www.ncbi.nlm.nih.gov/gene/?term=92691		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025793	92691	TMEM169	http://www.ncbi.nlm.nih.gov/gene/?term=92691		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025794	926	CD8B	http://www.ncbi.nlm.nih.gov/gene/?term=926	"CD8B1, LEU2, LY3, LYT3, P37 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025795	92703	TMEM183A	http://www.ncbi.nlm.nih.gov/gene/?term=92703	C1orf37	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025796	92703	TMEM183A	http://www.ncbi.nlm.nih.gov/gene/?term=92703	C1orf37	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025797	9270	ITGB1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=9270	"ICAP-1A, ICAP-1B, ICAP-1alpha, ICAP1, ICAP1A, ICAP1B "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025798	9270	ITGB1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=9270	"ICAP-1A, ICAP-1B, ICAP-1alpha, ICAP1, ICAP1A, ICAP1B "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025799	9270	ITGB1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=9270	"ICAP-1A, ICAP-1B, ICAP-1alpha, ICAP1, ICAP1A, ICAP1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025800	92714	ARRDC1	http://www.ncbi.nlm.nih.gov/gene/?term=92714		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025801	9271	PIWIL1	http://www.ncbi.nlm.nih.gov/gene/?term=9271	"CT80.1, HIWI, MIWI, PIWI "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025802	9274	BCL7C	http://www.ncbi.nlm.nih.gov/gene/?term=9274		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025803	9275	BCL7B	http://www.ncbi.nlm.nih.gov/gene/?term=9275		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025804	9275	BCL7B	http://www.ncbi.nlm.nih.gov/gene/?term=9275		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025805	9276	COPB2	http://www.ncbi.nlm.nih.gov/gene/?term=9276	beta'-COP	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025806	9276	COPB2	http://www.ncbi.nlm.nih.gov/gene/?term=9276	beta'-COP	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025807	9276	COPB2	http://www.ncbi.nlm.nih.gov/gene/?term=9276	beta'-COP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025808	9277	WDR46	http://www.ncbi.nlm.nih.gov/gene/?term=9277	"BING4, C6orf11, FP221, UTP7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025809	9278	ZBTB22	http://www.ncbi.nlm.nih.gov/gene/?term=9278	"BING1A, ZNF297, ZNF297A, fru, fruitless, ZBTB22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025810	9278	ZBTB22	http://www.ncbi.nlm.nih.gov/gene/?term=9278	"BING1, ZBTB22A, ZNF297, ZNF297A, fru, fruitless "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025811	92799	SHKBP1	http://www.ncbi.nlm.nih.gov/gene/?term=92799	"PP203, Sb1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025812	92799	SHKBP1	http://www.ncbi.nlm.nih.gov/gene/?term=92799	"PP203, Sb1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025813	92815	HIST3H2A	http://www.ncbi.nlm.nih.gov/gene/?term=92815		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025814	92815	HIST3H2A	http://www.ncbi.nlm.nih.gov/gene/?term=92815		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025815	9282	MED14	http://www.ncbi.nlm.nih.gov/gene/?term=9282	"CRSP150, CRSP2, CSRP, CXorf4, DRIP150, EXLM1, RGR1, TRAP170 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025816	9283	GPR37L1	http://www.ncbi.nlm.nih.gov/gene/?term=9283	"ET(B)R-LP-2, ETBR-LP-2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025817	9283	GPR37L1	http://www.ncbi.nlm.nih.gov/gene/?term=9283	"ET(B)R-LP-2, ETBR-LP-2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025818	92840	REEP6	http://www.ncbi.nlm.nih.gov/gene/?term=92840	"C19orf32, DP1L1, TB2L1, Yip2f "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025819	92840	REEP6	http://www.ncbi.nlm.nih.gov/gene/?term=92840	"C19orf32, DP1L1, TB2L1, Yip2f "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025820	92856	IMP4	http://www.ncbi.nlm.nih.gov/gene/?term=92856	BXDC4	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025821	92856	IMP4	http://www.ncbi.nlm.nih.gov/gene/?term=92856	BXDC4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025822	9289	ADGRG1	http://www.ncbi.nlm.nih.gov/gene/?term=9289	"BFPP, BPPR, GPR56, TM7LN4, TM7XN1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025823	9289	ADGRG1	http://www.ncbi.nlm.nih.gov/gene/?term=9289	"BFPP, BPPR, GPR56, TM7LN4, TM7XN1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025824	928	CD9	http://www.ncbi.nlm.nih.gov/gene/?term=928	"BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025825	928	CD9	http://www.ncbi.nlm.nih.gov/gene/?term=928	"BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025826	928	CD9	http://www.ncbi.nlm.nih.gov/gene/?term=928	"BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025827	92906	HNRNPLL	http://www.ncbi.nlm.nih.gov/gene/?term=92906	"HNRPLL, SRRF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025828	92906	HNRNPLL	http://www.ncbi.nlm.nih.gov/gene/?term=92906	"HNRPLL, SRRF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025829	92912	UBE2Q2	http://www.ncbi.nlm.nih.gov/gene/?term=92912		mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025830	92935	MARS2	http://www.ncbi.nlm.nih.gov/gene/?term=92935	"COXPD25, MetRS, mtMetRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025831	92949	ADAMTSL1	http://www.ncbi.nlm.nih.gov/gene/?term=92949	"ADAMTSL-1, ADAMTSR1, C9orf94, PUNCTIN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025832	92949	ADAMTSL1	http://www.ncbi.nlm.nih.gov/gene/?term=92949	"ADAMTSL-1, ADAMTSR1, C9orf94, PUNCTIN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025833	9294	S1PR2	http://www.ncbi.nlm.nih.gov/gene/?term=9294	"AGR16, DFNB68, EDG-5, EDG5, Gpcr13, H218, LPB2, S1P2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025834	9294	S1PR2	http://www.ncbi.nlm.nih.gov/gene/?term=9294	"AGR16, DFNB68, EDG-5, EDG5, Gpcr13, H218, LPB2, S1P2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025835	9294	S1PR2	http://www.ncbi.nlm.nih.gov/gene/?term=9294	"AGR16, EDG-5, EDG5, Gpcr13, H218, LPB2, S1P2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025836	9295	SRSF11	http://www.ncbi.nlm.nih.gov/gene/?term=9295	"NET2, SFRS11, dJ677H15.2, p54 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025837	9295	SRSF11	http://www.ncbi.nlm.nih.gov/gene/?term=9295	"NET2, SFRS11, dJ677H15.2, p54 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025838	9296	ATP6V1F	http://www.ncbi.nlm.nih.gov/gene/?term=9296	"ATP6S14, VATF, Vma7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025839	9296	ATP6V1F	http://www.ncbi.nlm.nih.gov/gene/?term=9296	"ATP6S14, VATF, Vma7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025840	92979	MARCH9	http://www.ncbi.nlm.nih.gov/gene/?term=92979	"MARCH-IX, RNF179 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025841	9297	SNORD29	http://www.ncbi.nlm.nih.gov/gene/?term=9297	"RNU29, U29 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025842	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00025843	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"The most abundant snoRNA found in the serum exosomes were SNORD100, SNORD27 and SNORD31 (Supplementary file). The functions of these snoRNA species are largely unknown; however, they have been detected in myeloma. "
RLID00025844	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025845	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025846	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00025847	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00025848	9298	SNORD31	http://www.ncbi.nlm.nih.gov/gene/?term=9298	"RNU31A, U31, SNORD31 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025849	9299	SNORD30	http://www.ncbi.nlm.nih.gov/gene/?term=9299	"RNU30, U30 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025850	9299	SNORD30	http://www.ncbi.nlm.nih.gov/gene/?term=9299	"RNU30, U30 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025851	9299	SNORD30	http://www.ncbi.nlm.nih.gov/gene/?term=9299	"RNU30, U30 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00025852	929	CD14	http://www.ncbi.nlm.nih.gov/gene/?term=929		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025853	92	ACVR2A	http://www.ncbi.nlm.nih.gov/gene/?term=92	"ACTRII, ACVR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025854	92	ACVR2A	http://www.ncbi.nlm.nih.gov/gene/?term=92	"ACTRII, ACVR2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025855	9300	SNORD28	http://www.ncbi.nlm.nih.gov/gene/?term=9300	"RNU28A, U28, SNORD28 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025856	9300	SNORD28	http://www.ncbi.nlm.nih.gov/gene/?term=9300	"RNU28A, U28, SNORD28 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025857	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00025858	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"The most abundant snoRNA found in the serum exosomes were SNORD100, SNORD27 and SNORD31 (Supplementary file). The functions of these snoRNA species are largely unknown; however, they have been detected in myeloma. "
RLID00025859	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025860	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025861	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 6. Ten Most Highly Expressed snoRNAs of Exosome I, Exosome II and W. Data are collected from Table 6. "
RLID00025862	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025863	9301	SNORD27	http://www.ncbi.nlm.nih.gov/gene/?term=9301	"RNU27, U27 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025864	9302	SNORD26	http://www.ncbi.nlm.nih.gov/gene/?term=9302	"RNU26, U26 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00025865	9302	SNORD26	http://www.ncbi.nlm.nih.gov/gene/?term=9302	"RNU26, U26 "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025866	9302	SNORD26	http://www.ncbi.nlm.nih.gov/gene/?term=9302	"RNU26, U26 "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00025867	9302	SNORD26	http://www.ncbi.nlm.nih.gov/gene/?term=9302	"RNU26, U26 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025868	9303	SNORD25	http://www.ncbi.nlm.nih.gov/gene/?term=9303	"RNU25, U25 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00025869	9304	SNORD22	http://www.ncbi.nlm.nih.gov/gene/?term=9304	"RNU22, U22 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00025870	9304	SNORD22	http://www.ncbi.nlm.nih.gov/gene/?term=9304	"RNU22, U22 "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025871	9304	SNORD22	http://www.ncbi.nlm.nih.gov/gene/?term=9304	"RNU22, U22 "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025872	9306	SOCS6	http://www.ncbi.nlm.nih.gov/gene/?term=9306	"CIS-4, CIS4, HSPC060, SOCS-4, SOCS-6, SOCS4, SSI4, STAI4, STATI4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025873	9306	SOCS6	http://www.ncbi.nlm.nih.gov/gene/?term=9306	"CIS-4, CIS4, HSPC060, SOCS-4, SOCS-6, SOCS4, SSI4, STAI4, STATI4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025874	93081	TEX30	http://www.ncbi.nlm.nih.gov/gene/?term=93081	C13orf27	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025875	93099	DMKN	http://www.ncbi.nlm.nih.gov/gene/?term=93099	"UNQ729, ZD52F10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025876	93100	NAPRT	http://www.ncbi.nlm.nih.gov/gene/?term=93100	"NAPRT1, PP3856 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025877	93100	NAPRT	http://www.ncbi.nlm.nih.gov/gene/?term=93100	"NAPRT1, PP3856 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025878	93109	TMEM44	http://www.ncbi.nlm.nih.gov/gene/?term=93109		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025879	93109	TMEM44	http://www.ncbi.nlm.nih.gov/gene/?term=93109		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025880	93145	OLFM2	http://www.ncbi.nlm.nih.gov/gene/?term=93145	"NOE2, NOELIN2, NOELIN2_V1, OlfC "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025881	9314	KLF4	http://www.ncbi.nlm.nih.gov/gene/?term=9314	"EZF, GKLF "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025882	9314	KLF4	http://www.ncbi.nlm.nih.gov/gene/?term=9314	"EZF, GKLF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025883	93183	PIGM	http://www.ncbi.nlm.nih.gov/gene/?term=93183	GPI-MT-I	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025884	93183	PIGM	http://www.ncbi.nlm.nih.gov/gene/?term=93183	GPI-MT-I	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025885	93183	PIGM	http://www.ncbi.nlm.nih.gov/gene/?term=93183	GPI-MT-I	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025886	9318	COPS2	http://www.ncbi.nlm.nih.gov/gene/?term=9318	"ALIEN, CSN2, SGN2, TRIP15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025887	9318	COPS2	http://www.ncbi.nlm.nih.gov/gene/?term=9318	"ALIEN, CSN2, SGN2, TRIP15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025888	9318	COPS2	http://www.ncbi.nlm.nih.gov/gene/?term=9318	"ALIEN, CSN2, SGN2, TRIP15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025889	93190	C1orf158	http://www.ncbi.nlm.nih.gov/gene/?term=93190		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025890	9319	TRIP13	http://www.ncbi.nlm.nih.gov/gene/?term=9319	16E1BP	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025891	9319	TRIP13	http://www.ncbi.nlm.nih.gov/gene/?term=9319	16E1BP	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025892	9320	TRIP12	http://www.ncbi.nlm.nih.gov/gene/?term=9320	"TRIP-12, ULF "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025893	9320	TRIP12	http://www.ncbi.nlm.nih.gov/gene/?term=9320	"TRIP-12, ULF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025894	93210	PGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=93210	"AGLA546, CAB2, PERLD1, PP1498, hCOS16 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025895	9321	TRIP11	http://www.ncbi.nlm.nih.gov/gene/?term=9321	"ACG1A, CEV14, GMAP-210, GMAP210, TRIP-11, TRIP230 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025896	9322	TRIP10	http://www.ncbi.nlm.nih.gov/gene/?term=9322	"CIP4, HSTP, STOT, STP, TRIP-10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025897	9322	TRIP10	http://www.ncbi.nlm.nih.gov/gene/?term=9322	"CIP4, HSTP, STOT, STP, TRIP-10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025898	9324	HMGN3	http://www.ncbi.nlm.nih.gov/gene/?term=9324	"PNAS-24, PNAS-25, TRIP7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025899	9325	TRIP4	http://www.ncbi.nlm.nih.gov/gene/?term=9325	"ASC-1, ASC1, HsT17391, SMABF1, ZC2HC5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025900	9325	TRIP4	http://www.ncbi.nlm.nih.gov/gene/?term=9325	"ASC-1, ASC1, HsT17391, ZC2HC5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025901	9326	ZNHIT3	http://www.ncbi.nlm.nih.gov/gene/?term=9326	TRIP3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025902	9328	GTF3C5	http://www.ncbi.nlm.nih.gov/gene/?term=9328	"TFIIIC63, TFIIICepsilon, TFiiiC2-63 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025903	9329	GTF3C4	http://www.ncbi.nlm.nih.gov/gene/?term=9329	"KAT12, TF3C-delta, TFIII90, TFIIIC290, TFIIIC90, TFIIICDELTA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025904	9330	GTF3C3	http://www.ncbi.nlm.nih.gov/gene/?term=9330	"TFIIIC102, TFIIICgamma, TFiiiC2-102 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025905	9330	GTF3C3	http://www.ncbi.nlm.nih.gov/gene/?term=9330	"TFIIIC102, TFIIICgamma, TFiiiC2-102 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025906	93323	HAUS8	http://www.ncbi.nlm.nih.gov/gene/?term=93323	"DGT4, HICE1, NY-SAR-48 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025907	9332	CD163	http://www.ncbi.nlm.nih.gov/gene/?term=9332	"M130, MM130 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025908	93343	MVB12A	http://www.ncbi.nlm.nih.gov/gene/?term=93343	"CFBP, FAM125A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025909	93343	MVB12A	http://www.ncbi.nlm.nih.gov/gene/?term=93343	"CFBP, FAM125A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025910	93343	MVB12A	http://www.ncbi.nlm.nih.gov/gene/?term=93343	"CFBP, FAM125A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025911	9337	CNOT8	http://www.ncbi.nlm.nih.gov/gene/?term=9337	"CAF1, CALIF, Caf1b, POP2, hCAF1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025912	9338	TCEAL1	http://www.ncbi.nlm.nih.gov/gene/?term=9338	"SIIR, WEX9, p21, pp21 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025913	933	CD22	http://www.ncbi.nlm.nih.gov/gene/?term=933	"SIGLEC-2, SIGLEC2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025914	93408	MYL10	http://www.ncbi.nlm.nih.gov/gene/?term=93408	"MYLC2PL, PLRLC "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025915	93408	MYL10	http://www.ncbi.nlm.nih.gov/gene/?term=93408	"MYLC2PL, PLRLC "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025916	9341	VAMP3	http://www.ncbi.nlm.nih.gov/gene/?term=9341	CEB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025917	9341	VAMP3	http://www.ncbi.nlm.nih.gov/gene/?term=9341	CEB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025918	9342	SNAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9342	"CEDNIK, SNAP-29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025919	9342	SNAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9342	"CEDNIK, SNAP-29 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025920	9342	SNAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9342	"CEDNIK, SNAP-29 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025921	9342	SNAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9342	"CEDNIK, SNAP-29 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025922	9342	SNAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9342	"CEDNIK, SNAP-29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025923	93436	ARMC6	http://www.ncbi.nlm.nih.gov/gene/?term=93436	R30923_1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025924	9343	EFTUD2	http://www.ncbi.nlm.nih.gov/gene/?term=9343	"MFDGA, MFDM, SNRNP116, Snrp116, Snu114, U5-116KD "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025925	9343	EFTUD2	http://www.ncbi.nlm.nih.gov/gene/?term=9343	"MFDGA, MFDM, SNRNP116, Snrp116, Snu114, U5-116KD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025926	9344	TAOK2	http://www.ncbi.nlm.nih.gov/gene/?term=9344	"MAP3K17, PSK, PSK1, PSK1-BETA, TAO1, TAO2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025927	93487	MAPK1IP1L	http://www.ncbi.nlm.nih.gov/gene/?term=93487	"C14orf32, MISS, c14_5346 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025928	93487	MAPK1IP1L	http://www.ncbi.nlm.nih.gov/gene/?term=93487	"C14orf32, MISS, c14_5346 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025929	93487	MAPK1IP1L	http://www.ncbi.nlm.nih.gov/gene/?term=93487	"C14orf32, MISS, c14_5346 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025930	93487	MAPK1IP1L	http://www.ncbi.nlm.nih.gov/gene/?term=93487	"C14orf32, MISS, c14_5346 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025931	9349	RPL23	http://www.ncbi.nlm.nih.gov/gene/?term=9349	"L23, rpL17 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025932	9349	RPL23	http://www.ncbi.nlm.nih.gov/gene/?term=9349	"L23, rpL17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025933	9351	SLC9A3R2	http://www.ncbi.nlm.nih.gov/gene/?term=9351	"E3KARP, NHE3RF2, NHERF-2, NHERF2, OCTS2, SIP-1, SIP1, TKA-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025934	9351	SLC9A3R2	http://www.ncbi.nlm.nih.gov/gene/?term=9351	"E3KARP, NHE3RF2, NHERF-2, NHERF2, OCTS2, SIP-1, SIP1, TKA-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025935	9352	TXNL1	http://www.ncbi.nlm.nih.gov/gene/?term=9352	"HEL-S-114, TRP32, TXL-1, TXNL, Txl "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025936	9352	TXNL1	http://www.ncbi.nlm.nih.gov/gene/?term=9352	"HEL-S-114, TRP32, TXL-1, TXNL, Txl "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025937	9352	TXNL1	http://www.ncbi.nlm.nih.gov/gene/?term=9352	"HEL-S-114, TRP32, TXL-1, TXNL, Txl "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025938	9353	SLIT2	http://www.ncbi.nlm.nih.gov/gene/?term=9353	"SLIL3, Slit-2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025939	9353	SLIT2	http://www.ncbi.nlm.nih.gov/gene/?term=9353	"SLIL3, Slit-2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025940	9354	UBE4A	http://www.ncbi.nlm.nih.gov/gene/?term=9354	"E4, UBOX2, UFD2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025941	9355	LHX2	http://www.ncbi.nlm.nih.gov/gene/?term=9355	"LH2, hLhx2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025942	9358	ITGBL1	http://www.ncbi.nlm.nih.gov/gene/?term=9358	"OSCP, TIED "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025943	93594	TBC1D31	http://www.ncbi.nlm.nih.gov/gene/?term=93594	"Gm85, WDR67 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025944	9360	PPIG	http://www.ncbi.nlm.nih.gov/gene/?term=9360	"CARS-Cyp, CYP, SCAF10, SRCyp "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025945	93611	FBXO44	http://www.ncbi.nlm.nih.gov/gene/?term=93611	"FBG3, FBX30, FBX6A, Fbx44, Fbxo6a "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025946	93611	FBXO44	http://www.ncbi.nlm.nih.gov/gene/?term=93611	"FBG3, FBX30, FBX6A, Fbx44, Fbxo6a "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025947	9361	LONP1	http://www.ncbi.nlm.nih.gov/gene/?term=9361	"CODASS, LON, LONP, LonHS, PIM1, PRSS15, hLON "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025948	9361	LONP1	http://www.ncbi.nlm.nih.gov/gene/?term=9361	"CODASS, LON, LONP, LonHS, PIM1, PRSS15, hLON "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025949	9361	LONP1	http://www.ncbi.nlm.nih.gov/gene/?term=9361	"CODASS, LON, LONP, LonHS, PIM1, PRSS15, hLON "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025950	93621	MRFAP1	http://www.ncbi.nlm.nih.gov/gene/?term=93621	"PAM14, PGR1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025951	93621	MRFAP1	http://www.ncbi.nlm.nih.gov/gene/?term=93621	"PAM14, PGR1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025952	93621	MRFAP1	http://www.ncbi.nlm.nih.gov/gene/?term=93621	"PAM14, PGR1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025953	93622	LOC93622	http://www.ncbi.nlm.nih.gov/gene/?term=93622		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025954	93627	TBCK	http://www.ncbi.nlm.nih.gov/gene/?term=93627	"HSPC302, TBCKL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025955	9364	RAB28	http://www.ncbi.nlm.nih.gov/gene/?term=9364	CORD18	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025956	93663	ARHGAP18	http://www.ncbi.nlm.nih.gov/gene/?term=93663	"MacGAP, SENEX, bA307O14.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025957	93664	CADPS2	http://www.ncbi.nlm.nih.gov/gene/?term=93664		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025958	93667	Olfm1	http://www.ncbi.nlm.nih.gov/gene/?term=93667	"D2Sut1e, Noe1 "	mRNA	Rattus norvegicus	25301173	Dendrite	Hippocampus	In situ hybridization	"Figure 2: In situ hybridization reveals species-specific patterns of localization in neuronal dendrites. Fluorescent Microscopy evaluation of biotin-conjugated oligoprobes on paraformaldehyde fixed 14-day cultured rat and mouse cortical neurons hybridized with nine biotin-conjugated oligoprobes detected with streptadivin-Alexa Fluor 568 (Invitrogen). For each probe images set, the small bottom left corner panels represent MAP2 immuno-staining. Scale bar = 20um. (A), Probes against SFRS16, ARHGDIA and HNRPK transcripts show higher dendritic localization in mouse neurons than in rat neurons (Red box). (B), Probes against ZFP410, COMMD3 and RSP6 transcripts show higher dendritic localization in rat neurons than in mouse neurons (Blue box). (C), Probes against UBA52, OLFM1 and H2AFZ transcripts show high dendritic localization in both rat and mouse neurons (Black box). Data are collected from Figure 2. "
RLID00025959	9367	RAB9A	http://www.ncbi.nlm.nih.gov/gene/?term=9367	RAB9	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025960	9367	RAB9A	http://www.ncbi.nlm.nih.gov/gene/?term=9367	RAB9	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025961	93683	Glce	http://www.ncbi.nlm.nih.gov/gene/?term=93683	"1110017N23Rik, AI747411, C130034A12Rik, Hsepi "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025962	93683	Glce	http://www.ncbi.nlm.nih.gov/gene/?term=93683	"1110017N23Rik, AI747411, C130034A12Rik, Hsepi "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025963	93688	Klhl1	http://www.ncbi.nlm.nih.gov/gene/?term=93688	mKIAA1490	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025964	9368	SLC9A3R1	http://www.ncbi.nlm.nih.gov/gene/?term=9368	"EBP50, NHERF, NHERF-1, NHERF1, NPHLOP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025965	9368	SLC9A3R1	http://www.ncbi.nlm.nih.gov/gene/?term=9368	"EBP50, NHERF, NHERF-1, NHERF1, NPHLOP2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025966	9368	SLC9A3R1	http://www.ncbi.nlm.nih.gov/gene/?term=9368	"EBP50, NHERF, NHERF-1, NHERF1, NPHLOP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00025967	9368	SLC9A3R1	http://www.ncbi.nlm.nih.gov/gene/?term=9368	"EBP50, NHERF, NHERF-1, NHERF1, NPHLOP2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025968	93691	Klf7	http://www.ncbi.nlm.nih.gov/gene/?term=93691	9830124P08Rik	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025969	93691	Klf7	http://www.ncbi.nlm.nih.gov/gene/?term=93691	9830124P08Rik	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00025970	93695	Gpnmb	http://www.ncbi.nlm.nih.gov/gene/?term=93695	"DC-HIL, Dchil, ipd "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00025971	93702	Pcdhgb5	http://www.ncbi.nlm.nih.gov/gene/?term=93702		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025972	93703	Pcdhgb6	http://www.ncbi.nlm.nih.gov/gene/?term=93703		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025973	93707	Pcdhgc4	http://www.ncbi.nlm.nih.gov/gene/?term=93707		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025974	9371	KIF3B	http://www.ncbi.nlm.nih.gov/gene/?term=9371	"FLA8, HH0048, KLP-11 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025975	9372	ZFYVE9	http://www.ncbi.nlm.nih.gov/gene/?term=9372	"MADHIP, NSP, PPP1R173, SARA, SMADIP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025976	93730	Lztfl1	http://www.ncbi.nlm.nih.gov/gene/?term=93730	"5530402H04Rik, 6130400H19Rik, AI414725, AW048545 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00025977	93736	Aff4	http://www.ncbi.nlm.nih.gov/gene/?term=93736	"AF5Q31, Alf4, Laf4l, MCEF "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025978	9373	PLAA	http://www.ncbi.nlm.nih.gov/gene/?term=9373	"DOA1, PLA2P, PLAP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025979	93742	Pard3	http://www.ncbi.nlm.nih.gov/gene/?term=93742	"AA960621, AI256638, Asip, D8Ertd580e, Par-3, Par3, Pard-3a, Phip, Pard3 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025980	93757	Immp2l	http://www.ncbi.nlm.nih.gov/gene/?term=93757	"AI853880, IMP2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025981	93759	Sirt1	http://www.ncbi.nlm.nih.gov/gene/?term=93759	"AA673258, SIR2L1, Sir2, Sir2a, Sir2alpha "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025982	93759	Sirt1	http://www.ncbi.nlm.nih.gov/gene/?term=93759	"AA673258, SIR2L1, Sir2, Sir2a, Sir2alpha "	mRNA	Mus musculus	24480879	Cytoplasm	B16F1 cell|melanoblasts	Immunostaining|RT-PCR	The subcellular fractionation of B16F1 cells showed SIRT1 expression in the cytoplasm (Figure 1c). Figure 1. Cytoplasmic SIRT1 promotes the migration of B16F1 cells. (f) SIRT1 small interfering RNAs (SIRT1-siRNAs) suppressed SIRT1 mRNA expression.
RLID00025983	9375	TM9SF2	http://www.ncbi.nlm.nih.gov/gene/?term=9375	P76	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025984	9375	TM9SF2	http://www.ncbi.nlm.nih.gov/gene/?term=9375	P76	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025985	9375	TM9SF2	http://www.ncbi.nlm.nih.gov/gene/?term=9375	P76	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025986	93762	Smarca5	http://www.ncbi.nlm.nih.gov/gene/?term=93762	"4933427E24Rik, D030040M08Rik, D330027N15Rik, MommeD4, Snf2h "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025987	93762	Smarca5	http://www.ncbi.nlm.nih.gov/gene/?term=93762	"4933427E24Rik, D030040M08Rik, D330027N15Rik, MommeD4, Snf2h "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00025988	9377	COX5A	http://www.ncbi.nlm.nih.gov/gene/?term=9377	"COX, COX-VA, VA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025989	9377	COX5A	http://www.ncbi.nlm.nih.gov/gene/?term=9377	"COX, COX-VA, VA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025990	93790	Nipa2	http://www.ncbi.nlm.nih.gov/gene/?term=93790	"2600017P10Rik, 3830408P04Rik, AB041581 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025991	9379	NRXN2	http://www.ncbi.nlm.nih.gov/gene/?term=9379		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025992	9380	GRHPR	http://www.ncbi.nlm.nih.gov/gene/?term=9380	"GLXR, GLYD, PH2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025993	9380	GRHPR	http://www.ncbi.nlm.nih.gov/gene/?term=9380	"GLXR, GLYD, PH2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00025994	9380	GRHPR	http://www.ncbi.nlm.nih.gov/gene/?term=9380	"GLXR, GLYD, PH2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025995	9381	OTOF	http://www.ncbi.nlm.nih.gov/gene/?term=9381	"AUNB1, DFNB6, DFNB9, FER1L2, NSRD9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025996	9382	COG1	http://www.ncbi.nlm.nih.gov/gene/?term=9382	"CDG2G, LDLB "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00025997	9382	COG1	http://www.ncbi.nlm.nih.gov/gene/?term=9382	"CDG2G, LDLB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00025998	93871	Brwd1	http://www.ncbi.nlm.nih.gov/gene/?term=93871	"5330419I02Rik, D530019K20Rik, G1-403-16, Wdr9, repro5 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00025999	93887	Pcdhb16	http://www.ncbi.nlm.nih.gov/gene/?term=93887	"Pcdhb8, PcdhbP "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026000	93888	Pcdhb17	http://www.ncbi.nlm.nih.gov/gene/?term=93888	"Pcdhb16, PcdhbQ, mKIAA1621 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026001	9388	LIPG	http://www.ncbi.nlm.nih.gov/gene/?term=9388	"EDL, EL, PRO719 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026002	9388	LIPG	http://www.ncbi.nlm.nih.gov/gene/?term=9388	"EDL, EL, PRO719 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026003	93893	Pcdhb22	http://www.ncbi.nlm.nih.gov/gene/?term=93893	"Pcdhb15, PcdhbV "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026004	9391	CIAO1	http://www.ncbi.nlm.nih.gov/gene/?term=9391	"CIA1, WDR39 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026005	9391	CIAO1	http://www.ncbi.nlm.nih.gov/gene/?term=9391	"CIA1, WDR39 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026006	9392	TGFBRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9392	"TRAP-1, TRAP1, VPS3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026007	9392	TGFBRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9392	"TRAP-1, TRAP1, VPS3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026008	9392	TGFBRAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9392	"TRAP-1, TRAP1, VPS3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026009	9394	HS6ST1	http://www.ncbi.nlm.nih.gov/gene/?term=9394	"HH15, HS6ST "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026010	9394	HS6ST1	http://www.ncbi.nlm.nih.gov/gene/?term=9394	"HH15, HS6ST "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026011	93961	B3galt5	http://www.ncbi.nlm.nih.gov/gene/?term=93961	"1190002B21Rik, AU045265, b3Galt-V "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026012	93973	ACTR8	http://www.ncbi.nlm.nih.gov/gene/?term=93973	"ARP8, INO80N, hArp8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026013	93973	ACTR8	http://www.ncbi.nlm.nih.gov/gene/?term=93973	"ARP8, INO80N, hArp8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026014	93974	ATPIF1	http://www.ncbi.nlm.nih.gov/gene/?term=93974	"ATPI, ATPIP, IP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026015	93974	ATPIF1	http://www.ncbi.nlm.nih.gov/gene/?term=93974	"ATPI, ATPIP, IP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026016	93986	FOXP2	http://www.ncbi.nlm.nih.gov/gene/?term=93986	"CAGH44, SPCH1, TNRC10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026017	93	ACVR2B	http://www.ncbi.nlm.nih.gov/gene/?term=93	"ACTRIIB, ActR-IIB, HTX4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026018	93	ACVR2B	http://www.ncbi.nlm.nih.gov/gene/?term=93	"ACTRIIB, ActR-IIB, HTX4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026019	94005	PIGS	http://www.ncbi.nlm.nih.gov/gene/?term=94005		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026020	94009	SERHL	http://www.ncbi.nlm.nih.gov/gene/?term=94009	"BK126B4.1, BK126B4.2, HS126B42, dJ222E13.1 "	lncRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026021	94015	TTYH2	http://www.ncbi.nlm.nih.gov/gene/?term=94015	C17orf29	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026022	9401	RECQL4	http://www.ncbi.nlm.nih.gov/gene/?term=9401	RECQ4	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026023	9401	RECQL4	http://www.ncbi.nlm.nih.gov/gene/?term=9401	RECQ4	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026024	94025	MUC16	http://www.ncbi.nlm.nih.gov/gene/?term=94025	CA125	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026025	94025	MUC16	http://www.ncbi.nlm.nih.gov/gene/?term=94025	CA125	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026026	9403	SEP15	http://www.ncbi.nlm.nih.gov/gene/?term=9403		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026027	94043	Tm2d1	http://www.ncbi.nlm.nih.gov/gene/?term=94043	"2310026L18Rik, AA990549, Bbp "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026028	9404	LPXN	http://www.ncbi.nlm.nih.gov/gene/?term=9404	LDPL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026029	94056	SYAP1	http://www.ncbi.nlm.nih.gov/gene/?term=94056	PRO3113	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026030	94061	Mrpl1	http://www.ncbi.nlm.nih.gov/gene/?term=94061	"2410002L03Rik, 5830418D04Rik, AI462572, L1mt "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026031	94067	Mrpl43	http://www.ncbi.nlm.nih.gov/gene/?term=94067	"4930442D21Rik, bMRP36a "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026032	9406965	SPRRNA.34	http://www.ncbi.nlm.nih.gov/gene/?term=9406965	SPRRNA.34	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.34
RLID00026033	9406	ZRANB2	http://www.ncbi.nlm.nih.gov/gene/?term=9406	"ZIS, ZIS1, ZIS2, ZNF265 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026034	9406	ZRANB2	http://www.ncbi.nlm.nih.gov/gene/?term=9406	"ZIS, ZIS1, ZIS2, ZNF265 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026035	9407007	SPRRNA.39	http://www.ncbi.nlm.nih.gov/gene/?term=9407007	SPRRNA.39	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.39
RLID00026036	9407146	SPRRNA.40	http://www.ncbi.nlm.nih.gov/gene/?term=9407146	SPRRNA.40	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.40
RLID00026037	9407213	snoR61	http://www.ncbi.nlm.nih.gov/gene/?term=9407213	SPNCRNA.445	snoRNA	Saccharomyces cerevisiae	25361970	Nucleolus	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPNCRNA.445
RLID00026038	9407306	SPRRNA.35	http://www.ncbi.nlm.nih.gov/gene/?term=9407306	SPRRNA.35	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.35
RLID00026039	9407315	SPRRNA.37	http://www.ncbi.nlm.nih.gov/gene/?term=9407315	SPRRNA.37	rRNA	Saccharomyces cerevisiae	25361970	Ribosome	-	PomBase	Data are collected from PomBase database: http://www.pombase.org/spombe/result/SPRRNA.37
RLID00026040	94081	SFXN1	http://www.ncbi.nlm.nih.gov/gene/?term=94081		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026041	94081	SFXN1	http://www.ncbi.nlm.nih.gov/gene/?term=94081		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026042	94081	SFXN1	http://www.ncbi.nlm.nih.gov/gene/?term=94081		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026043	94081	SFXN1	http://www.ncbi.nlm.nih.gov/gene/?term=94081		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026044	94097	SFXN5	http://www.ncbi.nlm.nih.gov/gene/?term=94097	BBG-TCC	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026045	94101	ORMDL1	http://www.ncbi.nlm.nih.gov/gene/?term=94101		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026046	94101	ORMDL1	http://www.ncbi.nlm.nih.gov/gene/?term=94101		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026047	94103	ORMDL3	http://www.ncbi.nlm.nih.gov/gene/?term=94103		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026048	94103	ORMDL3	http://www.ncbi.nlm.nih.gov/gene/?term=94103		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026049	94104	PAXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=94104	"BM020, C21orf66, FSAP105, GCFC, GCFC1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026050	94104	PAXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=94104	"BM020, C21orf66, FSAP105, GCFC, GCFC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026051	94107	TMEM203	http://www.ncbi.nlm.nih.gov/gene/?term=94107	HBEBP1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026052	94107	TMEM203	http://www.ncbi.nlm.nih.gov/gene/?term=94107	HBEBP1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026053	9410	SNRNP40	http://www.ncbi.nlm.nih.gov/gene/?term=9410	"40K, HPRP8BP, PRP8BP, PRPF8BP, SPF38, WDR57 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026054	9410	SNRNP40	http://www.ncbi.nlm.nih.gov/gene/?term=9410	"40K, HPRP8BP, PRP8BP, PRPF8BP, SPF38, WDR57 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026055	94111	Mepe	http://www.ncbi.nlm.nih.gov/gene/?term=94111	Of45	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026056	9411	ARHGAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9411	PARG1	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026057	9411	ARHGAP29	http://www.ncbi.nlm.nih.gov/gene/?term=9411	PARG1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026058	9412	MED21	http://www.ncbi.nlm.nih.gov/gene/?term=9412	"SRB7, SURB7, hSrb7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026059	94134	ARHGAP12	http://www.ncbi.nlm.nih.gov/gene/?term=94134		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026060	9415	FADS2	http://www.ncbi.nlm.nih.gov/gene/?term=9415	"D6D, DES6, FADSD6, LLCDL2, SLL0262, TU13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026061	9415	FADS2	http://www.ncbi.nlm.nih.gov/gene/?term=9415	"D6D, DES6, FADSD6, LLCDL2, SLL0262, TU13 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026062	9415	FADS2	http://www.ncbi.nlm.nih.gov/gene/?term=9415	"D6D, DES6, FADSD6, LLCDL2, SLL0262, TU13 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026063	94161	SNORD46	http://www.ncbi.nlm.nih.gov/gene/?term=94161	"RNU40, RNU46, U40, U46 "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00026064	94161	SNORD46	http://www.ncbi.nlm.nih.gov/gene/?term=94161	"RNU40, RNU46, U40, U46 "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026065	94162	SNORD38A	http://www.ncbi.nlm.nih.gov/gene/?term=94162	"RNU38A, U38A "	snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026066	94162	SNORD38A	http://www.ncbi.nlm.nih.gov/gene/?term=94162	"RNU38A, U38A "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00026067	94162	SNORD38A	http://www.ncbi.nlm.nih.gov/gene/?term=94162	"RNU38A, U38A "	snoRNA	Homo sapiens	25203660	Nucleus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00026068	94162	SNORD38A	http://www.ncbi.nlm.nih.gov/gene/?term=94162	"RNU38A, U38A "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026069	94163	SNORD38B	http://www.ncbi.nlm.nih.gov/gene/?term=94163	"RNU38B, U38B "	snoRNA	Homo sapiens	24255815	Exosome	Breast cancer cell	Next-generation sequencing	"Using these criteria, we obtained lower number of annotated transcripts (6,187 transcripts or 3,437 genes) compared to that when RPKM values were considered (Fig. S5 and Table S1). As a result, some transcripts showed high coverage with CDSs criteria (for example, ATPIF1) in exosomal RNA from MDA-MB-231 cells, even when the number of reads was small (less than 5) (Fig. 6B). Such genes were also taken into consideration in our analysis. Data are collected from Table S1. "
RLID00026070	94163	SNORD38B	http://www.ncbi.nlm.nih.gov/gene/?term=94163	"RNU38B, U38B "	snoRNA	Homo sapiens	25203660	Nucleolus	HeLa cell	Next-generation sequencing	"Further analysis of the 68 snoRNA loci represented by more than 10 reads in any given fraction showed that 63 mapped to box C/D and 5 to box H/ACA snoRNA loci, respectively (Table S1) showing that box C/D snoRNA-derived reads were highly frequent. Table S1 contains the reads subcellular distribution of the snoRNAs. "
RLID00026071	94163	SNORD38B	http://www.ncbi.nlm.nih.gov/gene/?term=94163	"RNU38B, U38B "	snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026072	94163	SNORD38B	http://www.ncbi.nlm.nih.gov/gene/?term=94163	"RNU38B, U38B "	snoRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026073	94167	Prdx6	http://www.ncbi.nlm.nih.gov/gene/?term=94167		mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00026074	9416	DDX23	http://www.ncbi.nlm.nih.gov/gene/?term=9416	"PRPF28, SNRNP100, U5-100K, U5-100KD, prp28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026075	9416	DDX23	http://www.ncbi.nlm.nih.gov/gene/?term=9416	"PRPF28, SNRNP100, U5-100K, U5-100KD, prp28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026076	94181	Nans	http://www.ncbi.nlm.nih.gov/gene/?term=94181	"4632418E04Rik, BB056474, Sas "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00026077	94186	Strn3	http://www.ncbi.nlm.nih.gov/gene/?term=94186	"Gs2na, SG2NA "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026078	94192	C1galt1	http://www.ncbi.nlm.nih.gov/gene/?term=94192	"2210410E06Rik, AV284120, T-synthase "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026079	9419	CRIPT	http://www.ncbi.nlm.nih.gov/gene/?term=9419	"HSPC139, SSMDF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026080	9419	CRIPT	http://www.ncbi.nlm.nih.gov/gene/?term=9419	"HSPC139, SSMDF "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026081	9419	CRIPT	http://www.ncbi.nlm.nih.gov/gene/?term=9419	"HSPC139, SSMDF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026082	9420	CYP7B1	http://www.ncbi.nlm.nih.gov/gene/?term=9420	"CBAS3, CP7B, SPG5A "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026083	94213	Ddx50	http://www.ncbi.nlm.nih.gov/gene/?term=94213	"4933429B04Rik, 8430408E17Rik, GU2, RH-II "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026084	94221	Gopc	http://www.ncbi.nlm.nih.gov/gene/?term=94221	"2210402P09Rik, AI844555, CAL, FIG, GOPC1, PIST "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026085	94229	Slc4a10	http://www.ncbi.nlm.nih.gov/gene/?term=94229	"NCBE, mKIAA4136 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026086	9422	ZNF264	http://www.ncbi.nlm.nih.gov/gene/?term=9422		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026087	9422	ZNF264	http://www.ncbi.nlm.nih.gov/gene/?term=9422		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026088	94239	H2AFV	http://www.ncbi.nlm.nih.gov/gene/?term=94239	"H2A.Z-2, H2AV "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026089	94239	H2AFV	http://www.ncbi.nlm.nih.gov/gene/?term=94239	"H2A.Z-2, H2AV "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026090	94239	H2AFV	http://www.ncbi.nlm.nih.gov/gene/?term=94239	"H2A.Z-2, H2AV "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026091	94239	H2AFV	http://www.ncbi.nlm.nih.gov/gene/?term=94239	"H2A.Z-2, H2AV "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026092	9424	KCNK6	http://www.ncbi.nlm.nih.gov/gene/?term=9424	"K2p6.1, KCNK8, TOSS, TWIK-2, TWIK2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026093	9425	CDYL	http://www.ncbi.nlm.nih.gov/gene/?term=9425	CDYL1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026094	9425	CDYL	http://www.ncbi.nlm.nih.gov/gene/?term=9425	CDYL1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026095	94274	PPP1R14A	http://www.ncbi.nlm.nih.gov/gene/?term=94274	"CPI-17, CPI17, PPP1INL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026096	9427	ECEL1	http://www.ncbi.nlm.nih.gov/gene/?term=9427	"DA5D, DINE, ECEX, XCE "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026097	94284	Ugt1a6a	http://www.ncbi.nlm.nih.gov/gene/?term=94284	"UDPGT, UDPGT 1-6, UGT1-06, UGT1.6, Ugt1a6, Ugt1a7 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026098	9429	ABCG2	http://www.ncbi.nlm.nih.gov/gene/?term=9429	"ABC15, ABCP, BCRP, BCRP1, BMDP, CD338, CDw338, EST157481, GOUT1, MRX, MXR, MXR-1, MXR1, UAQTL1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026099	94332	Cadm3	http://www.ncbi.nlm.nih.gov/gene/?term=94332	"BIgR, Igsf4b, Necl-1, Necl1, SynCAM3, Tsll1 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026100	94352	Loxl2	http://www.ncbi.nlm.nih.gov/gene/?term=94352	"1110004B06Rik, 4930526G11Rik, 9430067E15Rik "	lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026101	943	TNFRSF8	http://www.ncbi.nlm.nih.gov/gene/?term=943	"CD30, D1S166E, Ki-1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026102	9440	MED17	http://www.ncbi.nlm.nih.gov/gene/?term=9440	"CRSP6, CRSP77, DRIP80, TRAP80 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026103	9440	MED17	http://www.ncbi.nlm.nih.gov/gene/?term=9440	"CRSP6, CRSP77, DRIP80, TRAP80 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026104	9440	MED17	http://www.ncbi.nlm.nih.gov/gene/?term=9440	"CRSP6, CRSP77, DRIP80, TRAP80 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026105	9440	MED17	http://www.ncbi.nlm.nih.gov/gene/?term=9440	"CRSP6, CRSP77, DRIP80, TRAP80 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026106	9442	MED27	http://www.ncbi.nlm.nih.gov/gene/?term=9442	"CRAP34, CRSP34, CRSP8, MED3, TRAP37 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026107	9443	MED7	http://www.ncbi.nlm.nih.gov/gene/?term=9443	"ARC34, CRSP33, CRSP9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026108	9444	QKI	http://www.ncbi.nlm.nih.gov/gene/?term=9444	"Hqk, QK, QK1, QK3, hqkI "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026109	9444	QKI	http://www.ncbi.nlm.nih.gov/gene/?term=9444	"Hqk, QK, QK1, QK3, hqkI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026110	9445	ITM2B	http://www.ncbi.nlm.nih.gov/gene/?term=9445	"ABRI, BRI, BRI2, BRICD2B, E25B, E3-16, FBD, RDGCA, imBRI2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026111	9445	ITM2B	http://www.ncbi.nlm.nih.gov/gene/?term=9445	"ABRI, BRI, BRI2, BRICD2B, E25B, E3-16, FBD, RDGCA, imBRI2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026112	9445	ITM2B	http://www.ncbi.nlm.nih.gov/gene/?term=9445	"ABRI, BRI, BRI2, BRICD2B, E25B, E3-16, FBD, RDGCA, imBRI2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026113	9446	GSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=9446	"GSTO 1-1, GSTTLp28, HEL-S-21, P28, SPG-R "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026114	9446	GSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=9446	"GSTO 1-1, GSTTLp28, HEL-S-21, P28, SPG-R "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026115	9446	GSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=9446	"GSTO 1-1, GSTTLp28, HEL-S-21, P28, SPG-R "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026116	9448	MAP4K4	http://www.ncbi.nlm.nih.gov/gene/?term=9448	"FLH21957, HEL-S-31, HGK, MEKKK4, NIK "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026117	9448	MAP4K4	http://www.ncbi.nlm.nih.gov/gene/?term=9448	"FLH21957, HEL-S-31, HGK, MEKKK4, NIK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026118	9451	EIF2AK3	http://www.ncbi.nlm.nih.gov/gene/?term=9451	"PEK, PERK, WRS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026119	9451	EIF2AK3	http://www.ncbi.nlm.nih.gov/gene/?term=9451	"PEK, PERK, WRS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026120	9452	ITM2A	http://www.ncbi.nlm.nih.gov/gene/?term=9452	"BRICD2A, E25A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026121	9453	GGPS1	http://www.ncbi.nlm.nih.gov/gene/?term=9453	"GGPPS, GGPPS1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026122	9453	GGPS1	http://www.ncbi.nlm.nih.gov/gene/?term=9453	"GGPPS, GGPPS1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026123	9454	HOMER3	http://www.ncbi.nlm.nih.gov/gene/?term=9454	"HOMER-3, VESL3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026124	9459	ARHGEF6	http://www.ncbi.nlm.nih.gov/gene/?term=9459	"COOL2, Cool-2, MRX46, PIXA, alpha-PIX, alphaPIX "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026125	9459	ARHGEF6	http://www.ncbi.nlm.nih.gov/gene/?term=9459	"COOL2, Cool-2, MRX46, PIXA, alpha-PIX, alphaPIX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026126	9463	PICK1	http://www.ncbi.nlm.nih.gov/gene/?term=9463	"PICK, PRKCABP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026127	9467	SH3BP5	http://www.ncbi.nlm.nih.gov/gene/?term=9467	"SAB, SH3BP-5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026128	9468	PCYT1B	http://www.ncbi.nlm.nih.gov/gene/?term=9468	"CCTB, CTB "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026129	9468	PCYT1B	http://www.ncbi.nlm.nih.gov/gene/?term=9468	"CCTB, CTB "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026130	9469	CHST3	http://www.ncbi.nlm.nih.gov/gene/?term=9469	"C6ST, C6ST1, HSD "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026131	9470	EIF4E2	http://www.ncbi.nlm.nih.gov/gene/?term=9470	"4E-LP, 4EHP, EIF4EL3, IF4e "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026132	9470	EIF4E2	http://www.ncbi.nlm.nih.gov/gene/?term=9470	"4E-LP, 4EHP, EIF4EL3, IF4e "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026133	9470	EIF4E2	http://www.ncbi.nlm.nih.gov/gene/?term=9470	"4E-LP, 4EHP, EIF4EL3, IF4e "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026134	9474	ATG5	http://www.ncbi.nlm.nih.gov/gene/?term=9474	"APG5, APG5-LIKE, APG5L, ASP, hAPG5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026135	9474	ATG5	http://www.ncbi.nlm.nih.gov/gene/?term=9474	"APG5, APG5-LIKE, APG5L, ASP, hAPG5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026136	9475	ROCK2	http://www.ncbi.nlm.nih.gov/gene/?term=9475	ROCK-II	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026137	9475	ROCK2	http://www.ncbi.nlm.nih.gov/gene/?term=9475	ROCK-II	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026138	9475	ROCK2	http://www.ncbi.nlm.nih.gov/gene/?term=9475	ROCK-II	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026139	9477	MED20	http://www.ncbi.nlm.nih.gov/gene/?term=9477	"PRO0213, TRFP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026140	9477	MED20	http://www.ncbi.nlm.nih.gov/gene/?term=9477	"PRO0213, TRFP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026141	9479	MAPK8IP1	http://www.ncbi.nlm.nih.gov/gene/?term=9479	"IB1, JIP-1, JIP1, PRKM8IP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026142	947	CD34	http://www.ncbi.nlm.nih.gov/gene/?term=947		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026143	9482	STX8	http://www.ncbi.nlm.nih.gov/gene/?term=9482	CARB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026144	9482	STX8	http://www.ncbi.nlm.nih.gov/gene/?term=9482	CARB	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026145	9486	CHST10	http://www.ncbi.nlm.nih.gov/gene/?term=9486	"HNK-1ST, HNK1ST "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026146	9486	CHST10	http://www.ncbi.nlm.nih.gov/gene/?term=9486	"HNK-1ST, HNK1ST "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026147	9488	PIGB	http://www.ncbi.nlm.nih.gov/gene/?term=9488	"GPI-MT-III, PIG-B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026148	948	CD36	http://www.ncbi.nlm.nih.gov/gene/?term=948	"BDPLT10, CHDS7, FAT, GP3B, GP4, GPIV, PASIV, SCARB3 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026149	948	CD36	http://www.ncbi.nlm.nih.gov/gene/?term=948	"BDPLT10, CHDS7, FAT, GP3B, GP4, GPIV, PASIV, SCARB3 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026150	948	CD36	http://www.ncbi.nlm.nih.gov/gene/?term=948	"BDPLT10, CHDS7, FAT, GP3B, GP4, GPIV, PASIV, SCARB3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026151	9491	PSMF1	http://www.ncbi.nlm.nih.gov/gene/?term=9491	PI31	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026152	9491	PSMF1	http://www.ncbi.nlm.nih.gov/gene/?term=9491	PI31	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026153	9493	KIF23	http://www.ncbi.nlm.nih.gov/gene/?term=9493	"CHO1, KNSL5, MKLP-1, MKLP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026154	9493	KIF23	http://www.ncbi.nlm.nih.gov/gene/?term=9493	"CHO1, KNSL5, MKLP-1, MKLP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026155	9495	AKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9495	"AKAP75, AKAP79, H21 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026156	9495	AKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9495	"AKAP75, AKAP79, H21 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026157	9497	SLC4A7	http://www.ncbi.nlm.nih.gov/gene/?term=9497	"NBC2, NBC3, NBCN1, SBC2, SLC4A6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026158	9499	MYOT	http://www.ncbi.nlm.nih.gov/gene/?term=9499	"LGMD1, LGMD1A, MFM3, TTID, TTOD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026159	949	SCARB1	http://www.ncbi.nlm.nih.gov/gene/?term=949	"CD36L1, CLA-1, CLA1, HDLQTL6, SR-BI, SRB1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026160	94	ACVRL1	http://www.ncbi.nlm.nih.gov/gene/?term=94	"ACVRLK1, ALK-1, ALK1, HHT, HHT2, ORW2, SKR3, TSR-I "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026161	9501	RPH3AL	http://www.ncbi.nlm.nih.gov/gene/?term=9501	NOC2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026162	9501	RPH3AL	http://www.ncbi.nlm.nih.gov/gene/?term=9501	NOC2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026163	9501	RPH3AL	http://www.ncbi.nlm.nih.gov/gene/?term=9501	NOC2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026164	9507	ADAMTS4	http://www.ncbi.nlm.nih.gov/gene/?term=9507	"ADAMTS-2, ADAMTS-4, ADMP-1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026165	9507	ADAMTS4	http://www.ncbi.nlm.nih.gov/gene/?term=9507	"ADAMTS-2, ADAMTS-4, ADMP-1 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026166	9508	ADAMTS3	http://www.ncbi.nlm.nih.gov/gene/?term=9508	ADAMTS-4	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026167	9509	ADAMTS2	http://www.ncbi.nlm.nih.gov/gene/?term=9509	"ADAM-TS2, ADAMTS-2, ADAMTS-3, NPI, PC I-NP, PCI-NP, PCINP, PCPNI, PNPI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026168	950	SCARB2	http://www.ncbi.nlm.nih.gov/gene/?term=950	"AMRF, CD36L2, EPM4, HLGP85, LGP85, LIMP-2, LIMPII, SR-BII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026169	950	SCARB2	http://www.ncbi.nlm.nih.gov/gene/?term=950	"AMRF, CD36L2, EPM4, HLGP85, LGP85, LIMP-2, LIMPII, SR-BII "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026170	950	SCARB2	http://www.ncbi.nlm.nih.gov/gene/?term=950	"AMRF, CD36L2, EPM4, HLGP85, LGP85, LIMP-2, LIMPII, SR-BII "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026171	950	SCARB2	http://www.ncbi.nlm.nih.gov/gene/?term=950	"AMRF, CD36L2, EPM4, HLGP85, LGP85, LIMP-2, LIMPII, SR-BII "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026172	950	SCARB2	http://www.ncbi.nlm.nih.gov/gene/?term=950	"AMRF, CD36L2, EPM4, HLGP85, LGP85, LIMP-2, LIMPII, SR-BII "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026173	9510	ADAMTS1	http://www.ncbi.nlm.nih.gov/gene/?term=9510	"C3-C5, METH1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026174	9512	PMPCB	http://www.ncbi.nlm.nih.gov/gene/?term=9512	"Beta-MPP, MPP11, MPPB, MPPP52, P-52 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026175	9512	PMPCB	http://www.ncbi.nlm.nih.gov/gene/?term=9512	"Beta-MPP, MPP11, MPPB, MPPP52, P-52 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026176	9513	FXR2	http://www.ncbi.nlm.nih.gov/gene/?term=9513	"FMR1L2P, FXR2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026177	9513	FXR2	http://www.ncbi.nlm.nih.gov/gene/?term=9513	"FMR1L2, FXR2P "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026178	9514	GAL3ST1	http://www.ncbi.nlm.nih.gov/gene/?term=9514	CST	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026179	9516	LITAF	http://www.ncbi.nlm.nih.gov/gene/?term=9516	"PIG7, SIMPLE, TP53I7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026180	9516	LITAF	http://www.ncbi.nlm.nih.gov/gene/?term=9516	"PIG7, SIMPLE, TP53I7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026181	9517	SPTLC2	http://www.ncbi.nlm.nih.gov/gene/?term=9517	"HSN1C, LCB2, LCB2A, NSAN1C, SPT2, hLCB2a "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026182	9518	GDF15	http://www.ncbi.nlm.nih.gov/gene/?term=9518	"GDF-15, MIC-1, MIC1, NAG-1, PDF, PLAB, PTGFB "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026183	9518	GDF15	http://www.ncbi.nlm.nih.gov/gene/?term=9518	"GDF-15, MIC-1, MIC1, NAG-1, PDF, PLAB, PTGFB "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026184	9519	TBPL1	http://www.ncbi.nlm.nih.gov/gene/?term=9519	"MGC:8389, MGC:9620, STUD, TLF, TLP, TRF2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026185	9519	TBPL1	http://www.ncbi.nlm.nih.gov/gene/?term=9519	"MGC:8389, MGC:9620, STUD, TLF, TLP, TRF2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026186	9519	TBPL1	http://www.ncbi.nlm.nih.gov/gene/?term=9519	"MGC:8389, MGC:9620, STUD, TLF, TLP, TRF2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026187	951	CD37	http://www.ncbi.nlm.nih.gov/gene/?term=951	"GP52-40, TSPAN26 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026188	9520	NPEPPS	http://www.ncbi.nlm.nih.gov/gene/?term=9520	"AAP-S, MP100, PSA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026189	9520	NPEPPS	http://www.ncbi.nlm.nih.gov/gene/?term=9520	"AAP-S, MP100, PSA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026190	9520	NPEPPS	http://www.ncbi.nlm.nih.gov/gene/?term=9520	"AAP-S, MP100, PSA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026191	9521	EEF1E1	http://www.ncbi.nlm.nih.gov/gene/?term=9521	"AIMP3, P18 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026192	9521	EEF1E1	http://www.ncbi.nlm.nih.gov/gene/?term=9521	"AIMP3, P18 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026193	9521	EEF1E1	http://www.ncbi.nlm.nih.gov/gene/?term=9521	"AIMP3, P18 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026194	9522	SCAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=9522	"SCAMP, SCAMP37 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026195	9522	SCAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=9522	"SCAMP, SCAMP37 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026196	9522	SCAMP1	http://www.ncbi.nlm.nih.gov/gene/?term=9522	"SCAMP, SCAMP37 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026197	9524	TECR	http://www.ncbi.nlm.nih.gov/gene/?term=9524	"GPSN2, MRT14, SC2, TER "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026198	9525	VPS4B	http://www.ncbi.nlm.nih.gov/gene/?term=9525	"MIG1, SKD1, SKD1B, VPS4-2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026199	9526	MPDU1	http://www.ncbi.nlm.nih.gov/gene/?term=9526	"CDGIF, HBEBP2BPA, Lec35, My008, PP3958, PQLC5, SL15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026200	9526	MPDU1	http://www.ncbi.nlm.nih.gov/gene/?term=9526	"CDGIF, HBEBP2BPA, Lec35, My008, PP3958, PQLC5, SL15 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026201	9526	MPDU1	http://www.ncbi.nlm.nih.gov/gene/?term=9526	"CDGIF, HBEBP2BPA, Lec35, My008, PP3958, PQLC5, SL15 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026202	9527	GOSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9527	"GOLIM2, GOS-28, GOS28, GOS28/P28, GS28, P28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026203	9527	GOSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9527	"GOLIM2, GOS-28, GOS28, GOS28/P28, GS28, P28 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026204	9527	GOSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9527	"GOLIM2, GOS-28, GOS28, GOS28/P28, GS28, P28 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026205	9527	GOSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9527	"GOLIM2, GOS-28, GOS28, GOS28/P28, GS28, P28 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026206	9528	TMEM59	http://www.ncbi.nlm.nih.gov/gene/?term=9528	"C1orf8, DCF1, HSPC001, PRO195, UNQ169 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026207	9529	BAG5	http://www.ncbi.nlm.nih.gov/gene/?term=9529	BAG-5	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026208	9530	BAG4	http://www.ncbi.nlm.nih.gov/gene/?term=9530	"BAG-4, SODD "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026209	9530	BAG4	http://www.ncbi.nlm.nih.gov/gene/?term=9530	"BAG-4, SODD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026210	9532	BAG2	http://www.ncbi.nlm.nih.gov/gene/?term=9532	"BAG-2, dJ417I1.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026211	9532	BAG2	http://www.ncbi.nlm.nih.gov/gene/?term=9532	"BAG-2, dJ417I1.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026212	9533	POLR1C	http://www.ncbi.nlm.nih.gov/gene/?term=9533	"AC40, HLD11, RPA39, RPA40, RPA5, RPAC1, RPC40, TCS3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026213	9533	POLR1C	http://www.ncbi.nlm.nih.gov/gene/?term=9533	"AC40, HLD11, RPA39, RPA40, RPA5, RPAC1, RPC40, TCS3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026214	9537	TP53I11	http://www.ncbi.nlm.nih.gov/gene/?term=9537	PIG11	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026215	9538	EI24	http://www.ncbi.nlm.nih.gov/gene/?term=9538	"EPG4, PIG8, TP53I8 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026216	9538	EI24	http://www.ncbi.nlm.nih.gov/gene/?term=9538	"EPG4, PIG8, TP53I8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026217	953	ENTPD1	http://www.ncbi.nlm.nih.gov/gene/?term=953	"ATPDase, CD39, NTPDase-1, SPG64 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026218	953	ENTPD1	http://www.ncbi.nlm.nih.gov/gene/?term=953	"ATPDase, CD39, NTPDase-1, SPG64 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026219	953	ENTPD1	http://www.ncbi.nlm.nih.gov/gene/?term=953	"ATPDase, CD39, NTPDase-1, SPG64 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026220	9540	TP53I3	http://www.ncbi.nlm.nih.gov/gene/?term=9540	PIG3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026221	9540	TP53I3	http://www.ncbi.nlm.nih.gov/gene/?term=9540	PIG3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026222	9541	CIR1	http://www.ncbi.nlm.nih.gov/gene/?term=9541	CIR	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026223	9542	NRG2	http://www.ncbi.nlm.nih.gov/gene/?term=9542	"DON1, HRG2, NTAK "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026224	9545	RAB3D	http://www.ncbi.nlm.nih.gov/gene/?term=9545	"D2-2, GOV, RAB16, RAD3D "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026225	9546	APBA3	http://www.ncbi.nlm.nih.gov/gene/?term=9546	"MGC:15815, X11L2, mint3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026226	9546	APBA3	http://www.ncbi.nlm.nih.gov/gene/?term=9546	"MGC:15815, X11L2, mint3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026227	9550	ATP6V1G1	http://www.ncbi.nlm.nih.gov/gene/?term=9550	"ATP6G, ATP6G1, ATP6GL, ATP6J, Vma10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026228	9550	ATP6V1G1	http://www.ncbi.nlm.nih.gov/gene/?term=9550	"ATP6G, ATP6G1, ATP6GL, ATP6J, Vma10 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026229	9551	ATP5J2	http://www.ncbi.nlm.nih.gov/gene/?term=9551	ATP5JL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026230	9551	ATP5J2	http://www.ncbi.nlm.nih.gov/gene/?term=9551	ATP5JL	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026231	9552	SPAG7	http://www.ncbi.nlm.nih.gov/gene/?term=9552	"ACRP, FSA-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026232	9553	MRPL33	http://www.ncbi.nlm.nih.gov/gene/?term=9553	"C2orf1, L33mt, MRP-L33, RPL33L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026233	9553	MRPL33	http://www.ncbi.nlm.nih.gov/gene/?term=9553	"C2orf1, L33mt, MRP-L33, RPL33L "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026234	9554	SEC22B	http://www.ncbi.nlm.nih.gov/gene/?term=9554	"ERS-24, SEC22L1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026235	9555	H2AFY	http://www.ncbi.nlm.nih.gov/gene/?term=9555	"H2A.y, H2A/y, H2AF12M, MACROH2A1.1, mH2A1, macroH2A1.2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026236	9555	H2AFY	http://www.ncbi.nlm.nih.gov/gene/?term=9555	"H2A.y, H2A/y, H2AF12M, MACROH2A1.1, mH2A1, macroH2A1.2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026237	9556	C14orf2	http://www.ncbi.nlm.nih.gov/gene/?term=9556	"MP68, PLPM "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026238	9556	C14orf2	http://www.ncbi.nlm.nih.gov/gene/?term=9556	"MP68, PLPM "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026239	9557	CHD1L	http://www.ncbi.nlm.nih.gov/gene/?term=9557	"ALC1, CHDL "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026240	9559	VPS26A	http://www.ncbi.nlm.nih.gov/gene/?term=9559	"HB58, Hbeta58, PEP8A, VPS26 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026241	9559	VPS26A	http://www.ncbi.nlm.nih.gov/gene/?term=9559	"HB58, Hbeta58, PEP8A, VPS26 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026242	9559	VPS26A	http://www.ncbi.nlm.nih.gov/gene/?term=9559	"HB58, Hbeta58, PEP8A, VPS26 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026243	955	ENTPD6	http://www.ncbi.nlm.nih.gov/gene/?term=955	"CD39L2, IL-6SAG, IL6ST2, NTPDase-6, dJ738P15.3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026244	9562	MINPP1	http://www.ncbi.nlm.nih.gov/gene/?term=9562	"HIPER1, MINPP2, MIPP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026245	9562	MINPP1	http://www.ncbi.nlm.nih.gov/gene/?term=9562	"HIPER1, MINPP2, MIPP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026246	9563	H6PD	http://www.ncbi.nlm.nih.gov/gene/?term=9563	"CORTRD1, G6PDH, GDH "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026247	9563	H6PD	http://www.ncbi.nlm.nih.gov/gene/?term=9563	"CORTRD1, G6PDH, GDH "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026248	9563	H6PD	http://www.ncbi.nlm.nih.gov/gene/?term=9563	"CORTRD1, G6PDH, GDH "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026249	9563	H6PD	http://www.ncbi.nlm.nih.gov/gene/?term=9563	"CORTRD1, G6PDH, GDH "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026250	9564	BCAR1	http://www.ncbi.nlm.nih.gov/gene/?term=9564	"CAS, CAS1, CASS1, CRKAS, P130Cas "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026251	9567	GTPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=9567	"GP-1, GP1, HSPC018 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026252	9567	GTPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=9567	"GP-1, GP1, HSPC018 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026253	9567	GTPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=9567	"GP-1, GP1, HSPC018 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026254	9567	GTPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=9567	"GP-1, GP1, HSPC018 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026255	95681	CEP41	http://www.ncbi.nlm.nih.gov/gene/?term=95681	"JBTS15, TSGA14 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026256	9570	GOSR2	http://www.ncbi.nlm.nih.gov/gene/?term=9570	"Bos1, EPM6, GS27 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026257	9570	GOSR2	http://www.ncbi.nlm.nih.gov/gene/?term=9570	"Bos1, EPM6, GS27 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026258	9572	NR1D1	http://www.ncbi.nlm.nih.gov/gene/?term=9572	"EAR1, THRA1, THRAL, ear-1, hRev "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026259	9572	NR1D1	http://www.ncbi.nlm.nih.gov/gene/?term=9572	"EAR1, THRA1, THRAL, ear-1, hRev "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026260	9572	NR1D1	http://www.ncbi.nlm.nih.gov/gene/?term=9572	"EAR1, THRA1, THRAL, ear-1, hRev "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026261	9575	CLOCK	http://www.ncbi.nlm.nih.gov/gene/?term=9575	"KAT13D, bHLHe8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026262	9575	CLOCK	http://www.ncbi.nlm.nih.gov/gene/?term=9575	"KAT13D, bHLHe8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026263	9577	BRE	http://www.ncbi.nlm.nih.gov/gene/?term=9577	"BRCC4, BRCC45 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026264	9577	BRE	http://www.ncbi.nlm.nih.gov/gene/?term=9577	"BRCC4, BRCC45 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026265	9578	CDC42BPB	http://www.ncbi.nlm.nih.gov/gene/?term=9578	MRCKB	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026266	9578	CDC42BPB	http://www.ncbi.nlm.nih.gov/gene/?term=9578	MRCKB	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026267	9578	CDC42BPB	http://www.ncbi.nlm.nih.gov/gene/?term=9578	MRCKB	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026268	957	ENTPD5	http://www.ncbi.nlm.nih.gov/gene/?term=957	"CD39L4, NTPDase-5, PCPH "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026269	9581	PREPL	http://www.ncbi.nlm.nih.gov/gene/?term=9581		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026270	9581	PREPL	http://www.ncbi.nlm.nih.gov/gene/?term=9581		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026271	9581	PREPL	http://www.ncbi.nlm.nih.gov/gene/?term=9581		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026272	9583	ENTPD4	http://www.ncbi.nlm.nih.gov/gene/?term=9583	"LALP70, LAP70, LYSAL1, NTPDase-4, UDPase "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026273	9583	ENTPD4	http://www.ncbi.nlm.nih.gov/gene/?term=9583	"LALP70, LAP70, LYSAL1, NTPDase-4, UDPase "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026274	9583	ENTPD4	http://www.ncbi.nlm.nih.gov/gene/?term=9583	"LALP70, LAP70, LYSAL1, NTPDase-4, UDPase "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026275	9583	ENTPD4	http://www.ncbi.nlm.nih.gov/gene/?term=9583	"LALP70, LAP70, LYSAL1, NTPDase-4, UDPase "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026276	9583	ENTPD4	http://www.ncbi.nlm.nih.gov/gene/?term=9583	"LALP70, LAP70, LYSAL1, NTPDase-4, UDPase "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026277	9584	RBM39	http://www.ncbi.nlm.nih.gov/gene/?term=9584	"CAPER, CAPERalpha, FSAP59, HCC1, RNPC2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026278	9584	RBM39	http://www.ncbi.nlm.nih.gov/gene/?term=9584	"CAPER, CAPERalpha, FSAP59, HCC1, RNPC2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026279	9584	RBM39	http://www.ncbi.nlm.nih.gov/gene/?term=9584	"CAPER, CAPERalpha, FSAP59, HCC1, RNPC2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026280	9584	RBM39	http://www.ncbi.nlm.nih.gov/gene/?term=9584	"CAPER, CAPERalpha, FSAP59, HCC1, RNPC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026281	9585	KIF20B	http://www.ncbi.nlm.nih.gov/gene/?term=9585	"CT90, KRMP1, MPHOSPH1, MPP-1, MPP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026282	9585	KIF20B	http://www.ncbi.nlm.nih.gov/gene/?term=9585	"CT90, KRMP1, MPHOSPH1, MPP-1, MPP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026283	9586	CREB5	http://www.ncbi.nlm.nih.gov/gene/?term=9586	"CRE-BPA, CREB-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026284	9587	MAD2L1BP	http://www.ncbi.nlm.nih.gov/gene/?term=9587	CMT2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026285	9587	MAD2L1BP	http://www.ncbi.nlm.nih.gov/gene/?term=9587	CMT2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026286	9587	MAD2L1BP	http://www.ncbi.nlm.nih.gov/gene/?term=9587	CMT2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026287	9588	PRDX6	http://www.ncbi.nlm.nih.gov/gene/?term=9588	"1-Cys, AOP2, HEL-S-128m, NSGPx, PRX, aiPLA2, p29 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026288	9588	PRDX6	http://www.ncbi.nlm.nih.gov/gene/?term=9588	"1-Cys, AOP2, HEL-S-128m, NSGPx, PRX, aiPLA2, p29 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026289	9588	PRDX6	http://www.ncbi.nlm.nih.gov/gene/?term=9588	"1-Cys, AOP2, HEL-S-128m, NSGPx, PRX, aiPLA2, p29 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026290	958	CD40	http://www.ncbi.nlm.nih.gov/gene/?term=958	"Bp50, CDW40, TNFRSF5, p50 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026291	9590	AKAP12	http://www.ncbi.nlm.nih.gov/gene/?term=9590	"AKAP250, SSeCKS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026292	9590	AKAP12	http://www.ncbi.nlm.nih.gov/gene/?term=9590	"AKAP250, SSeCKS "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026293	9592	IER2	http://www.ncbi.nlm.nih.gov/gene/?term=9592	ETR101	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026294	9592	IER2	http://www.ncbi.nlm.nih.gov/gene/?term=9592	ETR101	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026295	9592	IER2	http://www.ncbi.nlm.nih.gov/gene/?term=9592	ETR101	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026296	95	ACY1	http://www.ncbi.nlm.nih.gov/gene/?term=95	"ACY-1, ACY1D, HEL-S-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026297	9600	PITPNM1	http://www.ncbi.nlm.nih.gov/gene/?term=9600	"DRES9, NIR2, PITPNM, RDGB, RDGB1, RDGBA, RDGBA1, Rd9 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026298	9600	PITPNM1	http://www.ncbi.nlm.nih.gov/gene/?term=9600	"DRES9, NIR2, PITPNM, RDGB, RDGB1, RDGBA, RDGBA1, Rd9 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026299	9601	PDIA4	http://www.ncbi.nlm.nih.gov/gene/?term=9601	"ERP70, ERP72, ERp-72 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026300	9601	PDIA4	http://www.ncbi.nlm.nih.gov/gene/?term=9601	"ERP70, ERP72, ERp-72 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026301	9603	NFE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=9603	NRF3	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026302	9603	NFE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=9603	NRF3	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026303	9604	RNF14	http://www.ncbi.nlm.nih.gov/gene/?term=9604	"ARA54, HFB30, HRIHFB2038, TRIAD2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026304	9604	RNF14	http://www.ncbi.nlm.nih.gov/gene/?term=9604	"ARA54, HFB30, HRIHFB2038, TRIAD2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026305	9604	RNF14	http://www.ncbi.nlm.nih.gov/gene/?term=9604	"ARA54, HFB30, HRIHFB2038, TRIAD2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026306	9605	VPS9D1	http://www.ncbi.nlm.nih.gov/gene/?term=9605	"ATP-BL, C16orf7 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026307	9609	RAB36	http://www.ncbi.nlm.nih.gov/gene/?term=9609		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026308	9609	RAB36	http://www.ncbi.nlm.nih.gov/gene/?term=9609		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026309	960	CD44	http://www.ncbi.nlm.nih.gov/gene/?term=960	"CDW44, CSPG8, ECMR-III, HCELL, HUTCH-I, IN, LHR, MC56, MDU2, MDU3, MIC4, Pgp1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026310	960	CD44	http://www.ncbi.nlm.nih.gov/gene/?term=960	"CDW44, CSPG8, ECMR-III, HCELL, HUTCH-I, IN, LHR, MC56, MDU2, MDU3, MIC4, Pgp1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026311	9610	RIN1	http://www.ncbi.nlm.nih.gov/gene/?term=9610		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026312	9611	NCOR1	http://www.ncbi.nlm.nih.gov/gene/?term=9611	"N-CoR, N-CoR1, PPP1R109, TRAC1, hN-CoR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026313	9611	NCOR1	http://www.ncbi.nlm.nih.gov/gene/?term=9611	"N-CoR, N-CoR1, PPP1R109, TRAC1, hN-CoR "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026314	9611	NCOR1	http://www.ncbi.nlm.nih.gov/gene/?term=9611	"N-CoR, N-CoR1, PPP1R109, TRAC1, hN-CoR "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026315	9611	NCOR1	http://www.ncbi.nlm.nih.gov/gene/?term=9611	"N-CoR, N-CoR1, PPP1R109, TRAC1, hN-CoR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026316	9612	NCOR2	http://www.ncbi.nlm.nih.gov/gene/?term=9612	"CTG26, N-CoR2, SMAP270, SMRT, SMRTE, SMRTE-tau, TNRC14, TRAC, TRAC-1, TRAC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026317	9615	GDA	http://www.ncbi.nlm.nih.gov/gene/?term=9615	"CYPIN, GUANASE, NEDASIN "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026318	9616	RNF7	http://www.ncbi.nlm.nih.gov/gene/?term=9616	"CKBBP1, ROC2, SAG "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026319	9616	RNF7	http://www.ncbi.nlm.nih.gov/gene/?term=9616	"CKBBP1, ROC2, SAG "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026320	9616	RNF7	http://www.ncbi.nlm.nih.gov/gene/?term=9616	"CKBBP1, ROC2, SAG "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026321	9618	TRAF4	http://www.ncbi.nlm.nih.gov/gene/?term=9618	"CART1, MLN62, RNF83 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026322	9618	TRAF4	http://www.ncbi.nlm.nih.gov/gene/?term=9618	"CART1, MLN62, RNF83 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026323	9618	TRAF4	http://www.ncbi.nlm.nih.gov/gene/?term=9618	"CART1, MLN62, RNF83 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026324	9619	ABCG1	http://www.ncbi.nlm.nih.gov/gene/?term=9619	"ABC8, WHITE1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026325	961	CD47	http://www.ncbi.nlm.nih.gov/gene/?term=961	"IAP, MER6, OA3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026326	961	CD47	http://www.ncbi.nlm.nih.gov/gene/?term=961	"IAP, MER6, OA3 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026327	961	CD47	http://www.ncbi.nlm.nih.gov/gene/?term=961	"IAP, MER6, OA3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026328	9628	RGS6	http://www.ncbi.nlm.nih.gov/gene/?term=9628	GAP	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026329	962	CD48	http://www.ncbi.nlm.nih.gov/gene/?term=962	"BCM1, BLAST, BLAST1, MEM-102, SLAMF2, hCD48, mCD48 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026330	9631	NUP155	http://www.ncbi.nlm.nih.gov/gene/?term=9631	"ATFB15, N155 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026331	9631	NUP155	http://www.ncbi.nlm.nih.gov/gene/?term=9631	"ATFB15, N155 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026332	9632	SEC24C	http://www.ncbi.nlm.nih.gov/gene/?term=9632		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026333	9632	SEC24C	http://www.ncbi.nlm.nih.gov/gene/?term=9632		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026334	9632	SEC24C	http://www.ncbi.nlm.nih.gov/gene/?term=9632		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026335	9632	SEC24C	http://www.ncbi.nlm.nih.gov/gene/?term=9632		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026336	9633	MTL5	http://www.ncbi.nlm.nih.gov/gene/?term=9633	"CXCDC2, MTLT, TESMIN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026337	9633	MTL5	http://www.ncbi.nlm.nih.gov/gene/?term=9633	"CXCDC2, MTLT, TESMIN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026338	9636	ISG15	http://www.ncbi.nlm.nih.gov/gene/?term=9636	"G1P2, IFI15, IMD38, IP17, UCRP, hUCRP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026339	9636	ISG15	http://www.ncbi.nlm.nih.gov/gene/?term=9636	"G1P2, IFI15, IMD38, IP17, UCRP, hUCRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026340	9637	FEZ2	http://www.ncbi.nlm.nih.gov/gene/?term=9637	HUM3CL	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026341	9638	FEZ1	http://www.ncbi.nlm.nih.gov/gene/?term=9638	UNC-76	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026342	9638	FEZ1	http://www.ncbi.nlm.nih.gov/gene/?term=9638	UNC-76	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026343	9638	FEZ1	http://www.ncbi.nlm.nih.gov/gene/?term=9638	UNC-76	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026344	9639	ARHGEF10	http://www.ncbi.nlm.nih.gov/gene/?term=9639	"GEF10, SNCV "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026345	963	CD53	http://www.ncbi.nlm.nih.gov/gene/?term=963	"MOX44, TSPAN25 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026346	9640	ZNF592	http://www.ncbi.nlm.nih.gov/gene/?term=9640	"CAMOS, SCAR5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026347	9641	IKBKE	http://www.ncbi.nlm.nih.gov/gene/?term=9641	"IKK-E, IKK-i, IKKE, IKKI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026348	9643	MORF4L2	http://www.ncbi.nlm.nih.gov/gene/?term=9643	"MORFL2, MRGX "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026349	9643	MORF4L2	http://www.ncbi.nlm.nih.gov/gene/?term=9643	"MORFL2, MRGX "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026350	96459	FNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=96459		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026351	96459	FNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=96459		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026352	96459	FNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=96459		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026353	9645	MICAL2	http://www.ncbi.nlm.nih.gov/gene/?term=9645	"MICAL-2PV1, MICAL2PV2, MICAL2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026354	9645	MICAL2	http://www.ncbi.nlm.nih.gov/gene/?term=9645	"MICAL-2, MICAL2PV1, MICAL2PV2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026355	9646	CTR9	http://www.ncbi.nlm.nih.gov/gene/?term=9646	"SH2BP1, TSBP, p150, p150TSP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026356	9647	PPM1F	http://www.ncbi.nlm.nih.gov/gene/?term=9647	"CAMKP, CaMKPase, FEM-2, POPX2, hFEM-2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026357	9647	PPM1F	http://www.ncbi.nlm.nih.gov/gene/?term=9647	"CAMKP, CaMKPase, FEM-2, POPX2, hFEM-2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026358	9650	MTFR1	http://www.ncbi.nlm.nih.gov/gene/?term=9650	"CHPPR, FAM54A2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026359	9652	TTC37	http://www.ncbi.nlm.nih.gov/gene/?term=9652	"KIAA0372, Ski3, THES "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026360	9652	TTC37	http://www.ncbi.nlm.nih.gov/gene/?term=9652	"KIAA0372, Ski3, THES "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026361	9653	HS2ST1	http://www.ncbi.nlm.nih.gov/gene/?term=9653	dJ604K5.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026362	9654	TTLL4	http://www.ncbi.nlm.nih.gov/gene/?term=9654		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026363	9655	SOCS5	http://www.ncbi.nlm.nih.gov/gene/?term=9655	"CIS6, CISH6, Cish5, SOCS-5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026364	9656	MDC1	http://www.ncbi.nlm.nih.gov/gene/?term=9656	NFBD1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026365	9657	IQCB1	http://www.ncbi.nlm.nih.gov/gene/?term=9657	"NPHP5, PIQ, SLSN5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026366	9657	IQCB1	http://www.ncbi.nlm.nih.gov/gene/?term=9657	"NPHP5, PIQ, SLSN5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026367	9659	PDE4DIP	http://www.ncbi.nlm.nih.gov/gene/?term=9659	"CMYA2, MMGL "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026368	9659	PDE4DIP	http://www.ncbi.nlm.nih.gov/gene/?term=9659	"CMYA2, MMGL "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026369	965	CD58	http://www.ncbi.nlm.nih.gov/gene/?term=965	"LFA-3, LFA3, ag3 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026370	96626	LIMS3	http://www.ncbi.nlm.nih.gov/gene/?term=96626	PINCH-3	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026371	9665	KIAA0430	http://www.ncbi.nlm.nih.gov/gene/?term=9665	"LKAP, MARF1, PPP1R34 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026372	9666	DZIP3	http://www.ncbi.nlm.nih.gov/gene/?term=9666	"PPP1R66, UURF2, hRUL138 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026373	9666	DZIP3	http://www.ncbi.nlm.nih.gov/gene/?term=9666	"PPP1R66, UURF2, hRUL138 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026374	9667	SAFB2	http://www.ncbi.nlm.nih.gov/gene/?term=9667		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026375	9667	SAFB2	http://www.ncbi.nlm.nih.gov/gene/?term=9667		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026376	9669	EIF5B	http://www.ncbi.nlm.nih.gov/gene/?term=9669	IF2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026377	9669	EIF5B	http://www.ncbi.nlm.nih.gov/gene/?term=9669	IF2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026378	966	CD59	http://www.ncbi.nlm.nih.gov/gene/?term=966	"16.3A5, 1F5, EJ16, EJ30, EL32, G344, HRF-20, HRF20, MAC-IP, MACIF, MEM43, MIC11, MIN1, MIN2, MIN3, MIRL, MSK21, p18-20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026379	966	CD59	http://www.ncbi.nlm.nih.gov/gene/?term=966	"16.3A5, 1F5, EJ16, EJ30, EL32, G344, HRF-20, HRF20, MAC-IP, MACIF, MEM43, MIC11, MIN1, MIN2, MIN3, MIRL, MSK21, p18-20 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026380	9670	IPO13	http://www.ncbi.nlm.nih.gov/gene/?term=9670	"IMP13, KAP13, LGL2, RANBP13 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026381	9671	WSCD2	http://www.ncbi.nlm.nih.gov/gene/?term=9671		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026382	9672	SDC3	http://www.ncbi.nlm.nih.gov/gene/?term=9672	"SDCN, SYND3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026383	9674	KIAA0040	http://www.ncbi.nlm.nih.gov/gene/?term=9674		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026384	96764	TGS1	http://www.ncbi.nlm.nih.gov/gene/?term=96764	"NCOA6IP, PIMT, PIPMT "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026385	96764	TGS1	http://www.ncbi.nlm.nih.gov/gene/?term=96764	"NCOA6IP, PIMT, PIPMT "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026386	96764	TGS1	http://www.ncbi.nlm.nih.gov/gene/?term=96764	"NCOA6IP, PIMT, PIPMT "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026387	9677	PPIP5K1	http://www.ncbi.nlm.nih.gov/gene/?term=9677	"HISPPD2A, IP6K, IPS1, VIP1, hsVIP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026388	9678	PHF14	http://www.ncbi.nlm.nih.gov/gene/?term=9678		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026389	9679	FAM53B	http://www.ncbi.nlm.nih.gov/gene/?term=9679	"KIAA0140, bA12J10.2, smp "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026390	967	CD63	http://www.ncbi.nlm.nih.gov/gene/?term=967	"LAMP-3, ME491, MLA1, OMA81H, TSPAN30 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026391	9682	KDM4A	http://www.ncbi.nlm.nih.gov/gene/?term=9682	"JHDM3A, JMJD2, JMJD2A, TDRD14A "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026392	9682	KDM4A	http://www.ncbi.nlm.nih.gov/gene/?term=9682	"JHDM3A, JMJD2, JMJD2A, TDRD14A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026393	9683	N4BP1	http://www.ncbi.nlm.nih.gov/gene/?term=9683		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026394	9685	CLINT1	http://www.ncbi.nlm.nih.gov/gene/?term=9685	"CLINT, ENTH, EPN4, EPNR "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026395	9685	CLINT1	http://www.ncbi.nlm.nih.gov/gene/?term=9685	"CLINT, ENTH, EPN4, EPNR "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026396	9685	CLINT1	http://www.ncbi.nlm.nih.gov/gene/?term=9685	"CLINT, ENTH, EPN4, EPNR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026397	9687	GREB1	http://www.ncbi.nlm.nih.gov/gene/?term=9687		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026398	9687	GREB1	http://www.ncbi.nlm.nih.gov/gene/?term=9687		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026399	9688	NUP93	http://www.ncbi.nlm.nih.gov/gene/?term=9688	"NIC96, NPHS12 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026400	9688	NUP93	http://www.ncbi.nlm.nih.gov/gene/?term=9688	NIC96	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026401	96891	C79246	http://www.ncbi.nlm.nih.gov/gene/?term=96891		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026402	9689	BZW1	http://www.ncbi.nlm.nih.gov/gene/?term=9689	"BZAP45, Nbla10236 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026403	9689	BZW1	http://www.ncbi.nlm.nih.gov/gene/?term=9689	"BZAP45, Nbla10236 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026404	9689	BZW1	http://www.ncbi.nlm.nih.gov/gene/?term=9689	"BZAP45, Nbla10236 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026405	968	CD68	http://www.ncbi.nlm.nih.gov/gene/?term=968	"GP110, LAMP4, SCARD1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026406	96907	C81001	http://www.ncbi.nlm.nih.gov/gene/?term=96907		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026407	9690	UBE3C	http://www.ncbi.nlm.nih.gov/gene/?term=9690	HECTH2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026408	9690	UBE3C	http://www.ncbi.nlm.nih.gov/gene/?term=9690	HECTH2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026409	9692	KIAA0391	http://www.ncbi.nlm.nih.gov/gene/?term=9692	"MRPP3, PRORP "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026410	9693	RAPGEF2	http://www.ncbi.nlm.nih.gov/gene/?term=9693	"CNrasGEF, NRAPGEP, PDZ-GEF1, PDZGEF1, RA-GEF, RA-GEF-1, Rap-GEP, nRap GEP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026411	9694	EMC2	http://www.ncbi.nlm.nih.gov/gene/?term=9694	"KIAA0103, TTC35 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026412	9695	EDEM1	http://www.ncbi.nlm.nih.gov/gene/?term=9695	EDEM	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026413	9695	EDEM1	http://www.ncbi.nlm.nih.gov/gene/?term=9695	EDEM	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026414	9695	EDEM1	http://www.ncbi.nlm.nih.gov/gene/?term=9695	EDEM	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026415	96961	C77609	http://www.ncbi.nlm.nih.gov/gene/?term=96961		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026416	96979	Ptges2	http://www.ncbi.nlm.nih.gov/gene/?term=96979	"0610038H10Rik, C79137, Gbf1, Mpges2, Pges2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026417	9697	TRAM2	http://www.ncbi.nlm.nih.gov/gene/?term=9697		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026418	9697	TRAM2	http://www.ncbi.nlm.nih.gov/gene/?term=9697		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026419	9698	PUM1	http://www.ncbi.nlm.nih.gov/gene/?term=9698	"HSPUM, PUMH, PUMH1, PUML1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026420	9699	RIMS2	http://www.ncbi.nlm.nih.gov/gene/?term=9699	"OBOE, RAB3IP3, RIM2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026421	9700	ESPL1	http://www.ncbi.nlm.nih.gov/gene/?term=9700	"ESP1, SEPA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026422	9700	ESPL1	http://www.ncbi.nlm.nih.gov/gene/?term=9700	"ESP1, SEPA "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026423	9700	ESPL1	http://www.ncbi.nlm.nih.gov/gene/?term=9700	"ESP1, SEPA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026424	9701	PPP6R2	http://www.ncbi.nlm.nih.gov/gene/?term=9701	"KIAA0685, PP6R2, SAP190, SAPS2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026425	9702	CEP57	http://www.ncbi.nlm.nih.gov/gene/?term=9702	"MVA2, PIG8, TSP57 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026426	9702	CEP57	http://www.ncbi.nlm.nih.gov/gene/?term=9702	"MVA2, PIG8, TSP57 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026427	9702	CEP57	http://www.ncbi.nlm.nih.gov/gene/?term=9702	"MVA2, PIG8, TSP57 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026428	97031	Tprn	http://www.ncbi.nlm.nih.gov/gene/?term=97031	"C430004E15Rik, C87750 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026429	9703	KIAA0100	http://www.ncbi.nlm.nih.gov/gene/?term=9703	"BCOX, BCOX1, CT101 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026430	9703	KIAA0100	http://www.ncbi.nlm.nih.gov/gene/?term=9703	"BCOX, BCOX1, CT101 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026431	9703	KIAA0100	http://www.ncbi.nlm.nih.gov/gene/?term=9703	"BCOX, BCOX1, CT101 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026432	9704	DHX34	http://www.ncbi.nlm.nih.gov/gene/?term=9704	"DDX34, HRH1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026433	9704	DHX34	http://www.ncbi.nlm.nih.gov/gene/?term=9704	"DDX34, HRH1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026434	97067	C78651	http://www.ncbi.nlm.nih.gov/gene/?term=97067		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026435	9709	HERPUD1	http://www.ncbi.nlm.nih.gov/gene/?term=9709	"HERP, Mif1, SUP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026436	970	CD70	http://www.ncbi.nlm.nih.gov/gene/?term=970	"CD27L, CD27LG, TNFSF7, TNLG8A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026437	9710	KIAA0355	http://www.ncbi.nlm.nih.gov/gene/?term=9710		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026438	97112	Nmd3	http://www.ncbi.nlm.nih.gov/gene/?term=97112	C87860	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026439	9711	RUBCN	http://www.ncbi.nlm.nih.gov/gene/?term=9711	"KIAA0226, RUBICON, SCAR15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026440	9712	USP6NL	http://www.ncbi.nlm.nih.gov/gene/?term=9712	"RNTRE, TRE2NL, USP6NL-IT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026441	97148	C78692	http://www.ncbi.nlm.nih.gov/gene/?term=97148		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026442	97165	Hmgb2	http://www.ncbi.nlm.nih.gov/gene/?term=97165	"C80539, HMG-2, Hmg2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026443	9716	AQR	http://www.ncbi.nlm.nih.gov/gene/?term=9716	"IBP160, fSAP164 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026444	9716	AQR	http://www.ncbi.nlm.nih.gov/gene/?term=9716	"IBP160, fSAP164 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026445	9718	ECE2	http://www.ncbi.nlm.nih.gov/gene/?term=9718		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026446	97225	C77815	http://www.ncbi.nlm.nih.gov/gene/?term=97225		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026447	9725	TMEM63A	http://www.ncbi.nlm.nih.gov/gene/?term=9725	KIAA0792	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026448	9725	TMEM63A	http://www.ncbi.nlm.nih.gov/gene/?term=9725	KIAA0792	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026449	9726	ZNF646	http://www.ncbi.nlm.nih.gov/gene/?term=9726		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026450	9727	RAB11FIP3	http://www.ncbi.nlm.nih.gov/gene/?term=9727	"CART1, Rab11-FIP3 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026451	9727	RAB11FIP3	http://www.ncbi.nlm.nih.gov/gene/?term=9727	"CART1, Rab11-FIP3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026452	9728	SECISBP2L	http://www.ncbi.nlm.nih.gov/gene/?term=9728	"SBP2L, SLAN "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026453	9731	CEP104	http://www.ncbi.nlm.nih.gov/gene/?term=9731	"CFAP256, GlyBP, JBTS25, KIAA0562, ROC22 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026454	9731	CEP104	http://www.ncbi.nlm.nih.gov/gene/?term=9731	"CFAP256, GlyBP, JBTS25, KIAA0562, ROC22 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026455	9733	SART3	http://www.ncbi.nlm.nih.gov/gene/?term=9733	"DSAP1, P100, RP11-13G14, TIP110, p110, p110(nrb) "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026456	9733	SART3	http://www.ncbi.nlm.nih.gov/gene/?term=9733	"DSAP1, P100, RP11-13G14, TIP110, p110, p110(nrb) "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026457	9733	SART3	http://www.ncbi.nlm.nih.gov/gene/?term=9733	"DSAP1, P100, RP11-13G14, TIP110, p110, p110(nrb) "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026458	9734	HDAC9	http://www.ncbi.nlm.nih.gov/gene/?term=9734	"HD7, HD9, HD7b, HDAC, HDRP, MITR, HDAC7, HDAC7B, HDAC9B, HDAC9FL "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00026459	9735	KNTC1	http://www.ncbi.nlm.nih.gov/gene/?term=9735	ROD	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026460	9736	USP34	http://www.ncbi.nlm.nih.gov/gene/?term=9736		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026461	9737	GPRASP1	http://www.ncbi.nlm.nih.gov/gene/?term=9737	"GASP, GASP-1, GASP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026462	97389	C80893	http://www.ncbi.nlm.nih.gov/gene/?term=97389		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026463	9738	CCP110	http://www.ncbi.nlm.nih.gov/gene/?term=9738	"CP110, Cep110 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026464	9739	SETD1A	http://www.ncbi.nlm.nih.gov/gene/?term=9739	"KMT2F, Set1, Set1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026465	9741	LAPTM4A	http://www.ncbi.nlm.nih.gov/gene/?term=9741	"HUMORF13, LAPTM4, MBNT, Mtrp "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026466	9741	LAPTM4A	http://www.ncbi.nlm.nih.gov/gene/?term=9741	"HUMORF13, LAPTM4, MBNT, Mtrp "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026467	9743	ARHGAP32	http://www.ncbi.nlm.nih.gov/gene/?term=9743	"GC-GAP, GRIT, PX-RICS, RICS, p200RhoGAP, p250GAP "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026468	97455	C78859	http://www.ncbi.nlm.nih.gov/gene/?term=97455		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026469	9746	CLSTN3	http://www.ncbi.nlm.nih.gov/gene/?term=9746	"CDHR14, CSTN3, alcbeta "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026470	97476	Fam90a1a	http://www.ncbi.nlm.nih.gov/gene/?term=97476	C86695	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026471	9747	TCAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9747	FAM115A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026472	97484	Cog8	http://www.ncbi.nlm.nih.gov/gene/?term=97484	"BB235941, C87832 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026473	97487	Cmtm4	http://www.ncbi.nlm.nih.gov/gene/?term=97487	"Cklfsf4, D19397, ENSMUSG00000051554, Gm9853 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026474	9748	SLK	http://www.ncbi.nlm.nih.gov/gene/?term=9748	"LOSK, STK2, bA16H23.1, se20-9 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026475	9748	SLK	http://www.ncbi.nlm.nih.gov/gene/?term=9748	"LOSK, STK2, bA16H23.1, se20-9 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026476	9748	SLK	http://www.ncbi.nlm.nih.gov/gene/?term=9748	"LOSK, STK2, bA16H23.1, se20-9 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026477	9749	PHACTR2	http://www.ncbi.nlm.nih.gov/gene/?term=9749	C6orf56	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026478	9751	SNPH	http://www.ncbi.nlm.nih.gov/gene/?term=9751		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026479	9752	PCDHA9	http://www.ncbi.nlm.nih.gov/gene/?term=9752	PCDH-ALPHA9	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026480	9752	PCDHA9	http://www.ncbi.nlm.nih.gov/gene/?term=9752	PCDH-ALPHA9	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026481	9755	TBKBP1	http://www.ncbi.nlm.nih.gov/gene/?term=9755	"ProSAPiP2, SINTBAD "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026482	97569	C87580	http://www.ncbi.nlm.nih.gov/gene/?term=97569		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026483	9759	HDAC4	http://www.ncbi.nlm.nih.gov/gene/?term=9759	"HD4, AHO3, BDMR, HDACA, HA6116, HDAC-4, HDAC-A "	mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00026484	975	CD81	http://www.ncbi.nlm.nih.gov/gene/?term=975	"CVID6, S5.7, TAPA1, TSPAN28 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026485	975	CD81	http://www.ncbi.nlm.nih.gov/gene/?term=975	"CVID6, S5.7, TAPA1, TSPAN28 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026486	975	CD81	http://www.ncbi.nlm.nih.gov/gene/?term=975	"CVID6, S5.7, TAPA1, TSPAN28 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026487	9761	MLEC	http://www.ncbi.nlm.nih.gov/gene/?term=9761	KIAA0152	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026488	9761	MLEC	http://www.ncbi.nlm.nih.gov/gene/?term=9761	KIAA0152	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026489	9762	LZTS3	http://www.ncbi.nlm.nih.gov/gene/?term=9762	PROSAPIP1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026490	9764	KIAA0513	http://www.ncbi.nlm.nih.gov/gene/?term=9764		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026491	9764	KIAA0513	http://www.ncbi.nlm.nih.gov/gene/?term=9764		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026492	9764	KIAA0513	http://www.ncbi.nlm.nih.gov/gene/?term=9764		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026493	9765	ZFYVE16	http://www.ncbi.nlm.nih.gov/gene/?term=9765	PPP1R69	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026494	9765	ZFYVE16	http://www.ncbi.nlm.nih.gov/gene/?term=9765	PPP1R69	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026495	97662	C86090	http://www.ncbi.nlm.nih.gov/gene/?term=97662		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026496	9766	SUSD6	http://www.ncbi.nlm.nih.gov/gene/?term=9766	"DRAGO, KIAA0247 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026497	9768	KIAA0101	http://www.ncbi.nlm.nih.gov/gene/?term=9768	"L5, NS5ATP9, OEATC, OEATC-1, OEATC1, PAF, PAF15, p15(PAF), p15/PAF, p15PAF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026498	976	ADGRE5	http://www.ncbi.nlm.nih.gov/gene/?term=976	"CD97, TM7LN1 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026499	9770	RASSF2	http://www.ncbi.nlm.nih.gov/gene/?term=9770	"CENP-34, RASFADIN "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026500	9770	RASSF2	http://www.ncbi.nlm.nih.gov/gene/?term=9770	"CENP-34, RASFADIN "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026501	97714	C78891	http://www.ncbi.nlm.nih.gov/gene/?term=97714		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026502	97726	C80165	http://www.ncbi.nlm.nih.gov/gene/?term=97726		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026503	9772	TMEM94	http://www.ncbi.nlm.nih.gov/gene/?term=9772	KIAA0195	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026504	9774	BCLAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9774	"BTF, bK211L9.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026505	9774	BCLAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9774	"BTF, bK211L9.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026506	9774	BCLAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9774	"BTF, bK211L9.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026507	9775	EIF4A3	http://www.ncbi.nlm.nih.gov/gene/?term=9775	"DDX48, MUK34, NMP265, NUK34, RCPS, eIF4AIII "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026508	9775	EIF4A3	http://www.ncbi.nlm.nih.gov/gene/?term=9775	"DDX48, MUK34, NMP265, NUK34, RCPS, eIF4AIII "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026509	9775	EIF4A3	http://www.ncbi.nlm.nih.gov/gene/?term=9775	"DDX48, MUK34, NMP265, NUK34, RCPS, eIF4AIII "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026510	9776	ATG13	http://www.ncbi.nlm.nih.gov/gene/?term=9776	"KIAA0652, PARATARG8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026511	9776	ATG13	http://www.ncbi.nlm.nih.gov/gene/?term=9776	"KIAA0652, PARATARG8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026512	9776	ATG13	http://www.ncbi.nlm.nih.gov/gene/?term=9776	"KIAA0652, PARATARG8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026513	9777	TM9SF4	http://www.ncbi.nlm.nih.gov/gene/?term=9777	dJ836N17.2	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026514	9777	TM9SF4	http://www.ncbi.nlm.nih.gov/gene/?term=9777	dJ836N17.2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026515	97783	C76336	http://www.ncbi.nlm.nih.gov/gene/?term=97783		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026516	97784	C76472	http://www.ncbi.nlm.nih.gov/gene/?term=97784		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026517	97787	C76872	http://www.ncbi.nlm.nih.gov/gene/?term=97787		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026518	9778	KIAA0232	http://www.ncbi.nlm.nih.gov/gene/?term=9778		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026519	9779	TBC1D5	http://www.ncbi.nlm.nih.gov/gene/?term=9779		mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026520	9779	TBC1D5	http://www.ncbi.nlm.nih.gov/gene/?term=9779		mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026521	9779	TBC1D5	http://www.ncbi.nlm.nih.gov/gene/?term=9779		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026522	977	CD151	http://www.ncbi.nlm.nih.gov/gene/?term=977	"GP27, MER2, PETA-3, RAPH, SFA1, TSPAN24 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026523	977	CD151	http://www.ncbi.nlm.nih.gov/gene/?term=977	"GP27, MER2, PETA-3, RAPH, SFA1, TSPAN24 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026524	9780	PIEZO1	http://www.ncbi.nlm.nih.gov/gene/?term=9780	"DHS, FAM38A, Mib "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026525	97820	4833439L19Rik	http://www.ncbi.nlm.nih.gov/gene/?term=97820	"4930558H15Rik, C81457, Kiaa1191, P33monox "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026526	9782	MATR3	http://www.ncbi.nlm.nih.gov/gene/?term=9782	"ALS21, MPD2, VCPDM "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026527	9783	RIMS3	http://www.ncbi.nlm.nih.gov/gene/?term=9783	"NIM3, RIM3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026528	9784	SNX17	http://www.ncbi.nlm.nih.gov/gene/?term=9784		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026529	9785	DHX38	http://www.ncbi.nlm.nih.gov/gene/?term=9785	"DDX38, PRP16, PRPF16 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026530	97863	Fam8a1	http://www.ncbi.nlm.nih.gov/gene/?term=97863	C78339	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026531	9787	DLGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9787	"DLG7, HURP "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026532	9787	DLGAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9787	"DLG7, HURP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026533	97884	B3galnt2	http://www.ncbi.nlm.nih.gov/gene/?term=97884	"A930105D20Rik, C80633, D230016N13Rik "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026534	9789	SPCS2	http://www.ncbi.nlm.nih.gov/gene/?term=9789		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026535	9789	SPCS2	http://www.ncbi.nlm.nih.gov/gene/?term=9789		mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026536	9791	PTDSS1	http://www.ncbi.nlm.nih.gov/gene/?term=9791	"LMHD, PSS1, PSSA "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026537	9791	PTDSS1	http://www.ncbi.nlm.nih.gov/gene/?term=9791	"LMHD, PSS1, PSSA "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026538	9792	SERTAD2	http://www.ncbi.nlm.nih.gov/gene/?term=9792	"Sei-2, TRIP-Br2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026539	9792	SERTAD2	http://www.ncbi.nlm.nih.gov/gene/?term=9792	"Sei-2, TRIP-Br2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026540	9793	CKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9793	"CHTOG, MSPS, TOG, TOGp, ch-TOG "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026541	9793	CKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9793	"CHTOG, MSPS, TOG, TOGp, ch-TOG "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026542	9794	MAML1	http://www.ncbi.nlm.nih.gov/gene/?term=9794	"Mam-1, Mam1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026543	9794	MAML1	http://www.ncbi.nlm.nih.gov/gene/?term=9794	"Mam-1, Mam1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026544	9797	TATDN2	http://www.ncbi.nlm.nih.gov/gene/?term=9797		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026545	9798	IST1	http://www.ncbi.nlm.nih.gov/gene/?term=9798	OLC1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026546	97	ACYP1	http://www.ncbi.nlm.nih.gov/gene/?term=97	ACYPE	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026547	98013	C78549	http://www.ncbi.nlm.nih.gov/gene/?term=98013		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026548	9801	MRPL19	http://www.ncbi.nlm.nih.gov/gene/?term=9801	"L19mt, MRP-L15, MRP-L19, MRPL15, RLX1, RPML15 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026549	9801	MRPL19	http://www.ncbi.nlm.nih.gov/gene/?term=9801	"L19mt, MRP-L15, MRP-L19, MRPL15, RLX1, RPML15 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026550	9802	DAZAP2	http://www.ncbi.nlm.nih.gov/gene/?term=9802	PRTB	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026551	9802	DAZAP2	http://www.ncbi.nlm.nih.gov/gene/?term=9802	PRTB	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026552	9804	TOMM20	http://www.ncbi.nlm.nih.gov/gene/?term=9804	"MAS20, MOM19, TOM20 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026553	9804	TOMM20	http://www.ncbi.nlm.nih.gov/gene/?term=9804	"MAS20, MOM19, TOM20 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026554	9805	SCRN1	http://www.ncbi.nlm.nih.gov/gene/?term=9805	SES1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026555	9805	SCRN1	http://www.ncbi.nlm.nih.gov/gene/?term=9805	SES1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026556	9805	SCRN1	http://www.ncbi.nlm.nih.gov/gene/?term=9805	SES1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026557	9806	SPOCK2	http://www.ncbi.nlm.nih.gov/gene/?term=9806	testican-2	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026558	9807	IP6K1	http://www.ncbi.nlm.nih.gov/gene/?term=9807	"IHPK1, PiUS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026559	9807	IP6K1	http://www.ncbi.nlm.nih.gov/gene/?term=9807	"IHPK1, PiUS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026560	9810	RNF40	http://www.ncbi.nlm.nih.gov/gene/?term=9810	"BRE1B, RBP95, STARING "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026561	9810	RNF40	http://www.ncbi.nlm.nih.gov/gene/?term=9810	"BRE1B, RBP95, STARING "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026562	9811	CTIF	http://www.ncbi.nlm.nih.gov/gene/?term=9811	"Gm672, KIAA0427 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026563	9812	KIAA0141	http://www.ncbi.nlm.nih.gov/gene/?term=9812	DELE	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026564	9812	KIAA0141	http://www.ncbi.nlm.nih.gov/gene/?term=9812	DELE	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026565	9813	EFCAB14	http://www.ncbi.nlm.nih.gov/gene/?term=9813	KIAA0494	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026566	98146	C78505	http://www.ncbi.nlm.nih.gov/gene/?term=98146		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026567	9816	URB2	http://www.ncbi.nlm.nih.gov/gene/?term=9816	"KIAA0133, NET10, NPA2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026568	9816	URB2	http://www.ncbi.nlm.nih.gov/gene/?term=9816	"KIAA0133, NET10, NPA2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026569	98170	Tmem132a	http://www.ncbi.nlm.nih.gov/gene/?term=98170	"6720481D13Rik, Hspa5bp1, Orai1, R74613 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026570	9817	KEAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9817	"INrf2, KLHL19 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026571	9817	KEAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9817	"INrf2, KLHL19 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026572	9817	KEAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9817	"INrf2, KLHL19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026573	9818	NUP58	http://www.ncbi.nlm.nih.gov/gene/?term=9818	"NUP45, NUPL1, PRO2463 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026574	9819	TSC22D2	http://www.ncbi.nlm.nih.gov/gene/?term=9819	"TILZ4a, TILZ4b, TILZ4c "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026575	9819	TSC22D2	http://www.ncbi.nlm.nih.gov/gene/?term=9819	"TILZ4a, TILZ4b, TILZ4c "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026576	9820	CUL7	http://www.ncbi.nlm.nih.gov/gene/?term=9820	"3M1, KIAA0076, dJ20C7.5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026577	9821	RB1CC1	http://www.ncbi.nlm.nih.gov/gene/?term=9821	"ATG17, CC1, FIP200, PPP1R131 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026578	9824	ARHGAP11A	http://www.ncbi.nlm.nih.gov/gene/?term=9824	GAP (1-12)	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026579	9824	ARHGAP11A	http://www.ncbi.nlm.nih.gov/gene/?term=9824	GAP (1-12)	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026580	9824	ARHGAP11A	http://www.ncbi.nlm.nih.gov/gene/?term=9824	GAP (1-12)	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026581	98267	Stk17b	http://www.ncbi.nlm.nih.gov/gene/?term=98267	"3110009A03Rik, AI120141, Drak2 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026582	9826	ARHGEF11	http://www.ncbi.nlm.nih.gov/gene/?term=9826	"GTRAP48, PDZ-RHOGEF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026583	9826	ARHGEF11	http://www.ncbi.nlm.nih.gov/gene/?term=9826	"GTRAP48, PDZ-RHOGEF "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026584	9827	RGP1	http://www.ncbi.nlm.nih.gov/gene/?term=9827	KIAA0258	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026585	9828	ARHGEF17	http://www.ncbi.nlm.nih.gov/gene/?term=9828	"P164RHOGEF, TEM4, p164-RhoGEF "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026586	9829	DNAJC6	http://www.ncbi.nlm.nih.gov/gene/?term=9829	"DJC6, PARK19 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026587	98303	D630023F18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=98303	AI314969	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026588	9830	TRIM14	http://www.ncbi.nlm.nih.gov/gene/?term=9830		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026589	9830	TRIM14	http://www.ncbi.nlm.nih.gov/gene/?term=9830		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026590	9832	JAKMIP2	http://www.ncbi.nlm.nih.gov/gene/?term=9832	"JAMIP2, NECC1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026591	98365	Slamf9	http://www.ncbi.nlm.nih.gov/gene/?term=98365	"2310026I04Rik, AI462096, CD2F-10, CD84-H1, Cd2f10, SF2001 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026592	9837	GINS1	http://www.ncbi.nlm.nih.gov/gene/?term=9837	PSF1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026593	9837	GINS1	http://www.ncbi.nlm.nih.gov/gene/?term=9837	PSF1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026594	98386	Lbr	http://www.ncbi.nlm.nih.gov/gene/?term=98386	"AI505894, ic "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026595	9839	ZEB2	http://www.ncbi.nlm.nih.gov/gene/?term=9839	"HSPC082, SIP-1, SIP1, SMADIP1, ZFHX1B "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026596	983	CDK1	http://www.ncbi.nlm.nih.gov/gene/?term=983	"CDC2, CDC28A, P34CDC2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026597	983	CDK1	http://www.ncbi.nlm.nih.gov/gene/?term=983	"CDC2, CDC28A, P34CDC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026598	98415	Nucks1	http://www.ncbi.nlm.nih.gov/gene/?term=98415	"2700010L10Rik, 8430423A01Rik, AI647518, C78391, Nucks "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026599	9842	PLEKHM1	http://www.ncbi.nlm.nih.gov/gene/?term=9842	"AP162, B2, OPTB6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026600	9843	HEPH	http://www.ncbi.nlm.nih.gov/gene/?term=9843	CPL	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026601	9843	HEPH	http://www.ncbi.nlm.nih.gov/gene/?term=9843	CPL	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026602	9844	ELMO1	http://www.ncbi.nlm.nih.gov/gene/?term=9844	"CED-12, CED12, ELMO-1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026603	9847	C2CD5	http://www.ncbi.nlm.nih.gov/gene/?term=9847	"CDP138, KIAA0528 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026604	9849	ZNF518A	http://www.ncbi.nlm.nih.gov/gene/?term=9849	ZNF518	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026605	9849	ZNF518A	http://www.ncbi.nlm.nih.gov/gene/?term=9849	ZNF518	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026606	9853	RUSC2	http://www.ncbi.nlm.nih.gov/gene/?term=9853	Iporin	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026607	9854	C2CD2L	http://www.ncbi.nlm.nih.gov/gene/?term=9854	"DLNB23, TMEM24 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026608	9857	CEP350	http://www.ncbi.nlm.nih.gov/gene/?term=9857	"CAP350, GM133 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026609	9857	CEP350	http://www.ncbi.nlm.nih.gov/gene/?term=9857	"CAP350, GM133 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026610	9858	PPP1R26	http://www.ncbi.nlm.nih.gov/gene/?term=9858	KIAA0649	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026611	9858	PPP1R26	http://www.ncbi.nlm.nih.gov/gene/?term=9858	KIAA0649	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026612	9859	CEP170	http://www.ncbi.nlm.nih.gov/gene/?term=9859	"FAM68A, KAB, KIAA0470 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026613	9859	CEP170	http://www.ncbi.nlm.nih.gov/gene/?term=9859	"FAM68A, KAB, KIAA0470 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026614	9860	LRIG2	http://www.ncbi.nlm.nih.gov/gene/?term=9860	"LIG-2, LIG2, UFS2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026615	9860	LRIG2	http://www.ncbi.nlm.nih.gov/gene/?term=9860	"LIG-2, LIG2, UFS2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026616	9861	PSMD6	http://www.ncbi.nlm.nih.gov/gene/?term=9861	"Rpn7, S10, SGA-113M, p42A, p44S10 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026617	9862	MED24	http://www.ncbi.nlm.nih.gov/gene/?term=9862	"ARC100, CRSP100, CRSP4, DRIP100, MED5, THRAP4, TRAP100 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026618	9862	MED24	http://www.ncbi.nlm.nih.gov/gene/?term=9862	"ARC100, CRSP100, CRSP4, DRIP100, MED5, THRAP4, TRAP100 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026619	9867	PJA2	http://www.ncbi.nlm.nih.gov/gene/?term=9867	"Neurodap1, RNF131 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026620	9867	PJA2	http://www.ncbi.nlm.nih.gov/gene/?term=9867	"Neurodap1, RNF131 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026621	98685	Trmt1l	http://www.ncbi.nlm.nih.gov/gene/?term=98685	"1190005F20Rik, AW226554, C1orf25, Trm1-like, Trm1l "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026622	9868	TOMM70	http://www.ncbi.nlm.nih.gov/gene/?term=9868	"TOMM70A, Tom70 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026623	9868	TOMM70	http://www.ncbi.nlm.nih.gov/gene/?term=9868		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026624	9869	SETDB1	http://www.ncbi.nlm.nih.gov/gene/?term=9869	"ESET, H3-K9-HMTase4, KG1T, KMT1E, TDRD21 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026625	9870	AREL1	http://www.ncbi.nlm.nih.gov/gene/?term=9870	KIAA0317	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026626	9870	AREL1	http://www.ncbi.nlm.nih.gov/gene/?term=9870	KIAA0317	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026627	98711	Rdh10	http://www.ncbi.nlm.nih.gov/gene/?term=98711	"3110069K09Rik, 4921506A21Rik, AI875664, AW549993, D1Ertd762e, m366Asp "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026628	9871	SEC24D	http://www.ncbi.nlm.nih.gov/gene/?term=9871	CLCRP2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026629	9871	SEC24D	http://www.ncbi.nlm.nih.gov/gene/?term=9871	CLCRP2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026630	98732	Rab3gap2	http://www.ncbi.nlm.nih.gov/gene/?term=98732	"1110059F07Rik, 2010002H18Rik, 5830469C09, AI851069, AW743433, RAB3-GAP150, mKIAA0839 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026631	98733	Obsl1	http://www.ncbi.nlm.nih.gov/gene/?term=98733	AW822216	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026632	9873	FCHSD2	http://www.ncbi.nlm.nih.gov/gene/?term=9873	"NWK, SH3MD3 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026633	9874	TLK1	http://www.ncbi.nlm.nih.gov/gene/?term=9874	PKU-beta	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026634	98758	Hnrnpf	http://www.ncbi.nlm.nih.gov/gene/?term=98758	"4833420I20Rik, AA407306, Hnrpf "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026635	9875	URB1	http://www.ncbi.nlm.nih.gov/gene/?term=9875	"C21orf108, NPA1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026636	9875	URB1	http://www.ncbi.nlm.nih.gov/gene/?term=9875	"C21orf108, NPA1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026637	9877	ZC3H11A	http://www.ncbi.nlm.nih.gov/gene/?term=9877	ZC3HDC11A	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026638	9877	ZC3H11A	http://www.ncbi.nlm.nih.gov/gene/?term=9877	ZC3HDC11A	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026639	9878	TOX4	http://www.ncbi.nlm.nih.gov/gene/?term=9878	"C14orf92, KIAA0737, LCP1, MIG7 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026640	9878	TOX4	http://www.ncbi.nlm.nih.gov/gene/?term=9878	"C14orf92, KIAA0737, LCP1, MIG7 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026641	9878	TOX4	http://www.ncbi.nlm.nih.gov/gene/?term=9878	"C14orf92, KIAA0737, LCP1, MIG7 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026642	9879	DDX46	http://www.ncbi.nlm.nih.gov/gene/?term=9879	"PRPF5, Prp5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026643	987	LRBA	http://www.ncbi.nlm.nih.gov/gene/?term=987	"BGL, CDC4L, CVID8, LAB300, LBA "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026644	987	LRBA	http://www.ncbi.nlm.nih.gov/gene/?term=987	"BGL, CDC4L, CVID8, LAB300, LBA "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026645	9880	ZBTB39	http://www.ncbi.nlm.nih.gov/gene/?term=9880	ZNF922	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026646	9881	TRANK1	http://www.ncbi.nlm.nih.gov/gene/?term=9881	LBA1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026647	9882	TBC1D4	http://www.ncbi.nlm.nih.gov/gene/?term=9882	"AS160, NIDDM5 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026648	9882	TBC1D4	http://www.ncbi.nlm.nih.gov/gene/?term=9882	"AS160, NIDDM5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026649	9883	POM121	http://www.ncbi.nlm.nih.gov/gene/?term=9883	"P145, POM121A "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026650	9885	OSBPL2	http://www.ncbi.nlm.nih.gov/gene/?term=9885	"DFNA67, DNFA67, ORP-2, ORP2 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026651	9885	OSBPL2	http://www.ncbi.nlm.nih.gov/gene/?term=9885	"DFNA67, DNFA67, ORP-2, ORP2 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026652	9885	OSBPL2	http://www.ncbi.nlm.nih.gov/gene/?term=9885	"DFNA67, DNFA67, ORP-2, ORP2 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026653	9886	RHOBTB1	http://www.ncbi.nlm.nih.gov/gene/?term=9886		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026654	98878	Ehd4	http://www.ncbi.nlm.nih.gov/gene/?term=98878	"2210022F10Rik, AI197390, AI846352, AV006278, Past2 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026655	9887	SMG7	http://www.ncbi.nlm.nih.gov/gene/?term=9887	"C1orf16, EST1C, SGA56M "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026656	9887	SMG7	http://www.ncbi.nlm.nih.gov/gene/?term=9887	"C1orf16, EST1C, SGA56M "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026657	9887	SMG7	http://www.ncbi.nlm.nih.gov/gene/?term=9887	"C1orf16, EST1C, SGA56M "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026658	988	CDC5L	http://www.ncbi.nlm.nih.gov/gene/?term=988	"CDC5, CDC5-LIKE, CEF1, PCDC5RP, dJ319D22.1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026659	988	CDC5L	http://www.ncbi.nlm.nih.gov/gene/?term=988	"CDC5, CDC5-LIKE, CEF1, PCDC5RP, dJ319D22.1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026660	988	CDC5L	http://www.ncbi.nlm.nih.gov/gene/?term=988	"CDC5, CDC5-LIKE, CEF1, PCDC5RP, dJ319D22.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026661	9894	TELO2	http://www.ncbi.nlm.nih.gov/gene/?term=9894	"CLK2, TEL2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026662	9895	TECPR2	http://www.ncbi.nlm.nih.gov/gene/?term=9895	"KIAA0329, SPG49 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026663	9896	FIG4	http://www.ncbi.nlm.nih.gov/gene/?term=9896	"ALS11, BTOP, CMT4J, KIAA0274, SAC3, YVS, dJ249I4.1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026664	9897	KIAA0196	http://www.ncbi.nlm.nih.gov/gene/?term=9897	"RTSC, RTSC1, SPG8 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026665	9897	KIAA0196	http://www.ncbi.nlm.nih.gov/gene/?term=9897	"RTSC, RTSC1, SPG8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026666	9897	KIAA0196	http://www.ncbi.nlm.nih.gov/gene/?term=9897	"RTSC, RTSC1, SPG8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026667	9897	KIAA0196	http://www.ncbi.nlm.nih.gov/gene/?term=9897	"RTSC, RTSC1, SPG8 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026668	98985	Clp1	http://www.ncbi.nlm.nih.gov/gene/?term=98985	"AI462438, Heab "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026669	9898	UBAP2L	http://www.ncbi.nlm.nih.gov/gene/?term=9898	"NICE-4, NICE4 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026670	9898	UBAP2L	http://www.ncbi.nlm.nih.gov/gene/?term=9898	"NICE-4, NICE4 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026671	9899	SV2B	http://www.ncbi.nlm.nih.gov/gene/?term=9899	HsT19680	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026672	98	ACYP2	http://www.ncbi.nlm.nih.gov/gene/?term=98	"ACYM, ACYP "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026673	99003	Qser1	http://www.ncbi.nlm.nih.gov/gene/?term=99003	"4732486I23Rik, AI502974 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026674	9901	SRGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=9901	"ARHGAP14, MEGAP, SRGAP2, WRP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026675	9902	MRC2	http://www.ncbi.nlm.nih.gov/gene/?term=9902	"CD280, CLEC13E, ENDO180, UPARAP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026676	99031	Osbpl6	http://www.ncbi.nlm.nih.gov/gene/?term=99031	"1110062M20Rik, AI596402, ORP-6, mKIAA4128 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026677	9903	KLHL21	http://www.ncbi.nlm.nih.gov/gene/?term=9903		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026678	99045	Mrps26	http://www.ncbi.nlm.nih.gov/gene/?term=99045	"AI648866, GI008, MRP-S13, MRP-S26, Rpms13 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026679	9905	SGSM2	http://www.ncbi.nlm.nih.gov/gene/?term=9905	RUTBC1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026680	9908	G3BP2	http://www.ncbi.nlm.nih.gov/gene/?term=9908		mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026681	9908	G3BP2	http://www.ncbi.nlm.nih.gov/gene/?term=9908		mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026682	9908	G3BP2	http://www.ncbi.nlm.nih.gov/gene/?term=9908		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026683	9909	DENND4B	http://www.ncbi.nlm.nih.gov/gene/?term=9909	KIAA0476	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026684	990	CDC6	http://www.ncbi.nlm.nih.gov/gene/?term=990	"CDC18L, HsCDC18, HsCDC6 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026685	990	CDC6	http://www.ncbi.nlm.nih.gov/gene/?term=990	"CDC18L, HsCDC18, HsCDC6 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026686	990	CDC6	http://www.ncbi.nlm.nih.gov/gene/?term=990	"CDC18L, HsCDC18, HsCDC6 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026687	990	CDC6	http://www.ncbi.nlm.nih.gov/gene/?term=990	"CDC18L, HsCDC18, HsCDC6 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026688	990	CDC6	http://www.ncbi.nlm.nih.gov/gene/?term=990	"CDC18L, HsCDC18, HsCDC6 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026689	9910	RABGAP1L	http://www.ncbi.nlm.nih.gov/gene/?term=9910	"HHL, TBC1D18 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026690	9910	RABGAP1L	http://www.ncbi.nlm.nih.gov/gene/?term=9910	"HHL, TBC1D18 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026691	99138	Stard7	http://www.ncbi.nlm.nih.gov/gene/?term=99138	"AI852671, AL022671, AW544915 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026692	9913	SUPT7L	http://www.ncbi.nlm.nih.gov/gene/?term=9913	"SPT7L, STAF65, STAF65(gamma), STAF65G, SUPT7H "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026693	9913	SUPT7L	http://www.ncbi.nlm.nih.gov/gene/?term=9913	"SPT7L, STAF65, STAF65(gamma), STAF65G, SUPT7H "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026694	9913	SUPT7L	http://www.ncbi.nlm.nih.gov/gene/?term=9913	"SPT7L, STAF65, STAF65(gamma), STAF65G, SUPT7H "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026695	9913	SUPT7L	http://www.ncbi.nlm.nih.gov/gene/?term=9913	"SPT7L, STAF65, STAF65(gamma), STAF65G, SUPT7H "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026696	9914	ATP2C2	http://www.ncbi.nlm.nih.gov/gene/?term=9914	SPCA2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026697	9915	ARNT2	http://www.ncbi.nlm.nih.gov/gene/?term=9915	"WEDAS, bHLHe1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026698	99167	Ssx2ip	http://www.ncbi.nlm.nih.gov/gene/?term=99167	"AU014939, AU042321, Adip "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026699	9917	FAM20B	http://www.ncbi.nlm.nih.gov/gene/?term=9917	gxk1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026700	9917	FAM20B	http://www.ncbi.nlm.nih.gov/gene/?term=9917	gxk1	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026701	9917	FAM20B	http://www.ncbi.nlm.nih.gov/gene/?term=9917	gxk1	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026702	9917	FAM20B	http://www.ncbi.nlm.nih.gov/gene/?term=9917	gxk1	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026703	9918	NCAPD2	http://www.ncbi.nlm.nih.gov/gene/?term=9918	"CAP-D2, CNAP1, hCAP-D2 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026704	9919	SEC16A	http://www.ncbi.nlm.nih.gov/gene/?term=9919	"KIAA0310, SEC16L, p250 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026705	9919	SEC16A	http://www.ncbi.nlm.nih.gov/gene/?term=9919	"KIAA0310, SEC16L, p250 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026706	991	CDC20	http://www.ncbi.nlm.nih.gov/gene/?term=991	"CDC20A, bA276H19.3, p55CDC "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026707	9921	RNF10	http://www.ncbi.nlm.nih.gov/gene/?term=9921	RIE2	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026708	9921	RNF10	http://www.ncbi.nlm.nih.gov/gene/?term=9921	RIE2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026709	9923	ZBTB40	http://www.ncbi.nlm.nih.gov/gene/?term=9923	ZNF923	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026710	9923	ZBTB40	http://www.ncbi.nlm.nih.gov/gene/?term=9923	ZNF923	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026711	9923	ZBTB40	http://www.ncbi.nlm.nih.gov/gene/?term=9923	ZNF923	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026712	9924	PAN2	http://www.ncbi.nlm.nih.gov/gene/?term=9924	USP52	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026713	9925	ZBTB5	http://www.ncbi.nlm.nih.gov/gene/?term=9925		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026714	9926	LPGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=9926	"FAM34A, FAM34A1, NET8 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026715	9926	LPGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=9926	"FAM34A, FAM34A1, NET8 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026716	9926	LPGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=9926	"FAM34A, FAM34A1, NET8 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026717	9926	LPGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=9926	"FAM34A, FAM34A1, NET8 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026718	9927	MFN2	http://www.ncbi.nlm.nih.gov/gene/?term=9927	"CMT2A, CMT2A2, CPRP1, HMSN6A, HSG, MARF "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026719	9928	KIF14	http://www.ncbi.nlm.nih.gov/gene/?term=9928	MKS12	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026720	9928	KIF14	http://www.ncbi.nlm.nih.gov/gene/?term=9928	MKS12	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026721	9929	JOSD1	http://www.ncbi.nlm.nih.gov/gene/?term=9929	dJ508I15.2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026722	9929	JOSD1	http://www.ncbi.nlm.nih.gov/gene/?term=9929	dJ508I15.2	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026723	9929	JOSD1	http://www.ncbi.nlm.nih.gov/gene/?term=9929	dJ508I15.2	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026724	9929	JOSD1	http://www.ncbi.nlm.nih.gov/gene/?term=9929	dJ508I15.2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026725	9931	HELZ	http://www.ncbi.nlm.nih.gov/gene/?term=9931	"DHRC, DRHC, HUMORF5 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026726	9931	HELZ	http://www.ncbi.nlm.nih.gov/gene/?term=9931	"DHRC, DRHC, HUMORF5 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026727	9931	HELZ	http://www.ncbi.nlm.nih.gov/gene/?term=9931	"DHRC, DRHC, HUMORF5 "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026728	9931	HELZ	http://www.ncbi.nlm.nih.gov/gene/?term=9931	"DHRC, DRHC, HUMORF5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026729	9933	PUM3	http://www.ncbi.nlm.nih.gov/gene/?term=9933	"HA-8, HLA-HA8, KIAA0020, PEN, PUF-A, PUF6, XTP5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026730	9936	CD302	http://www.ncbi.nlm.nih.gov/gene/?term=9936	"BIMLEC, CLEC13A, DCL-1, DCL1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026731	99375	Cul4a	http://www.ncbi.nlm.nih.gov/gene/?term=99375	"2810470J21Rik, AW495282 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026732	9937	DCLRE1A	http://www.ncbi.nlm.nih.gov/gene/?term=9937	"PSO2, SNM1, SNM1A "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026733	9937	DCLRE1A	http://www.ncbi.nlm.nih.gov/gene/?term=9937	"PSO2, SNM1, SNM1A "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026734	99382	Abtb2	http://www.ncbi.nlm.nih.gov/gene/?term=99382	"AW539457, BPOZ-2 "	mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026735	9939	RBM8A	http://www.ncbi.nlm.nih.gov/gene/?term=9939	"BOV-1A, BOV-1B, BOV-1C, C1DELq21.1, DEL1q21.1, MDS014, RBM8, RBM8B, TAR, Y14, ZNRP, ZRNP1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026736	9939	RBM8A	http://www.ncbi.nlm.nih.gov/gene/?term=9939	"BOV-1A, BOV-1B, BOV-1C, C1DELq21.1, DEL1q21.1, MDS014, RBM8, RBM8B, TAR, Y14, ZNRP, ZRNP1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026737	993	CDC25A	http://www.ncbi.nlm.nih.gov/gene/?term=993	CDC25A2	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026738	993	CDC25A	http://www.ncbi.nlm.nih.gov/gene/?term=993	CDC25A2	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026739	99413	AW555355	http://www.ncbi.nlm.nih.gov/gene/?term=99413		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026740	99413	AW555355	http://www.ncbi.nlm.nih.gov/gene/?term=99413		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026741	9943	OXSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9943	OSR1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026742	9943	OXSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9943	OSR1	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026743	9943	OXSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9943	OSR1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026744	99458	BB166591	http://www.ncbi.nlm.nih.gov/gene/?term=99458		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026745	99470	Magi3	http://www.ncbi.nlm.nih.gov/gene/?term=99470	"4732496O19Rik, 6530407C02Rik, AA407180, AI120132, mKIAA1634 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026746	99480	Dnttip2	http://www.ncbi.nlm.nih.gov/gene/?term=99480	"4930588M11Rik, AA408582, AU014960, HSU15552 "	mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026747	9948	WDR1	http://www.ncbi.nlm.nih.gov/gene/?term=9948	"AIP1, HEL-S-52, NORI-1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026748	9949	AMMECR1	http://www.ncbi.nlm.nih.gov/gene/?term=9949	AMMERC1	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026749	9949	AMMECR1	http://www.ncbi.nlm.nih.gov/gene/?term=9949	AMMERC1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026750	994	CDC25B	http://www.ncbi.nlm.nih.gov/gene/?term=994		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026751	994	CDC25B	http://www.ncbi.nlm.nih.gov/gene/?term=994		mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026752	9953	HS3ST3B1	http://www.ncbi.nlm.nih.gov/gene/?term=9953	"3-OST-3B, 3OST3B1, h3-OST-3B "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026753	9955	HS3ST3A1	http://www.ncbi.nlm.nih.gov/gene/?term=9955	"3-OST-3A, 3OST3A1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026754	99586	Dpyd	http://www.ncbi.nlm.nih.gov/gene/?term=99586	"AI315208, DPD, E330028L06Rik "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026755	9958	USP15	http://www.ncbi.nlm.nih.gov/gene/?term=9958	"UNPH-2, UNPH4 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026756	9958	USP15	http://www.ncbi.nlm.nih.gov/gene/?term=9958	"UNPH-2, UNPH4 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026757	995	CDC25C	http://www.ncbi.nlm.nih.gov/gene/?term=995	"CDC25, PPP1R60 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026758	995	CDC25C	http://www.ncbi.nlm.nih.gov/gene/?term=995	"CDC25, PPP1R60 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026759	9960	USP3	http://www.ncbi.nlm.nih.gov/gene/?term=9960	"SIH003, UBP "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026760	9961	MVP	http://www.ncbi.nlm.nih.gov/gene/?term=9961	"LRP, VAULT1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026761	9961	MVP	http://www.ncbi.nlm.nih.gov/gene/?term=9961	"LRP, VAULT1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026762	9962	SLC23A2	http://www.ncbi.nlm.nih.gov/gene/?term=9962	"NBTL1, SLC23A1, SVCT2, YSPL2, hSVCT2 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026763	9962	SLC23A2	http://www.ncbi.nlm.nih.gov/gene/?term=9962	"NBTL1, SLC23A1, SVCT2, YSPL2 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026764	99633	Adgrl2	http://www.ncbi.nlm.nih.gov/gene/?term=99633	"AI450192, CIRL-2, Gm619, Lec1, Lphh1, Lphn2, mKIAA0786 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026765	9967	THRAP3	http://www.ncbi.nlm.nih.gov/gene/?term=9967	TRAP150	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026766	9967	THRAP3	http://www.ncbi.nlm.nih.gov/gene/?term=9967	TRAP150	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026767	99683	Sec24b	http://www.ncbi.nlm.nih.gov/gene/?term=99683	"AI605202, SEC24 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026768	9968	MED12	http://www.ncbi.nlm.nih.gov/gene/?term=9968	"ARC240, CAGH45, FGS1, HOPA, MED12S, OHDOX, OKS, OPA1, TNRC11, TRAP230 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026769	9969	MED13	http://www.ncbi.nlm.nih.gov/gene/?term=9969	"ARC250, DRIP250, HSPC221, THRAP1, TRAP240 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026770	9969	MED13	http://www.ncbi.nlm.nih.gov/gene/?term=9969	"ARC250, DRIP250, HSPC221, THRAP1, TRAP240 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026771	996	CDC27	http://www.ncbi.nlm.nih.gov/gene/?term=996	"ANAPC3, APC3Hs, D0S1430E, D17S978E, H-NUC, HNUC, NUC2, CDC27 "	mRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026772	996	CDC27	http://www.ncbi.nlm.nih.gov/gene/?term=996	"ANAPC3, APC3Hs, D0S1430E, D17S978E, H-NUC, HNUC, NUC2, CDC27 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026773	996	CDC27	http://www.ncbi.nlm.nih.gov/gene/?term=996	"ANAPC3, APC3, CDC27Hs, D0S1430E, D17S978E, H-NUC, HNUC, NUC2 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026774	99712	Cept1	http://www.ncbi.nlm.nih.gov/gene/?term=99712	"9930118K05Rik, mCEPT1 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026775	9972	NUP153	http://www.ncbi.nlm.nih.gov/gene/?term=9972	"HNUP153, N153 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026776	9972	NUP153	http://www.ncbi.nlm.nih.gov/gene/?term=9972	"HNUP153, N153 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026777	99730	Taf13	http://www.ncbi.nlm.nih.gov/gene/?term=99730	"1810004N01Rik, 2010309N11Rik, AI847295, TAFII18 "	mRNA	Mus musculus	24152552	Axon	Motorneuron 	Microarray	"To identify SMN-associated mRNAs in these repertoires, we compared our microarray data with the transcriptome analyses of (1) axons from dorsal root ganglion neurons (Willis et al. 2007), (2) uninjured and regenerating cortical axons (Taylor et al. 2009), and (3) embryonic and adult sensory axons (Gumy et al. 2011). This identified 75 localized mRNAs present in SMN complexes (Fig. 4). Data are collected from Figure 4: SMN interacts with a subset of mRNAs known to be localized in axons.  "
RLID00026778	9973	CCS	http://www.ncbi.nlm.nih.gov/gene/?term=9973		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026779	9975	NR1D2	http://www.ncbi.nlm.nih.gov/gene/?term=9975	"BD73, EAR-1R, RVR "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026780	9975	NR1D2	http://www.ncbi.nlm.nih.gov/gene/?term=9975	"BD73, EAR-1R, RVR "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026781	9976	CLEC2B	http://www.ncbi.nlm.nih.gov/gene/?term=9976	"AICL, CLECSF2, HP10085, IFNRG1 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026782	9978	RBX1	http://www.ncbi.nlm.nih.gov/gene/?term=9978	"BA554C12.1, RNF75, ROC1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026783	9978	RBX1	http://www.ncbi.nlm.nih.gov/gene/?term=9978	"BA554C12.1, RNF75, ROC1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026784	9978	RBX1	http://www.ncbi.nlm.nih.gov/gene/?term=9978	"BA554C12.1, RNF75, ROC1 "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026785	9978	RBX1	http://www.ncbi.nlm.nih.gov/gene/?term=9978	"BA554C12.1, RNF75, ROC1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026786	997	CDC34	http://www.ncbi.nlm.nih.gov/gene/?term=997	"E2-CDC34, UBC3, UBCH3, UBE2R1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026787	997	CDC34	http://www.ncbi.nlm.nih.gov/gene/?term=997	"E2-CDC34, UBC3, UBCH3, UBE2R1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026788	9982	FGFBP1	http://www.ncbi.nlm.nih.gov/gene/?term=9982	"FGF-BP, FGF-BP1, FGFBP, FGFBP-1, HBP17 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026789	9984	THOC1	http://www.ncbi.nlm.nih.gov/gene/?term=9984	"HPR1, P84, P84N5 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026790	9986	RCE1	http://www.ncbi.nlm.nih.gov/gene/?term=9986	"FACE2A, RCE1B, RCE1 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026791	9987	HNRNPDL	http://www.ncbi.nlm.nih.gov/gene/?term=9987	"HNRNP, HNRPDL, JKTBP, JKTBP2, LGMD1G, laAUF1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026792	9987	HNRNPDL	http://www.ncbi.nlm.nih.gov/gene/?term=9987	"HNRNP, HNRPDL, JKTBP, JKTBP2, LGMD1G, laAUF1 "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026793	9987	HNRNPDL	http://www.ncbi.nlm.nih.gov/gene/?term=9987	"HNRNP, HNRPDL, JKTBP, JKTBP2, LGMD1G, laAUF1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026794	99889	Arfip1	http://www.ncbi.nlm.nih.gov/gene/?term=99889	"2310030I10Rik, Arfaptin, D3Ertd598e "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026795	9988	DMTF1	http://www.ncbi.nlm.nih.gov/gene/?term=9988	"DMP1, DMTF, MRUL, hDMP1 "	mRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026796	9989	PPP4R1	http://www.ncbi.nlm.nih.gov/gene/?term=9989	"MEG1, PP4(Rmeg), PP4R1 "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026797	998	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=998	"CDC42Hs, G25K, TKS "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026798	998	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=998	"CDC42Hs, G25K, TKS "	mRNA	Homo sapiens	22199352	Ribosome	HEK293 cell	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00026799	998	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=998	"CDC42Hs, G25K, TKS "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026800	998	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=998	"CDC42Hs, G25K, TKS "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026801	998	CDC42	http://www.ncbi.nlm.nih.gov/gene/?term=998	"CDC42Hs, G25K, TKS "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026802	9990	SLC12A6	http://www.ncbi.nlm.nih.gov/gene/?term=9990	"ACCPN, KCC3, KCC3A, KCC3B "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026803	9990	SLC12A6	http://www.ncbi.nlm.nih.gov/gene/?term=9990	"ACCPN, KCC3, KCC3A, KCC3B "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026804	9991	PTBP3	http://www.ncbi.nlm.nih.gov/gene/?term=9991	ROD1	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026805	99929	Tiparp	http://www.ncbi.nlm.nih.gov/gene/?term=99929	"ARTD14, AW558171, PARP7 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026806	9993	DGCR2	http://www.ncbi.nlm.nih.gov/gene/?term=9993	"DGS-C, IDD, LAN, SEZ-12 "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026807	9993	DGCR2	http://www.ncbi.nlm.nih.gov/gene/?term=9993	"DGS-C, IDD, LAN, SEZ-12 "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026808	9994	CASP8AP2	http://www.ncbi.nlm.nih.gov/gene/?term=9994	"CED-4, FLASH, RIP25 "	lncRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026809	9997	SCO2	http://www.ncbi.nlm.nih.gov/gene/?term=9997	"CEMCOX1, MYP6, SCO1L "	mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00026810	99982	Kdm1a	http://www.ncbi.nlm.nih.gov/gene/?term=99982	"1810043O07Rik, AA408884, Aof2, D4Ertd478e, Kdm1, Lsd1, mKIAA0601 "	mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026811	999	CDH1	http://www.ncbi.nlm.nih.gov/gene/?term=999	"Arc-1, CD324, CDHE, ECAD, LCAM, UVO "	mRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026812	999	CDH1	http://www.ncbi.nlm.nih.gov/gene/?term=999	"Arc-1, CD324, CDHE, ECAD, LCAM, UVO "	mRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00026813	999	CDH1	http://www.ncbi.nlm.nih.gov/gene/?term=999	"Arc-1, CD324, CDHE, ECAD, LCAM, UVO "	mRNA	Homo sapiens	21613539	Endoplasmic reticulum	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026814	9	NAT1	http://www.ncbi.nlm.nih.gov/gene/?term=9	"AAC1, MNAT, NAT-1, NATI "	mRNA	Homo sapiens	21613539	Cytosol	Myeloma cell	qRT-PCR	"The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, and mRNAs encoding topogenic signal-bearing proteins are translated on ER-bound ribosomes, with ER localization being conferred by the signal-recognition particle pathway. Data are collected from Supplemental Data - The gene lists selected by the described GO categories are listed. Gene ID and subcellular distribution values, in log2 as well as fractional ER enrichment are listed.  "
RLID00026815	AA153229	AA153229	http://www.ncbi.nlm.nih.gov/nuccore/AA153229		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026816	AA413531	AA413531	http://www.ncbi.nlm.nih.gov/nuccore/AA413531		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026817	AA690930	AA690930	http://www.ncbi.nlm.nih.gov/nuccore/AA690930		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026818	AA798895	AA798895	http://www.ncbi.nlm.nih.gov/nuccore/AA798895		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026819	AB048287	AB048287	http://www.ncbi.nlm.nih.gov/nuccore/AB048287		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00026820	AB055854	AB055854	http://www.ncbi.nlm.nih.gov/nuccore/AB055854		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026821	AB116666	Khps1	http://www.ncbi.nlm.nih.gov/nuccore/AB116666		lncRNA	Rattus norvegicus	15325271	Cytoplasm	Liver|Brain	In situ hybridization|Northern blot	"The expression of Khps1 in the primary cell culture preparation from rat fetuses was investigated (Fig. 2D). Expression was detected in the cytoplasm as well as nuclei in some cells, indicating that Khps1 is exported to the cytoplasm. "
RLID00026822	AB116666	Khps1	http://www.ncbi.nlm.nih.gov/nuccore/AB116666		lncRNA	Rattus norvegicus	15325271	Nucleus	Liver|Brain	In situ hybridization|Northern blot	"The expression of Khps1 in the primary cell culture preparation from rat fetuses was investigated (Fig. 2D). Expression was detected in the cytoplasm as well as nuclei in some cells, indicating that Khps1 is exported to the cytoplasm. "
RLID00026823	AC008472	Alpha-250	http://www.ncbi.nlm.nih.gov/nuccore/AC008472		lncRNA	Homo sapiens	7867928	Cytoplasm	HeLa cell	Binding assays	"Although alpha-280 is detected among both the cells' nuclear and cytoplasmic RNAs, the great majority of alpha-250 is found in the cytoplasmic subcellular compartment. "
RLID00026824	AC008472	Alpha-280	http://www.ncbi.nlm.nih.gov/nuccore/AC008472		lncRNA	Homo sapiens	7867928	Nucleus	HeLa cell	Binding assays	"Although alpha-280 is detected among both the cells' nuclear and cytoplasmic RNAs, the great majority of alpha-250 is found in the cytoplasmic subcellular compartment. As judged by its resistance to high concentrations of alpha-amanitin, cell-free transcription of alpha-250 and alpha-280 appears to involve RNA polymerase I. Tissue culture transfection and cell-free transcription experiments demonstrate that alpha-250 and alpha-280 stimulate S14 mRNA transcription, whereas free ribosomal protein S14 inhibits it. "
RLID00026825	AC008472	Alpha-280	http://www.ncbi.nlm.nih.gov/nuccore/AC008472		lncRNA	Homo sapiens	7867928	Cytoplasm	HeLa cell	Binding assays	"Although alpha-280 is detected among both the cells' nuclear and cytoplasmic RNAs, the great majority of alpha-250 is found in the cytoplasmic subcellular compartment. As judged by its resistance to high concentrations of alpha-amanitin, cell-free transcription of alpha-250 and alpha-280 appears to involve RNA polymerase I. Tissue culture transfection and cell-free transcription experiments demonstrate that alpha-250 and alpha-280 stimulate S14 mRNA transcription, whereas free ribosomal protein S14 inhibits it. "
RLID00026826	AF085738	AF085738	http://www.ncbi.nlm.nih.gov/nuccore/AF085738		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026827	AF145043	AF145043	http://www.ncbi.nlm.nih.gov/nuccore/?term=AF145043	Nerve growth factor(NGF) 	mRNA	Cervus elaphus	17215957	Axon	Antler	In situ hybridization|Northern blot	Denervation experiments suggested a causal relationship exists between NGF mRNA expression in arterial smooth muscle and sensory axons in the antler tip.
RLID00026828	AI118114	AI118114	http://www.ncbi.nlm.nih.gov/nuccore/AI118114		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026829	AI326469	AI326469	http://www.ncbi.nlm.nih.gov/nuccore/AI326469		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026830	AI414004	AI414004	http://www.ncbi.nlm.nih.gov/nuccore/AI414004		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026831	AI447935	AI447935	http://www.ncbi.nlm.nih.gov/nuccore/AI447935		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026832	AI448156	AI448156	http://www.ncbi.nlm.nih.gov/nuccore/AI448156		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026833	AI481875	AI481875	http://www.ncbi.nlm.nih.gov/nuccore/AI481875		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026834	AI506532	AI506532	http://www.ncbi.nlm.nih.gov/nuccore/AI506532		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026835	AI506565	AI506565	http://www.ncbi.nlm.nih.gov/nuccore/AI506565		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026836	AI506888	AI506888	http://www.ncbi.nlm.nih.gov/nuccore/AI506888		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026837	AI585789	AI585789	http://www.ncbi.nlm.nih.gov/nuccore/AI585789		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026838	AI585995	AI585995	http://www.ncbi.nlm.nih.gov/nuccore/AI585995		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026839	AI606070	AI606070	http://www.ncbi.nlm.nih.gov/nuccore/AI606070		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026840	AI643819	AI643819	http://www.ncbi.nlm.nih.gov/nuccore/AI643819		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026841	AI648759	AI648759	http://www.ncbi.nlm.nih.gov/nuccore/AI648759		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026842	AI843353	AI843353	http://www.ncbi.nlm.nih.gov/nuccore/AI843353		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026843	AJ409505	AJ409505	http://www.ncbi.nlm.nih.gov/nuccore/AJ409505		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026844	AK003956	AK003956	http://www.ncbi.nlm.nih.gov/nuccore/?term=AK003956		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00026845	AK006399	AK006399	http://www.ncbi.nlm.nih.gov/nuccore/AK006399		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026846	AK006751	AK006751	http://www.ncbi.nlm.nih.gov/nuccore/AK006751		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026847	AK012243	AK012243	http://www.ncbi.nlm.nih.gov/nuccore/AK012243		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026848	AK013287	AK013287	http://www.ncbi.nlm.nih.gov/nuccore/?term=AK013287		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00026849	AK013702	AK013702	http://www.ncbi.nlm.nih.gov/nuccore/AK013702		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026850	AK015332	AK015332	http://www.ncbi.nlm.nih.gov/nuccore/AK015332		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026851	AK015425	AK015425	http://www.ncbi.nlm.nih.gov/nuccore/AK015425		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00026852	AK016846	AK016846	http://www.ncbi.nlm.nih.gov/nuccore/AK016846		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026853	AK020545	AK020545	http://www.ncbi.nlm.nih.gov/nuccore/AK020545		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026854	AK021084	AK021084	http://www.ncbi.nlm.nih.gov/nuccore/AK021084		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026855	AK028006	AK028006	http://www.ncbi.nlm.nih.gov/nuccore/AK028006		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026856	AK029643	AK029643	http://www.ncbi.nlm.nih.gov/nuccore/AK029643		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026857	AK031372	AK031372	http://www.ncbi.nlm.nih.gov/nuccore/AK031372		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026858	AK032119	AK032119	http://www.ncbi.nlm.nih.gov/nuccore/AK032119		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026859	AK032198	AK032198	http://www.ncbi.nlm.nih.gov/nuccore/AK032198		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026860	AK032433	AK032433	http://www.ncbi.nlm.nih.gov/nuccore/AK032433		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026861	AK032710	AK032710	http://www.ncbi.nlm.nih.gov/nuccore/AK032710		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026862	AK032810	AK032810	http://www.ncbi.nlm.nih.gov/nuccore/AK032810		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026863	AK032971	AK032971	http://www.ncbi.nlm.nih.gov/nuccore/AK032971		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026864	AK033359	AK033359	http://www.ncbi.nlm.nih.gov/nuccore/AK033359		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026865	AK033546	AK033546	http://www.ncbi.nlm.nih.gov/nuccore/AK033546		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026866	AK033881	AK033881	http://www.ncbi.nlm.nih.gov/nuccore/AK033881		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026867	AK034929	AK034929	http://www.ncbi.nlm.nih.gov/nuccore/AK034929		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026868	AK035021	AK035021	http://www.ncbi.nlm.nih.gov/nuccore/AK035021		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026869	AK035820	AK035820	http://www.ncbi.nlm.nih.gov/nuccore/AK035820		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026870	AK037080	AK037080	http://www.ncbi.nlm.nih.gov/nuccore/AK037080		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026871	AK038908	AK038908	http://www.ncbi.nlm.nih.gov/nuccore/AK038908		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026872	AK039317	AK039317	http://www.ncbi.nlm.nih.gov/nuccore/AK039317		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026873	AK039415	AK039415	http://www.ncbi.nlm.nih.gov/nuccore/AK039415		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026874	AK039687	AK039687	http://www.ncbi.nlm.nih.gov/nuccore/AK039687		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026875	AK039697	AK039697	http://www.ncbi.nlm.nih.gov/nuccore/AK039697		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026876	AK039862	AK039862	http://www.ncbi.nlm.nih.gov/nuccore/AK039862		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026877	AK039914	AK039914	http://www.ncbi.nlm.nih.gov/nuccore/AK039914		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026878	AK040695	AK040695	http://www.ncbi.nlm.nih.gov/nuccore/AK040695		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026879	AK041029	AK041029	http://www.ncbi.nlm.nih.gov/nuccore/AK041029		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026880	AK041105	AK041105	http://www.ncbi.nlm.nih.gov/nuccore/AK041105		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026881	AK041297	AK041297	http://www.ncbi.nlm.nih.gov/nuccore/AK041297		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026882	AK041799	AK041799	http://www.ncbi.nlm.nih.gov/nuccore/AK041799		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026883	AK042227	AK042227	http://www.ncbi.nlm.nih.gov/nuccore/AK042227		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026884	AK042390	AK042390	http://www.ncbi.nlm.nih.gov/nuccore/AK042390		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026885	AK042797	AK042797	http://www.ncbi.nlm.nih.gov/nuccore/AK042797		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026886	AK043453	AK043453	http://www.ncbi.nlm.nih.gov/nuccore/AK043453		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026887	AK043655	AK043655	http://www.ncbi.nlm.nih.gov/nuccore/AK043655		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026888	AK043715	AK043715	http://www.ncbi.nlm.nih.gov/nuccore/AK043715		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026889	AK043785	AK043785	http://www.ncbi.nlm.nih.gov/nuccore/AK043785		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026890	AK044354	AK044354	http://www.ncbi.nlm.nih.gov/nuccore/AK044354		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026891	AK044373	AK044373	http://www.ncbi.nlm.nih.gov/nuccore/AK044373		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026892	AK044844	AK044844	http://www.ncbi.nlm.nih.gov/nuccore/AK044844		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026893	AK045229	AK045229	http://www.ncbi.nlm.nih.gov/nuccore/AK045229		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026894	AK045243	AK045243	http://www.ncbi.nlm.nih.gov/nuccore/AK045243		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026895	AK045559	AK045559	http://www.ncbi.nlm.nih.gov/nuccore/AK045559		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026896	AK046710	AK046710	http://www.ncbi.nlm.nih.gov/nuccore/AK046710		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026897	AK046731	AK046731	http://www.ncbi.nlm.nih.gov/nuccore/AK046731		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026898	AK046917	AK046917	http://www.ncbi.nlm.nih.gov/nuccore/AK046917		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026899	AK047329	AK047329	http://www.ncbi.nlm.nih.gov/nuccore/AK047329		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026900	AK047560	AK047560	http://www.ncbi.nlm.nih.gov/nuccore/AK047560		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026901	AK047744	AK047744	http://www.ncbi.nlm.nih.gov/nuccore/AK047744		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026902	AK047802	AK047802	http://www.ncbi.nlm.nih.gov/nuccore/AK047802		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026903	AK048192	AK048192	http://www.ncbi.nlm.nih.gov/nuccore/AK048192		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026904	AK048225	AK048225	http://www.ncbi.nlm.nih.gov/nuccore/AK048225		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026905	AK048391	AK048391	http://www.ncbi.nlm.nih.gov/nuccore/AK048391		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026906	AK048510	AK048510	http://www.ncbi.nlm.nih.gov/nuccore/AK048510		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026907	AK048712	AK048712	http://www.ncbi.nlm.nih.gov/nuccore/AK048712		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026908	AK049451	AK049451	http://www.ncbi.nlm.nih.gov/nuccore/AK049451		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026909	AK049757	AK049757	http://www.ncbi.nlm.nih.gov/nuccore/AK049757		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026910	AK049962	AK049962	http://www.ncbi.nlm.nih.gov/nuccore/AK049962		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026911	AK050685	AK050685	http://www.ncbi.nlm.nih.gov/nuccore/AK050685		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026912	AK050712	AK050712	http://www.ncbi.nlm.nih.gov/nuccore/AK050712		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026913	AK051340	AK051340	http://www.ncbi.nlm.nih.gov/nuccore/AK051340		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026914	AK051554	AK051554	http://www.ncbi.nlm.nih.gov/nuccore/AK051554		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026915	AK051785	AK051785	http://www.ncbi.nlm.nih.gov/nuccore/AK051785		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026916	AK051928	AK051928	http://www.ncbi.nlm.nih.gov/nuccore/AK051928		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026917	AK052078	AK052078	http://www.ncbi.nlm.nih.gov/nuccore/AK052078		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026918	AK052349	AK052349	http://www.ncbi.nlm.nih.gov/nuccore/AK052349		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026919	AK053610	AK053610	http://www.ncbi.nlm.nih.gov/nuccore/AK053610		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026920	AK053770	AK053770	http://www.ncbi.nlm.nih.gov/nuccore/AK053770		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026921	AK076845	AK076845	http://www.ncbi.nlm.nih.gov/nuccore/AK076845		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026922	AK076878	AK076878	http://www.ncbi.nlm.nih.gov/nuccore/AK076878		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026923	AK077428	AK077428	http://www.ncbi.nlm.nih.gov/nuccore/AK077428		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026924	AK078296	AK078296	http://www.ncbi.nlm.nih.gov/nuccore/AK078296		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026925	AK078359	AK078359	http://www.ncbi.nlm.nih.gov/nuccore/AK078359		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026926	AK078978	AK078978	http://www.ncbi.nlm.nih.gov/nuccore/AK078978		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026927	AK078983	AK078983	http://www.ncbi.nlm.nih.gov/nuccore/AK078983		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026928	AK079655	AK079655	http://www.ncbi.nlm.nih.gov/nuccore/AK079655		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026929	AK080153	AK080153	http://www.ncbi.nlm.nih.gov/nuccore/AK080153		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026930	AK080436	AK080436	http://www.ncbi.nlm.nih.gov/nuccore/AK080436		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026931	AK080586	AK080586	http://www.ncbi.nlm.nih.gov/nuccore/AK080586		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026932	AK081070	AK081070	http://www.ncbi.nlm.nih.gov/nuccore/AK081070		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026933	AK081105	AK081105	http://www.ncbi.nlm.nih.gov/nuccore/AK081105		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026934	AK081403	AK081403	http://www.ncbi.nlm.nih.gov/nuccore/AK081403		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026935	AK081423	AK081423	http://www.ncbi.nlm.nih.gov/nuccore/AK081423		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026936	AK082143	AK082143	http://www.ncbi.nlm.nih.gov/nuccore/AK082143		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026937	AK083508	AK083508	http://www.ncbi.nlm.nih.gov/nuccore/AK083508		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026938	AK084036	AK084036	http://www.ncbi.nlm.nih.gov/nuccore/AK084036		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026939	AK084095	AK084095	http://www.ncbi.nlm.nih.gov/nuccore/AK084095		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026940	AK084102	AK084102	http://www.ncbi.nlm.nih.gov/nuccore/AK084102		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026941	AK084115	AK084115	http://www.ncbi.nlm.nih.gov/nuccore/AK084115		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026942	AK084189	AK084189	http://www.ncbi.nlm.nih.gov/nuccore/AK084189		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026943	AK084363	AK084363	http://www.ncbi.nlm.nih.gov/nuccore/AK084363		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026944	AK084753	AK084753	http://www.ncbi.nlm.nih.gov/nuccore/AK084753		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026945	AK084755	AK084755	http://www.ncbi.nlm.nih.gov/nuccore/AK084755		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026946	AK085609	AK085609	http://www.ncbi.nlm.nih.gov/nuccore/AK085609		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026947	AK085783	AK085783	http://www.ncbi.nlm.nih.gov/nuccore/AK085783		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026948	AK085978	AK085978	http://www.ncbi.nlm.nih.gov/nuccore/AK085978		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026949	AK086030	AK086030	http://www.ncbi.nlm.nih.gov/nuccore/AK086030		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026950	AK086184	AK086184	http://www.ncbi.nlm.nih.gov/nuccore/AK086184		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026951	AK086690	AK086690	http://www.ncbi.nlm.nih.gov/nuccore/AK086690		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026952	AK087613	AK087613	http://www.ncbi.nlm.nih.gov/nuccore/AK087613		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026953	AK089491	AK089491	http://www.ncbi.nlm.nih.gov/nuccore/AK089491		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026954	AK089590	AK089590	http://www.ncbi.nlm.nih.gov/nuccore/AK089590		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026955	AK089614	AK089614	http://www.ncbi.nlm.nih.gov/nuccore/AK089614		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026956	AK089617	AK089617	http://www.ncbi.nlm.nih.gov/nuccore/AK089617		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026957	AK089620	AK089620	http://www.ncbi.nlm.nih.gov/nuccore/AK089620		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026958	AK089735	AK089735	http://www.ncbi.nlm.nih.gov/nuccore/AK089735		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026959	AK089776	AK089776	http://www.ncbi.nlm.nih.gov/nuccore/AK089776		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026960	AK089849	AK089849	http://www.ncbi.nlm.nih.gov/nuccore/AK089849		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026961	AK089870	AK089870	http://www.ncbi.nlm.nih.gov/nuccore/AK089870		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026962	AK090205	AK090205	http://www.ncbi.nlm.nih.gov/nuccore/AK090205		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026963	AK090293	AK090293	http://www.ncbi.nlm.nih.gov/nuccore/AK090293		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026964	AK131756	AK131756	http://www.ncbi.nlm.nih.gov/nuccore/AK131756		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026965	AK131878	AK131878	http://www.ncbi.nlm.nih.gov/nuccore/AK131878		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026966	AK132507	AK132507	http://www.ncbi.nlm.nih.gov/nuccore/AK132507		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026967	AK132620	AK132620	http://www.ncbi.nlm.nih.gov/nuccore/AK132620		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026968	AK132818	AK132818	http://www.ncbi.nlm.nih.gov/nuccore/AK132818		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026969	AK132844	AK132844	http://www.ncbi.nlm.nih.gov/nuccore/AK132844		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026970	AK133692	AK133692	http://www.ncbi.nlm.nih.gov/nuccore/AK133692		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026971	AK133765	AK133765	http://www.ncbi.nlm.nih.gov/nuccore/AK133765		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026972	AK133808	AK133808	http://www.ncbi.nlm.nih.gov/nuccore/AK133808		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026973	AK134145	AK134145	http://www.ncbi.nlm.nih.gov/nuccore/AK134145		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026974	AK135459	AK135459	http://www.ncbi.nlm.nih.gov/nuccore/AK135459		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026975	AK135695	AK135695	http://www.ncbi.nlm.nih.gov/nuccore/AK135695		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026976	AK135830	AK135830	http://www.ncbi.nlm.nih.gov/nuccore/AK135830		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026977	AK136392	AK136392	http://www.ncbi.nlm.nih.gov/nuccore/AK136392		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026978	AK136693	AK136693	http://www.ncbi.nlm.nih.gov/nuccore/AK136693		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026979	AK136989	AK136989	http://www.ncbi.nlm.nih.gov/nuccore/AK136989		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026980	AK137670	AK137670	http://www.ncbi.nlm.nih.gov/nuccore/AK137670		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026981	AK138107	AK138107	http://www.ncbi.nlm.nih.gov/nuccore/AK138107		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026982	AK138425	AK138425	http://www.ncbi.nlm.nih.gov/nuccore/AK138425		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026983	AK138551	AK138551	http://www.ncbi.nlm.nih.gov/nuccore/AK138551		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026984	AK138620	AK138620	http://www.ncbi.nlm.nih.gov/nuccore/AK138620		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026985	AK138862	AK138862	http://www.ncbi.nlm.nih.gov/nuccore/AK138862		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026986	AK138914	AK138914	http://www.ncbi.nlm.nih.gov/nuccore/AK138914		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026987	AK139228	AK139228	http://www.ncbi.nlm.nih.gov/nuccore/AK139228		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026988	AK139316	AK139316	http://www.ncbi.nlm.nih.gov/nuccore/AK139316		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026989	AK139755	AK139755	http://www.ncbi.nlm.nih.gov/nuccore/AK139755		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026990	AK139932	AK139932	http://www.ncbi.nlm.nih.gov/nuccore/AK139932		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026991	AK140106	AK140106	http://www.ncbi.nlm.nih.gov/nuccore/AK140106		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026992	AK140518	AK140518	http://www.ncbi.nlm.nih.gov/nuccore/AK140518		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026993	AK140787	AK140787	http://www.ncbi.nlm.nih.gov/nuccore/AK140787		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026994	AK140835	AK140835	http://www.ncbi.nlm.nih.gov/nuccore/AK140835		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026995	AK140883	AK140883	http://www.ncbi.nlm.nih.gov/nuccore/AK140883		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026996	AK140958	AK140958	http://www.ncbi.nlm.nih.gov/nuccore/AK140958		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026997	AK141540	AK141540	http://www.ncbi.nlm.nih.gov/nuccore/AK141540		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026998	AK141628	AK141628	http://www.ncbi.nlm.nih.gov/nuccore/AK141628		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00026999	AK142013	AK142013	http://www.ncbi.nlm.nih.gov/nuccore/AK142013		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027000	AK142410	AK142410	http://www.ncbi.nlm.nih.gov/nuccore/AK142410		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027001	AK142416	AK142416	http://www.ncbi.nlm.nih.gov/nuccore/AK142416		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027002	AK142482	AK142482	http://www.ncbi.nlm.nih.gov/nuccore/AK142482		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027003	AK142778	AK142778	http://www.ncbi.nlm.nih.gov/nuccore/AK142778		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027004	AK142958	AK142958	http://www.ncbi.nlm.nih.gov/nuccore/AK142958		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027005	AK143034	AK143034	http://www.ncbi.nlm.nih.gov/nuccore/AK143034		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027006	AK143146	AK143146	http://www.ncbi.nlm.nih.gov/nuccore/AK143146		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027007	AK144104	AK144104	http://www.ncbi.nlm.nih.gov/nuccore/AK144104		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027008	AK144201	AK144201	http://www.ncbi.nlm.nih.gov/nuccore/AK144201		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027009	AK144914	AK144914	http://www.ncbi.nlm.nih.gov/nuccore/AK144914		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027010	AK149037	AK149037	http://www.ncbi.nlm.nih.gov/nuccore/AK149037		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027011	AK149172	AK149172	http://www.ncbi.nlm.nih.gov/nuccore/AK149172		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027012	AK149691	AK149691	http://www.ncbi.nlm.nih.gov/nuccore/AK149691		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027013	AK150079	AK150079	http://www.ncbi.nlm.nih.gov/nuccore/AK150079		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027014	AK153753	AK153753	http://www.ncbi.nlm.nih.gov/nuccore/AK153753		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027015	AK155780	AK155780	http://www.ncbi.nlm.nih.gov/nuccore/AK155780		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027016	AK156229	AK156229	http://www.ncbi.nlm.nih.gov/nuccore/AK156229		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027017	AK156578	AK156578	http://www.ncbi.nlm.nih.gov/nuccore/AK156578		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027018	AK156672	AK156672	http://www.ncbi.nlm.nih.gov/nuccore/AK156672		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027019	AK156802	AK156802	http://www.ncbi.nlm.nih.gov/nuccore/AK156802		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027020	AK157094	AK157094	http://www.ncbi.nlm.nih.gov/nuccore/AK157094		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027021	AK157185	AK157185	http://www.ncbi.nlm.nih.gov/nuccore/AK157185		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027022	AK157495	AK157495	http://www.ncbi.nlm.nih.gov/nuccore/AK157495		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027023	AK157498	AK157498	http://www.ncbi.nlm.nih.gov/nuccore/AK157498		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027024	AK157530	AK157530	http://www.ncbi.nlm.nih.gov/nuccore/AK157530		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027025	AK157564	AK157564	http://www.ncbi.nlm.nih.gov/nuccore/AK157564		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027026	AK158741	AK158741	http://www.ncbi.nlm.nih.gov/nuccore/AK158741		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027027	AK158887	AK158887	http://www.ncbi.nlm.nih.gov/nuccore/AK158887		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027028	AK162735	AK162735	http://www.ncbi.nlm.nih.gov/nuccore/AK162735		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027029	AK162998	AK162998	http://www.ncbi.nlm.nih.gov/nuccore/AK162998		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027030	AK171827	AK171827	http://www.ncbi.nlm.nih.gov/nuccore/AK171827		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027031	AK180240	AK180240	http://www.ncbi.nlm.nih.gov/nuccore/AK180240		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027032	AK191463	AK191463	http://www.ncbi.nlm.nih.gov/nuccore/AK191463		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027033	AK197782	AK197782	http://www.ncbi.nlm.nih.gov/nuccore/AK197782		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027034	AK212600	AK212600	http://www.ncbi.nlm.nih.gov/nuccore/AK212600		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027035	AK214167	AK214167	http://www.ncbi.nlm.nih.gov/nuccore/AK214167		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027036	AU016662	AU016662	http://www.ncbi.nlm.nih.gov/nuccore/AU016662		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027037	AU019880	AU019880	http://www.ncbi.nlm.nih.gov/nuccore/AU019880		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027038	AU022045	AU022045	http://www.ncbi.nlm.nih.gov/nuccore/AU022045		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027039	AU040911	AU040911	http://www.ncbi.nlm.nih.gov/nuccore/AU040911		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027040	AU042851	AU042851	http://www.ncbi.nlm.nih.gov/nuccore/AU042851		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027041	AV045102	AV045102	http://www.ncbi.nlm.nih.gov/nuccore/AV045102		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027042	AV057789	AV057789	http://www.ncbi.nlm.nih.gov/nuccore/AV057789		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027043	AV110871	AV110871	http://www.ncbi.nlm.nih.gov/nuccore/AV110871		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027044	AV127023	AV127023	http://www.ncbi.nlm.nih.gov/nuccore/AV127023		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027045	AV170241	AV170241	http://www.ncbi.nlm.nih.gov/nuccore/AV170241		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027046	AV213405	AV213405	http://www.ncbi.nlm.nih.gov/nuccore/AV213405		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027047	AV216984	AV216984	http://www.ncbi.nlm.nih.gov/nuccore/AV216984		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027048	AV229195	AV229195	http://www.ncbi.nlm.nih.gov/nuccore/AV229195		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027049	AV271189	AV271189	http://www.ncbi.nlm.nih.gov/nuccore/AV271189		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027050	AV309800	AV309800	http://www.ncbi.nlm.nih.gov/nuccore/AV309800		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027051	AV337624	AV337624	http://www.ncbi.nlm.nih.gov/nuccore/AV337624		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027052	AW121856	AW121856	http://www.ncbi.nlm.nih.gov/nuccore/AW121856		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027053	AW123678	AW123678	http://www.ncbi.nlm.nih.gov/nuccore/AW123678		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027054	AW494074	AW494074	http://www.ncbi.nlm.nih.gov/nuccore/AW494074		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027055	AW495413	AW495413	http://www.ncbi.nlm.nih.gov/nuccore/AW495413		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027056	AW543447	AW543447	http://www.ncbi.nlm.nih.gov/nuccore/AW543447		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027057	AW543705	AW543705	http://www.ncbi.nlm.nih.gov/nuccore/?term=AW543705		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00027058	AW544672	AW544672	http://www.ncbi.nlm.nih.gov/nuccore/AW544672		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027059	AW553423	AW553423	http://www.ncbi.nlm.nih.gov/nuccore/AW553423		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027060	AW555202	AW555202	http://www.ncbi.nlm.nih.gov/nuccore/AW555202		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027061	AW555368	AW555368	http://www.ncbi.nlm.nih.gov/nuccore/AW555368		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027062	AW556834	AW556834	http://www.ncbi.nlm.nih.gov/nuccore/AW556834		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027063	AW557641	AW557641	http://www.ncbi.nlm.nih.gov/nuccore/AW557641		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027064	AW558862	AW558862	http://www.ncbi.nlm.nih.gov/nuccore/AW558862		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027065	AW909306	AW909306	http://www.ncbi.nlm.nih.gov/nuccore/AW909306		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027066	AY178855	AY178855	http://www.ncbi.nlm.nih.gov/nuccore/AY178855		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027067	BB012661	BB012661	http://www.ncbi.nlm.nih.gov/nuccore/BB012661		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027068	BB016866	BB016866	http://www.ncbi.nlm.nih.gov/nuccore/BB016866		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027069	BB017018	BB017018	http://www.ncbi.nlm.nih.gov/nuccore/BB017018		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027070	BB043897	BB043897	http://www.ncbi.nlm.nih.gov/nuccore/BB043897		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027071	BB051562	BB051562	http://www.ncbi.nlm.nih.gov/nuccore/BB051562		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027072	BB080140	BB080140	http://www.ncbi.nlm.nih.gov/nuccore/BB080140		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027073	BB085906	BB085906	http://www.ncbi.nlm.nih.gov/nuccore/BB085906		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027074	BB097040	BB097040	http://www.ncbi.nlm.nih.gov/nuccore/BB097040		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027075	BB099980	BB099980	http://www.ncbi.nlm.nih.gov/nuccore/BB099980		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027076	BB117670	BB117670	http://www.ncbi.nlm.nih.gov/nuccore/BB117670		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027077	BB121580	BB121580	http://www.ncbi.nlm.nih.gov/nuccore/BB121580		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027078	BB158810	BB158810	http://www.ncbi.nlm.nih.gov/nuccore/BB158810		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027079	BB183984	BB183984	http://www.ncbi.nlm.nih.gov/nuccore/BB183984		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027080	BB193921	BB193921	http://www.ncbi.nlm.nih.gov/nuccore/BB193921		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027081	BB195788	BB195788	http://www.ncbi.nlm.nih.gov/nuccore/BB195788		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027082	BB205199	BB205199	http://www.ncbi.nlm.nih.gov/nuccore/BB205199		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027083	BB223643	BB223643	http://www.ncbi.nlm.nih.gov/nuccore/BB223643		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027084	BB241135	BB241135	http://www.ncbi.nlm.nih.gov/nuccore/BB241135		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027085	BB255841	BB255841	http://www.ncbi.nlm.nih.gov/nuccore/BB255841		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027086	BB273287	BB273287	http://www.ncbi.nlm.nih.gov/nuccore/BB273287		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027087	BB276575	BB276575	http://www.ncbi.nlm.nih.gov/nuccore/BB276575		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027088	BB315798	BB315798	http://www.ncbi.nlm.nih.gov/nuccore/BB315798		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027089	BB335101	BB335101	http://www.ncbi.nlm.nih.gov/nuccore/BB335101		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027090	BB344838	BB344838	http://www.ncbi.nlm.nih.gov/nuccore/BB344838		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027091	BB345991	BB345991	http://www.ncbi.nlm.nih.gov/nuccore/BB345991		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027092	BB359521	BB359521	http://www.ncbi.nlm.nih.gov/nuccore/BB359521		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027093	BB381966	BB381966	http://www.ncbi.nlm.nih.gov/nuccore/?term=BB381966		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00027094	BB393078	BB393078	http://www.ncbi.nlm.nih.gov/nuccore/BB393078		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027095	BB470306	BB470306	http://www.ncbi.nlm.nih.gov/nuccore/BB470306		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027096	BB473929	BB473929	http://www.ncbi.nlm.nih.gov/nuccore/BB473929		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027097	BB496295	BB496295	http://www.ncbi.nlm.nih.gov/nuccore/BB496295		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027098	BB521034	BB521034	http://www.ncbi.nlm.nih.gov/nuccore/BB521034		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027099	BB529352	BB529352	http://www.ncbi.nlm.nih.gov/nuccore/BB529352		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027100	BB662083	BB662083	http://www.ncbi.nlm.nih.gov/nuccore/BB662083		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027101	BB703378	BB703378	http://www.ncbi.nlm.nih.gov/nuccore/BB703378		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027102	BB709387	BB709387	http://www.ncbi.nlm.nih.gov/nuccore/BB709387		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027103	BB710064	BB710064	http://www.ncbi.nlm.nih.gov/nuccore/BB710064		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027104	BB712583	BB712583	http://www.ncbi.nlm.nih.gov/nuccore/BB712583		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027105	BB713391	BB713391	http://www.ncbi.nlm.nih.gov/nuccore/BB713391		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027106	BB728372	BB728372	http://www.ncbi.nlm.nih.gov/nuccore/BB728372		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027107	BB735036	BB735036	http://www.ncbi.nlm.nih.gov/nuccore/BB735036		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027108	BB754142	BB754142	http://www.ncbi.nlm.nih.gov/nuccore/BB754142		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027109	BB763701	BB763701	http://www.ncbi.nlm.nih.gov/nuccore/BB763701		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027110	BB767243	BB767243	http://www.ncbi.nlm.nih.gov/nuccore/BB767243		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027111	BB794742	BB794742	http://www.ncbi.nlm.nih.gov/nuccore/BB794742		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027112	BB829165	BB829165	http://www.ncbi.nlm.nih.gov/nuccore/BB829165		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027113	BC003764	BC003764	http://www.ncbi.nlm.nih.gov/nuccore/?term=BC003764		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00027114	BC018588	BC018588	http://www.ncbi.nlm.nih.gov/nuccore/BC018588		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027115	BC021831	BC021831	http://www.ncbi.nlm.nih.gov/nuccore/BC021831		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027116	BC024416	BC024416	http://www.ncbi.nlm.nih.gov/nuccore/BC024416		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027117	BC029124	BC029124	http://www.ncbi.nlm.nih.gov/nuccore/BC029124		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027118	BC030004	BC030004	http://www.ncbi.nlm.nih.gov/nuccore/BC030004		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027119	BC035532	BC035532	http://www.ncbi.nlm.nih.gov/nuccore/BC035532		lncRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027120	BC035679	BC035679	http://www.ncbi.nlm.nih.gov/nuccore/BC035679		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027121	BC038538	BC038538	http://www.ncbi.nlm.nih.gov/nuccore/BC038538		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027122	BC038887	BC038887	http://www.ncbi.nlm.nih.gov/nuccore/BC038887		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027123	BC055052	BC055052	http://www.ncbi.nlm.nih.gov/nuccore/BC055052		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027124	BC058854	BC058854	http://www.ncbi.nlm.nih.gov/nuccore/BC058854		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027125	BC065566	BC065566	http://www.ncbi.nlm.nih.gov/nuccore/BC065566		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027126	BC067836	BC067836	http://www.ncbi.nlm.nih.gov/nuccore/BC067836		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027127	BC071254	BC071254	http://www.ncbi.nlm.nih.gov/nuccore/BC071254		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027128	BC075654	BC075654	http://www.ncbi.nlm.nih.gov/nuccore/BC075654		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027129	BC127080	BC127080	http://www.ncbi.nlm.nih.gov/nuccore/BC127080		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00027130	BE628832	BE628832	http://www.ncbi.nlm.nih.gov/nuccore/BE628832		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027131	BE650311	BE650311	http://www.ncbi.nlm.nih.gov/nuccore/BE650311		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027132	BE945748	BE945748	http://www.ncbi.nlm.nih.gov/nuccore/BE945748		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027133	BE948370	BE948370	http://www.ncbi.nlm.nih.gov/nuccore/BE948370		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027134	BE951647	BE951647	http://www.ncbi.nlm.nih.gov/nuccore/BE951647		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027135	BE987947	BE987947	http://www.ncbi.nlm.nih.gov/nuccore/BE987947		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027136	BE992875	BE992875	http://www.ncbi.nlm.nih.gov/nuccore/BE992875		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027137	BF148780	BF148780	http://www.ncbi.nlm.nih.gov/nuccore/BF148780		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027138	BF166000	BF166000	http://www.ncbi.nlm.nih.gov/nuccore/BF166000		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027139	BF227338	BF227338	http://www.ncbi.nlm.nih.gov/nuccore/BF227338		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027140	BF321332	BF321332	http://www.ncbi.nlm.nih.gov/nuccore/BF321332		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027141	BF455409	BF455409	http://www.ncbi.nlm.nih.gov/nuccore/BF455409		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027142	BF730541	BF730541	http://www.ncbi.nlm.nih.gov/nuccore/BF730541		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027143	BG063240	BG063240	http://www.ncbi.nlm.nih.gov/nuccore/BG063240		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027144	BG065705	BG065705	http://www.ncbi.nlm.nih.gov/nuccore/BG065705		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027145	BG066175	BG066175	http://www.ncbi.nlm.nih.gov/nuccore/BG066175		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027146	BG066346	BG066346	http://www.ncbi.nlm.nih.gov/nuccore/BG066346		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027147	BG066533	BG066533	http://www.ncbi.nlm.nih.gov/nuccore/BG066533		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027148	BG066727	BG066727	http://www.ncbi.nlm.nih.gov/nuccore/BG066727		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027149	BG066746	BG066746	http://www.ncbi.nlm.nih.gov/nuccore/BG066746		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027150	BG066901	BG066901	http://www.ncbi.nlm.nih.gov/nuccore/BG066901		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027151	BG067289	BG067289	http://www.ncbi.nlm.nih.gov/nuccore/BG067289		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027152	BG067993	BG067993	http://www.ncbi.nlm.nih.gov/nuccore/BG067993		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027153	BG068123	BG068123	http://www.ncbi.nlm.nih.gov/nuccore/BG068123		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027154	BG068591	BG068591	http://www.ncbi.nlm.nih.gov/nuccore/BG068591		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027155	BG068672	BG068672	http://www.ncbi.nlm.nih.gov/nuccore/BG068672		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027156	BG068681	BG068681	http://www.ncbi.nlm.nih.gov/nuccore/BG068681		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027157	BG068807	BG068807	http://www.ncbi.nlm.nih.gov/nuccore/BG068807		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027158	BG068932	BG068932	http://www.ncbi.nlm.nih.gov/nuccore/BG068932		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027159	BG068986	BG068986	http://www.ncbi.nlm.nih.gov/nuccore/BG068986		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027160	BG068989	BG068989	http://www.ncbi.nlm.nih.gov/nuccore/BG068989		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027161	BG069080	BG069080	http://www.ncbi.nlm.nih.gov/nuccore/BG069080		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027162	BG069109	BG069109	http://www.ncbi.nlm.nih.gov/nuccore/BG069109		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027163	BG069648	BG069648	http://www.ncbi.nlm.nih.gov/nuccore/BG069648		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027164	BG069857	BG069857	http://www.ncbi.nlm.nih.gov/nuccore/BG069857		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027165	BG069991	BG069991	http://www.ncbi.nlm.nih.gov/nuccore/BG069991		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027166	BG070566	BG070566	http://www.ncbi.nlm.nih.gov/nuccore/BG070566		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027167	BG070611	BG070611	http://www.ncbi.nlm.nih.gov/nuccore/BG070611		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027168	BG070655	BG070655	http://www.ncbi.nlm.nih.gov/nuccore/BG070655		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027169	BG070910	BG070910	http://www.ncbi.nlm.nih.gov/nuccore/BG070910		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027170	BG071002	BG071002	http://www.ncbi.nlm.nih.gov/nuccore/BG071002		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027171	BG071600	BG071600	http://www.ncbi.nlm.nih.gov/nuccore/BG071600		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027172	BG072319	BG072319	http://www.ncbi.nlm.nih.gov/nuccore/BG072319		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027173	BG073432	BG073432	http://www.ncbi.nlm.nih.gov/nuccore/BG073432		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027174	BG073921	BG073921	http://www.ncbi.nlm.nih.gov/nuccore/BG073921		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027175	BG074150	BG074150	http://www.ncbi.nlm.nih.gov/nuccore/BG074150		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027176	BG074624	BG074624	http://www.ncbi.nlm.nih.gov/nuccore/BG074624		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027177	BG074662	BG074662	http://www.ncbi.nlm.nih.gov/nuccore/BG074662		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027178	BG075370	BG075370	http://www.ncbi.nlm.nih.gov/nuccore/BG075370		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027179	BG076014	BG076014	http://www.ncbi.nlm.nih.gov/nuccore/BG076014		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027180	BG076325	BG076325	http://www.ncbi.nlm.nih.gov/nuccore/BG076325		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027181	BG078857	BG078857	http://www.ncbi.nlm.nih.gov/nuccore/BG078857		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027182	BG083020	BG083020	http://www.ncbi.nlm.nih.gov/nuccore/BG083020		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027183	BG083989	BG083989	http://www.ncbi.nlm.nih.gov/nuccore/BG083989		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027184	BG141806	BG141806	http://www.ncbi.nlm.nih.gov/nuccore/BG141806		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027185	BG297038	1300007C21Rik	http://www.ncbi.nlm.nih.gov/nuccore/BG297038		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027186	BG796845	BG796845	http://www.ncbi.nlm.nih.gov/nuccore/?term=BG796845		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00027187	BG963792	BG963792	http://www.ncbi.nlm.nih.gov/nuccore/BG963792		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027188	BG966742	BG966742	http://www.ncbi.nlm.nih.gov/nuccore/BG966742		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027189	BG976607	BG976607	http://www.ncbi.nlm.nih.gov/nuccore/BG976607		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027190	BI076698	BI076698	http://www.ncbi.nlm.nih.gov/nuccore/BI076698		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027191	BI076708	BI076708	http://www.ncbi.nlm.nih.gov/nuccore/BI076708		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027192	BI076711	BI076711	http://www.ncbi.nlm.nih.gov/nuccore/BI076711		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027193	BI076834	BI076834	http://www.ncbi.nlm.nih.gov/nuccore/BI076834		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027194	BI499978	BI499978	http://www.ncbi.nlm.nih.gov/nuccore/BI499978		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027195	BI651113	BI651113	http://www.ncbi.nlm.nih.gov/nuccore/BI651113		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027196	BI736050	BI736050	http://www.ncbi.nlm.nih.gov/nuccore/BI736050		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027197	BI963564	BI963564	http://www.ncbi.nlm.nih.gov/nuccore/BI963564		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027198	BJ625728	BJ625728	http://www.ncbi.nlm.nih.gov/nuccore/?term=BJ625728		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00027199	BM115860	BM115860	http://www.ncbi.nlm.nih.gov/nuccore/BM115860		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027200	BM117404	BM117404	http://www.ncbi.nlm.nih.gov/nuccore/BM117404		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027201	BM117570	BM117570	http://www.ncbi.nlm.nih.gov/nuccore/BM117570		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027202	BM195235	BM195235	http://www.ncbi.nlm.nih.gov/nuccore/BM195235		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027203	BM198753	BM198753	http://www.ncbi.nlm.nih.gov/nuccore/BM198753		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027204	BM213788	BM213788	http://www.ncbi.nlm.nih.gov/nuccore/BM213788		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027205	BM222792	BM222792	http://www.ncbi.nlm.nih.gov/nuccore/?term=BM222792		mRNA	Mus musculus	18451862	Pseudopodium	Migrating cell	qRT-PCR	About 50 RNAs were significantly enriched in pseudopodia in response to both migratory stimuli (table 1 and S1). Data are collected from Table 1 and S1.
RLID00027206	BM225255	BM225255	http://www.ncbi.nlm.nih.gov/nuccore/BM225255		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027207	BM232203	BM232203	http://www.ncbi.nlm.nih.gov/nuccore/BM232203		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027208	BM239430	4833416J08Rik	http://www.ncbi.nlm.nih.gov/nuccore/BM239430		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027209	BM241271	BM241271	http://www.ncbi.nlm.nih.gov/nuccore/BM241271		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027210	BM247957	BM247957	http://www.ncbi.nlm.nih.gov/nuccore/BM247957		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027211	BQ176181	BQ176181	http://www.ncbi.nlm.nih.gov/nuccore/BQ176181		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027212	BX647987	BX647987	http://www.ncbi.nlm.nih.gov/nuccore/BX647987		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027213	BX772720	BX772720	http://www.ncbi.nlm.nih.gov/nuccore/?term=BX772720		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00027214	C77540	C77540	http://www.ncbi.nlm.nih.gov/nuccore/C77540		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027215	C79035	C79035	http://www.ncbi.nlm.nih.gov/nuccore/C79035		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027216	C79752	C79752	http://www.ncbi.nlm.nih.gov/nuccore/C79752		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027217	C81225	C81225	http://www.ncbi.nlm.nih.gov/nuccore/C81225		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027218	C86506	C86506	http://www.ncbi.nlm.nih.gov/nuccore/C86506		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027219	CA971768	CA971768	http://www.ncbi.nlm.nih.gov/nuccore/?term=CA971768		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00027220	DQ359732	DQ359732	http://www.ncbi.nlm.nih.gov/nuccore/?term=DQ359732		mRNA	Spisula solidissima	22356233	Centrosome	Oocyte	RT-PCR	"TABLE 1: Similarity between centrosome-associated RNAs and viral sequences (from ref. [32], with modifications). Data are collected from Table 1. "
RLID00027221	DQ539895	piR-7	http://www.ncbi.nlm.nih.gov/nuccore/DQ539895		piRNA	Mus musculus	18204908	Nucleolus	Sertoli cell	In situ hybridization|Northern blot|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00027222	DQ548893	piR-17005	http://www.ncbi.nlm.nih.gov/nuccore/DQ548893		piRNA	Mus musculus	18204908	Nucleolus	Sertoli cell	In situ hybridization|Northern blot|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00027223	DQ548925	piR-17037	http://www.ncbi.nlm.nih.gov/nuccore/DQ548925		piRNA	Mus musculus	18204908	Nucleolus	Sertoli cell	In situ hybridization|Northern blot|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00027224	DQ548931	piR-17043	http://www.ncbi.nlm.nih.gov/nuccore/DQ548931		piRNA	Mus musculus	18204908	Nucleolus	Sertoli cell	In situ hybridization|Northern blot|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00027225	DQ548968	piR-17080	http://www.ncbi.nlm.nih.gov/nuccore/DQ548968		piRNA	Mus musculus	18204908	Nucleolus	Sertoli cell	In situ hybridization|Northern blot|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00027226	DQ571378	piR-31490	http://www.ncbi.nlm.nih.gov/nuccore/DQ571378		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027227	DQ571524	piR-31636	http://www.ncbi.nlm.nih.gov/nuccore/DQ571524		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027228	DQ571525	piR-31637	http://www.ncbi.nlm.nih.gov/nuccore/DQ571525		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027229	DQ571526	piR-31638	http://www.ncbi.nlm.nih.gov/nuccore/DQ571526		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027230	DQ571874	piR-31986	http://www.ncbi.nlm.nih.gov/nuccore/DQ571874		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027231	DQ571875	piR-31987	http://www.ncbi.nlm.nih.gov/nuccore/DQ571875		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027232	DQ579193	piR-47305	http://www.ncbi.nlm.nih.gov/nuccore/DQ579193		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027233	DQ582036	piR-32148	http://www.ncbi.nlm.nih.gov/nuccore/DQ582036		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027234	DQ582264	piR-32376	http://www.ncbi.nlm.nih.gov/nuccore/DQ582264		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027235	DQ582459	piR-32571	http://www.ncbi.nlm.nih.gov/nuccore/DQ582459		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027236	DQ582567	piR-32679	http://www.ncbi.nlm.nih.gov/nuccore/DQ582567		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027237	DQ584697	piR-51809	http://www.ncbi.nlm.nih.gov/nuccore/DQ584697		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027238	DQ584698	piR-51810	http://www.ncbi.nlm.nih.gov/nuccore/DQ584698		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027239	DQ590013	piR-57125	http://www.ncbi.nlm.nih.gov/nuccore/DQ590013		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027240	DQ590407	piR-57519	http://www.ncbi.nlm.nih.gov/nuccore/DQ590407		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027241	DQ591357	piR-58469	http://www.ncbi.nlm.nih.gov/nuccore/DQ591357		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027242	DQ592931	piR-33043	http://www.ncbi.nlm.nih.gov/nuccore/DQ592931		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027243	DQ593039	piR-33151	http://www.ncbi.nlm.nih.gov/nuccore/DQ593039		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027244	DQ593292	piR-33404	http://www.ncbi.nlm.nih.gov/nuccore/DQ593292		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027245	DQ593325	piR-33437	http://www.ncbi.nlm.nih.gov/nuccore/DQ593325		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027246	DQ593671	piR-33783	http://www.ncbi.nlm.nih.gov/nuccore/DQ593671		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027247	DQ594453	piR-60565	http://www.ncbi.nlm.nih.gov/nuccore/DQ594453		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027248	DQ594465	piR-60577	http://www.ncbi.nlm.nih.gov/nuccore/DQ594465		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027249	DQ595535	piR-61647	http://www.ncbi.nlm.nih.gov/nuccore/DQ595535		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027250	DQ595539	piR-61651	http://www.ncbi.nlm.nih.gov/nuccore/DQ595539		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027251	DQ596276	piR-34342	http://www.ncbi.nlm.nih.gov/nuccore/DQ596276		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027252	DQ596468	piR-34534	http://www.ncbi.nlm.nih.gov/nuccore/DQ596468		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027253	DQ596469	piR-34535	http://www.ncbi.nlm.nih.gov/nuccore/DQ596469		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027254	DQ596470	piR-34536	http://www.ncbi.nlm.nih.gov/nuccore/DQ596470		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027255	DQ596738	piR-34804	http://www.ncbi.nlm.nih.gov/nuccore/DQ596738		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027256	DQ596805	piR-34871	http://www.ncbi.nlm.nih.gov/nuccore/DQ596805		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027257	DQ597155	piR-35221	http://www.ncbi.nlm.nih.gov/nuccore/DQ597155		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027258	DQ597347	piR-35413	http://www.ncbi.nlm.nih.gov/nuccore/DQ597347		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027259	DQ597403	piR-35469	http://www.ncbi.nlm.nih.gov/nuccore/DQ597403		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027260	DQ597482	piR-35548	http://www.ncbi.nlm.nih.gov/nuccore/DQ597482		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027261	DQ597483	piR-35549	http://www.ncbi.nlm.nih.gov/nuccore/DQ597483		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027262	DQ597484	piR-35550	http://www.ncbi.nlm.nih.gov/nuccore/DQ597484		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027263	DQ597975	piR-36041	http://www.ncbi.nlm.nih.gov/nuccore/DQ597975		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027264	DQ597990	piR-36056	http://www.ncbi.nlm.nih.gov/nuccore/DQ597990		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027265	DQ597997	piR-36063	http://www.ncbi.nlm.nih.gov/nuccore/DQ597997		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027266	DQ598159	piR-36225	http://www.ncbi.nlm.nih.gov/nuccore/DQ598159		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027267	DQ598167	piR-36233	http://www.ncbi.nlm.nih.gov/nuccore/DQ598167		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027268	DQ598175	piR-36241	http://www.ncbi.nlm.nih.gov/nuccore/DQ598175		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027269	DQ598263	piR-36329	http://www.ncbi.nlm.nih.gov/nuccore/DQ598263		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027270	DQ598375	piR-36441	http://www.ncbi.nlm.nih.gov/nuccore/DQ598375		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027271	DQ598641	piR-36707	http://www.ncbi.nlm.nih.gov/nuccore/DQ598641		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027272	DQ598675	piR-36741	http://www.ncbi.nlm.nih.gov/nuccore/DQ598675		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027273	DQ598677	piR-36743	http://www.ncbi.nlm.nih.gov/nuccore/DQ598677		piRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027274	DQ600436	piR-38502	http://www.ncbi.nlm.nih.gov/nuccore/DQ600436		piRNA	Homo sapiens	24602614	Mitochondrion	Hela cell|HEK293 cell	Next-generation sequencing	"Fig. 1：Mitochondrial genomic location of the 29 piRNAs. The panel has two tracks: the 29-piRNAs (upper track) and mtDNA annotations (lower track). The piRNAs are located throughout mitochondrial genome, including rRNA regions, tRNA regions, and protein-coding regions. Data are collected from Figure 1. "
RLID00027275	DQ869571	DQ869571	http://www.ncbi.nlm.nih.gov/nuccore/?term=DQ869571	CheFz1 mRNA	mRNA	Clytia hemisphaerica	17355179	Cytoplasm	Eggs|Embryo|Planula larvae	In situ hybridization	"In situ hybridisation of C. hemisphaerica eggs, embryos, and planula larvae (fixed at 1 and 3 d after fertilisation), showing the concentration of CheFz1 RNA (top row) in the animal cytoplasm of the egg and around the nuclei during first cleavage, and its graded oral-aboral distribution in blastula and early gastrula stages. "
RLID00027276	DQ869572	DQ869572	http://www.ncbi.nlm.nih.gov/nuccore/?term=DQ869572	CheFz3 RNA	mRNA	Clytia hemisphaerica	17355179	Vegetal	Eggs|Embryo|Planula larvae	In situ hybridization	"CheFz3, whose RNA is localised at the egg vegetal cortex, was found to oppose CheFz1 function and to define an aboral territory. "
RLID00027277	DY566077	DY566077	http://www.ncbi.nlm.nih.gov/nuccore/?term=DY566077		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00027278	EB732697	EB732697	http://www.ncbi.nlm.nih.gov/nuccore/?term=EB732697		mRNA	Xenopus laevis	26337391	Vegetal	Oocyte	In situ hybridization	FIGURE 1: Identification of novel vegetally localizing RNAs in X. laevis oocytes. Data are collected from Figure 1.
RLID00027279	EF565083	lncRNA_ES2	http://www.ncbi.nlm.nih.gov/nuccore/EF565083		lncRNA	Homo sapiens	22193719	Nucleus	Embryonic stem cell	qRT-PCR|Microarray	"By means of RNA fractionation followed by quantitative PCR (qPCR), we found that lncRNA_ES1, lncRNA_ES2 and lncRNA_ES3 were preferentially retained in the nucleus (Figure 5A). "
RLID00027280	ENSG00000194297	RNU1-75P	http://asia.ensembl.org/id/ENSG00000194297		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027281	ENSG00000199308	RNU6-222P	http://asia.ensembl.org/id/ENSG00000199308		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027282	ENSG00000199313	RNU4-82P	http://asia.ensembl.org/id/ENSG00000199313		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027283	ENSG00000199325	RNU4-39P	http://asia.ensembl.org/id/ENSG00000199325		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027284	ENSG00000199488	RNU1-70P	http://asia.ensembl.org/id/ENSG00000199488		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027285	ENSG00000199562	RNU6-37P	http://asia.ensembl.org/id/ENSG00000199562		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027286	ENSG00000199664	RNU6-1266P	http://asia.ensembl.org/id/ENSG00000199664		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027287	ENSG00000199695	RNU6-1128P	http://asia.ensembl.org/id/ENSG00000199695		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027288	ENSG00000199709	RNU4-23P	http://asia.ensembl.org/id/ENSG00000199709		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027289	ENSG00000199731	RNU6-1079P	http://asia.ensembl.org/id/ENSG00000199731		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027290	ENSG00000199805	RNU1-134P	http://asia.ensembl.org/id/ENSG00000199805		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027291	ENSG00000199812	RNU6-428P	http://asia.ensembl.org/id/ENSG00000199812		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027292	ENSG00000200026	U8	http://asia.ensembl.org/id/ENSG00000200026		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027293	ENSG00000200062	RNU4-58P	http://asia.ensembl.org/id/ENSG00000200062		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027294	ENSG00000200107	RNU6-1249P	http://asia.ensembl.org/id/ENSG00000200107		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027295	ENSG00000200183	RNU6-238P	http://asia.ensembl.org/id/ENSG00000200183		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027296	ENSG00000200296	RNU1-83P	http://asia.ensembl.org/id/ENSG00000200296		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027297	ENSG00000200496	U8	http://asia.ensembl.org/id/ENSG00000200496		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027298	ENSG00000200597	RNU1-87P	http://asia.ensembl.org/id/ENSG00000200597		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027299	ENSG00000200728	RNU6-271P	http://asia.ensembl.org/id/ENSG00000200728		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027300	ENSG00000200731	RNU1-124P	http://asia.ensembl.org/id/ENSG00000200731		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027301	ENSG00000200779	RNU6-105P	http://asia.ensembl.org/id/ENSG00000200779		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027302	ENSG00000200889	RNU4-13P	http://asia.ensembl.org/id/ENSG00000200889		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027303	ENSG00000200903	RNU1-42P	http://asia.ensembl.org/id/ENSG00000200903		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027304	ENSG00000200972	RNU5A-8P	http://asia.ensembl.org/id/ENSG00000200972		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027305	ENSG00000200975	RNU1-7P	http://asia.ensembl.org/id/ENSG00000200975		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027306	ENSG00000201104	RNU6-11P	http://asia.ensembl.org/id/ENSG00000201104		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027307	ENSG00000201180	RNU6-115P	http://asia.ensembl.org/id/ENSG00000201180		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027308	ENSG00000201223	RNU6-1305P	http://asia.ensembl.org/id/ENSG00000201223		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027309	ENSG00000201291	RNU1-34P	http://asia.ensembl.org/id/ENSG00000201291		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027310	ENSG00000201317	RNU4-59P	http://asia.ensembl.org/id/ENSG00000201317		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027311	ENSG00000201372	RNU6-1251P	http://asia.ensembl.org/id/ENSG00000201372		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027312	ENSG00000201388	SNORA68	http://asia.ensembl.org/id/ENSG00000201388		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027313	ENSG00000201441	RNU6-646P	http://asia.ensembl.org/id/ENSG00000201441		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027314	ENSG00000201458	RNU4-4P	http://asia.ensembl.org/id/ENSG00000201458		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027315	ENSG00000201474	RNU6-164P	http://asia.ensembl.org/id/ENSG00000201474		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027316	ENSG00000201517	RNU6-707P	http://asia.ensembl.org/id/ENSG00000201517		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027317	ENSG00000201614	RNU4-19P	http://asia.ensembl.org/id/ENSG00000201614		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027318	ENSG00000201616	RNU1-91P	http://asia.ensembl.org/id/ENSG00000201616		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027319	ENSG00000201648	RNU4-91P	http://asia.ensembl.org/id/ENSG00000201648		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027320	ENSG00000201852	RNU6-702P	http://asia.ensembl.org/id/ENSG00000201852		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027321	ENSG00000201910	RNU1-140P	http://asia.ensembl.org/id/ENSG00000201910		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027322	ENSG00000201922	RNU1-43P	http://asia.ensembl.org/id/ENSG00000201922		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027323	ENSG00000202199	RNU1-115P	http://asia.ensembl.org/id/ENSG00000202199		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027324	ENSG00000202300	RNU6-487P	http://asia.ensembl.org/id/ENSG00000202300		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027325	ENSG00000202313	RNU1-64P	http://asia.ensembl.org/id/ENSG00000202313		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027326	ENSG00000202317	RNU1-84P	http://asia.ensembl.org/id/ENSG00000202317		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027327	ENSG00000202380	RNU1-55P	http://asia.ensembl.org/id/ENSG00000202380		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027328	ENSG00000202534	RNU6-1329P	http://asia.ensembl.org/id/ENSG00000202534		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027329	ENSG00000206593	RNU6-47P	http://asia.ensembl.org/id/ENSG00000206593		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027330	ENSG00000206599	RNU6-841P	http://asia.ensembl.org/id/ENSG00000206599		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027331	ENSG00000206600	RNU6-25P	http://asia.ensembl.org/id/ENSG00000206600		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027332	ENSG00000206601	RNU6-431P	http://asia.ensembl.org/id/ENSG00000206601		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027333	ENSG00000206629	RNU1-63P	http://asia.ensembl.org/id/ENSG00000206629		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027334	ENSG00000206675	RNU6-32P	http://asia.ensembl.org/id/ENSG00000206675		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027335	ENSG00000206744	RNU6-620P	http://asia.ensembl.org/id/ENSG00000206744		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027336	ENSG00000206772	RNU6-44P	http://asia.ensembl.org/id/ENSG00000206772		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027337	ENSG00000206820	RNU1-138P	http://asia.ensembl.org/id/ENSG00000206820		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027338	ENSG00000206833	RNU6-20P	http://asia.ensembl.org/id/ENSG00000206833		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027339	ENSG00000206875	RNU6-761P	http://asia.ensembl.org/id/ENSG00000206875		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027340	ENSG00000206900	RNU6-98P	http://asia.ensembl.org/id/ENSG00000206900		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027341	ENSG00000206908	RNU1-136P	http://asia.ensembl.org/id/ENSG00000206908		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027342	ENSG00000206932	RNU6-4P	http://asia.ensembl.org/id/ENSG00000206932		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027343	ENSG00000206954	RNU6-1201P	http://asia.ensembl.org/id/ENSG00000206954		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027344	ENSG00000206965	RNU6-5P	http://asia.ensembl.org/id/ENSG00000206965		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027345	ENSG00000206972	RNU6-17P	http://asia.ensembl.org/id/ENSG00000206972		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027346	ENSG00000206973	RNU6-1145P	http://asia.ensembl.org/id/ENSG00000206973		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027347	ENSG00000206975	RNU6-13P	http://asia.ensembl.org/id/ENSG00000206975		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027348	ENSG00000206981	RNU6-40P	http://asia.ensembl.org/id/ENSG00000206981		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027349	ENSG00000207000	RNU6-820P	http://asia.ensembl.org/id/ENSG00000207000		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027350	ENSG00000207003	RNU6-611P	http://asia.ensembl.org/id/ENSG00000207003		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027351	ENSG00000207029	RNU6-43P	http://asia.ensembl.org/id/ENSG00000207029		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027352	ENSG00000207041	RNU6-3P	http://asia.ensembl.org/id/ENSG00000207041		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027353	ENSG00000207052	RNU6-378P	http://asia.ensembl.org/id/ENSG00000207052		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027354	ENSG00000207083	RNU6-22P	http://asia.ensembl.org/id/ENSG00000207083		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027355	ENSG00000207099	RNU6-166P	http://asia.ensembl.org/id/ENSG00000207099		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027356	ENSG00000207110	RNU1-106P	http://asia.ensembl.org/id/ENSG00000207110		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027357	ENSG00000207138	RNU6-869P	http://asia.ensembl.org/id/ENSG00000207138		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027358	ENSG00000207154	RNU1-46P	http://asia.ensembl.org/id/ENSG00000207154		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027359	ENSG00000207175	RNU1-67P	http://asia.ensembl.org/id/ENSG00000207175		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027360	ENSG00000207182	RNU1-44P	http://asia.ensembl.org/id/ENSG00000207182		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027361	ENSG00000207201	RNU1-148P	http://asia.ensembl.org/id/ENSG00000207201		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027362	ENSG00000207256	RNU6-880P	http://asia.ensembl.org/id/ENSG00000207256		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027363	ENSG00000207257	RNU6-18P	http://asia.ensembl.org/id/ENSG00000207257		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027364	ENSG00000207296	RNU6-140P	http://asia.ensembl.org/id/ENSG00000207296		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027365	ENSG00000207307	RNU6-145P	http://asia.ensembl.org/id/ENSG00000207307		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027366	ENSG00000207322	RNU1-89P	http://asia.ensembl.org/id/ENSG00000207322		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027367	ENSG00000207334	RNU6-12P	http://asia.ensembl.org/id/ENSG00000207334		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027368	ENSG00000207336	RNU6-658P	http://asia.ensembl.org/id/ENSG00000207336		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027369	ENSG00000207352	RNU6-540P	http://asia.ensembl.org/id/ENSG00000207352		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027370	ENSG00000207367	RNU6-29P	http://asia.ensembl.org/id/ENSG00000207367		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027371	ENSG00000207434	RNU6-1072P	http://asia.ensembl.org/id/ENSG00000207434		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027372	ENSG00000207454	RNU6-1104P	http://asia.ensembl.org/id/ENSG00000207454		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027373	ENSG00000207472	RNU6-41P	http://asia.ensembl.org/id/ENSG00000207472		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027374	ENSG00000207483	RNU6-1067P	http://asia.ensembl.org/id/ENSG00000207483		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027375	ENSG00000207511	RNU6-771P	http://asia.ensembl.org/id/ENSG00000207511		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027376	ENSG00000210841	RNU6ATAC26P	http://asia.ensembl.org/id/ENSG00000210841		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027377	ENSG00000212144	U8	http://asia.ensembl.org/id/ENSG00000212144		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027378	ENSG00000212153	RNU1-82P	http://asia.ensembl.org/id/ENSG00000212153		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027379	ENSG00000212170	RNU1-77P	http://asia.ensembl.org/id/ENSG00000212170		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027380	ENSG00000212424	RNU1-119P	http://asia.ensembl.org/id/ENSG00000212424		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027381	ENSG00000212473	RNU1-101P	http://asia.ensembl.org/id/ENSG00000212473		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027382	ENSG00000212550	RNU1-78P	http://asia.ensembl.org/id/ENSG00000212550		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027383	ENSG00000212605	RNU1-56P	http://asia.ensembl.org/id/ENSG00000212605		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027384	ENSG00000221038	RNU6ATAC7P	http://asia.ensembl.org/id/ENSG00000221038		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027385	ENSG00000221562	RNU6ATAC10P	http://asia.ensembl.org/id/ENSG00000221562		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027386	ENSG00000221719	SNORA3	http://asia.ensembl.org/id/ENSG00000221719		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027387	ENSG00000222126	RNU2-9P	http://asia.ensembl.org/id/ENSG00000222126		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027388	ENSG00000222177	RNU4-30P	http://asia.ensembl.org/id/ENSG00000222177		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027389	ENSG00000222222	RNU2-17P	http://asia.ensembl.org/id/ENSG00000222222		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027390	ENSG00000222276	RNU2-33P	http://asia.ensembl.org/id/ENSG00000222276		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027391	ENSG00000222293	RNU2-36P	http://asia.ensembl.org/id/ENSG00000222293		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027392	ENSG00000222355	RNU2-29P	http://asia.ensembl.org/id/ENSG00000222355		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027393	ENSG00000222389	RNU2-28P	http://asia.ensembl.org/id/ENSG00000222389		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027394	ENSG00000222414	RNU2-59P	http://asia.ensembl.org/id/ENSG00000222414		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027395	ENSG00000222438	RNU6-1077P	http://asia.ensembl.org/id/ENSG00000222438		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027396	ENSG00000222440	RNU2-26P	http://asia.ensembl.org/id/ENSG00000222440		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027397	ENSG00000222449	RNU6-1140P	http://asia.ensembl.org/id/ENSG00000222449		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027398	ENSG00000222477	RNU2-23P	http://asia.ensembl.org/id/ENSG00000222477		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027399	ENSG00000222501	RNU4-25P	http://asia.ensembl.org/id/ENSG00000222501		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027400	ENSG00000222612	RNU2-52P	http://asia.ensembl.org/id/ENSG00000222612		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027401	ENSG00000222624	RNU2-15P	http://asia.ensembl.org/id/ENSG00000222624		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027402	ENSG00000222626	RNU2-48P	http://asia.ensembl.org/id/ENSG00000222626		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027403	ENSG00000222627	RNU2-37P	http://asia.ensembl.org/id/ENSG00000222627		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027404	ENSG00000222640	RNU2-51P	http://asia.ensembl.org/id/ENSG00000222640		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027405	ENSG00000222644	RNU2-16P	http://asia.ensembl.org/id/ENSG00000222644		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027406	ENSG00000222650	RNU2-70P	http://asia.ensembl.org/id/ENSG00000222650		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027407	ENSG00000222724	RNU2-63P	http://asia.ensembl.org/id/ENSG00000222724		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027408	ENSG00000222760	RNU4-53P	http://asia.ensembl.org/id/ENSG00000222760		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027409	ENSG00000222788	RNU2-38P	http://asia.ensembl.org/id/ENSG00000222788		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027410	ENSG00000222810	RNU2-68P	http://asia.ensembl.org/id/ENSG00000222810		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027411	ENSG00000222923	RNU2-41P	http://asia.ensembl.org/id/ENSG00000222923		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027412	ENSG00000222985	RNU2-14P	http://asia.ensembl.org/id/ENSG00000222985		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027413	ENSG00000223001	RNU2-61P	http://asia.ensembl.org/id/ENSG00000223001		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027414	ENSG00000223078	RNU2-55P	http://asia.ensembl.org/id/ENSG00000223078		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027415	ENSG00000223119	RNU6-1139P	http://asia.ensembl.org/id/ENSG00000223119		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027416	ENSG00000223125	RNU2-32P	http://asia.ensembl.org/id/ENSG00000223125		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027417	ENSG00000223247	RNU2-64P	http://asia.ensembl.org/id/ENSG00000223247		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027418	ENSG00000223327	RNU2-71P	http://asia.ensembl.org/id/ENSG00000223327		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027419	ENSG00000228549	RP11-108M9.3	http://asia.ensembl.org/id/ENSG00000228549		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027420	ENSG00000232019	AC074183.4	http://asia.ensembl.org/id/ENSG00000232019		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027421	ENSG00000232533	AC093673.5	http://asia.ensembl.org/id/ENSG00000232533		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027422	ENSG00000233421	RP5-875O13.1	http://asia.ensembl.org/id/ENSG00000233421		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027423	ENSG00000233461	RP11-295G20.2	http://asia.ensembl.org/id/ENSG00000233461		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027424	ENSG00000234949	AC104667.3	http://asia.ensembl.org/id/ENSG00000234949		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027425	ENSG00000236663	AP001631.9	http://asia.ensembl.org/id/ENSG00000236663		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027426	ENSG00000238554	RNU1-88P	http://asia.ensembl.org/id/ENSG00000238554		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027427	ENSG00000238561	RNU6ATAC28P	http://asia.ensembl.org/id/ENSG00000238561		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027428	ENSG00000238833	RNU1-131P	http://asia.ensembl.org/id/ENSG00000238833		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027429	ENSG00000239023	RNU1-98P	http://asia.ensembl.org/id/ENSG00000239023		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027430	ENSG00000239128	snoU13	http://asia.ensembl.org/id/ENSG00000239128		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027431	ENSG00000239178	RNU6-671P	http://asia.ensembl.org/id/ENSG00000239178		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027432	ENSG00000246350	RP5-1186N24.3	http://asia.ensembl.org/id/ENSG00000246350		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027433	ENSG00000250920	RP11-297P16.4	http://asia.ensembl.org/id/ENSG00000250920		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027434	ENSG00000251629	RP11-774D14.1	http://asia.ensembl.org/id/ENSG00000251629		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027435	ENSG00000251870	RNU2-69P	http://asia.ensembl.org/id/ENSG00000251870		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027436	ENSG00000251954	RNU6-496P	http://asia.ensembl.org/id/ENSG00000251954		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027437	ENSG00000251955	RNU6-27P	http://asia.ensembl.org/id/ENSG00000251955		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027438	ENSG00000252018	RNU2-30P	http://asia.ensembl.org/id/ENSG00000252018		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027439	ENSG00000252145	RNU6-1225P	http://asia.ensembl.org/id/ENSG00000252145		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027440	ENSG00000252201	RNU6-1058P	http://asia.ensembl.org/id/ENSG00000252201		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027441	ENSG00000252213	SNORA74	http://asia.ensembl.org/id/ENSG00000252213		snoRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027442	ENSG00000252237	RNU4-54P	http://asia.ensembl.org/id/ENSG00000252237		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027443	ENSG00000252247	RNU6-70P	http://asia.ensembl.org/id/ENSG00000252247		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027444	ENSG00000252311	RNU1-103P	http://asia.ensembl.org/id/ENSG00000252311		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027445	ENSG00000252373	RNU6-358P	http://asia.ensembl.org/id/ENSG00000252373		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027446	ENSG00000252468	RNU2-57P	http://asia.ensembl.org/id/ENSG00000252468		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027447	ENSG00000252635	RNU2-56P	http://asia.ensembl.org/id/ENSG00000252635		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027448	ENSG00000252636	RNU6-826P	http://asia.ensembl.org/id/ENSG00000252636		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027449	ENSG00000252839	RNU6-419P	http://asia.ensembl.org/id/ENSG00000252839		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027450	ENSG00000252847	RNU2-46P	http://asia.ensembl.org/id/ENSG00000252847		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027451	ENSG00000252850	RNU1-117P	http://asia.ensembl.org/id/ENSG00000252850		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027452	ENSG00000253086	RNU6-537P	http://asia.ensembl.org/id/ENSG00000253086		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027453	ENSG00000253089	RNU1-104P	http://asia.ensembl.org/id/ENSG00000253089		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027454	ENSG00000253097	RNU2-19P	http://asia.ensembl.org/id/ENSG00000253097		snRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027455	ENSG00000253190	AC084082.3	http://asia.ensembl.org/id/ENSG00000253190		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027456	ENSG00000254144	RP11-661A12.4	http://asia.ensembl.org/id/ENSG00000254144		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027457	ENSG00000260464	RP4-561L24.3	http://asia.ensembl.org/id/ENSG00000260464		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027458	ENSG00000261183	RP11-532F12.5	http://asia.ensembl.org/id/ENSG00000261183		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027459	ENSG00000261441	RP11-217B1.2	http://asia.ensembl.org/id/ENSG00000261441		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027460	ENSG00000261519	RP11-403P17.4	http://asia.ensembl.org/id/ENSG00000261519		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027461	ENSG00000261889	RP11-473M20.16	http://asia.ensembl.org/id/ENSG00000261889		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027462	ENSG00000262899	LA16c-360H6.3	http://asia.ensembl.org/id/ENSG00000262899		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027463	ENSG00000264727	RP11-680C21.1	http://asia.ensembl.org/id/ENSG00000264727		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027464	ENSG00000265091	RP11-835E18.5	http://asia.ensembl.org/id/ENSG00000265091		lncRNA	Homo sapiens	24393600	Cytosol	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027465	ENSG00000265706	SNORD53_SNORD92	http://asia.ensembl.org/id/ENSG00000265706		snoRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027466	ENSG00000266208	CTD-2267D19.3	http://asia.ensembl.org/id/ENSG00000266208		mRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027467	ENSG00000267321	RP11-1094M14.11	http://asia.ensembl.org/id/ENSG00000267321		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027468	ENSG00000271739	U1	http://asia.ensembl.org/id/ENSG00000271739		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027469	ENSG00000272086	CTD-2186M15.3	http://asia.ensembl.org/id/ENSG00000272086		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027470	ENSG00000272189	RP3-325F22.5	http://asia.ensembl.org/id/ENSG00000272189		lncRNA	Homo sapiens	24393600	Ribosome	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027471	ENSG00000272292	U6	http://asia.ensembl.org/id/ENSG00000272292		snRNA	Homo sapiens	24393600	Nucleus	Colon cancer cell	Next-generation sequencing	"The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes. Data were collected from additional file 5: Table showing the normalized read counts for each cluster in Figure 4A. "
RLID00027472	EU069824	EU069824	http://www.ncbi.nlm.nih.gov/nuccore/?term=EU069824		mRNA	Spisula solidissima	22356233	Centrosome	Oocyte	RT-PCR	"TABLE 1: Similarity between centrosome-associated RNAs and viral sequences (from ref. [32], with modifications). Data are collected from Table 1. "
RLID00027473	EU199802	EU199802	http://www.ncbi.nlm.nih.gov/nuccore/?term=EU199802 		mRNA	Clytia hemisphaerica	22309706	Germ plasm	Oocyte	In situ hybridization	Figure 2: Perinuclear concentration of “germ plasm�in growing oocytes. A-E: Characteristic perinuclear distribution of the five mRNAs in very early oocyte stages (cyt: cytoplasm; nu: nucleus). Data are collected from Figure 2.
RLID00027474	JQ397273	JQ397273	http://www.ncbi.nlm.nih.gov/nuccore/?term=JQ397273		mRNA	Clytia hemisphaerica	22309706	Germ plasm	Oocyte	In situ hybridization	Figure 2: Perinuclear concentration of “germ plasm�in growing oocytes. A-E: Characteristic perinuclear distribution of the five mRNAs in very early oocyte stages (cyt: cytoplasm; nu: nucleus). Data are collected from Figure 2.
RLID00027475	JQ397274	JQ397274	http://www.ncbi.nlm.nih.gov/nuccore/?term=JQ397274		mRNA	Clytia hemisphaerica	22309706	Germ plasm	Oocyte	In situ hybridization	Figure 2: Perinuclear concentration of “germ plasm�in growing oocytes. A-E: Characteristic perinuclear distribution of the five mRNAs in very early oocyte stages (cyt: cytoplasm; nu: nucleus). Data are collected from Figure 2.
RLID00027476	JQ397275	JQ397275	http://www.ncbi.nlm.nih.gov/nuccore/?term=JQ397275		mRNA	Clytia hemisphaerica	22309706	Germ plasm	Oocyte	In situ hybridization	Figure 2: Perinuclear concentration of “germ plasm�in growing oocytes. A-E: Characteristic perinuclear distribution of the five mRNAs in very early oocyte stages (cyt: cytoplasm; nu: nucleus). Data are collected from Figure 2.
RLID00027477	JQ397276	JQ397276	http://www.ncbi.nlm.nih.gov/nuccore/?term=JQ397276		mRNA	Clytia hemisphaerica	22309706	Germ plasm	Oocyte	In situ hybridization	Figure 2: Perinuclear concentration of “germ plasm�in growing oocytes. A-E: Characteristic perinuclear distribution of the five mRNAs in very early oocyte stages (cyt: cytoplasm; nu: nucleus). Data are collected from Figure 2.
RLID00027478	KC190025	LincRNA-EPS	http://www.ncbi.nlm.nih.gov/nuccore/KC190025		lncRNA	Mus musculus	22155924	Nucleus	293T cell	RT-PCR	"RT-PCR analysis revealed that LincRNA-EPS was predominantly detected in the nuclear fraction (Supplemental Fig. S3A,B). "
RLID00027479	KR095173	AS-IL1A	http://www.ncbi.nlm.nih.gov/nuccore/?term=KR095173		lncRNA	Mus musculus	26179904	Nucleus	Macrophage	qRT-PCR	AS-IL1α is located in the nucleus and did not alter the stability of IL-1α mRNA.  AS-IL1a was primarily nuclear (Fig. 4A).
RLID00027480	L36162	L36162	http://www.ncbi.nlm.nih.gov/nuccore/L36162		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00027481	M18237	M18237	http://www.ncbi.nlm.nih.gov/nuccore/M18237		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027482	M73818	M73818	http://www.ncbi.nlm.nih.gov/nuccore/M73818		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00027483	MI0000060	hsa-let-7a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000060	hsa-let-7a-1L	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027484	MI0000060	hsa-let-7a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000060	hsa-let-7a-1L	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027485	MI0000060	hsa-let-7a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000060	hsa-let-7a-1L	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027486	MI0000061	hsa-let-7a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000061	hsa-let-7a-2L	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027487	MI0000061	hsa-let-7a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000061	hsa-let-7a-2L	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027488	MI0000061	hsa-let-7a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000061	hsa-let-7a-2L	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027489	MI0000062	hsa-let-7a-3	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000062	hsa-let-7a-3L	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027490	MI0000062	hsa-let-7a-3	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000062	hsa-let-7a-3L	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027491	MI0000062	hsa-let-7a-3	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000062	hsa-let-7a-3L	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027492	MI0000063	hsa-let-7b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000063	hsa-let-7bL	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027493	MI0000063	hsa-let-7b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000063	hsa-let-7bL	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00027494	MI0000063	hsa-let-7b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000063	hsa-let-7bL	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00027495	MI0000063	hsa-let-7b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000063	hsa-let-7bL	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027496	MI0000063	hsa-let-7b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000063	hsa-let-7bL	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization	"In situ hybridization of pre-mir-302a, pre-let-7b and mir-365, using specific labelled locked nucleic acids and confocal microscopy, demonstrated that these miRNA were localized in mitochondria of human myoblasts.  Strikingly, we also observed that two pre-miRNAs, pre-mir302a and pre-let-7b were located within mitochondria surrounding the nucleus (Figures 5E, F).   The present study demonstrated for the first time the localization of pre-miRNA (pre-mir-302a, pre-let-7b) and miRNA in human mitochondria isolated from muscular cells. "
RLID00027497	MI0000063	hsa-let-7b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000063	hsa-let-7bL	miRNA	Homo sapiens	21637849	Nucleus	Skeletal muscular cell	In situ hybridizationq|qRT-PCR	Mir 365 exhibited a strong signal in the mitochondria but also in some areas of the nucleus (Figure 3D). The same observation was made for pre-let-7b (Figure 3E). 
RLID00027498	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027499	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00027500	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027501	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00027502	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00027503	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027504	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027505	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027506	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027507	MI0000064	hsa-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000064	hsa-let-7cL	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00027508	MI0000065	hsa-let-7d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000065	hsa-let-7dL	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027509	MI0000065	hsa-let-7d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000065	hsa-let-7dL	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00027510	MI0000066	hsa-let-7e	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000066	hsa-let-7eL	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027511	MI0000067	hsa-let-7f-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000067	hsa-let-7f-1L	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027512	MI0000067	hsa-let-7f-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000067	hsa-let-7f-1L	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027513	MI0000067	hsa-let-7f-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000067	hsa-let-7f-1L	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027514	MI0000068	hsa-let-7f-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000068	hsa-let-7f-2L	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027515	MI0000068	hsa-let-7f-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000068	hsa-let-7f-2L	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027516	MI0000069	hsa-mir-15a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000069	hsa-mir-15	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027517	MI0000070	hsa-mir-16-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000070	"hsa-mir-16-13, hsa-mir-16 "	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027518	MI0000072	hsa-mir-18a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000072	hsa-mir-18	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027519	MI0000074	hsa-mir-19b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000074		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027520	MI0000076	hsa-mir-20a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000076	hsa-mir-20	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027521	MI0000076	hsa-mir-20a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000076	hsa-mir-20	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027522	MI0000076	hsa-mir-20a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000076	hsa-mir-20	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027523	MI0000077	hsa-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000077		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027524	MI0000077	hsa-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000077		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027525	MI0000077	hsa-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000077		miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027526	MI0000077	hsa-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000077		miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027527	MI0000077	hsa-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000077		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027528	MI0000077	hsa-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000077		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027529	MI0000080	hsa-mir-24-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000080		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027530	MI0000080	hsa-mir-24-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000080		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027531	MI0000081	hsa-mir-24-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000081		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027532	MI0000081	hsa-mir-24-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000081		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027533	MI0000081	hsa-mir-24-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000081		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027534	MI0000083	hsa-mir-26a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000083	hsa-mir-26a	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027535	MI0000083	hsa-mir-26a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000083	hsa-mir-26a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027536	MI0000083	hsa-mir-26a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000083	hsa-mir-26a	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027537	MI0000085	hsa-mir-27a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000085	hsa-mir-27	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027538	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027539	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027540	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00027541	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027542	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027543	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027544	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027545	MI0000088	hsa-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000088	hsa-mir-30	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027546	MI0000090	hsa-mir-32	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000090		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027547	MI0000095	hsa-mir-93	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000095	"hsa-mir-93-7.1, hsa-mir-93-1 "	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027548	MI0000095	hsa-mir-93	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000095	"hsa-mir-93-7.1, hsa-mir-93-1 "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027549	MI0000097	hsa-mir-95	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000097	hsa-mir-95-4	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027550	MI0000097	hsa-mir-95	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000097	hsa-mir-95-4	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00027551	MI0000098	hsa-mir-96	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000098	hsa-mir-96-7	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027552	MI0000100	hsa-mir-98	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000100	hsa-mir-98-X	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027553	MI0000100	hsa-mir-98	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000100	hsa-mir-98-X	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027554	MI0000101	hsa-mir-99a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000101	"hsa-mir-99-21, hsa-mir-99 "	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027555	MI0000102	hsa-mir-100	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000102	hsa-mir-100-11	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027556	MI0000102	hsa-mir-100	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000102	hsa-mir-100-11	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027557	MI0000103	hsa-mir-101-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000103	"hsa-mir-101-1, hsa-mir-101 "	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027558	MI0000108	hsa-mir-103a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000108	"hsa-mir-103-20, hsa-mir-103-2 "	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027559	MI0000109	hsa-mir-103a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000109	"hsa-mir-103-5, hsa-mir-103-1 "	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027560	MI0000115	hsa-mir-16-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000115	hsa-mir-16-3	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027561	MI0000118	dme-mir-2a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000118		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027562	MI0000127	dme-mir-7	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000127		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027563	MI0000128	dme-mir-8	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000128		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027564	MI0000128	dme-mir-8	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000128		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027565	MI0000131	dme-mir-11	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000131		miRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027566	MI0000131	dme-mir-11	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000131		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027567	MI0000131	dme-mir-11	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000131		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027568	MI0000136	dme-mir-14	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000136		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027569	MI0000136	dme-mir-14	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000136		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027570	MI0000146	mmu-mir-99a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000146		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00027571	MI0000146	mmu-mir-99a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000146		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.17b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00027572	MI0000150	mmu-mir-124-3	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000150	"mmu-mir-124a, mmu-mir-124a-3 "	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.12b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00027573	MI0000152	mmu-mir-125b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000152	mmu-mir-125b	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00027574	MI0000152	mmu-mir-125b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000152	mmu-mir-125b	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.14b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00027575	MI0000160	mmu-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000160		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00027576	MI0000160	mmu-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000160		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.15b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00027577	MI0000254	hsa-mir-30c-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000254	hsa-mir-30c	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027578	MI0000255	hsa-mir-30d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000255		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027579	MI0000257	mmu-mir-143	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000257		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Individual microRNAs showed a wide range of relative enrichment ratios (fig.3). The lowest ratio was observed with mir-143, which was ?7-fold less abundant in the SYN fraction than in the total homogenate, whereas on the other hand, mir-200c was ?5-fold more abundant in the SYN fraction. "
RLID00027580	MI0000261	hsa-mir-139	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000261		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027581	MI0000263	hsa-mir-7-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000263		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027582	MI0000263	hsa-mir-7-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000263		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027583	MI0000263	hsa-mir-7-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000263		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027584	MI0000269	hsa-mir-181a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000269	hsa-mir-181a	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027585	MI0000272	hsa-mir-182	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000272	hsa-mir-182-as	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027586	MI0000273	hsa-mir-183	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000273		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027587	MI0000279	hsa-mir-196a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000279	hsa-mir-196-2	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027588	MI0000279	hsa-mir-196a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000279	hsa-mir-196-2	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027589	MI0000284	hsa-mir-204	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000284		miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027590	MI0000285	hsa-mir-205	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000285		miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027591	MI0000289	hsa-mir-181a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000289	hsa-mir-213	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027592	MI0000292	hsa-mir-216a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000292	hsa-mir-216	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027593	MI0000292	hsa-mir-216a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000292	hsa-mir-216	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027594	MI0000296	hsa-mir-219a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000296	hsa-mir-219	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027595	MI0000298	hsa-mir-221	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000298		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027596	MI0000300	hsa-mir-223	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000300		miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027597	MI0000343	dme-mir-263a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000343	dme-mir-263	miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027598	MI0000354	dme-mir-184	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000354		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027599	MI0000354	dme-mir-184	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000354		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027600	MI0000356	dme-mir-275	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000356		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027601	MI0000357	dme-mir-92a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000357		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027602	MI0000363	dme-mir-279	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000363		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027603	MI0000363	dme-mir-279	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000363		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027604	MI0000367	dme-mir-282	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000367		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027605	MI0000368	dme-mir-283	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000368		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027606	MI0000370	dme-mir-281-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000370		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027607	MI0000370	dme-mir-281-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000370		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027608	MI0000378	dme-mir-100	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000378		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027609	MI0000387	dme-bantam	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000387	"dme-bantam, bantam "	miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027610	MI0000409	dme-mir-303	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000409		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027611	MI0000410	dme-mir-31b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000410		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027612	MI0000413	dme-mir-9c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000413		miRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027613	MI0000430	dme-mir-318	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000430		miRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00027614	MI0000433	hsa-let-7g	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000433		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027615	MI0000433	hsa-let-7g	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000433		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00027616	MI0000434	hsa-let-7i	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000434		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027617	MI0000434	hsa-let-7i	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000434		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00027618	MI0000434	hsa-let-7i	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000434		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027619	MI0000438	hsa-mir-15b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000438		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027620	MI0000439	hsa-mir-23b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000439		miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027621	MI0000456	hsa-mir-140	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000456		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027622	MI0000458	hsa-mir-142	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000458		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027623	MI0000462	hsa-mir-152	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000462		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027624	MI0000462	hsa-mir-152	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000462		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027625	MI0000462	hsa-mir-152	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000462		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027626	MI0000462	hsa-mir-152	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000462		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027627	MI0000462	hsa-mir-152	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000462		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027628	MI0000466	hsa-mir-9-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000466		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027629	MI0000467	hsa-mir-9-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000467		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027630	MI0000468	hsa-mir-9-3	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000468		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027631	MI0000469	hsa-mir-125a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000469		miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027632	MI0000471	hsa-mir-126	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000471		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027633	MI0000471	hsa-mir-126	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000471		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027634	MI0000474	hsa-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000474		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027635	MI0000474	hsa-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000474		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027636	MI0000474	hsa-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000474		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027637	MI0000476	hsa-mir-138-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000476		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027638	MI0000476	hsa-mir-138-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000476		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027639	MI0000483	hsa-mir-186	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000483		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027640	MI0000483	hsa-mir-186	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000483		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027641	MI0000484	hsa-mir-188	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000484		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027642	MI0000621	mmu-mir-339	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000621		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00027643	MI0000621	mmu-mir-339	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000621		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.16b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00027644	MI0000694	mmu-mir-200c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000694		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Individual microRNAs showed a wide range of relative enrichment ratios (fig.3). The lowest ratio was observed with mir-143, which was ?7-fold less abundant in the SYN fraction than in the total homogenate, whereas on the other hand, mir-200c was ?5-fold more abundant in the SYN fraction. "
RLID00027645	MI0000725	mmu-mir-125b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000725		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00027646	MI0000725	mmu-mir-125b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000725		miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.13b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00027647	MI0000727	hsa-mir-128-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000727	hsa-mir-128b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00027648	MI0000734	hsa-mir-106b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000734		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027649	MI0000734	hsa-mir-106b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000734		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027650	MI0000738	hsa-mir-302a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000738	hsa-mir-302	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00027651	MI0000738	hsa-mir-302a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000738	hsa-mir-302	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization	"In situ hybridization of pre-mir-302a, pre-let-7b and mir-365, using specific labelled locked nucleic acids and confocal microscopy, demonstrated that these miRNA were localized in mitochondria of human myoblasts.  Strikingly, we also observed that two pre-miRNAs, pre-mir302a and pre-let-7b were located within mitochondria surrounding the nucleus (Figures 5E, F).  The present study demonstrated for the first time the localization of pre-miRNA (pre-mir-302a, pre-let-7b) and miRNA in human mitochondria isolated from muscular cells. "
RLID00027652	MI0000739	hsa-mir-101-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000739		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027653	MI0000746	hsa-mir-99b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000746		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027654	MI0000746	hsa-mir-99b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000746		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027655	MI0000749	hsa-mir-30e	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000749		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027656	MI0000750	hsa-mir-26a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000750		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027657	MI0000760	hsa-mir-361	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000760		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027658	MI0000767	hsa-mir-365a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000767	hsa-mir-365-1	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"In situ hybridization of pre-mir-302a, pre-let-7b and mir-365, using specific labelled locked nucleic acids and confocal microscopy, demonstrated that these miRNA were localized in mitochondria of human myoblasts. "
RLID00027659	MI0000767	hsa-mir-365a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000767	hsa-mir-365-1	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization	"In situ hybridization of pre-mir-302a, pre-let-7b and mir-367, using specific labelled locked nucleic acids and confocal microscopy, demonstrated that these miRNA were localized in mitochondria of human myoblasts. The top-20 most detected microRNA in the mitochondria of the human myotubes were mir-720, 133b, 1974, 24, 133a, 125a-5p, 1979, 103, 125b, 103, 221, 23a, let-7b, 423-3p, 106a, 23b, 92a, 193b and 365. Among them, the mir-365, detected by in situ hybridization, was confirmed. "
RLID00027660	MI0000767	hsa-mir-365a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000767	hsa-mir-365-1	miRNA	Homo sapiens	21637849	Nucleus	Skeletal muscular cell	In situ hybridizationq|qRT-PCR	Mir 365 exhibited a strong signal in the mitochondria but also in some areas of the nucleus (Figure 3D). The same observation was made for pre-let-7b (Figure 3E). 
RLID00027661	MI0000778	hsa-mir-370	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000778		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027662	MI0000778	hsa-mir-370	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000778		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027663	MI0000778	hsa-mir-370	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000778		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027664	MI0000782	hsa-mir-374a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000782	hsa-mir-374	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027665	MI0000786	hsa-mir-378a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000786	hsa-mir-378	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027666	MI0000786	hsa-mir-378a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000786	hsa-mir-378	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027667	MI0000787	hsa-mir-379	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000787		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027668	MI0000791	hsa-mir-383	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000791		miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00027669	MI0000809	hsa-mir-151a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000809	hsa-mir-151	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027670	MI0000810	hsa-mir-135b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000810		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027671	MI0000811	hsa-mir-148b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000811		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027672	MI0000811	hsa-mir-148b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000811		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027673	MI0000813	hsa-mir-324	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000813		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027674	MI0000815	hsa-mir-339	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000815		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027675	MI0000815	hsa-mir-339	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000815		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027676	MI0000825	hsa-mir-345	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000825		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027677	MI0000856	rno-mir-25	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000856		miRNA	Rattus norvegicus	25919946	Cell body	DRG neurons	Fluorescence in situ hybridization	"In cultured DRG neurons, pre-miRNA-25 was visible by FISH in cell body and axons (arrows). "
RLID00027678	MI0000856	rno-mir-25	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000856		miRNA	Rattus norvegicus	25919946	Axon	DRG neurons	Fluorescence in situ hybridization	"In cultured DRG neurons, pre-miRNA-25 was visible by FISH in cell body and axons (arrows). "
RLID00027679	MI0000907	rno-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000907		miRNA	Rattus norvegicus	23651854	Dendrite	Hippocampus	Fluorescence in situ hybridization|qRT-PCR	"We found that the neuronal precursor-miRNA-134 (pre-miR-134) accumulates in dendrites of hippocampal neurons and at synapses in vivo.   Together, our data obtained with synaptosomes, FISH, and compartmentalized neuron cultures support a specific localization of endogenous pre-miR-134 in dendrites of primary hippocampal neurons and at synapses in vivo. "
RLID00027680	MI0000907	rno-mir-134	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000907		miRNA	Rattus norvegicus	23651854	Synapse	Hippocampus	Fluorescence in situ hybridization|qRT-PCR	"We found that the neuronal precursor-miRNA-134 (pre-miR-134) accumulates in dendrites of hippocampal neurons and at synapses in vivo.   Together, our data obtained with synaptosomes, FISH, and compartmentalized neuron cultures support a specific localization of endogenous pre-miR-134 in dendrites of primary hippocampal neurons and at synapses in vivo. "
RLID00027681	MI0000912	rno-mir-138-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000912		miRNA	Rattus norvegicus	25919946	Cell body	DRG neurons	PCR	"Amplicons for pre-miRNAs-138-1, 150 and 320 were readily visualized in RNA prepared from the cell body. "
RLID00027682	MI0000920	rno-mir-150	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000920		miRNA	Rattus norvegicus	25919946	Cell body	DRG neurons	PCR	"Amplicons for pre-miRNAs-138-1, 150 and 320 were readily visualized in RNA prepared from the cell body. "
RLID00027683	MI0000972	rno-mir-320	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000972		miRNA	Rattus norvegicus	25919946	Cell body	DRG neurons	PCR	"Amplicons for pre-miRNAs-138-1, 150 and 320 were readily visualized in RNA prepared from the cell body. "
RLID00027684	MI0001150	hsa-mir-196b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001150		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027685	MI0001445	hsa-mir-423	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001445		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027686	MI0001445	hsa-mir-423	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001445		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027687	MI0001448	hsa-mir-425	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001448		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027688	MI0001448	hsa-mir-425	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001448		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027689	MI0001448	hsa-mir-425	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001448		miRNA	Homo sapiens	24937531	Exosome	Plasma	qRT-PCR	"For miRNome analysis, two homogeneous samples were created: one by pooling 2 μL of RNA from exosomes of diabetic patients and the other by pooling RNA from exosomes of control subjects. After reverse transcription (mirCURY LNA universal cDNA synthesis kit; Exiqon), the reaction was performed on a serum/plasma focus miRNA PCR panel 384 well (V1.R) (Exiqon) using the ABI 7900HT (Applied Biosystems). The most stable miRNAs (miR-425 and miR-423-5p) were identified by NormFinder and GeNorm, validated on each sample, and used as normalizators for circulating miRNAs. "
RLID00027690	MI0001652	hsa-mir-450a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001652	"hsa-mir-450, hsa-mir-450-1 "	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027691	MI0001723	hsa-mir-433	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001723		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027692	MI0001724	rno-mir-433	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001724		miRNA	Rattus norvegicus	25919946	Axon	DRG neurons	Fluorescence in situ hybridization	"Pre-miRNA-433 in the axons of cultured DRG neurons, and sciatic nerve FISH samples showed clear increase in pre-miRNA-433 in axons in vivo after sciatic nerve crush "
RLID00027693	MI0001729	hsa-mir-451a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001729	hsa-mir-451	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027694	MI0001729	hsa-mir-451a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001729	hsa-mir-451	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027695	MI0001729	hsa-mir-451a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001729	hsa-mir-451	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027696	MI0001733	hsa-mir-452	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001733		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027697	MI0001733	hsa-mir-452	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001733		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027698	MI0001733	hsa-mir-452	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0001733		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027699	MI0002412	ssc-mir-106a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002412		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027700	MI0002413	ssc-mir-122	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002413	ssc-mir-122a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027701	MI0002414	ssc-mir-125b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002414	ssc-mir-125b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027702	MI0002417	ssc-mir-145	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002417		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027703	MI0002418	ssc-mir-148a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002418		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027704	MI0002419	ssc-mir-15b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002419		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027705	MI0002420	ssc-mir-181b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002420	ssc-mir-181b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027706	MI0002421	ssc-mir-184	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002421		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027707	MI0002427	ssc-mir-23a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002427		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027708	MI0002428	ssc-mir-24-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002428	ssc-mir-24	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027709	MI0002429	ssc-mir-26a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002429		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027710	MI0002430	ssc-mir-28	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002430		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027711	MI0002431	ssc-mir-29b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002431	ssc-mir-29b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027712	MI0002433	ssc-mir-323	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002433		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027713	MI0002434	ssc-mir-326	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002434		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027714	MI0002435	ssc-mir-7-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002435	ssc-mir-7	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027715	MI0002437	ssc-mir-140	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002437		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027716	MI0002438	ssc-mir-181c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002438		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027717	MI0002439	ssc-mir-183	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002439		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027718	MI0002440	ssc-mir-205	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002440		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027719	MI0002442	ssc-mir-27a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002442		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027720	MI0002445	ssc-let-7c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002445		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027721	MI0002446	ssc-let-7f-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002446	ssc-let-7f	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027722	MI0002447	ssc-let-7i	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002447		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027723	MI0002448	ssc-mir-103-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002448	ssc-mir-103	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027724	MI0002449	ssc-mir-107	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002449		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027725	MI0002450	ssc-mir-124a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002450	ssc-mir-124a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027726	MI0002451	ssc-mir-128-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002451	"ssc-mir-128a, ssc-mir-128 "	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027727	MI0002453	ssc-mir-139	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002453		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027728	MI0002455	ssc-mir-18a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002455	ssc-mir-18	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027729	MI0002456	ssc-mir-186	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002456		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027730	MI0002458	ssc-mir-204	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002458		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027731	MI0002459	ssc-mir-21	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002459		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027732	MI0002460	ssc-mir-29c	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002460		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027733	MI0002461	ssc-mir-30c-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002461	ssc-mir-30c	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027734	MI0002462	ssc-mir-9-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002462		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027735	MI0002463	ssc-mir-9-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002463		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027736	MI0002465	hsa-mir-410	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002465		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027737	MI0002468	hsa-mir-484	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002468		miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027738	MI0002470	hsa-mir-486-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0002470	hsa-mir-486	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027739	MI0003139	hsa-mir-181d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003139		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027740	MI0003184	hsa-mir-500a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003184	hsa-mir-500	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027741	MI0003184	hsa-mir-500a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003184	hsa-mir-500	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027742	MI0003185	hsa-mir-501	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003185		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027743	MI0003187	hsa-mir-450a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003187	hsa-mir-450-2	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027744	MI0003188	hsa-mir-503	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003188		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027745	MI0003188	hsa-mir-503	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003188		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027746	MI0003189	hsa-mir-504	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003189		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027747	MI0003513	hsa-mir-455	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003513		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027748	MI0003560	hsa-mir-92b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003560		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027749	MI0003591	hsa-mir-584	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003591		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027750	MI0003609	hsa-mir-597	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003609		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027751	MI0003610	hsa-mir-598	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003610		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027752	MI0003641	hsa-mir-627	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003641		miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00027753	MI0003642	hsa-mir-628	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003642		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027754	MI0003643	hsa-mir-629	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003643		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027755	MI0003643	hsa-mir-629	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003643		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027756	MI0003646	hsa-mir-33b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003646		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027757	MI0003646	hsa-mir-33b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003646		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027758	MI0003685	hsa-mir-421	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003685		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027759	MI0003686	hsa-mir-542	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003686		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027760	MI0003686	hsa-mir-542	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003686		miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027761	MI0003686	hsa-mir-542	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003686		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027762	MI0003763	hsa-mir-767	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003763		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027763	MI0003763	hsa-mir-767	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003763		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027764	MI0003780	hsa-mir-1296	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003780		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027765	MI0003815	hsa-mir-1301	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003815		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00027766	MI0003815	hsa-mir-1301	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003815		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027767	MI0003815	hsa-mir-1301	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0003815		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027768	MI0005416	hsa-mir-675	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005416		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027769	MI0005532	hsa-mir-874	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005532		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00027770	MI0005532	hsa-mir-874	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005532		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00027771	MI0005559	hsa-mir-744	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005559		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027772	MI0005559	hsa-mir-744	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005559		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027773	MI0005561	hsa-mir-877	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005561		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027774	MI0005562	hsa-mir-887	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005562		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER).
RLID00027775	MI0005762	hsa-mir-940	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005762		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027776	MI0006273	hsa-mir-1180	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006273		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027777	MI0006273	hsa-mir-1180	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006273		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027778	MI0006273	hsa-mir-1180	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006273		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027779	MI0006311	hsa-mir-1225	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006311		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027780	MI0006313	hsa-mir-1226	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006313		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027781	MI0006326	hsa-mir-1236	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006326		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027782	MI0006353	hsa-mir-1291	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006353		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027783	MI0006353	hsa-mir-1291	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006353		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027784	MI0006383	hsa-mir-1248	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006383		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027785	MI0006383	hsa-mir-1248	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006383		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027786	MI0006419	hsa-mir-1277	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006419		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027787	MI0006442	hsa-mir-664a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006442	hsa-mir-664	miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027788	MI0006442	hsa-mir-664a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006442	hsa-mir-664	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027789	MI0006444	hsa-mir-1307	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006444		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027790	MI0006444	hsa-mir-1307	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0006444		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027791	MI0007077	ssc-mir-99b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0007077		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027792	MI0007258	hsa-mir-1537	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0007258		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027793	MI0007261	hsa-mir-103b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0007261	hsa-mir-103-1-as	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027794	MI0007262	hsa-mir-103b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0007262	hsa-mir-103-2-as	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027795	MI0008211	ssc-mir-15a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008211		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027796	MI0008213	ssc-mir-16-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008213	ssc-mir-16-2	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027797	MI0008214	ssc-mir-17	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008214		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027798	MI0008215	ssc-mir-30b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008215		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027799	MI0008216	ssc-mir-34a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008216		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027800	MI0008217	ssc-mir-130a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008217		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027801	MI0008218	ssc-mir-185	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008218		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027802	MI0008219	ssc-mir-199b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008219		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027803	MI0008220	ssc-mir-210	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008220		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027804	MI0008221	ssc-mir-221	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008221		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027805	MI0008329	hsa-mir-1908	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0008329		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027806	MI0010678	ssc-mir-101-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010678	ssc-mir-101a-1	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027807	MI0010679	ssc-mir-101-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010679	ssc-mir-101a-2	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027808	MI0010680	ssc-mir-124a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010680		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027809	MI0010681	ssc-mir-133a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010681	ssc-mir-133a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027810	MI0010682	ssc-mir-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010682	ssc-mir-1a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027811	MI0010685	ssc-mir-146b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010685		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027812	MI0010686	ssc-mir-181a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010686	ssc-mir-181a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027813	MI0010688	ssc-mir-30a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0010688		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027814	MI0011284	hsa-mir-2277	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0011284		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027815	MI0011284	hsa-mir-2277	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0011284		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027816	MI0013084	ssc-mir-206	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013084		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027817	MI0013085	ssc-let-7a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013085	ssc-let-7a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027818	MI0013086	ssc-let-7e	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013086		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027819	MI0013087	ssc-let-7g	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013087		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027820	MI0013088	ssc-mir-378-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013088	ssc-mir-378	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027821	MI0013090	ssc-mir-29a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013090		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027822	MI0013091	ssc-mir-30d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013091		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027823	MI0013092	ssc-mir-30e	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013092		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027824	MI0013093	ssc-mir-199a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013093	ssc-mir-199a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027825	MI0013094	ssc-mir-128-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013094		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027826	MI0013095	ssc-mir-191	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013095		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027827	MI0013097	ssc-mir-320	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013097		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027828	MI0013098	ssc-mir-143	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013098		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027829	MI0013100	ssc-mir-151	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013100		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027830	MI0013101	ssc-mir-10a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013101		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027831	MI0013102	ssc-mir-10b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013102		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027832	MI0013103	ssc-mir-486-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013103	ssc-mir-486	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027833	MI0013104	ssc-mir-152	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013104		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027834	MI0013105	ssc-mir-103-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013105		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027835	MI0013106	ssc-mir-181a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013106		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027836	MI0013107	ssc-mir-181b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013107		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027837	MI0013108	ssc-mir-181d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013108		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027838	MI0013109	ssc-mir-27b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013109		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027839	MI0013110	ssc-mir-340-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013110	ssc-mir-340	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027840	MI0013111	ssc-mir-24-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013111		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027841	MI0013112	ssc-mir-23b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013112		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027842	MI0013113	ssc-mir-193a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013113		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027843	MI0013114	ssc-mir-99a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013114		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027844	MI0013115	ssc-mir-125a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013115		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027845	MI0013117	ssc-mir-345-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013117	ssc-mir-345	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027846	MI0013118	ssc-mir-148b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013118		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027847	MI0013120	ssc-mir-365-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013120		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027848	MI0013122	ssc-mir-98	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013122		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027849	MI0013124	ssc-mir-92a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013124		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027850	MI0013125	ssc-mir-92a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013125		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027851	MI0013127	ssc-mir-192	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013127		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027852	MI0013128	ssc-mir-100	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013128		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027853	MI0013130	ssc-mir-374a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013130		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027854	MI0013131	ssc-mir-374b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013131		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027855	MI0013132	ssc-mir-34c-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013132	ssc-mir-34c	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3’UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027856	MI0013134	ssc-mir-142	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013134		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027857	MI0013136	ssc-mir-130b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013136		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027858	MI0013137	ssc-mir-196b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013137	ssc-mir-196b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027859	MI0013139	ssc-mir-497	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013139		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027860	MI0013142	ssc-mir-331	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013142		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027861	MI0013143	ssc-mir-504	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013143		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027862	MI0013144	ssc-mir-127	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013144		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027863	MI0013145	ssc-mir-361	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013145		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027864	MI0013147	ssc-mir-1307	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013147		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027865	MI0013148	ssc-mir-1306	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013148		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027866	MI0013149	ssc-mir-339-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013149	ssc-mir-339	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027867	MI0013151	ssc-mir-222	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013151		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027868	MI0013152	ssc-mir-676-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013152	ssc-mir-676	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027869	MI0013153	ssc-mir-342	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013153		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027870	MI0013156	ssc-mir-935	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013156		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027871	MI0013158	ssc-mir-328	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013158		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027872	MI0013159	ssc-mir-19b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013159		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027873	MI0013160	ssc-mir-19b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013160		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027874	MI0013161	ssc-mir-574	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013161		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027875	MI0013162	ssc-mir-1839	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013162		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027876	MI0013164	ssc-mir-1285	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013164		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027877	MI0013166	ssc-mir-500	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013166		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027878	MI0013167	ssc-mir-324	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013167		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027879	MI0013169	ssc-mir-129a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013169	ssc-mir-129	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027880	MI0013171	ssc-mir-505	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013171		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027881	MI0013172	ssc-mir-125b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0013172		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027882	MI0014189	hsa-mir-3160-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0014189		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027883	MI0014769	ssc-mir-744	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0014769		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027884	MI0014770	ssc-mir-22	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0014770		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027885	MI0014771	ssc-mir-363-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0014771	ssc-mir-363	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027886	MI0014772	ssc-mir-299	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0014772		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027887	MI0014773	ssc-mir-338	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0014773		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027888	MI0015903	hsa-mir-500b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015903		miRNA	Homo sapiens	22058130	Cytoplasm	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027889	MI0015906	ssc-mir-296	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015906		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027890	MI0015910	ssc-mir-4331	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015910		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027891	MI0015911	ssc-mir-382	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015911		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027892	MI0015913	ssc-mir-362	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015913		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027893	MI0015917	ssc-mir-4332	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015917		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027894	MI0015922	ssc-mir-1271	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0015922		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027895	MI0016618	ssc-mir-30c-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016618		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027896	MI0016620	ssc-mir-149	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016620		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027897	MI0016621	ssc-mir-199a-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016621		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027898	MI0016622	ssc-mir-378-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016622		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027899	MI0016623	ssc-mir-451	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016623		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027900	MI0016691	csi-MIR156	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016691		miRNA	Citrus sinensis	26033697	Nucleus	-	Immunoprecipitation	The co-immunoprecipitation of viral 24K protein with pre-miR156a or pre-miR171a suggests that the alteration in the processing of these precursors might be caused by a direct or indirect interaction with this particular viral protein. This result is also consistent with the nuclear localization of both miRNA precursors and the CPsV 24K protein. 
RLID00027901	MI0016699	csi-MIR171a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016699		miRNA	Citrus sinensis	26033697	Nucleus	-	Immunoprecipitation	The co-immunoprecipitation of viral 24K protein with pre-miR156a or pre-miR171a suggests that the alteration in the processing of these precursors might be caused by a direct or indirect interaction with this particular viral protein. This result is also consistent with the nuclear localization of both miRNA precursors and the CPsV 24K protein. 
RLID00027902	MI0016792	hsa-mir-4449	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0016792		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00027903	MI0017360	hsa-mir-451b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017360		miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027904	MI0017984	ssc-let-7a-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017984		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027905	MI0017986	ssc-mir-129b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017986		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027906	MI0017988	ssc-mir-190b	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017988	ssc-mir-190	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027907	MI0017990	ssc-mir-219a	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017990	ssc-mir-219	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027908	MI0017991	ssc-mir-429	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017991		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027909	MI0017992	ssc-mir-486-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017992		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027910	MI0017993	ssc-mir-491	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017993		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027911	MI0017996	ssc-mir-1343	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017996		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027912	MI0017997	ssc-mir-2320	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0017997		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027913	MI0022120	ssc-let-7d	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0022120		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027914	MI0022121	ssc-let-7f-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0022121		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027915	MI0022124	ssc-mir-20b-1	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0022124		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027916	MI0022125	ssc-mir-20b-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0022125		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027917	MI0022128	ssc-mir-34c-2	http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0022128		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00027918	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00027919	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00027920	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00027921	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00027922	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24937531	Circulating	Plasma	qRT-PCR	"Quantitative RT-PCR validation confirmed the significant up-regulation of miR-326 (P = .004) and down-regulation of let-7a (P < .001) and let-7f (P = .003). Notably, an inverse negative correlation was found between circulating miR-326 and its putative target adiponectin (p = -0.479, P = .009).  "
RLID00027923	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00027924	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00027925	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00027926	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00027927	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00027928	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00027929	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22427800	Exosome	Serum	RT-PCR	The miRNAs tested in serum and saliva samples are shown in Table 1. These miRNAs were selected because they are either ubiquitously expressed or have been reported as biomarkers (Table 1). The relative concentration of these microRNAs was determined by calculating the difference of Ct values between the exosome samples and the exosome-depleted supernatant. A 1-unit difference in the Ct value between the miRNAs isolated from the exosomal pellet or supernatant represents a 2-fold difference in the amount of input miRNA. Data are collected from Table 1: List of miRNAs tested in serum and saliva samples.
RLID00027930	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00027931	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00027932	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00027933	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00027934	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00027935	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00027936	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00027937	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00027938	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00027939	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00027940	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00027941	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00027942	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00027943	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027944	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00027945	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00027946	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027947	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027948	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00027949	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027950	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027951	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	26304123	Endoplasmic reticulum	HEK293 cell	Northern blo|RT-PCR	"To confirm the association of miRNA and Ago2 protein with rER and associated structures, we fractionated isotonic HEK293 cell lysates on a 3-30% OptiPrep gradient and analyzed the individual fractions. We observed that the majority of Ago2 and let-7a miRNA accumulated with the ER-positive fractions (Fig. 1C). "
RLID00027952	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00027953	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00027954	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00027955	MIMAT0000062	hsa-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062	hsa-let-7a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00027956	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22884882	Circulating	Plasma	Microarray	"To explore a potential novel biomarker, we examined the cellular and plasma miRNA profiles in adult T-cell leukemia (ATL) characterized by diverse clinical features. Methods and results : Using CD4-positive cells isolated from 2 non-infected healthy individuals, 3 chronic ATL patients and 3 acute ATL patients, cellular miRNAs were profiled by microarray. The microarray screened 5 miRNAs namely miR-155, let-7g, miR-126, miR-130a and let-7b because of the large difference in their expression in diseased vs. that of healthy controls. "
RLID00027957	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00027958	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00027959	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00027960	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00027961	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00027962	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00027963	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00027964	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00027965	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00027966	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00027967	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00027968	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00027969	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00027970	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00027971	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00027972	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00027973	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00027974	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00027975	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00027976	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00027977	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00027978	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00027979	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00027980	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00027981	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00027982	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00027983	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00027984	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00027985	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00027986	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00027987	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027988	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00027989	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00027990	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027991	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00027992	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-133a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00027993	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00027994	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00027995	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00027996	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00027997	MIMAT0000063	hsa-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000063	hsa-let-7b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00027998	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00027999	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23424776	Circulating	Blood	qRT-PCR|Microarray	"Five miRNAs (let-7c, miR-16, miR- 449, miR-181a and miR-181b) were found to exhibit similar expression patterns (p < 0.05) in peripheral blood when compared to data obtained by using bone marrow aspirates from MM patients in other studies.  "
RLID00028000	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028001	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028002	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028003	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00028004	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028005	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028006	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028007	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028008	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00028009	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028010	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028011	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028012	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028013	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028014	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028015	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028016	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028017	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028018	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028019	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028020	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028021	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028022	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028023	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028024	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028025	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028026	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-135a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00028027	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028028	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028029	MIMAT0000064	hsa-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000064		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028030	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028031	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028032	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028033	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028034	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24577456	Circulating	Serum	qRT-PCR|Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00028035	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028036	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028037	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028038	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028039	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028040	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028041	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028042	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028043	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028044	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028045	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00028046	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00028047	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028048	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028049	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028050	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028051	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028052	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028053	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028054	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028055	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028056	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028057	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028058	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028059	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028060	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028061	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	20864815	Cytoplasm	Colon cancer cell	RT-PCR|Northern blot|Microarray	"MicroRNAs such as let-7d, miR-19a, miR-19b and miR-200b, demonstrated nuclear localization at a level similar to that of cytoplasm. "
RLID00028062	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-136a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00028063	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028064	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028065	MIMAT0000065	hsa-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000065	hsa-let-7d	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028066	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	21690488	Circulating	Plasma	qRT-PCR	"The expressions of selected miRNAs (miR-296-5p, let-7e, and a human cytomegalovirus [HCMV]-encoded miRNA, hcmv-miR-UL112) were validated independently in plasma samples from 24 hypertensive patients and 22 control subjects. "
RLID00028067	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028068	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028069	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028070	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028071	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028072	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028073	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028074	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028075	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	21924071	Circulating	Plasma	Microarray	"MiR-296-5p (Fold change 0.47, P = 0.013) and miR-133b (Fold change 0.57, P = 0.033) were consistently down-regulated in the patient plasma, whereas let-7e (Fold change 1.62, P = 0.009) and hcmv-miR-UL112 (Fold change 2.72, P = 0.004), one human cytomegalovirus encoded microRNAs, were up-regulated in the patient samples.  "
RLID00028076	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028077	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028078	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028079	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028080	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00028081	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00028082	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028083	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028084	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028085	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028086	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028087	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028088	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028089	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028090	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028091	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028092	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028093	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028094	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	19628621	Nucleolus	Myoblast	Microarray 	"Five miRNAs, miR-340-5p, miR-351, miR-494, miR-664, and let-7e, were significantly concentrated (two- to eightfold) in the nucleolus compared with the nucleoplasm and/or the cytoplasm (Fig. 2A; Supplemental Table 1). "
RLID00028095	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-138a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00028096	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028097	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028098	MIMAT0000066	hsa-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000066	hsa-let-7e	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028099	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028100	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028101	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028102	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24937531	Circulating	Plasma	qRT-PCR	"Quantitative RT-PCR validation confirmed the significant up-regulation of miR-326 (P = .004) and down-regulation of let-7a (P < .001) and let-7f (P = .003). Notably, an inverse negative correlation was found between circulating miR-326 and its putative target adiponectin (p = -0.479, P = .009).  "
RLID00028103	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028104	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028105	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028106	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028107	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028108	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028109	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028110	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00028111	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028112	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028113	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028114	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028115	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028116	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028117	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028118	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028119	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028120	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028121	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028122	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028123	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028124	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028125	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028126	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-139a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00028127	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028128	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028129	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028130	MIMAT0000067	hsa-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000067	hsa-let-7f	miRNA	Homo sapiens	22997154	Circulating	Plasma	Microarray	"Co-transfection with HBV replicative constructs suggested that let-7f, miR-939 and miR-638 can modulate HBV replication. Therefore, we propose that the miRNA profile constitutes a novel circulating marker that can help to predict response to IFN treatment in CHB patients. "
RLID00028131	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028132	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028133	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028134	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028135	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028136	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028137	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028138	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028139	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00028140	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028141	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028142	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028143	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028144	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028145	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028146	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028147	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028148	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028149	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028150	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028151	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028152	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028153	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028154	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028155	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028156	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028157	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028158	MIMAT0000068	hsa-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000068	hsa-miR-15a	miRNA	Homo sapiens	24130905	Circulating	Plasma	RT-PCR	"Overall expression levels of circulating miRNAs: most miRNAs from the designated list were successfully detected (with Ct values between 18 and 35) in virtually all samples. The highest signal was detected for miR-451, -223, -15a, -486-5p, -16, and -21, which is in agreement with literature data "
RLID00028159	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00028160	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	20883153	Circulating	Plasma	qRT-PCR|Microarray	"In mild TBI patients (GCS score >=12), miR-765 levels were unchanged, while the plasma levels of miR-92a and miR-16 were significantly increased within the first 24h of injury compared to healthy volunteers, and had AUC values of 0.78 and 0.82, respectively. "
RLID00028161	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028162	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028163	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028164	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028165	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028166	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028167	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028168	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028169	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028170	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028171	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028172	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028173	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00028174	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028175	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028176	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028177	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028178	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028179	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028180	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028181	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028182	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028183	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028184	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028185	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028186	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028187	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028188	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00028189	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028190	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028191	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028192	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028193	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22529849	Exosome	Kidney cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028194	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028195	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028196	MIMAT0000069	hsa-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069	hsa-miR-16	miRNA	Homo sapiens	24130905	Circulating	Plasma	RT-PCR	"Overall expression levels of circulating miRNAs: most miRNAs from the designated list were successfully detected (with Ct values between 18 and 35) in virtually all samples. The highest signal was detected for miR-451, -223, -15a, -486-5p, -16, and -21, which is in agreement with literature data "
RLID00028197	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00028198	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028199	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23056289	Circulating	Serum	qRT-PCR	"Circulating miR-17, miR-20a, miR-29c, and miR-223 combined as non-invasive biomarkers in nasopharyngeal carcinoma. "
RLID00028200	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028201	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	24456939	Circulating	Plasma	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00028202	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028203	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028204	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028205	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028206	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028207	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00028208	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028209	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028210	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028211	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028212	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028213	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028214	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028215	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028216	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028217	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028218	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028219	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028220	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028221	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028222	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028223	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028224	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00028225	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028226	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028227	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028228	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028229	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028230	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028231	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028232	MIMAT0000070	hsa-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000070	"hsa-miR-17-5p, hsa-miR-17 "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028233	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00028234	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028235	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00028236	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028237	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028238	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028239	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028240	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	21203553	Mitochondrion	Prostate epithelial cell	Northern blot|RT-PCR|Microarray	Our study demonstrates that miR-17* is a negative regulator for three important antioxidant enzymes located in mitochondria.
RLID00028241	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028242	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028243	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028244	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028245	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028246	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028247	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028248	MIMAT0000071	hsa-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000071	"hsa-miR-17-3p, hsa-miR-17* "	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00028249	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028250	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028251	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028252	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028253	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028254	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028255	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028256	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028257	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028258	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028259	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028260	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028261	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028262	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028263	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028264	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028265	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028266	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028267	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028268	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028269	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028270	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028271	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028272	MIMAT0000072	hsa-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000072	"hsa-miR-18, hsa-miR-18a "	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028273	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028274	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028275	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028276	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028277	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028278	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028279	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028280	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028281	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028282	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028283	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028284	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028285	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028286	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028287	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028288	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028289	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00028290	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028291	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028292	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028293	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028294	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00028295	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	20864815	Cytoplasm	Colon cancer cell	RT-PCR|Northern blot|Microarray	"MicroRNAs such as let-7d, miR-19a, miR-19b and miR-200b, demonstrated nuclear localization at a level similar to that of cytoplasm. "
RLID00028296	MIMAT0000073	hsa-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000073	hsa-miR-19a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028297	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028298	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028299	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028300	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028301	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028302	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028303	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028304	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028305	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028306	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028307	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028308	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028309	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028310	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028311	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028312	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028313	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028314	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028315	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028316	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028317	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028318	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028319	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028320	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00028321	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028322	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028323	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028324	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028325	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00028326	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00028327	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	20864815	Cytoplasm	Colon cancer cell	RT-PCR|Northern blot|Microarray	"MicroRNAs such as let-7d, miR-19a, miR-19b and miR-200b, demonstrated nuclear localization at a level similar to that of cytoplasm. "
RLID00028328	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028329	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028330	MIMAT0000074	hsa-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000074	hsa-miR-19b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00028331	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	20145944	Circulating	Blood	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00028332	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028333	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00028334	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23056289	Circulating	Serum	qRT-PCR	"Circulating miR-17, miR-20a, miR-29c, and miR-223 combined as non-invasive biomarkers in nasopharyngeal carcinoma. "
RLID00028335	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028336	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	24456939	Circulating	Serum	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00028337	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028338	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028339	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028340	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028341	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028342	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028343	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028344	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028345	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028346	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028347	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028348	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00028349	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028350	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028351	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028352	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028353	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028354	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028355	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028356	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028357	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028358	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028359	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028360	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028361	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028362	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028363	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028364	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028365	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028366	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028367	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	23940654	Cytoplasm	HeLa cell	qRT-PCR|In situ hybridization	"The miRNA identified in the qPCR screen to be nucleolus-excluded, miR-20a, was indeed found by ISH to be mostly cytoplasmic.  "
RLID00028368	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028369	MIMAT0000075	hsa-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000075	"hsa-miR-20, hsa-miR-20a "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00028370	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00028371	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22105822	Circulating	plasma	qRT-PCR	"Our study revealed that plasma miR-122, miR-192, miR-21, miR-223, miR-26a, miR-27a, and miR-801 were potential circulating markers for diagnosing HCC. The microRNA panel with the seven microRNAs from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of HCC, especially for patients with early BCLC stages (0 and A). "
RLID00028372	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00028373	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028374	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028375	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028376	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028377	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24456939	Circulating	Gastric juice	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00028378	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24456939	Circulating	Plasma	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00028379	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028380	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028381	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028382	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028383	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028384	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00028385	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028386	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028387	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028388	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	21601258	Exosome	Ascites	qRT-PCR	"Fig. 2. Biochemical marker analysis of exosomes. (A) Exosomes isolated from ascites or pleural effusions of tumor or LC patients were analyzed using the indi cated mAb followed by peroxidase-conjugated secondary antibody and ECL detection. 10 μ g exosomes were applied per lane. Note that HSP70, ADAM10, Annexin-1 and CD9 are considered as general exosome markers. HLA-DR was used as a marker for immune cell derived exosomes. Note that in BrCa patients #9�4 samples were derived from pleural effusions and #15 and 16 were from ascites. (B) The content of the indicated miRNAs was quantified by real-time RT-PCR in exosomes from ascites of OvCa (n=10) or LC patients (n=6) or BrCa pleural effusions (n=7). Note, that low Ct values re fl ect high expression levels of the respective miRNA. P-values in the fi gure are indicated as follows: * < 0.05, ** < 0.01 *** < 0.001. Data are collected from Figure 2. "
RLID00028389	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028390	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22895844	Exosome	Colon|Liver|Lung	qRT-PCR	"When the RNA species within exosomes derived from the three CRC cell lines were examined, the mRNAs of housekeeping genes such as ACTB and GAPDH, the microRNAs such as miR-21, miR-192 and miR-221, and the natural antisense RNAs of LRRC24, MDM2 and CDKN1A genes, were detected. "
RLID00028391	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028392	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23559272	Circulating	Serum	Microarray	"Using microarray-based expression profiling followed by real-time quantitative polymerase chain reaction validation, we compared the levels of a series of circulating miRNAs (miR-21, miR-155, miR-182, and miR-197) in serum from patients with lung cancer (n = 65), pulmonary tuberculosis (n = 29), pneumonia (n = 29), and transudate (n = 16) compared with matched healthy controls (n = 37). "
RLID00028393	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028394	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24373621	Circulating	Plasma	qRT-PCR	"Unsupervised clustering of the expression profiles using the six most regulated miRNAs (miR-425-5p, miR-21-5p, miR-106b-5p, miR-590-5p, miR-574-3p, miR-885-3p) significantly (p = 0.012) separated plasma samples collected prior to treatment from plasma samples collected after two days of radiochemotherapy. "
RLID00028395	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028396	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028397	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028398	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028399	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028400	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028401	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028402	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028403	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028404	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028405	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028406	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028407	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00028408	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028409	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028410	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028411	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028412	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028413	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00028414	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00028415	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22529849	Exosome	Placenta	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028416	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22529849	Exosome	Kidney cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028417	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028418	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028419	MIMAT0000076	hsa-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076	hsa-miR-21	miRNA	Homo sapiens	24130905	Circulating	Plasma	RT-PCR	"Overall expression levels of circulating miRNAs: most miRNAs from the designated list were successfully detected (with Ct values between 18 and 35) in virtually all samples. The highest signal was detected for miR-451, -223, -15a, -486-5p, -16, and -21, which is in agreement with literature data "
RLID00028420	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028421	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028422	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028423	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00028424	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028425	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028426	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028427	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028428	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028429	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028430	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028431	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028432	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028433	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028434	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028435	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028436	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028437	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028438	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028439	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028440	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028441	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028442	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028443	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028444	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028445	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028446	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028447	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028448	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028449	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028450	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028451	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028452	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028453	MIMAT0000077	hsa-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000077	hsa-miR-22	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028454	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00028455	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028456	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028457	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028458	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00028459	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00028460	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028461	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028462	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028463	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028464	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028465	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028466	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028467	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028468	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028469	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028470	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028471	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028472	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028473	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028474	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028475	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028476	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028477	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028478	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028479	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028480	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00028481	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00028482	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028483	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028484	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028485	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028486	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028487	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028488	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028489	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028490	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028491	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028492	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028493	MIMAT0000078	hsa-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000078	hsa-miR-23a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028494	MIMAT0000079	hsa-miR-24-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000079	"hsa-miR-189, hsa-miR-24-1* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028495	MIMAT0000079	hsa-miR-24-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000079	"hsa-miR-189, hsa-miR-24-1* "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028496	MIMAT0000079	hsa-miR-24-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000079	"hsa-miR-189, hsa-miR-24-1* "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028497	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23424776	Circulating	Blood	qRT-PCR|Microarray	"Five miRNAs (let-7c, miR-16, miR- 449, miR-181a and miR-181b) were found to exhibit similar expression patterns (p < 0.05) in peripheral blood when compared to data obtained by using bone marrow aspirates from MM patients in other studies.  "
RLID00028498	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028499	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028500	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028501	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028502	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028503	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028504	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028505	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028506	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028507	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028508	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028509	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028510	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028511	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028512	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028513	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028514	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028515	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028516	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028517	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028518	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028519	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028520	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028521	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028522	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028523	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00028524	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028525	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028526	MIMAT0000080	hsa-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000080	hsa-miR-24	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028527	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028528	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028529	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028530	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028531	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028532	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028533	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028534	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028535	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028536	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028537	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028538	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028539	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028540	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028541	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028542	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028543	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028544	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028545	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028546	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028547	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028548	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028549	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028550	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028551	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028552	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028553	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028554	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028555	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00028556	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028557	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028558	MIMAT0000081	hsa-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000081	hsa-miR-25	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028559	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	20857419	Circulating	Serum	Microarray	"Microarray analysis of miRNAs was performed on human aortic SMCs undergoing phenotypic switching in response to serum withdrawal, and identified 31 significantly regulated entities. We chose the highly conserved candidate miRNA-26a for additional studies.  "
RLID00028560	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	22105822	Circulating	plasma	qRT-PCR	"Our study revealed that plasma miR-122, miR-192, miR-21, miR-223, miR-26a, miR-27a, and miR-801 were potential circulating markers for diagnosing HCC. The microRNA panel with the seven microRNAs from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of HCC, especially for patients with early BCLC stages (0 and A). "
RLID00028561	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028562	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028563	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028564	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028565	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028566	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028567	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028568	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028569	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028570	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028571	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028572	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028573	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00028574	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028575	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028576	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028577	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028578	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028579	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028580	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028581	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028582	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028583	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028584	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028585	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028586	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028587	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00028588	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028589	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028590	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028591	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028592	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028593	MIMAT0000082	hsa-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000082	hsa-miR-26a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028594	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028595	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028596	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028597	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028598	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028599	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028600	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028601	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028602	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028603	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028604	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028605	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028606	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028607	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028608	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028609	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028610	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028611	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028612	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028613	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028614	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028615	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028616	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028617	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028618	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028619	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028620	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028621	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028622	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028623	MIMAT0000083	hsa-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000083	hsa-miR-26b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028624	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22105822	Circulating	Plasma	qRT-PCR	"Our study revealed that plasma miR-122, miR-192, miR-21, miR-223, miR-26a, miR-27a, and miR-801 were potential circulating markers for diagnosing HCC. The microRNA panel with the seven microRNAs from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of HCC, especially for patients with early BCLC stages (0 and A). "
RLID00028625	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028626	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028627	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028628	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028629	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	24456939	Circulating	Serum	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00028630	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028631	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028632	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028633	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028634	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028635	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028636	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028637	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028638	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028639	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028640	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028641	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028642	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028643	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028644	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028645	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028646	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028647	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028648	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028649	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028650	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028651	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028652	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028653	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00028654	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00028655	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028656	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028657	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028658	MIMAT0000084	hsa-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000084	hsa-miR-27a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028659	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028660	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028661	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028662	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028663	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028664	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028665	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028666	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028667	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028668	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028669	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028670	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00028671	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028672	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028673	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028674	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028675	MIMAT0000085	hsa-miR-28-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000085	hsa-miR-28	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00028676	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00028677	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028678	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028679	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028680	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028681	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028682	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028683	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028684	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028685	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028686	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028687	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028688	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028689	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	19951903	Microvesicle	Plasma	qRT-PCR|Microarray	"Thus, miR-29a was up-regulated in both blood microvesicles and colon tissue of IBS patients with increased membrane permeability.  "
RLID00028690	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028691	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028692	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028693	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028694	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028695	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028696	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028697	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028698	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028699	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028700	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028701	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028702	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028703	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028704	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028705	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00028706	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028707	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028708	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028709	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028710	MIMAT0000086	hsa-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000086	hsa-miR-29a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028711	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028712	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028713	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028714	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028715	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028716	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028717	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028718	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028719	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028720	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028721	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028722	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028723	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028724	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028725	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028726	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028727	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028728	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028729	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028730	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028731	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028732	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028733	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028734	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028735	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028736	MIMAT0000087	hsa-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000087	"hsa-miR-30a-5p, hsa-miR-30a "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028737	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028738	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028739	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028740	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028741	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028742	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028743	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028744	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028745	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028746	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028747	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028748	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028749	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028750	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028751	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00028752	MIMAT0000088	hsa-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000088	"hsa-miR-30a-3p, hsa-miR-30a* "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028753	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028754	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028755	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028756	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028757	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028758	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028759	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028760	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028761	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028762	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028763	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028764	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028765	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028766	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028767	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028768	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00028769	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028770	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028771	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028772	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028773	MIMAT0000089	hsa-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000089	hsa-miR-31	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028774	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028775	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028776	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028777	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028778	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028779	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028780	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028781	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028782	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028783	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028784	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028785	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028786	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00028787	MIMAT0000090	hsa-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000090	hsa-miR-32	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028788	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028789	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028790	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028791	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028792	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028793	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028794	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028795	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028796	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028797	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028798	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028799	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028800	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028801	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028802	MIMAT0000091	hsa-miR-33a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000091	"hsa-miR-33, hsa-miR-33a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028803	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00028804	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00028805	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	20883153	Circulating	Plasma	qRT-PCR|Microarray	"In mild TBI patients (GCS score >=12), miR-765 levels were unchanged, while the plasma levels of miR-92a and miR-16 were significantly increased within the first 24h of injury compared to healthy volunteers, and had AUC values of 0.78 and 0.82, respectively. "
RLID00028806	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00028807	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	21383985	Circulating	Plasma	qRT-PCR	DLBCL patients with low plasma miR-92a relapsed significantly compared with those with normal range plasma miR-92a (5/12 versus 1/22; P?=?.007 by the chi-square test; Table 1).
RLID00028808	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00028809	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00028810	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00028811	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028812	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028813	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028814	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028815	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028816	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028817	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028818	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00028819	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028820	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028821	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22427800	Circulating	Serum	RT-PCR	The miRNAs tested in serum and saliva samples are shown in Table 1. These miRNAs were selected because they are either ubiquitously expressed or have been reported as biomarkers (Table 1). The relative concentration of these microRNAs was determined by calculating the difference of Ct values between the exosome samples and the exosome-depleted supernatant. A 1-unit difference in the Ct value between the miRNAs isolated from the exosomal pellet or supernatant represents a 2-fold difference in the amount of input miRNA. Data are collected from Table 1: List of miRNAs tested in serum and saliva samples.
RLID00028822	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028823	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028824	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028825	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028826	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028827	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028828	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028829	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028830	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028831	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028832	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028833	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028834	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00028835	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00028836	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00028837	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028838	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028839	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028840	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028841	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24105805	Cytoplasm	Umbilical vein endothelial cell	TEPA-PCL	"Our data indicated that miR-92a-C formulated in TEPA-PCL accumulated in and was spread throughout the cytoplasm in a time-dependent manner, and was taken up into the cells by macropinosome-mediated endocytosis. "
RLID00028842	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028843	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028844	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028845	MIMAT0000092	hsa-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000092	"hsa-miR-92, hsa-miR-92a "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00028846	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00028847	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028848	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028849	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028850	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028851	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028852	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00028853	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028854	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028855	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028856	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028857	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028858	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028859	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028860	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00028861	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00028862	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028863	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00028864	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028865	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028866	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00028867	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028868	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028869	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028870	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028871	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00028872	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028873	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028874	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028875	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028876	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028877	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028878	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028879	MIMAT0000093	hsa-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000093	hsa-miR-93	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028880	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028881	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028882	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028883	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028884	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028885	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028886	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028887	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028888	MIMAT0000094	hsa-miR-95-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000094		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00028889	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00028890	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00028891	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028892	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028893	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028894	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028895	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028896	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00028897	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00028898	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028899	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028900	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028901	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00028902	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028903	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028904	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028905	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028906	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028907	MIMAT0000095	hsa-miR-96-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000095	hsa-miR-96	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028908	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028909	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028910	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028911	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028912	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028913	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00028914	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028915	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028916	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028917	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028918	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028919	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028920	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028921	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00028922	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00028923	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028924	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028925	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028926	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00028927	MIMAT0000096	hsa-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000096	hsa-miR-98	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028928	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00028929	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028930	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028931	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028932	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00028933	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00028934	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028935	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028936	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00028937	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028938	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028939	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028940	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028941	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028942	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028943	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028944	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028945	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028946	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028947	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028948	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028949	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00028950	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028951	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028952	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028953	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028954	MIMAT0000097	hsa-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000097	hsa-miR-99a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00028955	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028956	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028957	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00028958	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00028959	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00028960	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028961	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00028962	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028963	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028964	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00028965	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00028966	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028967	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00028968	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00028969	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00028970	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028971	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028972	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028973	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00028974	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00028975	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00028976	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028977	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028978	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028979	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00028980	MIMAT0000098	hsa-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000098	hsa-miR-100	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00028981	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028982	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00028983	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028984	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00028985	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028986	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00028987	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00028988	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00028989	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00028990	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00028991	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00028992	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028993	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00028994	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00028995	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00028996	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00028997	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028998	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00028999	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029000	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029001	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00029002	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029003	MIMAT0000099	hsa-miR-101-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000099	hsa-miR-101	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029004	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029005	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029006	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00029007	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029008	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029009	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029010	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029011	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029012	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029013	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029014	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	17204650	Nucleus	HeLa cell	In situ hybridization|RT-PCR	"We showed that human miR-29b, in contrast to other studied animal miRNAs, is predominantly localized to the nucleus. "
RLID00029015	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029016	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00029017	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029018	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029019	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029020	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029021	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029022	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00029023	MIMAT0000100	hsa-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000100	hsa-miR-29b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029024	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00029025	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00029026	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029027	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029028	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029029	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00029030	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029031	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029032	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00029033	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029034	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029035	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029036	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029037	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029038	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029039	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029040	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029041	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029042	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029043	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029044	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029045	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00029046	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029047	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029048	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029049	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029050	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029051	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00029052	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029053	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029054	MIMAT0000101	hsa-miR-103a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000101	"hsa-miR-103, hsa-miR-103a "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029055	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029056	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029057	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029058	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029059	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029060	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029061	MIMAT0000102	hsa-miR-105-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000102	hsa-miR-105	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029062	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	20145944	Circulating	Blood	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00029063	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00029064	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029065	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24456939	Circulating	Gastric juice	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00029066	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24456939	Circulating	Plasma	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00029067	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029068	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00029069	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029070	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00029071	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029072	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029073	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029074	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029075	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24670448	Circulating	Plasma	Microarray|RT-PCR	The plasma levels of miR-106a expression were significantly higher in the cancer patients than in the healthy control group (P=0.012).
RLID00029076	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00029077	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029078	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029079	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029080	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029081	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029082	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029083	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029084	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00029085	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029086	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029087	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029088	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029089	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029090	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029091	MIMAT0000103	hsa-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000103	hsa-miR-106a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029092	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00029093	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029094	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029095	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029096	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00029097	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00029098	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029099	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00029100	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029101	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029102	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029103	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029104	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029105	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029106	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00029107	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029108	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029109	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00029110	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029111	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029112	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029113	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029114	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00029115	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029116	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029117	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029118	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029119	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029120	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029121	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029122	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029123	MIMAT0000104	hsa-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000104		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029124	MIMAT0000121	mmu-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000121	mmu-let-7g	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029125	MIMAT0000121	mmu-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000121	mmu-let-7g	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029126	MIMAT0000121	mmu-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000121	mmu-let-7g	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029127	MIMAT0000121	mmu-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000121	mmu-let-7g	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	"Supplementary information, Figure S4 Screening for the target miRNAs of miR-709 in the nucleus via microarray assay (only top 44 miRNAs were showed). Data are collected from Figure S4. "
RLID00029128	MIMAT0000121	mmu-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000121	mmu-let-7g	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029129	MIMAT0000122	mmu-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000122	mmu-let-7i	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029130	MIMAT0000122	mmu-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000122	mmu-let-7i	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029131	MIMAT0000122	mmu-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000122	mmu-let-7i	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029132	MIMAT0000122	mmu-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000122	mmu-let-7i	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029133	MIMAT0000123	mmu-miR-1a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000123	"mmu-miR-1, mmu-miR-1a "	miRNA	Mus musculus	25083871	Mitochondrion	Myoblast	qRT-PCR|Northern blot|CLIP-seq	"Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. "
RLID00029134	MIMAT0000123	mmu-miR-1a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000123	"mmu-miR-1, mmu-miR-1a "	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029135	MIMAT0000123	mmu-miR-1a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000123	"mmu-miR-1, mmu-miR-1a "	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00029136	MIMAT0000124	mmu-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000124	mmu-miR-15b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029137	MIMAT0000124	mmu-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000124	mmu-miR-15b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029138	MIMAT0000124	mmu-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000124	mmu-miR-15b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029139	MIMAT0000124	mmu-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000124	mmu-miR-15b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029140	MIMAT0000124	mmu-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000124	mmu-miR-15b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029141	MIMAT0000125	mmu-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000125	mmu-miR-23b	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029142	MIMAT0000125	mmu-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000125	mmu-miR-23b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029143	MIMAT0000125	mmu-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000125	mmu-miR-23b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029144	MIMAT0000125	mmu-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000125	mmu-miR-23b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029145	MIMAT0000125	mmu-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000125	mmu-miR-23b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029146	MIMAT0000125	mmu-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000125	mmu-miR-23b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029147	MIMAT0000126	mmu-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000126	mmu-miR-27b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029148	MIMAT0000126	mmu-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000126	mmu-miR-27b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029149	MIMAT0000126	mmu-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000126	mmu-miR-27b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029150	MIMAT0000126	mmu-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000126	mmu-miR-27b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029151	MIMAT0000127	mmu-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000127	mmu-miR-29b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029152	MIMAT0000127	mmu-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000127	mmu-miR-29b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029153	MIMAT0000127	mmu-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000127	mmu-miR-29b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029154	MIMAT0000127	mmu-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000127	mmu-miR-29b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029155	MIMAT0000127	mmu-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000127	mmu-miR-29b	miRNA	Mus musculus	17204650	Nucleus	NIH 3T3 cell	Fluorescence in situ hybridization	"miR-29b also shows mitotic accumulation and nuclear enrichment in murine NIH 3T3 cells (fig. S6), demonstrating the conservation of this pathway in other mammalian cell lines. "
RLID00029156	MIMAT0000127	mmu-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000127	mmu-miR-29b	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029157	MIMAT0000128	mmu-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000128	"mmu-miR-30a-5p, mmu-miR-30a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029158	MIMAT0000128	mmu-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000128	"mmu-miR-30a-5p, mmu-miR-30a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029159	MIMAT0000130	mmu-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000130	mmu-miR-30b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029160	MIMAT0000130	mmu-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000130	mmu-miR-30b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029161	MIMAT0000130	mmu-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000130	mmu-miR-30b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029162	MIMAT0000130	mmu-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000130	mmu-miR-30b	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029163	MIMAT0000131	mmu-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000131	mmu-miR-99a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029164	MIMAT0000131	mmu-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000131	mmu-miR-99a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029165	MIMAT0000131	mmu-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000131	mmu-miR-99a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029166	MIMAT0000131	mmu-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000131	mmu-miR-99a	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.11b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00029167	MIMAT0000131	mmu-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000131	mmu-miR-99a	miRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	Table 2: Enrichment ratios (synaptoneurosomes/total homogenate) of selected mature microRNAs measured by real-time qRT-PCR. Data are collected from Table 2.
RLID00029168	MIMAT0000132	mmu-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000132	mmu-miR-99b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029169	MIMAT0000132	mmu-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000132	mmu-miR-99b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029170	MIMAT0000133	mmu-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000133	mmu-miR-101a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029171	MIMAT0000133	mmu-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000133	mmu-miR-101a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029172	MIMAT0000133	mmu-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000133	mmu-miR-101a	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00029173	MIMAT0000133	mmu-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000133	mmu-miR-101a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029174	MIMAT0000133	mmu-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000133	mmu-miR-101a	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029175	MIMAT0000134	mmu-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000134	"mmu-miR-124a, mmu-miR-124 "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029176	MIMAT0000134	mmu-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000134	"mmu-miR-124a, mmu-miR-124 "	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00029177	MIMAT0000134	mmu-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000134	"mmu-miR-124a, mmu-miR-124 "	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig. 7b, the microRNA precursors were all predominantly associated with the PSD fraction. In contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B. "
RLID00029178	MIMAT0000134	mmu-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000134	"mmu-miR-124a, mmu-miR-124 "	miRNA	Mus musculus	24784359	Dendrite	Hippocampus	Fluorescence in situ hybridization|qRT-PCR	"In contrast, we detected significant concentrations of miR-124 in dendrites. We conclude that GluA2 is a predominantly somatically restricted mRNA, while miR-124 is present in somata and in dendrites. Using these probes, we detected clear dendritic signals for miR-124.  Together with the fact that RT-qPCR experiments revealed significant concentrations of miR-124 in synaptosome fractions (Figure 2), our results provide strong evidence that miR-124 is dendritically localized in mouse hippocampal neurons. "
RLID00029179	MIMAT0000134	mmu-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000134	"mmu-miR-124a, mmu-miR-124 "	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029180	MIMAT0000135	mmu-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000135	mmu-miR-125a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029181	MIMAT0000135	mmu-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000135	mmu-miR-125a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029182	MIMAT0000135	mmu-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000135	mmu-miR-125a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029183	MIMAT0000135	mmu-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000135	mmu-miR-125a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029184	MIMAT0000135	mmu-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000135	mmu-miR-125a	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029185	MIMAT0000135	mmu-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000135	mmu-miR-125a	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029186	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029187	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029188	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029189	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029190	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00029191	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig. 8b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00029192	MIMAT0000136	mmu-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000136	mmu-miR-125b	miRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	Table 2: Enrichment ratios (synaptoneurosomes/total homogenate) of selected mature microRNAs measured by real-time qRT-PCR. Data are collected from Table 2.
RLID00029193	MIMAT0000137	mmu-miR-126a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000137		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029194	MIMAT0000137	mmu-miR-126a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000137		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029195	MIMAT0000137	mmu-miR-126a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000137		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029196	MIMAT0000137	mmu-miR-126a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000137		miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029197	MIMAT0000138	mmu-miR-126a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000138		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029198	MIMAT0000138	mmu-miR-126a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000138		miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029199	MIMAT0000138	mmu-miR-126a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000138		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029200	MIMAT0000138	mmu-miR-126a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000138		miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029201	MIMAT0000139	mmu-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000139	mmu-miR-127	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029202	MIMAT0000140	mmu-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000140	"mmu-miR-128a, mmu-miR-128 "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029203	MIMAT0000141	mmu-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000141	mmu-miR-130a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029204	MIMAT0000141	mmu-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000141	mmu-miR-130a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029205	MIMAT0000141	mmu-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000141	mmu-miR-130a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	"Supplementary information, Figure S4 Screening for the target miRNAs of miR-709 in the nucleus via microarray assay (only top 44 miRNAs were showed). Data are collected from Figure S4. "
RLID00029206	MIMAT0000141	mmu-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000141	mmu-miR-130a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029207	MIMAT0000142	mmu-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000142	mmu-miR-9	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029208	MIMAT0000142	mmu-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000142	mmu-miR-9	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029209	MIMAT0000143	mmu-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000143	mmu-miR-9*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029210	MIMAT0000143	mmu-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000143	mmu-miR-9*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029211	MIMAT0000143	mmu-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000143	mmu-miR-9*	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029212	MIMAT0000144	mmu-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000144	mmu-miR-132	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029213	MIMAT0000144	mmu-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000144	mmu-miR-132	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029214	MIMAT0000144	mmu-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000144	mmu-miR-132	miRNA	Mus musculus	24381269	Axon	Dorsal root ganglion	qRT-PCR	"High axonal expression and preferential localization were observed for miR-132, a miRNA previously known for roles in dendrites and dysregulation in major neurologic diseases. miR-132 knockdown reduced extension of cultured DRG axons, whereas overexpression increased extension. "
RLID00029215	MIMAT0000144	mmu-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000144	mmu-miR-132	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029216	MIMAT0000144	mmu-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000144	mmu-miR-132	miRNA	Mus musculus	20506192	Dendrite	Hippocampal neuroprogenitors	In situ hybridization	"Several miRNAs are found to be localized and functioning in dendrites and synapses. Among them, miR-132 and miR-137 are both enriched in dendritic spines, but whereas miR-132 represses spine volume, miR-137 shows no effect on spine volume.  "
RLID00029217	MIMAT0000145	mmu-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000145	mmu-miR-133a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029218	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029219	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00029220	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"As shown in fig. 6, microRNA precursors were readily detected within the SYN fraction, at levels that were comparable to the total homogenate. Data are collected from Figure 6. "
RLID00029221	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig. 9b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00029222	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	23897634	Synapse	Neuron ball cultures	Fluorescence in situ hybridization	"Moreover, of these 12 miRNAs, six were significantly enriched in axons when compared with the mean cell body–axon gradient calculated from all miRNAs (Table 1). miR-134, which was reported to be enriched in synapses (Schratt et al., 2006), and detected in axonal growth cones by FISH (Han et al., 2011) was also enriched in axons in our preparation, although the Ct value of cell bodies was below our cutoff value (i.e., 33; Table 1).  "
RLID00029223	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"Moreover, of these 12 miRNAs, six were significantly enriched in axons when compared with the mean cell body–axon gradient calculated from all miRNAs (Table 1). miR-134, which was reported to be enriched in synapses (Schratt et al., 2006), and detected in axonal growth cones by FISH (Han et al., 2011) was also enriched in axons in our preparation, although the Ct value of cell bodies was below our cutoff value (i.e., 33; Table 1).  "
RLID00029224	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	24874920	Dendrite	Hippocampus	In situ hybridization	"MicroRNA-134 (miR-134) is enriched in dendrites of hippocampal neurons, where it negatively regulates spine volume. Recent work identified upregulation of miR-134 in experimental and human epilepsy. "
RLID00029225	MIMAT0000146	mmu-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000146	mmu-miR-134	miRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	Table 2: Enrichment ratios (synaptoneurosomes/total homogenate) of selected mature microRNAs measured by real-time qRT-PCR. Data are collected from Table 2.
RLID00029226	MIMAT0000147	mmu-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000147	mmu-miR-135a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029227	MIMAT0000147	mmu-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000147	mmu-miR-135a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029228	MIMAT0000147	mmu-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000147	mmu-miR-135a	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029229	MIMAT0000148	mmu-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000148	mmu-miR-136	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029230	MIMAT0000149	mmu-miR-137-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000149	mmu-miR-137	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029231	MIMAT0000149	mmu-miR-137-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000149	mmu-miR-137	miRNA	Mus musculus	20506192	Dendrite	Hippocampal neuroprogenitors	In situ hybridization	"Several miRNAs are found to be localized and functioning in dendrites and synapses. Among them, miR-132 and miR-137 are both enriched in dendritic spines, but whereas miR-132 represses spine volume, miR-137 shows no effect on spine volume.  "
RLID00029232	MIMAT0000149	mmu-miR-137-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000149	mmu-miR-137	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029233	MIMAT0000150	mmu-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000150	mmu-miR-138	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029234	MIMAT0000150	mmu-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000150	mmu-miR-138	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029235	MIMAT0000150	mmu-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000150	mmu-miR-138	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029236	MIMAT0000150	mmu-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000150	mmu-miR-138	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029237	MIMAT0000151	mmu-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000151	mmu-miR-140	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029238	MIMAT0000151	mmu-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000151	mmu-miR-140	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029239	MIMAT0000152	mmu-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000152	mmu-miR-140*	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029240	MIMAT0000152	mmu-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000152	mmu-miR-140*	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029241	MIMAT0000152	mmu-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000152	mmu-miR-140*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029242	MIMAT0000152	mmu-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000152	mmu-miR-140*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029243	MIMAT0000154	mmu-miR-142a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000154	mmu-miR-142-5p	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029244	MIMAT0000154	mmu-miR-142a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000154	mmu-miR-142-5p	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029245	MIMAT0000154	mmu-miR-142a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000154	mmu-miR-142-5p	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029246	MIMAT0000154	mmu-miR-142a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000154	mmu-miR-142-5p	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029247	MIMAT0000154	mmu-miR-142a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000154	mmu-miR-142-5p	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029248	MIMAT0000154	mmu-miR-142a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000154	mmu-miR-142-5p	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00029249	MIMAT0000155	mmu-miR-142a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000155	mmu-miR-142-3p	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029250	MIMAT0000155	mmu-miR-142a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000155	mmu-miR-142-3p	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029251	MIMAT0000155	mmu-miR-142a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000155	mmu-miR-142-3p	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029252	MIMAT0000155	mmu-miR-142a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000155	mmu-miR-142-3p	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029253	MIMAT0000155	mmu-miR-142a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000155	mmu-miR-142-3p	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00029254	MIMAT0000156	mmu-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000156	mmu-miR-144	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029255	MIMAT0000157	mmu-miR-145a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000157	"mmu-miR-145, mmu-miR-145-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029256	MIMAT0000157	mmu-miR-145a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000157	"mmu-miR-145, mmu-miR-145-5p "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029257	MIMAT0000157	mmu-miR-145a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000157	"mmu-miR-145, mmu-miR-145-5p "	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029258	MIMAT0000157	mmu-miR-145a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000157	"mmu-miR-145, mmu-miR-145-5p "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029259	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029260	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029261	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029262	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00029263	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029264	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00029265	MIMAT0000158	mmu-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000158	"mmu-miR-146, mmu-miR-146a "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029266	MIMAT0000159	mmu-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000159	mmu-miR-149	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029267	MIMAT0000159	mmu-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000159	mmu-miR-149	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029268	MIMAT0000160	mmu-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000160	mmu-miR-150	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029269	MIMAT0000160	mmu-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000160	mmu-miR-150	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029270	MIMAT0000160	mmu-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000160	mmu-miR-150	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029271	MIMAT0000160	mmu-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000160	mmu-miR-150	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029272	MIMAT0000160	mmu-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000160	mmu-miR-150	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029273	MIMAT0000161	mmu-miR-151-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000161	mmu-miR-151	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029274	MIMAT0000161	mmu-miR-151-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000161	mmu-miR-151	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029275	MIMAT0000162	mmu-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000162	mmu-miR-152	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029276	MIMAT0000162	mmu-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000162	mmu-miR-152	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029277	MIMAT0000162	mmu-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000162	mmu-miR-152	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029278	MIMAT0000163	mmu-miR-153-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000163	mmu-miR-153	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029279	MIMAT0000164	mmu-miR-154-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000164	mmu-miR-154	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029280	MIMAT0000165	mmu-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000165	mmu-miR-155	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029281	MIMAT0000165	mmu-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000165	mmu-miR-155	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029282	MIMAT0000165	mmu-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000165	mmu-miR-155	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00029283	MIMAT0000209	mmu-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000209	mmu-miR-129	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029284	MIMAT0000209	mmu-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000209	mmu-miR-129	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029285	MIMAT0000210	mmu-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000210	mmu-miR-181a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029286	MIMAT0000210	mmu-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000210	mmu-miR-181a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029287	MIMAT0000210	mmu-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000210	mmu-miR-181a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029288	MIMAT0000211	mmu-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000211	mmu-miR-182	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029289	MIMAT0000211	mmu-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000211	mmu-miR-182	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029290	MIMAT0000211	mmu-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000211	mmu-miR-182	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029291	MIMAT0000211	mmu-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000211	mmu-miR-182	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029292	MIMAT0000211	mmu-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000211	mmu-miR-182	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029293	MIMAT0000211	mmu-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000211	mmu-miR-182	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029294	MIMAT0000212	mmu-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000212	mmu-miR-183	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029295	MIMAT0000212	mmu-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000212	mmu-miR-183	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029296	MIMAT0000212	mmu-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000212	mmu-miR-183	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029297	MIMAT0000213	mmu-miR-184-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000213	mmu-miR-184	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029298	MIMAT0000213	mmu-miR-184-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000213	mmu-miR-184	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029299	MIMAT0000213	mmu-miR-184-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000213	mmu-miR-184	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029300	MIMAT0000214	mmu-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000214	mmu-miR-185	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029301	MIMAT0000214	mmu-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000214	mmu-miR-185	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029302	MIMAT0000214	mmu-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000214	mmu-miR-185	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029303	MIMAT0000214	mmu-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000214	mmu-miR-185	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029304	MIMAT0000214	mmu-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000214	mmu-miR-185	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029305	MIMAT0000215	mmu-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000215	mmu-miR-186	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029306	MIMAT0000216	mmu-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000216	mmu-miR-187	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029307	MIMAT0000216	mmu-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000216	mmu-miR-187	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00029308	MIMAT0000216	mmu-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000216	mmu-miR-187	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029309	MIMAT0000217	mmu-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000217	mmu-miR-188	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029310	MIMAT0000217	mmu-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000217	mmu-miR-188	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029311	MIMAT0000217	mmu-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000217	mmu-miR-188	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00029312	MIMAT0000217	mmu-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000217	mmu-miR-188	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029313	MIMAT0000217	mmu-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000217	mmu-miR-188	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029314	MIMAT0000217	mmu-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000217	mmu-miR-188	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029315	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029316	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029317	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029318	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029319	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	18204908	Nucleolus	Spermatocyte	In situ hybridization|Microarray	"Hybridization signals with all miRNA probes tested localized to the Sertoli cells (Figure 5A), with some also present in the cytoplasm of the germ cells (miR-214) and others (miR-24) having a distinct localization pattern in the nuclei of spermatocytes (Figure 5A).  "
RLID00029320	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029321	MIMAT0000219	mmu-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000219	mmu-miR-24	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029322	MIMAT0000220	mmu-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000220	"mmu-miR-190, mmu-miR-190-5p "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029323	MIMAT0000220	mmu-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000220	"mmu-miR-190, mmu-miR-190-5p "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029324	MIMAT0000221	mmu-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000221	mmu-miR-191	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00029325	MIMAT0000221	mmu-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000221	mmu-miR-191	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029326	MIMAT0000221	mmu-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000221	mmu-miR-191	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029327	MIMAT0000221	mmu-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000221	mmu-miR-191	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029328	MIMAT0000221	mmu-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000221	mmu-miR-191	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029329	MIMAT0000221	mmu-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000221	mmu-miR-191	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00029330	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22105822	Circulating	plasma	qRT-PCR	"Our study revealed that plasma miR-122, miR-192, miR-21, miR-223, miR-26a, miR-27a, and miR-801 were potential circulating markers for diagnosing HCC. The microRNA panel with the seven microRNAs from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of HCC, especially for patients with early BCLC stages (0 and A). "
RLID00029331	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029332	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029333	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029334	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00029335	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00029336	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00029337	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029338	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029339	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029340	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00029341	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029342	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22895844	Exosome	Colon|Liver|Lung	qRT-PCR	"When the RNA species within exosomes derived from the three CRC cell lines were examined, the mRNAs of housekeeping genes such as ACTB and GAPDH, the microRNAs such as miR-21, miR-192 and miR-221, and the natural antisense RNAs of LRRC24, MDM2 and CDKN1A genes, were detected. "
RLID00029343	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029344	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029345	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029346	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029347	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029348	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029349	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029350	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029351	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029352	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00029353	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029354	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029355	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029356	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029357	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00029358	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029359	MIMAT0000222	hsa-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000222	hsa-miR-192	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029360	MIMAT0000223	mmu-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000223	"mmu-miR-193, mmu-miR-193-3p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029361	MIMAT0000224	mmu-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000224	mmu-miR-194	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029362	MIMAT0000224	mmu-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000224	mmu-miR-194	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029363	MIMAT0000224	mmu-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000224	mmu-miR-194	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00029364	MIMAT0000224	mmu-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000224	mmu-miR-194	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029365	MIMAT0000225	mmu-miR-195a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000225	"mmu-miR-195, mmu-miR-195-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029366	MIMAT0000225	mmu-miR-195a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000225	"mmu-miR-195, mmu-miR-195-5p "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029367	MIMAT0000225	mmu-miR-195a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000225	"mmu-miR-195, mmu-miR-195-5p "	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029368	MIMAT0000225	mmu-miR-195a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000225	"mmu-miR-195, mmu-miR-195-5p "	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00029369	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00029370	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029371	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029372	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029373	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00029374	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029375	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029376	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029377	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029378	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029379	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029380	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029381	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029382	MIMAT0000226	hsa-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000226	hsa-miR-196a	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029383	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00029384	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029385	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029386	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029387	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029388	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029389	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029390	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029391	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029392	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029393	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029394	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23559272	Circulating	Serum	Microarray	"Using microarray-based expression profiling followed by real-time quantitative polymerase chain reaction validation, we compared the levels of a series of circulating miRNAs (miR-21, miR-155, miR-182, and miR-197) in serum from patients with lung cancer (n = 65), pulmonary tuberculosis (n = 29), pneumonia (n = 29), and transudate (n = 16) compared with matched healthy controls (n = 37). "
RLID00029395	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029396	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029397	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029398	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029399	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029400	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029401	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029402	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00029403	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029404	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029405	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029406	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029407	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029408	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029409	MIMAT0000227	hsa-miR-197-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000227	hsa-miR-197	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029410	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029411	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029412	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029413	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029414	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00029415	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00029416	MIMAT0000228	hsa-miR-198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000228		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029417	MIMAT0000230	mmu-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000230	mmu-miR-199a*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029418	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029419	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029420	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029421	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029422	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029423	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029424	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00029425	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00029426	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00029427	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029428	MIMAT0000231	hsa-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000231	hsa-miR-199a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029429	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029430	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029431	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029432	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029433	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029434	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029435	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029436	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029437	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029438	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029439	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00029440	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029441	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029442	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029443	MIMAT0000232	hsa-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000232	hsa-miR-199a*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029444	MIMAT0000233	mmu-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000233	mmu-miR-200b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029445	MIMAT0000233	mmu-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000233	mmu-miR-200b	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029446	MIMAT0000235	mmu-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000235	mmu-miR-202	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029447	MIMAT0000235	mmu-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000235	mmu-miR-202	miRNA	Mus musculus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00029448	MIMAT0000235	mmu-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000235	mmu-miR-202	miRNA	Mus musculus	18204908	Nucleolus	Spermatocyte	In situ hybridization|Microarray	"This round mass contained little DNA and appeared in the surrounding DNA as a darker structure resembling the nucleolus (Thiry 1993). Other miRNAs tested miR-320, 20 and 202 exhibited similar patterns except that miR-320 localized to the Sertoli cell nucleolus and also displayed a diffuse pattern in the nucleus but not in the cytoplasm of germ cells (data not shown). "
RLID00029449	MIMAT0000236	mmu-miR-203-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000236	mmu-miR-203	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029450	MIMAT0000236	mmu-miR-203-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000236	mmu-miR-203	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029451	MIMAT0000237	mmu-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000237	mmu-miR-204	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029452	MIMAT0000239	mmu-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000239	mmu-miR-206	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029453	MIMAT0000240	mmu-miR-207	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000240		miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00029454	MIMAT0000241	hsa-miR-208a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000241	hsa-miR-208	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029455	MIMAT0000241	hsa-miR-208a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000241	hsa-miR-208	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029456	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029457	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	24456939	Circulating	Gastric juice	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00029458	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029459	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029460	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029461	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029462	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029463	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029464	MIMAT0000242	hsa-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000242	hsa-miR-129	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029465	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029466	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029467	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029468	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00029469	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029470	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029471	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029472	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029473	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029474	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029475	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029476	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029477	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00029478	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029479	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00029480	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029481	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029482	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029483	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029484	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00029485	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029486	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029487	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029488	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029489	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	25376581	Exosome	Saliva	RNA-seq	"Previous reports suggested that the majority of miRNAs in saliva were concentrated in exosomes. We tested the presence of miRNAs in exosome and nonexosome fractions of saliva in a subset of samples (Fig. 1C; online Supplemental Fig. 4). Two miRNAs (miR-223-3p and miR-148a-3p) detected in RNA-Seq data of multiple individuals were chosen for this experiment. As shown in Fig. 1C, both miRNAs can be detected in all 3 individuals, and they are predominantly present in the exosomal RNA fraction in 2 of 3 individuals. For 1 individual (S1), both miRNAs were detected in both exosomal and nonexosomal fractions. "
RLID00029490	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029491	MIMAT0000243	hsa-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000243	hsa-miR-148a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029492	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00029493	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029494	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029495	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029496	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00029497	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029498	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00029499	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029500	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029501	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029502	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029503	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029504	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029505	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029506	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029507	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029508	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029509	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029510	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029511	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029512	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029513	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029514	MIMAT0000244	hsa-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000244	hsa-miR-30c	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029515	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	20194856	Circulating	Serum	Next-generation sequencing	"Endogenous circulating miRNAs are stable, are well protected from RNases, and remain stable even after being subjected to harsh conditions. Eleven serum miRNAs were found to be altered more than five-fold by Solexa sequencing between longer-survival and shorter-survival groups, and levels of four miRNAs (ie, miR-486, miR-30d, miR-1 and miR-501) were significantly associated with overall survival. "
RLID00029516	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029517	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029518	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029519	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029520	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029521	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029522	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00029523	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029524	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029525	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029526	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029527	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029528	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029529	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029530	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029531	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00029532	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029533	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029534	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029535	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029536	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00029537	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029538	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029539	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029540	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029541	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029542	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029543	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029544	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029545	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029546	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029547	MIMAT0000245	hsa-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000245	hsa-miR-30d	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029548	MIMAT0000246	mmu-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000246	"mmu-miR-122a, mmu-miR-122 "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029549	MIMAT0000246	mmu-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000246	"mmu-miR-122a, mmu-miR-122 "	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00029550	MIMAT0000246	mmu-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000246	"mmu-miR-122a, mmu-miR-122 "	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029551	MIMAT0000247	mmu-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000247	mmu-miR-143	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029552	MIMAT0000247	mmu-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000247	mmu-miR-143	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029553	MIMAT0000247	mmu-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000247	mmu-miR-143	miRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	Table 2: Enrichment ratios (synaptoneurosomes/total homogenate) of selected mature microRNAs measured by real-time qRT-PCR. Data are collected from Table 2.
RLID00029554	MIMAT0000247	mmu-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000247	mmu-miR-143	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00029555	MIMAT0000248	mmu-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000248	mmu-miR-30e	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029556	MIMAT0000248	mmu-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000248	mmu-miR-30e	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00029557	MIMAT0000248	mmu-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000248	mmu-miR-30e	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00029558	MIMAT0000248	mmu-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000248	mmu-miR-30e	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00029559	MIMAT0000249	mmu-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000249	mmu-miR-30e*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00029560	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029561	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029562	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029563	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029564	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029565	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029566	MIMAT0000250	hsa-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000250	hsa-miR-139	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029567	MIMAT0000251	hsa-miR-147a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000251	hsa-miR-147	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029568	MIMAT0000251	hsa-miR-147a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000251	hsa-miR-147	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029569	MIMAT0000251	hsa-miR-147a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000251	hsa-miR-147	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029570	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00029571	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029572	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029573	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029574	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029575	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00029576	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029577	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029578	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029579	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029580	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00029581	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029582	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029583	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029584	MIMAT0000252	hsa-miR-7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000252	hsa-miR-7	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029585	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	20145944	Circulating	Semen	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00029586	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00029587	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029588	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029589	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029590	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029591	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029592	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029593	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029594	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029595	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029596	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029597	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00029598	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029599	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029600	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029601	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00029602	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029603	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00029604	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00029605	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00029606	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00029607	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029608	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029609	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029610	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029611	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029612	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029613	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029614	MIMAT0000253	hsa-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000253	hsa-miR-10a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029615	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	21398193	Circulating	Blood	qRT-PCR	"Figure 3: Elevated levels of RNA and miRs in blood of lung cancer patients. The box plot shows the significantly different amounts of RNA, miR10b, miR34a, miR141 and miR155 which circulate in blood of healthy individuals (n = 28), patients with benign lung disease (n = 7) and patients with lung cancer (n = 35).  "
RLID00029616	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029617	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029618	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029619	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029620	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029621	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029622	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029623	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029624	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029625	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00029626	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029627	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029628	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029629	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00029630	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00029631	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00029632	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00029633	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00029634	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029635	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029636	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029637	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029638	MIMAT0000254	hsa-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000254	hsa-miR-10b	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00029639	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	21398193	Circulating	Blood	qRT-PCR	"Figure 3: Elevated levels of RNA and miRs in blood of lung cancer patients. The box plot shows the significantly different amounts of RNA, miR10b, miR34a, miR141 and miR155 which circulate in blood of healthy individuals (n = 28), patients with benign lung disease (n = 7) and patients with lung cancer (n = 35).  "
RLID00029640	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029641	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24456939	Circulating	Serum	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00029642	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029643	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029644	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029645	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029646	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029647	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029648	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029649	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00029650	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029651	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029652	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029653	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029654	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029655	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029656	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029657	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029658	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029659	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00029660	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00029661	MIMAT0000255	hsa-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000255	hsa-miR-34a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029662	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	23424776	Circulating	Blood	qRT-PCR|Microarray	"Five miRNAs (let-7c, miR-16, miR- 449, miR-181a and miR-181b) were found to exhibit similar expression patterns (p < 0.05) in peripheral blood when compared to data obtained by using bone marrow aspirates from MM patients in other studies.  "
RLID00029663	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029664	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029665	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029666	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029667	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00029668	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029669	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029670	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029671	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00029672	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029673	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029674	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029675	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029676	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029677	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029678	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00029679	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029680	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029681	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029682	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029683	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029684	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029685	MIMAT0000256	hsa-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000256	hsa-miR-181a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029686	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00029687	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23424776	Circulating	Blood	qRT-PCR|Microarray	"Five miRNAs (let-7c, miR-16, miR- 449, miR-181a and miR-181b) were found to exhibit similar expression patterns (p < 0.05) in peripheral blood when compared to data obtained by using bone marrow aspirates from MM patients in other studies.  "
RLID00029688	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029689	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029690	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029691	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23805240	Circulating	Plasma	qRT-PCR	"Circulating microRNAs as a Fingerprint for Liver Cirrhosis. Our study demonstrated that the combined detection of miR-106b and miR-181b has a considerable clinical value to diagnose patients with liver cirrhosis, especially those at early stage. "
RLID00029692	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00029693	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029694	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029695	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029696	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029697	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029698	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029699	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00029700	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00029701	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029702	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029703	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029704	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029705	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029706	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029707	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029708	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029709	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029710	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029711	MIMAT0000257	hsa-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000257	hsa-miR-181b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029712	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029713	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029714	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029715	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029716	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029717	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029718	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029719	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029720	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029721	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029722	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00029723	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00029724	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029725	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029726	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029727	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029728	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029729	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029730	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029731	MIMAT0000258	hsa-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000258	hsa-miR-181c	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029732	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029733	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029734	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029735	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029736	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029737	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029738	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00029739	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029740	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029741	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029742	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029743	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23559272	Circulating	Serum	Microarray	"Using microarray-based expression profiling followed by real-time quantitative polymerase chain reaction validation, we compared the levels of a series of circulating miRNAs (miR-21, miR-155, miR-182, and miR-197) in serum from patients with lung cancer (n = 65), pulmonary tuberculosis (n = 29), pneumonia (n = 29), and transudate (n = 16) compared with matched healthy controls (n = 37). "
RLID00029744	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029745	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029746	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029747	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029748	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029749	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00029750	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029751	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029752	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00029753	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029754	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029755	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029756	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029757	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00029758	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029759	MIMAT0000259	hsa-miR-182-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000259	hsa-miR-182	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029760	MIMAT0000260	hsa-miR-182-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000260	hsa-miR-182*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029761	MIMAT0000260	hsa-miR-182-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000260	hsa-miR-182*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029762	MIMAT0000260	hsa-miR-182-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000260	hsa-miR-182*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00029763	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00029764	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029765	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029766	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029767	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029768	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029769	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029770	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00029771	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029772	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029773	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029774	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029775	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029776	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029777	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029778	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029779	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00029780	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029781	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029782	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029783	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029784	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029785	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029786	MIMAT0000261	hsa-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000261	hsa-miR-183	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029787	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029788	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029789	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029790	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029791	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029792	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029793	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029794	MIMAT0000262	hsa-miR-187-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000262	hsa-miR-187	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029795	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029796	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029797	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029798	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029799	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029800	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00029801	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029802	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029803	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029804	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029805	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029806	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00029807	MIMAT0000263	hsa-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000263	hsa-miR-199b	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00029808	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029809	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029810	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00029811	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00029812	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00029813	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029814	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029815	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029816	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029817	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029818	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00029819	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029820	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029821	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029822	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029823	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029824	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029825	MIMAT0000264	hsa-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000264	hsa-miR-203a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029826	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00029827	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029828	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029829	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029830	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029831	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00029832	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029833	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029834	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029835	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00029836	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029837	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029838	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00029839	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029840	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029841	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029842	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029843	MIMAT0000265	hsa-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000265	hsa-miR-204	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029844	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00029845	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029846	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029847	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00029848	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	21601258	Exosome	Ascites	qRT-PCR	"Fig. 2. Biochemical marker analysis of exosomes. (A) Exosomes isolated from ascites or pleural effusions of tumor or LC patients were analyzed using the indi cated mAb followed by peroxidase-conjugated secondary antibody and ECL detection. 10 μ g exosomes were applied per lane. Note that HSP70, ADAM10, Annexin-1 and CD9 are considered as general exosome markers. HLA-DR was used as a marker for immune cell derived exosomes. Note that in BrCa patients #9�4 samples were derived from pleural effusions and #15 and 16 were from ascites. (B) The content of the indicated miRNAs was quantified by real-time RT-PCR in exosomes from ascites of OvCa (n=10) or LC patients (n=6) or BrCa pleural effusions (n=7). Note, that low Ct values re fl ect high expression levels of the respective miRNA. P-values in the fi gure are indicated as follows: * < 0.05, ** < 0.01 *** < 0.001. Data are collected from Figure 2. "
RLID00029849	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029850	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029851	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029852	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029853	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029854	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	25422181	Cytoplasm	Head|Neck tumor tissue	In situ hybridization	"LNA-ISH revealed that miR-205 exhibited significant differential cytoplasmic and nuclear staining among inflammation, benign and malignant tumors of head and neck. miR-205 was not only exclusively expressed in squamous epithelial malignancy. "
RLID00029855	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029856	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029857	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	25422181	Nucleus	Head|Neck tumor tissue	In situ hybridization	"LNA-ISH revealed that miR-205 exhibited significant differential cytoplasmic and nuclear staining among inflammation, benign and malignant tumors of head and neck. miR-205 was not only exclusively expressed in squamous epithelial malignancy. "
RLID00029858	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029859	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029860	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029861	MIMAT0000266	hsa-miR-205-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000266	hsa-miR-205	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029862	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029863	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029864	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029865	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00029866	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029867	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029868	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00029869	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029870	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029871	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029872	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029873	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029874	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029875	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029876	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029877	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029878	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029879	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029880	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029881	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029882	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029883	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029884	MIMAT0000267	hsa-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000267		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029885	MIMAT0000268	hsa-miR-211-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000268	hsa-miR-211	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029886	MIMAT0000268	hsa-miR-211-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000268	hsa-miR-211	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029887	MIMAT0000268	hsa-miR-211-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000268	hsa-miR-211	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029888	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029889	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029890	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00029891	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00029892	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029893	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029894	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029895	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029896	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029897	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029898	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029899	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029900	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029901	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029902	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029903	MIMAT0000269	hsa-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000269	hsa-miR-212	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029904	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029905	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029906	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029907	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029908	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029909	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029910	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029911	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029912	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029913	MIMAT0000270	hsa-miR-181a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000270	"hsa-miR-213, hsa-miR-181a* "	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029914	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00029915	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029916	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029917	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029918	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00029919	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029920	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029921	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029922	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029923	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029924	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029925	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029926	MIMAT0000271	hsa-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000271	hsa-miR-214	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029927	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029928	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029929	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029930	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029931	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029932	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029933	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029934	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029935	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029936	MIMAT0000272	hsa-miR-215-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000272		miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029937	MIMAT0000273	hsa-miR-216a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000273	"hsa-miR-216, hsa-miR-216a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029938	MIMAT0000273	hsa-miR-216a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000273	"hsa-miR-216, hsa-miR-216a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029939	MIMAT0000274	hsa-miR-217	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000274		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029940	MIMAT0000274	hsa-miR-217	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000274		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029941	MIMAT0000274	hsa-miR-217	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000274		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029942	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00029943	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029944	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029945	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029946	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029947	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00029948	MIMAT0000275	hsa-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000275	hsa-miR-218	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029949	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029950	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029951	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029952	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029953	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00029954	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029955	MIMAT0000276	hsa-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000276	hsa-miR-219	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00029956	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029957	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029958	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029959	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029960	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00029961	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00029962	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029963	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029964	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029965	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	22895844	Exosome	Colon|Liver|Lung	qRT-PCR	"When the RNA species within exosomes derived from the three CRC cell lines were examined, the mRNAs of housekeeping genes such as ACTB and GAPDH, the microRNAs such as miR-21, miR-192 and miR-221, and the natural antisense RNAs of LRRC24, MDM2 and CDKN1A genes, were detected. "
RLID00029966	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029967	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029968	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029969	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00029970	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00029971	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00029972	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029973	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00029974	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029975	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00029976	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00029977	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00029978	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029979	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00029980	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00029981	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00029982	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00029983	MIMAT0000278	hsa-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000278	hsa-miR-221	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00029984	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00029985	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029986	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00029987	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00029988	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00029989	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00029990	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00029991	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00029992	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00029993	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00029994	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00029995	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00029996	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00029997	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00029998	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00029999	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030000	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030001	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00030002	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030003	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030004	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030005	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030006	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030007	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030008	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00030009	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030010	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030011	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030012	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030013	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030014	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030015	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030016	MIMAT0000279	hsa-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000279	hsa-miR-222	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030017	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00030018	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	22105822	Circulating	plasma	qRT-PCR	"Our study revealed that plasma miR-122, miR-192, miR-21, miR-223, miR-26a, miR-27a, and miR-801 were potential circulating markers for diagnosing HCC. The microRNA panel with the seven microRNAs from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of HCC, especially for patients with early BCLC stages (0 and A). "
RLID00030019	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23056289	Circulating	Serum	qRT-PCR	"Circulating miR-17, miR-20a, miR-29c, and miR-223 combined as non-invasive biomarkers in nasopharyngeal carcinoma. "
RLID00030020	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030021	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030022	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030023	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030024	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030025	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030026	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030027	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030028	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030029	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	21939504	Exosome	Macrophage	RT-PCR	"MiR-223, a miRNA specific for IL-4-activated macrophages, was detected within the exosomes released by macrophages and was significantly elevated in the co-cultivated SKBR3 and MDA-MB-231 cells. "
RLID00030030	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030031	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030032	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00030033	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030034	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030035	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030036	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	25376581	Exosome	Saliva	RNA-seq	"Previous reports suggested that the majority of miRNAs in saliva were concentrated in exosomes. We tested the presence of miRNAs in exosome and nonexosome fractions of saliva in a subset of samples (Fig. 1C; online Supplemental Fig. 4). Two miRNAs (miR-223-3p and miR-148a-3p) detected in RNA-Seq data of multiple individuals were chosen for this experiment. As shown in Fig. 1C, both miRNAs can be detected in all 3 individuals, and they are predominantly present in the exosomal RNA fraction in 2 of 3 individuals. For 1 individual (S1), both miRNAs were detected in both exosomal and nonexosomal fractions. "
RLID00030037	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	22529849	Exosome	Breast cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030038	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030039	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030040	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	24130905	Circulating	Plasma	RT-PCR	"Overall expression levels of circulating miRNAs: most miRNAs from the designated list were successfully detected (with Ct values between 18 and 35) in virtually all samples. The highest signal was detected for miR-451, -223, -15a, -486-5p, -16, and -21, which is in agreement with literature data "
RLID00030041	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00030042	MIMAT0000280	hsa-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000280	hsa-miR-223	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00030043	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030044	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00030045	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030046	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030047	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030048	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030049	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030050	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030051	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030052	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030053	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030054	MIMAT0000281	hsa-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000281	hsa-miR-224	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030055	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030056	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030057	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030058	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030059	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030060	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030061	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030062	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030063	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030064	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030065	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030066	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	20864815	Cytoplasm	Colon cancer cell	RT-PCR|Northern blot|Microarray	"MicroRNAs such as let-7d, miR-19a, miR-19b and miR-200b, demonstrated nuclear localization at a level similar to that of cytoplasm. "
RLID00030067	MIMAT0000318	hsa-miR-200b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000318	hsa-miR-200b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030068	MIMAT0000366	mmu-miR-290a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000366	mmu-miR-290	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030069	MIMAT0000366	mmu-miR-290a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000366	mmu-miR-290	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00030070	MIMAT0000367	mmu-miR-291a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000367	mmu-miR-291-5p	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030071	MIMAT0000368	mmu-miR-291a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000368	mmu-miR-291-3p	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00030072	MIMAT0000369	mmu-miR-292a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000369	mmu-miR-292-5p	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030073	MIMAT0000370	mmu-miR-292a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000370	mmu-miR-292-3p	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00030074	MIMAT0000370	mmu-miR-292a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000370	mmu-miR-292-3p	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00030075	MIMAT0000372	mmu-miR-294-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000372	mmu-miR-294	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00030076	MIMAT0000373	mmu-miR-295-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000373	mmu-miR-295	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00030077	MIMAT0000374	mmu-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000374	mmu-miR-296	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030078	MIMAT0000374	mmu-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000374	mmu-miR-296	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030079	MIMAT0000374	mmu-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000374	mmu-miR-296	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00030080	MIMAT0000374	mmu-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000374	mmu-miR-296	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00030081	MIMAT0000375	mmu-miR-297a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000375	"mmu-miR-297, mmu-miR-297a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030082	MIMAT0000375	mmu-miR-297a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000375	"mmu-miR-297, mmu-miR-297a "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00030083	MIMAT0000376	mmu-miR-298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000376	mmu-miR-298	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030084	MIMAT0000376	mmu-miR-298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000376	mmu-miR-298	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030085	MIMAT0000376	mmu-miR-298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000376	mmu-miR-298	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030086	MIMAT0000378	mmu-miR-300-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000378	mmu-miR-300	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030087	MIMAT0000379	mmu-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000379	"mmu-miR-301, mmu-miR-301a "	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00030088	MIMAT0000379	mmu-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000379	"mmu-miR-301, mmu-miR-301a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030089	MIMAT0000379	mmu-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000379	"mmu-miR-301, mmu-miR-301a "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00030090	MIMAT0000379	mmu-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000379	"mmu-miR-301, mmu-miR-301a "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00030091	MIMAT0000381	mmu-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000381	mmu-miR-34c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030092	MIMAT0000381	mmu-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000381	mmu-miR-34c	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00030093	MIMAT0000382	mmu-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000382	mmu-miR-34b	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00030094	MIMAT0000383	mmu-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000383	mmu-let-7d	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030095	MIMAT0000383	mmu-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000383	mmu-let-7d	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030096	MIMAT0000383	mmu-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000383	mmu-let-7d	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030097	MIMAT0000383	mmu-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000383	mmu-let-7d	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	"Supplementary information, Figure S4 Screening for the target miRNAs of miR-709 in the nucleus via microarray assay (only top 44 miRNAs were showed). Data are collected from Figure S4. "
RLID00030098	MIMAT0000383	mmu-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000383	mmu-let-7d	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00030099	MIMAT0000384	mmu-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000384	mmu-let-7d*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030100	MIMAT0000385	mmu-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000385	mmu-miR-106a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030101	MIMAT0000385	mmu-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000385	mmu-miR-106a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030102	MIMAT0000385	mmu-miR-106a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000385	mmu-miR-106a	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00030103	MIMAT0000386	mmu-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000386	mmu-miR-106b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030104	MIMAT0000386	mmu-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000386	mmu-miR-106b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030105	MIMAT0000386	mmu-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000386	mmu-miR-106b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030106	MIMAT0000387	mmu-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000387	mmu-miR-130b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00030107	MIMAT0000387	mmu-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000387	mmu-miR-130b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00030108	MIMAT0000387	mmu-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000387	mmu-miR-130b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00030109	MIMAT0000387	mmu-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000387	mmu-miR-130b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00030110	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00030111	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22884882	Circulating	Plasma	Microarray	"To explore a potential novel biomarker, we examined the cellular and plasma miRNA profiles in adult T-cell leukemia (ATL) characterized by diverse clinical features. Methods and results : Using CD4-positive cells isolated from 2 non-infected healthy individuals, 3 chronic ATL patients and 3 acute ATL patients, cellular miRNAs were profiled by microarray. The microarray screened 5 miRNAs namely miR-155, let-7g, miR-126, miR-130a and let-7b because of the large difference in their expression in diseased vs. that of healthy controls. "
RLID00030112	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030113	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030114	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00030115	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030116	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030117	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030118	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030119	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030120	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030121	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030122	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030123	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030124	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030125	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00030126	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030127	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030128	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030129	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030130	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030131	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030132	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030133	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030134	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030135	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure (Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030136	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030137	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030138	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00030139	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030140	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030141	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030142	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-140a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00030143	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030144	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030145	MIMAT0000414	hsa-let-7g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000414	hsa-let-7g	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030146	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030147	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030148	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030149	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00030150	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030151	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00030152	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030153	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030154	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030155	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030156	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030157	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030158	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030159	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00030160	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030161	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030162	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030163	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030164	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030165	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030166	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030167	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030168	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030169	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030170	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030171	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030172	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030173	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-141a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00030174	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	22529849	Exosome	Gastric cancer cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030175	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030176	MIMAT0000415	hsa-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000415	hsa-let-7i	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030177	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	20194856	Circulating	Serum	Next-generation sequencing	"Endogenous circulating miRNAs are stable, are well protected from RNases, and remain stable even after being subjected to harsh conditions. Eleven serum miRNAs were found to be altered more than five-fold by Solexa sequencing between longer-survival and shorter-survival groups, and levels of four miRNAs (ie, miR-486, miR-30d, miR-1 and miR-501) were significantly associated with overall survival. "
RLID00030178	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030179	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	24456939	Circulating	Serum	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00030180	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030181	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030182	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030183	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030184	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030185	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030186	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030187	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030188	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030189	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	22529849	Exosome	Myocard	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030190	MIMAT0000416	hsa-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000416	hsa-miR-1	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030191	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030192	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030193	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030194	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030195	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00030196	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030197	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030198	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030199	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030200	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030201	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030202	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030203	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030204	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030205	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030206	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00030207	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030208	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030209	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030210	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030211	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030212	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030213	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030214	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030215	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030216	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00030217	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030218	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030219	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030220	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030221	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030222	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030223	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030224	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030225	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030226	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030227	MIMAT0000417	hsa-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000417	hsa-miR-15b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030228	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00030229	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030230	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030231	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030232	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030233	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030234	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030235	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030236	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030237	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030238	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030239	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030240	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030241	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030242	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030243	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030244	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030245	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030246	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030247	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030248	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030249	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030250	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030251	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030252	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030253	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030254	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030255	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030256	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030257	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030258	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030259	MIMAT0000418	hsa-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000418	hsa-miR-23b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030260	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030261	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030262	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030263	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030264	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030265	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030266	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030267	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030268	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030269	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030270	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030271	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030272	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030273	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030274	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030275	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00030276	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030277	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030278	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030279	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030280	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030281	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030282	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030283	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030284	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030285	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030286	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00030287	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030288	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030289	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030290	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030291	MIMAT0000419	hsa-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000419	hsa-miR-27b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030292	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030293	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030294	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030295	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030296	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030297	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030298	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030299	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030300	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030301	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030302	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030303	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030304	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030305	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030306	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030307	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030308	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030309	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030310	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030311	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030312	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030313	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030314	MIMAT0000420	hsa-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000420	hsa-miR-30b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030315	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00030316	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	22105822	Circulating	plasma	qRT-PCR	"Our study revealed that plasma miR-122, miR-192, miR-21, miR-223, miR-26a, miR-27a, and miR-801 were potential circulating markers for diagnosing HCC. The microRNA panel with the seven microRNAs from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of HCC, especially for patients with early BCLC stages (0 and A). "
RLID00030317	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030318	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030319	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030320	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00030321	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030322	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030323	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030324	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030325	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030326	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030327	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030328	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030329	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030330	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030331	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00030332	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030333	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030334	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	26304123	Endoplasmic reticulum	HEK293 cell	qRT-PCR	"This phenomenon is not HEK293- or let-7a miRNA-specific, and we documented a similar observation for a let-7a reporter in RAW264.7 mouse monocyte/macrophage cells and also for an miR-122 reporter in Huh7 cells expressing miR-122 (Fig. 1, G–I). Data are collected from Figure 1. "
RLID00030335	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030336	MIMAT0000421	hsa-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000421	"hsa-miR-122a, hsa-miR-122 "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030337	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00030338	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030339	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030340	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030341	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030342	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030343	MIMAT0000422	hsa-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000422	"hsa-miR-124a, hsa-miR-124 "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030344	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00030345	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030346	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030347	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030348	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00030349	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030350	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030351	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030352	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00030353	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030354	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030355	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030356	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030357	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030358	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00030359	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030360	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030361	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030362	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030363	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030364	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030365	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030366	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030367	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00030368	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030369	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24627568	Circulating	Plasma	qRT-PCR	"The plasma levels of miR-320b and miR-125b were significantly lower in patients with AMI when compared with controls, and these miRNAs may be involved in the pathogenesis of coronary heart disease. "
RLID00030370	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030371	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030372	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030373	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030374	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00030375	MIMAT0000423	hsa-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000423	hsa-miR-125b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030376	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030377	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030378	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030379	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030380	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030381	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030382	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030383	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030384	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030385	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030386	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030387	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030388	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030389	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030390	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030391	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030392	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030393	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030394	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030395	MIMAT0000424	hsa-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000424	hsa-miR-128a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030396	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030397	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030398	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030399	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030400	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030401	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030402	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030403	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00030404	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030405	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030406	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030407	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	22884882	Circulating	Plasma	Microarray	"To explore a potential novel biomarker, we examined the cellular and plasma miRNA profiles in adult T-cell leukemia (ATL) characterized by diverse clinical features. Methods and results : Using CD4-positive cells isolated from 2 non-infected healthy individuals, 3 chronic ATL patients and 3 acute ATL patients, cellular miRNAs were profiled by microarray. The microarray screened 5 miRNAs namely miR-155, let-7g, miR-126, miR-130a and let-7b because of the large difference in their expression in diseased vs. that of healthy controls. "
RLID00030408	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030409	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030410	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030411	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00030412	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030413	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030414	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030415	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030416	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030417	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030418	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030419	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030420	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030421	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00030422	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030423	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030424	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030425	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030426	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00030427	MIMAT0000425	hsa-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000425	hsa-miR-130a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030428	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030429	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00030430	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030431	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030432	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030433	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030434	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030435	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030436	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030437	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030438	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030439	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030440	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030441	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030442	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030443	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030444	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030445	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030446	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030447	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030448	MIMAT0000426	hsa-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000426	hsa-miR-132	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030449	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030450	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030451	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030452	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030453	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030454	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030455	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030456	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030457	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030458	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030459	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030460	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	22529849	Exosome	Myocard	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030461	MIMAT0000427	hsa-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000427		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030462	MIMAT0000428	hsa-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000428	hsa-miR-135a	miRNA	Homo sapiens	20145944	Circulating	Semen	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00030463	MIMAT0000428	hsa-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000428	hsa-miR-135a	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030464	MIMAT0000428	hsa-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000428	hsa-miR-135a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030465	MIMAT0000428	hsa-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000428	hsa-miR-135a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030466	MIMAT0000428	hsa-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000428	hsa-miR-135a	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00030467	MIMAT0000428	hsa-miR-135a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000428	hsa-miR-135a	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030468	MIMAT0000429	hsa-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000429		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030469	MIMAT0000429	hsa-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000429		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030470	MIMAT0000429	hsa-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000429		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030471	MIMAT0000429	hsa-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000429		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030472	MIMAT0000429	hsa-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000429		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030473	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00030474	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030475	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030476	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030477	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030478	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030479	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030480	MIMAT0000430	hsa-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000430	hsa-miR-138	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030481	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030482	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030483	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030484	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030485	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030486	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030487	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030488	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030489	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030490	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030491	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030492	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030493	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030494	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00030495	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030496	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030497	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030498	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030499	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030500	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00030501	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030502	MIMAT0000431	hsa-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000431	hsa-miR-140	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030503	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	18663219	Circulating	Serum	qRT-PCR	"Circulating microRNAs as stable blood-based markers for cancer detection. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. "
RLID00030504	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	21398193	Circulating	Blood	qRT-PCR	"Figure 3: Elevated levels of RNA and miRs in blood of lung cancer patients. The box plot shows the significantly different amounts of RNA, miR10b, miR34a, miR141 and miR155 which circulate in blood of healthy individuals (n = 28), patients with benign lung disease (n = 7) and patients with lung cancer (n = 35).  "
RLID00030505	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030506	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030507	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030508	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030509	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030510	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030511	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030512	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00030513	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030514	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030515	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00030516	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030517	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030518	MIMAT0000432	hsa-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000432	hsa-miR-141	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030519	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030520	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030521	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030522	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030523	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030524	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030525	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030526	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030527	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030528	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030529	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030530	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00030531	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00030532	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030533	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030534	MIMAT0000433	hsa-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433		miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00030535	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030536	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030537	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030538	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030539	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	22427800	Exosome	Serum	RT-PCR	The miRNAs tested in serum and saliva samples are shown in Table 1. These miRNAs were selected because they are either ubiquitously expressed or have been reported as biomarkers (Table 1). The relative concentration of these microRNAs was determined by calculating the difference of Ct values between the exosome samples and the exosome-depleted supernatant. A 1-unit difference in the Ct value between the miRNAs isolated from the exosomal pellet or supernatant represents a 2-fold difference in the amount of input miRNA. Data are collected from Table 1: List of miRNAs tested in serum and saliva samples.
RLID00030540	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030541	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030542	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030543	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	19951903	Microvesicle	Plasma	qRT-PCR|Microarray	"We found several miRNAs whose expression was consistently up-regulated in blood microvesicles samples from IBS patients with increased membrane permeability compared to controls (Figure 2A-lower, left panel). Three up-regulated miRNAs with a p<0.001 were identified: miR-142-3p, miRNA-29a and miR-148b (Figure 2A-lower, left panel). "
RLID00030544	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030545	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030546	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030547	MIMAT0000434	hsa-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000434		miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00030548	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00030549	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030550	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030551	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030552	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030553	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030554	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030555	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030556	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00030557	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030558	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00030559	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030560	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030561	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00030562	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030563	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030564	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030565	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030566	MIMAT0000435	hsa-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000435	hsa-miR-143	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00030567	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	20145944	Circulating	Blood	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00030568	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030569	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030570	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030571	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030572	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	25017274	Circulating	Serum	qRT-PCR	"The expression of four miRNAs (miR-1233, miR-520, miR-210, miR-144) was validated by quantitative real-time polymerase chain reaction analysis. MiR-1233 was the most overexpressed in the serum of women who later developed sPE. Circulating miRNAs deserve further investigation in order to explore their potential role in the pathogenesis of preeclampsia. In particular, miR-1233 might represent a potential marker of early sPE. "
RLID00030573	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030574	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030575	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030576	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030577	MIMAT0000436	hsa-miR-144-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000436	hsa-miR-144	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030578	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030579	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030580	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030581	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030582	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030583	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030584	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030585	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030586	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00030587	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030588	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030589	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030590	MIMAT0000437	hsa-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000437	hsa-miR-145	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030591	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030592	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030593	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030594	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030595	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030596	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030597	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030598	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030599	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030600	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030601	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030602	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030603	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030604	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030605	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030606	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030607	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030608	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030609	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030610	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00030611	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030612	MIMAT0000438	hsa-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000438		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030613	MIMAT0000439	hsa-miR-153-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000439		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030614	MIMAT0000439	hsa-miR-153-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000439		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030615	MIMAT0000439	hsa-miR-153-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000439		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030616	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030617	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030618	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030619	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030620	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00030621	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030622	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00030623	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030624	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030625	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00030626	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030627	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030628	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030629	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030630	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030631	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030632	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030633	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030634	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030635	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030636	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030637	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030638	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030639	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030640	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00030641	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030642	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00030643	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030644	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00030645	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00030646	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030647	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030648	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030649	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030650	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030651	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030652	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00030653	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR|In situ hybridization	"Through in situ hybridisation, we have localised these miRNAs, including miR-191 and miR-484, in the nucleolus of a diversity of human and rodent cell lines.  Four cleolar miRNAs; miR191, miR-484, miR-574-3p and miR-193b, were tested in our ISH experiments, and all four miRNAs exhibit strong nucleolar localisation (Figure 2A).  "
RLID00030654	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030655	MIMAT0000440	hsa-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000440	hsa-miR-191	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030656	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030657	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00030658	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030659	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030660	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030661	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030662	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030663	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030664	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030665	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030666	MIMAT0000441	hsa-miR-9-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000441	hsa-miR-9	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030667	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00030668	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030669	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030670	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030671	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030672	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030673	MIMAT0000442	hsa-miR-9-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000442	hsa-miR-9*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030674	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030675	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030676	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030677	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030678	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030679	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030680	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030681	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030682	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030683	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030684	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030685	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030686	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030687	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030688	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030689	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030690	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030691	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030692	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00030693	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030694	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030695	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030696	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030697	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030698	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030699	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00030700	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00030701	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030702	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030703	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030704	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030705	MIMAT0000443	hsa-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000443	hsa-miR-125a	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030706	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030707	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030708	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030709	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030710	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030711	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030712	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030713	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030714	MIMAT0000444	hsa-miR-126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000444	hsa-miR-126*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00030715	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00030716	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030717	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030718	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030719	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030720	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030721	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030722	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030723	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030724	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	22884882	Circulating	Plasma	Microarray|qRT-PCR	"To explore a potential novel biomarker, we examined the cellular and plasma miRNA profiles in adult T-cell leukemia (ATL) characterized by diverse clinical features. Methods and results : Using CD4-positive cells isolated from 2 non-infected healthy individuals, 3 chronic ATL patients and 3 acute ATL patients, cellular miRNAs were profiled by microarray. The microarray screened 5 miRNAs namely miR-155, let-7g, miR-126, miR-130a and let-7b because of the large difference in their expression in diseased vs. that of healthy controls. "
RLID00030725	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030726	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030727	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030728	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030729	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030730	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030731	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030732	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030733	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030734	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030735	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030736	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030737	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030738	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030739	MIMAT0000445	hsa-miR-126-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000445	hsa-miR-126	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030740	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00030741	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030742	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030743	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030744	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030745	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030746	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030747	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00030748	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030749	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030750	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030751	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030752	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00030753	MIMAT0000446	hsa-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000446	hsa-miR-127	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030754	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030755	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00030756	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030757	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030758	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030759	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030760	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030761	MIMAT0000447	hsa-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000447		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030762	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030763	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030764	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030765	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030766	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00030767	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030768	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030769	MIMAT0000448	hsa-miR-136-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000448	hsa-miR-136	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030770	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00030771	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030772	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030773	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030774	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030775	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00030776	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030777	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030778	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00030779	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030780	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030781	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030782	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030783	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030784	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030785	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030786	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030787	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030788	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030789	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030790	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00030791	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030792	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030793	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030794	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00030795	MIMAT0000449	hsa-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000449	"hsa-miR-146, hsa-miR-146a "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030796	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030797	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030798	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030799	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030800	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030801	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030802	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030803	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030804	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030805	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030806	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030807	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030808	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030809	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030810	MIMAT0000450	hsa-miR-149-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000450	hsa-miR-149	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030811	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00030812	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030813	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030814	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030815	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030816	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	19823581	Exosome	Plasma	qRT-PCR|Microarray	MiR-150 levels in plasma are significantly reduced in sepsis patients compared with controls and correlate with the Level of sepsis severity.
RLID00030817	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030818	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030819	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030820	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030821	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030822	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030823	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030824	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030825	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00030826	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030827	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030828	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00030829	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030830	MIMAT0000451	hsa-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000451	hsa-miR-150	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00030831	MIMAT0000452	hsa-miR-154-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000452	hsa-miR-154	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030832	MIMAT0000452	hsa-miR-154-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000452	hsa-miR-154	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030833	MIMAT0000452	hsa-miR-154-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000452	hsa-miR-154	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030834	MIMAT0000452	hsa-miR-154-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000452	hsa-miR-154	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030835	MIMAT0000453	hsa-miR-154-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000453	hsa-miR-154*	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00030836	MIMAT0000453	hsa-miR-154-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000453	hsa-miR-154*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030837	MIMAT0000453	hsa-miR-154-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000453	hsa-miR-154*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030838	MIMAT0000453	hsa-miR-154-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000453	hsa-miR-154*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030839	MIMAT0000453	hsa-miR-154-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000453	hsa-miR-154*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030840	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00030841	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030842	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030843	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030844	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030845	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030846	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030847	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030848	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00030849	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00030850	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030851	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030852	MIMAT0000454	hsa-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000454		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030853	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	20145944	Circulating	Blood	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00030854	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030855	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030856	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030857	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030858	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030859	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030860	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030861	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030862	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030863	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030864	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030865	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030866	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030867	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030868	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030869	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030870	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030871	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00030872	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030873	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030874	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030875	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030876	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030877	MIMAT0000455	hsa-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000455	hsa-miR-185	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030878	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030879	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030880	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030881	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030882	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00030883	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030884	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030885	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030886	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030887	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030888	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030889	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030890	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030891	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030892	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00030893	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030894	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030895	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030896	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030897	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030898	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00030899	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030900	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030901	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030902	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030903	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030904	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030905	MIMAT0000456	hsa-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000456	hsa-miR-186	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030906	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030907	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030908	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030909	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030910	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030911	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030912	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030913	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00030914	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030915	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030916	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030917	MIMAT0000457	hsa-miR-188-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000457	hsa-miR-188	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030918	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030919	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030920	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030921	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030922	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030923	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030924	MIMAT0000458	hsa-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000458	hsa-miR-190	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00030925	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030926	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030927	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030928	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030929	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030930	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030931	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030932	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030933	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00030934	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030935	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030936	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00030937	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00030938	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030939	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030940	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00030941	MIMAT0000459	hsa-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000459	"hsa-miR-193, hsa-miR-193a "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00030942	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030943	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030944	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00030945	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00030946	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030947	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030948	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030949	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030950	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030951	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030952	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00030953	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030954	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030955	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030956	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030957	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030958	MIMAT0000460	hsa-miR-194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000460	hsa-miR-194	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00030959	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00030960	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00030961	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030962	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030963	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030964	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030965	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030966	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00030967	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030968	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00030969	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00030970	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030971	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030972	MIMAT0000461	hsa-miR-195-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000461	hsa-miR-195	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00030973	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030974	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030975	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00030976	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030977	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030978	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00030979	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00030980	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00030981	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00030982	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00030983	MIMAT0000462	hsa-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000462		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00030984	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030985	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00030986	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00030987	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00030988	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00030989	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00030990	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00030991	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00030992	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00030993	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00030994	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00030995	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00030996	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00030997	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00030998	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	19011622	Microvesicle	Glioblastoma cell	qRT-PCR|Microarray	"Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles (Supplementary Table 1). Data are collected from Table S1. "
RLID00030999	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00031000	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031001	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031002	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031003	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031004	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031005	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031006	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00031007	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031008	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00031009	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00031010	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00031011	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00031012	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00031013	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031014	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031015	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031016	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031017	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00031018	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031019	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22529849	Exosome	Glioblastoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031020	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031021	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031022	MIMAT0000510	hsa-miR-320a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000510	hsa-miR-320	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031023	MIMAT0000513	mmu-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000513	mmu-miR-19b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031024	MIMAT0000513	mmu-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000513	mmu-miR-19b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031025	MIMAT0000513	mmu-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000513	mmu-miR-19b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031026	MIMAT0000513	mmu-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000513	mmu-miR-19b	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031027	MIMAT0000513	mmu-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000513	mmu-miR-19b	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031028	MIMAT0000514	mmu-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000514	mmu-miR-30c	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031029	MIMAT0000514	mmu-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000514	mmu-miR-30c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031030	MIMAT0000514	mmu-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000514	mmu-miR-30c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031031	MIMAT0000514	mmu-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000514	mmu-miR-30c	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031032	MIMAT0000514	mmu-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000514	mmu-miR-30c	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031033	MIMAT0000515	mmu-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000515	mmu-miR-30d	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031034	MIMAT0000515	mmu-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000515	mmu-miR-30d	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031035	MIMAT0000516	mmu-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000516	mmu-miR-148a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031036	MIMAT0000516	mmu-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000516	mmu-miR-148a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031037	MIMAT0000516	mmu-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000516	mmu-miR-148a	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031038	MIMAT0000517	mmu-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000517	mmu-miR-192	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031039	MIMAT0000517	mmu-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000517	mmu-miR-192	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031040	MIMAT0000517	mmu-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000517	mmu-miR-192	miRNA	Mus musculus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00031041	MIMAT0000517	mmu-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000517	mmu-miR-192	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031042	MIMAT0000517	mmu-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000517	mmu-miR-192	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031043	MIMAT0000518	mmu-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000518	mmu-miR-196a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031044	MIMAT0000521	mmu-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000521	mmu-let-7a	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031045	MIMAT0000521	mmu-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000521	mmu-let-7a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031046	MIMAT0000521	mmu-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000521	mmu-let-7a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031047	MIMAT0000521	mmu-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000521	mmu-let-7a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	"Supplementary information, Figure S4 Screening for the target miRNAs of miR-709 in the nucleus via microarray assay (only top 44 miRNAs were showed). Data are collected from Figure S4. "
RLID00031048	MIMAT0000521	mmu-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000521	mmu-let-7a	miRNA	Mus musculus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00031049	MIMAT0000522	mmu-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000522	mmu-let-7b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031050	MIMAT0000522	mmu-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000522	mmu-let-7b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031051	MIMAT0000522	mmu-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000522	mmu-let-7b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031052	MIMAT0000522	mmu-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000522	mmu-let-7b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031053	MIMAT0000522	mmu-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000522	mmu-let-7b	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031054	MIMAT0000523	mmu-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000523	mmu-let-7c	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031055	MIMAT0000523	mmu-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000523	mmu-let-7c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031056	MIMAT0000523	mmu-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000523	mmu-let-7c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031057	MIMAT0000523	mmu-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000523	mmu-let-7c	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031058	MIMAT0000524	mmu-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000524	mmu-let-7e	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031059	MIMAT0000524	mmu-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000524	mmu-let-7e	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031060	MIMAT0000524	mmu-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000524	mmu-let-7e	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031061	MIMAT0000524	mmu-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000524	mmu-let-7e	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031062	MIMAT0000524	mmu-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000524	mmu-let-7e	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031063	MIMAT0000524	mmu-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000524	mmu-let-7e	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031064	MIMAT0000525	mmu-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000525	mmu-let-7f	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031065	MIMAT0000525	mmu-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000525	mmu-let-7f	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031066	MIMAT0000525	mmu-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000525	mmu-let-7f	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (?42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031067	MIMAT0000525	mmu-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000525	mmu-let-7f	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031068	MIMAT0000525	mmu-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000525	mmu-let-7f	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	"Supplementary information, Figure S4 Screening for the target miRNAs of miR-709 in the nucleus via microarray assay (only top 44 miRNAs were showed). Data are collected from Figure S4. "
RLID00031069	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031070	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031071	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031072	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031073	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031074	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031075	MIMAT0000526	mmu-miR-15a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000526	mmu-miR-15a	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00031076	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031077	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031078	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031079	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031080	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031081	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00031082	MIMAT0000527	mmu-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000527	mmu-miR-16	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00031083	MIMAT0000528	mmu-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000528	"mmu-miR-18, mmu-miR-18a "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031084	MIMAT0000528	mmu-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000528	"mmu-miR-18, mmu-miR-18a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031085	MIMAT0000528	mmu-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000528	"mmu-miR-18, mmu-miR-18a "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031086	MIMAT0000529	mmu-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000529	"mmu-miR-20, mmu-miR-20a "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031087	MIMAT0000529	mmu-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000529	"mmu-miR-20, mmu-miR-20a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031088	MIMAT0000529	mmu-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000529	"mmu-miR-20, mmu-miR-20a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031089	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031090	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031091	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031092	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031093	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031094	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00031095	MIMAT0000530	mmu-miR-21a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000530	"mmu-miR-21, mmu-miR-21-5p "	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00031096	MIMAT0000531	mmu-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000531	mmu-miR-22	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031097	MIMAT0000531	mmu-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000531	mmu-miR-22	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031098	MIMAT0000531	mmu-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000531	mmu-miR-22	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031099	MIMAT0000531	mmu-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000531	mmu-miR-22	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031100	MIMAT0000531	mmu-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000531	mmu-miR-22	miRNA	Mus musculus	19266099	Microvesicle	Embryonic stem cell	qRT-PCR	"Figure 5: ESMVs contain miRNAs. The relative abundance of several miRNAs in ESMVs compared with ESCs was determined by real time quantitative RT-PCR. The miRNAs tested include miR-16 (lane 1), miR-21 (lane 2), miR-22 (lane 3), miR-290 (lane 4), miR-291-3p (lane 5), miR-292-3p (lane 6), miR-294 (lane 7), miR-295 (lane 8), and the small nuclear RNA, RNU6b (lane 9). Data are collected from Figure 5. "
RLID00031101	MIMAT0000532	mmu-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000532	mmu-miR-23a	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031102	MIMAT0000532	mmu-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000532	mmu-miR-23a	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031103	MIMAT0000532	mmu-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000532	mmu-miR-23a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031104	MIMAT0000532	mmu-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000532	mmu-miR-23a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031105	MIMAT0000532	mmu-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000532	mmu-miR-23a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031106	MIMAT0000533	mmu-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000533	mmu-miR-26a	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031107	MIMAT0000533	mmu-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000533	mmu-miR-26a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031108	MIMAT0000533	mmu-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000533	mmu-miR-26a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031109	MIMAT0000533	mmu-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000533	mmu-miR-26a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031110	MIMAT0000534	mmu-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000534	mmu-miR-26b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031111	MIMAT0000534	mmu-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000534	mmu-miR-26b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031112	MIMAT0000534	mmu-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000534	mmu-miR-26b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031113	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031114	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031115	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031116	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031117	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031118	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031119	MIMAT0000535	mmu-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000535	mmu-miR-29a	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031120	MIMAT0000536	mmu-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000536	mmu-miR-29c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031121	MIMAT0000536	mmu-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000536	mmu-miR-29c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031122	MIMAT0000536	mmu-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000536	mmu-miR-29c	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031123	MIMAT0000536	mmu-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000536	mmu-miR-29c	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031124	MIMAT0000536	mmu-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000536	mmu-miR-29c	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031125	MIMAT0000537	mmu-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000537	mmu-miR-27a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031126	MIMAT0000537	mmu-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000537	mmu-miR-27a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031127	MIMAT0000537	mmu-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000537	mmu-miR-27a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031128	MIMAT0000538	mmu-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000538	mmu-miR-31	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031129	MIMAT0000538	mmu-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000538	mmu-miR-31	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031130	MIMAT0000538	mmu-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000538	mmu-miR-31	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031131	MIMAT0000538	mmu-miR-31-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000538	mmu-miR-31	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031132	MIMAT0000539	mmu-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000539	"mmu-miR-92, mmu-miR-92a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031133	MIMAT0000539	mmu-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000539	"mmu-miR-92, mmu-miR-92a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031134	MIMAT0000539	mmu-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000539	"mmu-miR-92, mmu-miR-92a "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031135	MIMAT0000540	mmu-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000540	mmu-miR-93	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031136	MIMAT0000540	mmu-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000540	mmu-miR-93	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031137	MIMAT0000540	mmu-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000540	mmu-miR-93	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031138	MIMAT0000542	mmu-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000542	mmu-miR-34a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031139	MIMAT0000544	mmu-miR-129-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000544	mmu-miR-129-3p	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031140	MIMAT0000545	mmu-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000545	mmu-miR-98	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031141	MIMAT0000545	mmu-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000545	mmu-miR-98	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031142	MIMAT0000546	mmu-miR-103-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000546	mmu-miR-103	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031143	MIMAT0000546	mmu-miR-103-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000546	mmu-miR-103	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031144	MIMAT0000546	mmu-miR-103-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000546	mmu-miR-103	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031145	MIMAT0000546	mmu-miR-103-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000546	mmu-miR-103	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031146	MIMAT0000547	rno-miR-322-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000547		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031147	MIMAT0000547	rno-miR-322-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000547		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031148	MIMAT0000548	mmu-miR-322-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000548	"mmu-miR-322-5p, mmu-miR-424, mmu-miR-322 "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031149	MIMAT0000548	mmu-miR-322-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000548	"mmu-miR-322-5p, mmu-miR-424, mmu-miR-322 "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031150	MIMAT0000548	mmu-miR-322-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000548	"mmu-miR-322-5p, mmu-miR-424, mmu-miR-322 "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031151	MIMAT0000548	mmu-miR-322-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000548	"mmu-miR-322-5p, mmu-miR-424, mmu-miR-322 "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031152	MIMAT0000549	mmu-miR-322-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000549	"mmu-miR-322-3p, mmu-miR-322, mmu-miR-322* "	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031153	MIMAT0000549	mmu-miR-322-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000549	"mmu-miR-322-3p, mmu-miR-322, mmu-miR-322* "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031154	MIMAT0000550	rno-miR-323-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000550	rno-miR-323	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031155	MIMAT0000550	rno-miR-323-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000550	rno-miR-323	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00031156	MIMAT0000551	mmu-miR-323-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000551	mmu-miR-323	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031157	MIMAT0000552	rno-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000552	"rno-miR-301, rno-miR-301a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031158	MIMAT0000552	rno-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000552	"rno-miR-301, rno-miR-301a "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031159	MIMAT0000552	rno-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000552	"rno-miR-301, rno-miR-301a "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031160	MIMAT0000552	rno-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000552	"rno-miR-301, rno-miR-301a "	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031161	MIMAT0000553	rno-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000553		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031162	MIMAT0000554	rno-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000554		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031163	MIMAT0000555	mmu-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000555		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031164	MIMAT0000555	mmu-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000555		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031165	MIMAT0000556	mmu-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000556		miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031166	MIMAT0000556	mmu-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000556		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031167	MIMAT0000556	mmu-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000556		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031168	MIMAT0000556	mmu-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000556		miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031169	MIMAT0000557	rno-miR-325-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000557	rno-miR-325	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031170	MIMAT0000558	mmu-miR-325-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000558	"mmu-miR-325, mmu-miR-325* "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031171	MIMAT0000559	mmu-miR-326-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000559	mmu-miR-326	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031172	MIMAT0000559	mmu-miR-326-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000559	mmu-miR-326	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031173	MIMAT0000560	rno-miR-326-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000560	rno-miR-326	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031174	MIMAT0000560	rno-miR-326-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000560	rno-miR-326	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031175	MIMAT0000561	rno-miR-327	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000561		miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031176	MIMAT0000561	rno-miR-327	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000561		miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00031177	MIMAT0000562	rno-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000562	rno-let-7d	miRNA	Rattus norvegicus	17592044	Dendrite	Hippocampus	In situ hybridization|RT-PCR	"Dendritic miRNAs appeared punctate by in situ hybridization (Fig. 4), a pattern typical of many dendritic mRNA populations.  Fogure 4: miRNAs appear granular by in situ hybridization in cultured hippocampal neurons. (A) rno-miR-26a. (B) High power of rno-miR-26a puncta; (C) rno-miR-92; (D) rno-let-7d; and (E) rno-124a. Images were acquired using a confocal microscope. (A,C,D,E) Scale bar, 50 um; (B) scale bar, 5  um. "
RLID00031178	MIMAT0000564	rno-miR-328a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000564	"rno-miR-328, rno-miR-328a "	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00031179	MIMAT0000565	mmu-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000565	mmu-miR-328	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031180	MIMAT0000565	mmu-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000565	mmu-miR-328	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031181	MIMAT0000565	mmu-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000565	mmu-miR-328	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031182	MIMAT0000565	mmu-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000565	mmu-miR-328	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031183	MIMAT0000565	mmu-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000565	mmu-miR-328	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00031184	MIMAT0000566	rno-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000566	rno-miR-329	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031185	MIMAT0000566	rno-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000566	rno-miR-329	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031186	MIMAT0000566	rno-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000566	rno-miR-329	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00031187	MIMAT0000566	rno-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000566	rno-miR-329	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00031188	MIMAT0000567	mmu-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000567	mmu-miR-329	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031189	MIMAT0000570	rno-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000570	rno-miR-331	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031190	MIMAT0000571	mmu-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000571	mmu-miR-331	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031191	MIMAT0000571	mmu-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000571	mmu-miR-331	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031192	MIMAT0000573	rno-miR-140-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000573	rno-miR-140	miRNA	Rattus norvegicus	19106625	Mitochondrion	livers	qRT-PCR|Microarray	"To further define whether the miRNAs were present within the mitochondria, we used deoxycholic acid (DCA) to induce opening of the mitochondrial megapore channel33 and induction of the mitochondria permeability transition (MPT) in the isolated mitochondria.This disruption of mitochondrial integrity resulted in a significant loss of miRNAs by RT-PCR in the DCA treated mitochondria relative to the control vehicle group. The release of miR-130a and b, miR-320 and miR-494 was about 50% and that of miR-140 almost 80%. "
RLID00031193	MIMAT0000574	rno-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000574	rno-miR-140*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031194	MIMAT0000574	rno-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000574	rno-miR-140*	miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00031195	MIMAT0000575	rno-miR-335	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000575		miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00031196	MIMAT0000578	mmu-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000578	mmu-miR-337	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031197	MIMAT0000578	mmu-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000578	mmu-miR-337	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031198	MIMAT0000579	rno-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000579	rno-miR-148b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031199	MIMAT0000580	mmu-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000580	mmu-miR-148b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031200	MIMAT0000580	mmu-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000580	mmu-miR-148b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031201	MIMAT0000582	mmu-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000582	mmu-miR-338	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031202	MIMAT0000582	mmu-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000582	mmu-miR-338	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031203	MIMAT0000582	mmu-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000582	mmu-miR-338	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031204	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031205	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031206	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031207	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Nevertheless, the qRT-PCR method did confirm that both miR-339 and miR-350 were significantly SYN-enriched "
RLID00031208	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Synaptosomes were extracted with non-ionic detergent and measurements were made of the soluble extract vs. the insoluble residue (i.e., the PSD fraction). As shown in fig.10b, the microRNA precursors were all predominantly associated with the PSD fractionIn contrast, the mature microRNAs were predominantly detected in the Triton-soluble fraction (fig. 7b). Data are collected from Figure 7B.. "
RLID00031209	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	Table 2: Enrichment ratios (synaptoneurosomes/total homogenate) of selected mature microRNAs measured by real-time qRT-PCR. Data are collected from Table 2.
RLID00031210	MIMAT0000584	mmu-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000584	mmu-miR-339	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031211	MIMAT0000586	mmu-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000586	mmu-miR-340	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031212	MIMAT0000586	mmu-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000586	mmu-miR-340	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031213	MIMAT0000586	mmu-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000586	mmu-miR-340	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031214	MIMAT0000588	mmu-miR-341-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000588	mmu-miR-341	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031215	MIMAT0000589	rno-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000589	rno-miR-342	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00031216	MIMAT0000590	mmu-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000590	mmu-miR-342	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031217	MIMAT0000590	mmu-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000590	mmu-miR-342	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031218	MIMAT0000590	mmu-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000590	mmu-miR-342	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031219	MIMAT0000590	mmu-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000590		miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031220	MIMAT0000592	rno-miR-344a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000592	"rno-miR-344, rno-miR-344-3p "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031221	MIMAT0000593	mmu-miR-344-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000593	mmu-miR-344	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031222	MIMAT0000593	mmu-miR-344-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000593	mmu-miR-344	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00031223	MIMAT0000595	mmu-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000595	mmu-miR-345	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031224	MIMAT0000595	mmu-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000595	mmu-miR-345	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031225	MIMAT0000596	rno-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000596		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031226	MIMAT0000597	mmu-miR-346-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000597	mmu-miR-346	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031227	MIMAT0000598	rno-miR-347	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000598		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031228	MIMAT0000598	rno-miR-347	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000598		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031229	MIMAT0000600	rno-miR-129-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000600	rno-miR-129	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031230	MIMAT0000602	rno-miR-20a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000602	"rno-miR-20, rno-miR-20a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031231	MIMAT0000605	mmu-miR-350-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000605	mmu-miR-350	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031232	MIMAT0000605	mmu-miR-350-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000605	mmu-miR-350	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031233	MIMAT0000605	mmu-miR-350-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000605	mmu-miR-350	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031234	MIMAT0000605	mmu-miR-350-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000605	mmu-miR-350	miRNA	Mus musculus	18410515	Synapse	Forebrains	qRT-PCR|Microarray	"Nevertheless, the qRT-PCR method did confirm that both miR-339 and miR-350 were significantly SYN-enriched "
RLID00031235	MIMAT0000605	mmu-miR-350-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000605	mmu-miR-350	miRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR|Microarray	Table 2: Enrichment ratios (synaptoneurosomes/total homogenate) of selected mature microRNAs measured by real-time qRT-PCR. Data are collected from Table 2.
RLID00031236	MIMAT0000605	mmu-miR-350-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000605	mmu-miR-350	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031237	MIMAT0000606	rno-miR-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000606	"rno-miR-7, rno-miR-7a "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031238	MIMAT0000606	rno-miR-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000606	"rno-miR-7, rno-miR-7a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031239	MIMAT0000606	rno-miR-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000606	"rno-miR-7, rno-miR-7a "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031240	MIMAT0000607	rno-miR-7a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000607	"rno-miR-7*, rno-miR-7a*, rno-miR-7a-1* "	miRNA	Rattus norvegicus	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031241	MIMAT0000608	rno-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000608		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031242	MIMAT0000608	rno-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000608		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00031243	MIMAT0000608	rno-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000608		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Five miRNAs, miR-340-5p, miR-351, miR-494, miR-664, and let-7e, were significantly concentrated (two- to eightfold) in the nucleolus compared with the nucleoplasm and/or the cytoplasm (Fig. 2A; Supplemental Table 1). "
RLID00031244	MIMAT0000609	mmu-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000609	mmu-miR-351	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031245	MIMAT0000609	mmu-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000609	mmu-miR-351	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031246	MIMAT0000609	mmu-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000609	mmu-miR-351	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031247	MIMAT0000609	mmu-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000609	mmu-miR-351	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031248	MIMAT0000609	mmu-miR-351-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000609	mmu-miR-351	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031249	MIMAT0000610	rno-miR-352	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000610		miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00031250	MIMAT0000612	mmu-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000612	mmu-miR-135b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031251	MIMAT0000613	rno-miR-151-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000613	"rno-miR-151*, rno-miR-151 "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00031252	MIMAT0000613	rno-miR-151-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000613	"rno-miR-151*, rno-miR-151 "	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00031253	MIMAT0000616	mmu-miR-101b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000616	mmu-miR-101b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031254	MIMAT0000616	mmu-miR-101b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000616	mmu-miR-101b	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031255	MIMAT0000616	mmu-miR-101b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000616	mmu-miR-101b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031256	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	24259014	Circulating	Serum	Microarray	"Elevated Serum Level of MicroRNA (miRNA)-200c nd miRNA-371-5p in Children with Kawasaki Disease. Two miRNAs, miR-200c and miR-371-5p, were differentially expressed between children with and without KD (Fig.2). Both miRNAs were significantly upregulated in the KD group compared with the control group (p=0.032 in both). "
RLID00031257	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031258	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031259	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00031260	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031261	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	21601258	Exosome	Ascites	qRT-PCR	"Fig. 2. Biochemical marker analysis of exosomes. (A) Exosomes isolated from ascites or pleural effusions of tumor or LC patients were analyzed using the indi cated mAb followed by peroxidase-conjugated secondary antibody and ECL detection. 10 μ g exosomes were applied per lane. Note that HSP70, ADAM10, Annexin-1 and CD9 are considered as general exosome markers. HLA-DR was used as a marker for immune cell derived exosomes. Note that in BrCa patients #9�4 samples were derived from pleural effusions and #15 and 16 were from ascites. (B) The content of the indicated miRNAs was quantified by real-time RT-PCR in exosomes from ascites of OvCa (n=10) or LC patients (n=6) or BrCa pleural effusions (n=7). Note, that low Ct values re fl ect high expression levels of the respective miRNA. P-values in the fi gure are indicated as follows: * < 0.05, ** < 0.01 *** < 0.001. Data are collected from Figure 2. "
RLID00031262	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031263	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031264	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031265	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031266	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031267	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00031268	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031269	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00031270	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00031271	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031272	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031273	MIMAT0000617	hsa-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000617	hsa-miR-200c	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031274	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00031275	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	21398193	Circulating	Blood	qRT-PCR	"Figure 3: Elevated levels of RNA and miRs in blood of lung cancer patients. The box plot shows the significantly different amounts of RNA, miR10b, miR34a, miR141 and miR155 which circulate in blood of healthy individuals (n = 28), patients with benign lung disease (n = 7) and patients with lung cancer (n = 35).  "
RLID00031276	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031277	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031278	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031279	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00031280	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031281	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031282	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031283	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22884882	Circulating	Plasma	Microarray|qRT-PCR	"To explore a potential novel biomarker, we examined the cellular and plasma miRNA profiles in adult T-cell leukemia (ATL) characterized by diverse clinical features. Methods and results : Using CD4-positive cells isolated from 2 non-infected healthy individuals, 3 chronic ATL patients and 3 acute ATL patients, cellular miRNAs were profiled by microarray. The microarray screened 5 miRNAs namely miR-155, let-7g, miR-126, miR-130a and let-7b because of the large difference in their expression in diseased vs. that of healthy controls. "
RLID00031284	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031285	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23559272	Circulating	Serum	Microarray	"Using microarray-based expression profiling followed by real-time quantitative polymerase chain reaction validation, we compared the levels of a series of circulating miRNAs (miR-21, miR-155, miR-182, and miR-197) in serum from patients with lung cancer (n = 65), pulmonary tuberculosis (n = 29), pneumonia (n = 29), and transudate (n = 16) compared with matched healthy controls (n = 37). "
RLID00031286	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031287	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031288	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031289	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031290	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031291	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031292	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031293	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031294	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031295	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031296	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22529849	Exosome	Kidney cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031297	MIMAT0000646	hsa-miR-155-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000646	hsa-miR-155	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00031298	MIMAT0000647	mmu-miR-107-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000647	mmu-miR-107	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031299	MIMAT0000647	mmu-miR-107-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000647	mmu-miR-107	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031300	MIMAT0000647	mmu-miR-107-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000647	mmu-miR-107	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031301	MIMAT0000648	mmu-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000648	mmu-miR-10a	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031302	MIMAT0000648	mmu-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000648	mmu-miR-10a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031303	MIMAT0000648	mmu-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000648	mmu-miR-10a	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031304	MIMAT0000648	mmu-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000648	mmu-miR-10a	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00031305	MIMAT0000649	mmu-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000649	"mmu-miR-17-5p, mmu-miR-17 "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031306	MIMAT0000649	mmu-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000649	"mmu-miR-17-5p, mmu-miR-17 "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031307	MIMAT0000649	mmu-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000649	"mmu-miR-17-5p, mmu-miR-17 "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031308	MIMAT0000649	mmu-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000649	"mmu-miR-17-5p, mmu-miR-17 "	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00031309	MIMAT0000649	mmu-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000649	"mmu-miR-17-5p, mmu-miR-17 "	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031310	MIMAT0000650	mmu-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000650	"mmu-miR-17-3p, mmu-miR-17* "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031311	MIMAT0000650	mmu-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000650	"mmu-miR-17-3p, mmu-miR-17* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031312	MIMAT0000651	mmu-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000651	mmu-miR-19a	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031313	MIMAT0000651	mmu-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000651	mmu-miR-19a	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031314	MIMAT0000651	mmu-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000651	mmu-miR-19a	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031315	MIMAT0000652	mmu-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000652	mmu-miR-25	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031316	MIMAT0000652	mmu-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000652	mmu-miR-25	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031317	MIMAT0000652	mmu-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000652	mmu-miR-25	miRNA	Mus musculus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00031318	MIMAT0000652	mmu-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000652	mmu-miR-25	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031319	MIMAT0000653	mmu-miR-28a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000653	"mmu-miR-28, mmu-miR-28-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031320	MIMAT0000653	mmu-miR-28a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000653	"mmu-miR-28, mmu-miR-28-5p "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031321	MIMAT0000653	mmu-miR-28a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000653	"mmu-miR-28, mmu-miR-28-5p "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031322	MIMAT0000654	mmu-miR-32-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000654	mmu-miR-32	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031323	MIMAT0000655	mmu-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000655	mmu-miR-100	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031324	MIMAT0000655	mmu-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000655	mmu-miR-100	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031325	MIMAT0000656	mmu-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000656	mmu-miR-139	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031326	MIMAT0000656	mmu-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000656	mmu-miR-139	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031327	MIMAT0000657	mmu-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000657	mmu-miR-200c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031328	MIMAT0000657	mmu-miR-200c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000657	mmu-miR-200c	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031329	MIMAT0000658	mmu-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000658	mmu-miR-210	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031330	MIMAT0000658	mmu-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000658	mmu-miR-210	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00031331	MIMAT0000658	mmu-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000658	mmu-miR-210	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031332	MIMAT0000659	mmu-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000659	mmu-miR-212	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031333	MIMAT0000659	mmu-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000659	mmu-miR-212	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031334	MIMAT0000660	mmu-miR-181a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000660	"mmu-miR-213, mmu-miR-181a*, mmu-miR-181a-1* "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031335	MIMAT0000660	mmu-miR-181a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000660	"mmu-miR-213, mmu-miR-181a*, mmu-miR-181a-1* "	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031336	MIMAT0000661	mmu-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000661	mmu-miR-214	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031337	MIMAT0000661	mmu-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000661	mmu-miR-214	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031338	MIMAT0000661	mmu-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000661	mmu-miR-214	miRNA	Mus musculus	18204908	Cytoplasm	Spermatocyte	In situ hybridization|Microarray	"Hybridization signals with all miRNA probes tested localized to the Sertoli cells (Figure 5A), with some also present in the cytoplasm of the germ cells (miR-214) and others (miR-24) having a distinct localization pattern in the nuclei of spermatocytes (Figure 5A).  "
RLID00031339	MIMAT0000661	mmu-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000661	mmu-miR-214	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031340	MIMAT0000663	mmu-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000663	mmu-miR-218	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031341	MIMAT0000663	mmu-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000663	mmu-miR-218	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031342	MIMAT0000663	mmu-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000663	mmu-miR-218	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031343	MIMAT0000663	mmu-miR-218-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000663	mmu-miR-218	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00031344	MIMAT0000664	mmu-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000664	mmu-miR-219	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031345	MIMAT0000664	mmu-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000664	mmu-miR-219	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031346	MIMAT0000664	mmu-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000664	mmu-miR-219	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031347	MIMAT0000664	mmu-miR-219a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000664	mmu-miR-219	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031348	MIMAT0000665	mmu-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000665	mmu-miR-223	miRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"We found strong concordance when ranking the different RNAs based on their abundance in the shuttle RNA. We calculated the correlation between the (ranked) small shuttle RNA sequencing data of the replicates. A high correlation was observed between the replicates (Pearson’s correlation 0.97, P-value <2.2e-16; Supplementary Figure S1). Data are collected from Figure S1. "
RLID00031349	MIMAT0000665	mmu-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000665	mmu-miR-223	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031350	MIMAT0000665	mmu-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000665	mmu-miR-223	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031351	MIMAT0000665	mmu-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000665	mmu-miR-223	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031352	MIMAT0000665	mmu-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000665	mmu-miR-223	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031353	MIMAT0000665	mmu-miR-223-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000665	mmu-miR-223	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00031354	MIMAT0000666	mmu-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000666	mmu-miR-320	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031355	MIMAT0000666	mmu-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000666	mmu-miR-320	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031356	MIMAT0000666	mmu-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000666	mmu-miR-320	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031357	MIMAT0000666	mmu-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000666	mmu-miR-320	miRNA	Mus musculus	18204908	Nucleolus	Spermatocyte	In situ hybridization|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00031358	MIMAT0000666	mmu-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000666	mmu-miR-320	miRNA	Mus musculus	18204908	Nucleus	Spermatocyte	In situ hybridization|Microarray	"FISH analysis of piRNA localization revealed a strong signal in the nucleolus of Sertoli cells, in agreement with our observed miRNA pattern. The images of the two piRNAs shown in Figure 6S are essentially identical to all piRNAs tested. This nucleolar localization was abolished in MIWI-null testis (Figure 6C; Sertoli cell, insert, yellow arrow). The effect of MIWI deletion is surprising since expression of MIWI protein was reported in the cytoplasm of spermatocytes and spermatids but not Sertoli cells (Deng & Lin 2002, Kotaja et al. 2006). It is possible that the greater levels of expression in spermatocytes and spermatids have obscured visual- ization of MIWI staining in the Sertoli cells where MIWI could be responsible for localization of piRNAs to the nucleolus and possibly their processing. In meiotic spreads, only piR-7 and piR-17005 showed strong localization to the dense body, chromosome cores and possibly telomeres, while the other three (piR-17037, 17043, 17080) showed very weak or no association (Figure 6D). MIWI deletion did not affect piRNAs localization in the meiotic nucleus. "
RLID00031359	MIMAT0000666	mmu-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000666	mmu-miR-320	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031360	MIMAT0000667	mmu-miR-33-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000667	mmu-miR-33	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031361	MIMAT0000669	mmu-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000669	mmu-miR-221	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031362	MIMAT0000669	mmu-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000669	mmu-miR-221	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031363	MIMAT0000669	mmu-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000669	mmu-miR-221	miRNA	Mus musculus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00031364	MIMAT0000669	mmu-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000669	mmu-miR-221	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031365	MIMAT0000670	mmu-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000670	mmu-miR-222	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031366	MIMAT0000670	mmu-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000670	mmu-miR-222	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031367	MIMAT0000670	mmu-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000670	mmu-miR-222	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031368	MIMAT0000670	mmu-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000670	mmu-miR-222	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031369	MIMAT0000671	mmu-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000671	mmu-miR-224	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031370	MIMAT0000671	mmu-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000671	mmu-miR-224	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00031371	MIMAT0000673	mmu-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000673	mmu-miR-181b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031372	MIMAT0000673	mmu-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000673	mmu-miR-181b	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031373	MIMAT0000673	mmu-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000673	mmu-miR-181b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00031374	MIMAT0000674	mmu-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000674	mmu-miR-181c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031375	MIMAT0000674	mmu-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000674	mmu-miR-181c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031376	MIMAT0000674	mmu-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000674	mmu-miR-181c	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031377	MIMAT0000677	mmu-miR-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000677	"mmu-miR-7, mmu-miR-7a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031378	MIMAT0000677	mmu-miR-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000677	"mmu-miR-7, mmu-miR-7a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031379	MIMAT0000678	mmu-miR-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000678	mmu-miR-7b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031380	MIMAT0000678	mmu-miR-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000678	mmu-miR-7b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031381	MIMAT0000678	mmu-miR-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000678	mmu-miR-7b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031382	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031383	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031384	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23805240	Circulating	Plasma	qRT-PCR	"Circulating microRNAs as a Fingerprint for Liver Cirrhosis. Our study demonstrated that the combined detection of miR-106b and miR-181b has a considerable clinical value to diagnose patients with liver cirrhosis, especially those at early stage. "
RLID00031385	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24456939	Circulating	Plasma	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00031386	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031387	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031388	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031389	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00031390	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031391	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031392	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031393	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031394	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031395	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00031396	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00031397	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031398	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031399	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031400	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00031401	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031402	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031403	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00031404	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00031405	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031406	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031407	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031408	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031409	MIMAT0000680	hsa-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000680	hsa-miR-106b	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00031410	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23056289	Circulating	Serum	qRT-PCR	"Circulating miR-17, miR-20a, miR-29c, and miR-223 combined as non-invasive biomarkers in nasopharyngeal carcinoma. "
RLID00031411	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031412	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031413	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031414	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031415	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00031416	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031417	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031418	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031419	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031420	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031421	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031422	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031423	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00031424	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031425	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031426	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031427	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031428	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031429	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031430	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031431	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031432	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031433	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031434	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031435	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031436	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031437	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031438	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00031439	MIMAT0000681	hsa-miR-29c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000681	hsa-miR-29c	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031440	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031441	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031442	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031443	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	21601258	Exosome	Ascites	qRT-PCR	"Fig. 2. Biochemical marker analysis of exosomes. (A) Exosomes isolated from ascites or pleural effusions of tumor or LC patients were analyzed using the indi cated mAb followed by peroxidase-conjugated secondary antibody and ECL detection. 10 μ g exosomes were applied per lane. Note that HSP70, ADAM10, Annexin-1 and CD9 are considered as general exosome markers. HLA-DR was used as a marker for immune cell derived exosomes. Note that in BrCa patients #9�4 samples were derived from pleural effusions and #15 and 16 were from ascites. (B) The content of the indicated miRNAs was quantified by real-time RT-PCR in exosomes from ascites of OvCa (n=10) or LC patients (n=6) or BrCa pleural effusions (n=7). Note, that low Ct values re fl ect high expression levels of the respective miRNA. P-values in the fi gure are indicated as follows: * < 0.05, ** < 0.01 *** < 0.001. Data are collected from Figure 2. "
RLID00031444	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031445	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031446	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031447	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031448	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031449	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00031450	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031451	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031452	MIMAT0000682	hsa-miR-200a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000682	hsa-miR-200a	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031453	MIMAT0000683	hsa-miR-302a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000683	hsa-miR-302a*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031454	MIMAT0000683	hsa-miR-302a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000683	hsa-miR-302a*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031455	MIMAT0000684	hsa-miR-302a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000684	hsa-miR-302a	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031456	MIMAT0000684	hsa-miR-302a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000684	hsa-miR-302a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031457	MIMAT0000684	hsa-miR-302a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000684	hsa-miR-302a	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031458	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031459	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031460	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031461	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031462	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031463	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031464	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00031465	MIMAT0000685	hsa-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000685	"hsa-miR-34b, hsa-miR-34b* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031466	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00031467	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031468	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031469	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031470	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031471	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031472	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031473	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031474	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031475	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00031476	MIMAT0000686	hsa-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000686	hsa-miR-34c	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031477	MIMAT0000687	hsa-miR-299-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000687	"hsa-miR-299, hsa-miR-299-5p "	miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031478	MIMAT0000687	hsa-miR-299-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000687	"hsa-miR-299, hsa-miR-299-5p "	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031479	MIMAT0000687	hsa-miR-299-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000687	"hsa-miR-299, hsa-miR-299-5p "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031480	MIMAT0000687	hsa-miR-299-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000687	"hsa-miR-299, hsa-miR-299-5p "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031481	MIMAT0000687	hsa-miR-299-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000687	"hsa-miR-299, hsa-miR-299-5p "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031482	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031483	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031484	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00031485	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031486	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031487	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031488	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031489	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00031490	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031491	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00031492	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031493	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031494	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031495	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031496	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031497	MIMAT0000688	hsa-miR-301a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000688	"hsa-miR-301, hsa-miR-301a "	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031498	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	18954897	Circulating	Serum	qRT-PCR	Fig. 2. Median fold-change differences in differentially expressed miRNAs between patient and control serum. Data are collected from Figure 2.
RLID00031499	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031500	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031501	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031502	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031503	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031504	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031505	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031506	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00031507	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031508	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031509	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031510	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031511	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031512	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031513	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031514	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031515	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031516	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031517	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00031518	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00031519	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00031520	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031521	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031522	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031523	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031524	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031525	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031526	MIMAT0000689	hsa-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000689	hsa-miR-99b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031527	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	21690488	Circulating	Plasma	qRT-PCR	"The expressions of selected miRNAs (miR-296-5p, let-7e, and a human cytomegalovirus [HCMV]-encoded miRNA, hcmv-miR-UL112) were validated independently in plasma samples from 24 hypertensive patients and 22 control subjects. "
RLID00031528	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00031529	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031530	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031531	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	21924071	Circulating	Plasma	Microarray	"MiR-296-5p (Fold change 0.47, P = 0.013) and miR-133b (Fold change 0.57, P = 0.033) were consistently down-regulated in the patient plasma, whereas let-7e (Fold change 1.62, P = 0.009) and hcmv-miR-UL112 (Fold change 2.72, P = 0.004), one human cytomegalovirus encoded microRNAs, were up-regulated in the patient samples.  "
RLID00031532	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031533	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031534	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031535	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031536	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031537	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031538	MIMAT0000690	hsa-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000690	hsa-miR-296	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031539	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031540	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031541	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031542	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00031543	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031544	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031545	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031546	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031547	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031548	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031549	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031550	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031551	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031552	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031553	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031554	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031555	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031556	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031557	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00031558	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00031559	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00031560	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031561	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031562	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031563	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031564	MIMAT0000691	hsa-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000691	hsa-miR-130b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031565	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031566	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031567	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031568	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031569	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031570	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031571	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031572	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031573	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031574	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031575	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00031576	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00031577	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031578	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00031579	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031580	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031581	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031582	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031583	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031584	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031585	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031586	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031587	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00031588	MIMAT0000692	hsa-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000692	"hsa-miR-30e-5p, hsa-miR-30e "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031589	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031590	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031591	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031592	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031593	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031594	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031595	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031596	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031597	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031598	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031599	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031600	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031601	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031602	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031603	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00031604	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031605	MIMAT0000693	hsa-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000693	"hsa-miR-30e-3p, hsa-miR-30e* "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031606	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031607	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031608	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00031609	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031610	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00031611	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031612	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031613	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00031614	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031615	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031616	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031617	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031618	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031619	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00031620	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00031621	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031622	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031623	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031624	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031625	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031626	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031627	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031628	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031629	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031630	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031631	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00031632	MIMAT0000703	hsa-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000703	hsa-miR-361	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031633	MIMAT0000704	mmu-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000704	mmu-miR-361	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031634	MIMAT0000704	mmu-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000704	mmu-miR-361	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031635	MIMAT0000704	mmu-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000704	mmu-miR-361	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031636	MIMAT0000704	mmu-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000704	mmu-miR-361	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031637	MIMAT0000704	mmu-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000704	mmu-miR-361	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031638	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031639	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031640	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031641	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031642	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031643	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031644	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031645	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031646	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031647	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00031648	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031649	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031650	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031651	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031652	MIMAT0000705	hsa-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000705	hsa-miR-362	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00031653	MIMAT0000706	mmu-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000706	mmu-miR-362	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00031654	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031655	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031656	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031657	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00031658	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00031659	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031660	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031661	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031662	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031663	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031664	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031665	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031666	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031667	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031668	MIMAT0000707	hsa-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000707	hsa-miR-363	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031669	MIMAT0000708	mmu-miR-363-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000708	mmu-miR-363	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031670	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031671	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031672	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031673	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031674	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031675	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031676	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031677	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031678	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00031679	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00031680	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031681	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031682	MIMAT0000710	hsa-miR-365a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000710	hsa-miR-365	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031683	MIMAT0000711	mmu-miR-365-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000711	mmu-miR-365	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031684	MIMAT0000711	mmu-miR-365-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000711	mmu-miR-365	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031685	MIMAT0000711	mmu-miR-365-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000711	mmu-miR-365	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00031686	MIMAT0000714	hsa-miR-302b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000714	hsa-miR-302b*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031687	MIMAT0000715	hsa-miR-302b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000715	hsa-miR-302b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031688	MIMAT0000715	hsa-miR-302b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000715	hsa-miR-302b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031689	MIMAT0000715	hsa-miR-302b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000715	hsa-miR-302b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031690	MIMAT0000716	hsa-miR-302c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000716	hsa-miR-302c*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031691	MIMAT0000717	hsa-miR-302c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000717	hsa-miR-302c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031692	MIMAT0000717	hsa-miR-302c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000717	hsa-miR-302c	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031693	MIMAT0000717	hsa-miR-302c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000717	hsa-miR-302c	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031694	MIMAT0000717	hsa-miR-302c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000717	hsa-miR-302c	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031695	MIMAT0000718	hsa-miR-302d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000718	hsa-miR-302d	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031696	MIMAT0000719	hsa-miR-367-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000719	hsa-miR-367	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031697	MIMAT0000719	hsa-miR-367-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000719	hsa-miR-367	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031698	MIMAT0000720	hsa-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000720	"hsa-miR-368, hsa-miR-376c "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031699	MIMAT0000720	hsa-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000720	"hsa-miR-368, hsa-miR-376c "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031700	MIMAT0000720	hsa-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000720	"hsa-miR-368, hsa-miR-376c "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031701	MIMAT0000720	hsa-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000720	"hsa-miR-368, hsa-miR-376c "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031702	MIMAT0000720	hsa-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000720	"hsa-miR-368, hsa-miR-376c "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031703	MIMAT0000720	hsa-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000720	"hsa-miR-368, hsa-miR-376c "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031704	MIMAT0000721	hsa-miR-369-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000721	hsa-miR-369	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031705	MIMAT0000721	hsa-miR-369-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000721	hsa-miR-369	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031706	MIMAT0000721	hsa-miR-369-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000721	hsa-miR-369	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031707	MIMAT0000721	hsa-miR-369-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000721	hsa-miR-369	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00031708	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031709	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00031710	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031711	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031712	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031713	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031714	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031715	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031716	MIMAT0000722	hsa-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000722		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031717	MIMAT0000723	hsa-miR-371a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000723	"hsa-miR-371, hsa-miR-371-3p "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031718	MIMAT0000723	hsa-miR-371a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000723	"hsa-miR-371, hsa-miR-371-3p "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031719	MIMAT0000724	hsa-miR-372-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000724		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031720	MIMAT0000724	hsa-miR-372-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000724		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031721	MIMAT0000725	hsa-miR-373-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000725	hsa-miR-373*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031722	MIMAT0000725	hsa-miR-373-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000725	hsa-miR-373*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031723	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031724	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031725	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031726	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031727	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031728	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031729	MIMAT0000726	hsa-miR-373-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000726	hsa-miR-373	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031730	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031731	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031732	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031733	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031734	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031735	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031736	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031737	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00031738	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00031739	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031740	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031741	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031742	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031743	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031744	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031745	MIMAT0000727	hsa-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000727	"hsa-miR-374, hsa-miR-374a "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031746	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00031747	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031748	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031749	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031750	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031751	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031752	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031753	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031754	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23461060	Circulating	Serum	qRT-PCR	"The circulating serum levels of miR-375 in patients who had distal gastric adenocarcinoma were also much lower than normal controls (p < 0.001). As a biomarker, miR-375 yielded a receiver operating characteristic area under the curve of 0.835. "
RLID00031755	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031756	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031757	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031758	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031759	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00031760	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031761	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031762	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00031763	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00031764	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00031765	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031766	MIMAT0000728	hsa-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000728		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031767	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031768	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00031769	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031770	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031771	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031772	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031773	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031774	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031775	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031776	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031777	MIMAT0000729	hsa-miR-376a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000729	hsa-miR-376a	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00031778	MIMAT0000730	hsa-miR-377-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000730	hsa-miR-377	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00031779	MIMAT0000730	hsa-miR-377-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000730	hsa-miR-377	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031780	MIMAT0000730	hsa-miR-377-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000730	hsa-miR-377	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031781	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031782	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031783	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031784	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031785	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031786	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031787	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00031788	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031789	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031790	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031791	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031792	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031793	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031794	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031795	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031796	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031797	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031798	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00031799	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031800	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031801	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031802	MIMAT0000731	hsa-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000731	"hsa-miR-378, hsa-miR-378* "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031803	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031804	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031805	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031806	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00031807	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031808	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031809	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031810	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031811	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00031812	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031813	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031814	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031815	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00031816	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031817	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031818	MIMAT0000732	hsa-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000732	"hsa-miR-422b, hsa-miR-378 "	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00031819	MIMAT0000733	hsa-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000733	hsa-miR-379	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031820	MIMAT0000733	hsa-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000733	hsa-miR-379	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031821	MIMAT0000733	hsa-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000733	hsa-miR-379	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031822	MIMAT0000733	hsa-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000733	hsa-miR-379	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031823	MIMAT0000733	hsa-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000733	hsa-miR-379	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031824	MIMAT0000733	hsa-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000733	hsa-miR-379	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031825	MIMAT0000734	hsa-miR-380-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000734	"hsa-miR-380-5p, hsa-miR-380* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031826	MIMAT0000734	hsa-miR-380-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000734	"hsa-miR-380-5p, hsa-miR-380* "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031827	MIMAT0000735	hsa-miR-380-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000735	"hsa-miR-380-3p, hsa-miR-380 "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031828	MIMAT0000735	hsa-miR-380-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000735	"hsa-miR-380-3p, hsa-miR-380 "	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031829	MIMAT0000735	hsa-miR-380-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000735	"hsa-miR-380-3p, hsa-miR-380 "	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031830	MIMAT0000736	hsa-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000736	hsa-miR-381	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00031831	MIMAT0000736	hsa-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000736	hsa-miR-381	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031832	MIMAT0000736	hsa-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000736	hsa-miR-381	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031833	MIMAT0000736	hsa-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000736	hsa-miR-381	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00031834	MIMAT0000736	hsa-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000736	hsa-miR-381	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031835	MIMAT0000736	hsa-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000736	hsa-miR-381	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00031836	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031837	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00031838	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031839	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031840	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031841	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031842	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00031843	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031844	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031845	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031846	MIMAT0000737	hsa-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000737	hsa-miR-382	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031847	MIMAT0000738	hsa-miR-383-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000738		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031848	MIMAT0000738	hsa-miR-383-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000738		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031849	MIMAT0000739	mmu-miR-375-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000739	mmu-miR-375	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031850	MIMAT0000741	mmu-miR-377-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000741	mmu-miR-377	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00031851	MIMAT0000742	mmu-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000742	"mmu-miR-378, mmu-miR-378*, mmu-miR-378-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00031852	MIMAT0000742	mmu-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000742	"mmu-miR-378, mmu-miR-378*, mmu-miR-378-5p "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031853	MIMAT0000743	mmu-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000743	mmu-miR-379	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031854	MIMAT0000743	mmu-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000743	mmu-miR-379	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00031855	MIMAT0000744	mmu-miR-380-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000744		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031856	MIMAT0000746	mmu-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000746	mmu-miR-381	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00031857	MIMAT0000746	mmu-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000746	mmu-miR-381	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00031858	MIMAT0000747	mmu-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000747	mmu-miR-382	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00031859	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031860	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031861	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031862	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031863	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	25165030	Circulating	Serum	RT-PCR	"Although serum microRNAs (miRNAs) play essential roles in the diagnosis of various diseases, little is known about circulating miRNAs in the aging process. Solexa sequencing demonstrated 17 markedly altered miRNAs in the aging process. Quantitative reversn-PCR analysis identified five downregulated miRNAs (miR-29b, miR-106b, miR-130b, miR-142-5p, and miR-340) and three upregulated miRNAs (miR-92a, miR-222, and miR-375) with age.  "
RLID00031864	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031865	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031866	MIMAT0000750	hsa-miR-340-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000750	"hsa-miR-340, hsa-miR-340* "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031867	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031868	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031869	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031870	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031871	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031872	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031873	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031874	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031875	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031876	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031877	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031878	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031879	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031880	MIMAT0000751	hsa-miR-330-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000751	hsa-miR-330	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031881	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00031882	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031883	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031884	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031885	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00031886	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031887	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031888	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031889	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031890	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031891	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031892	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031893	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00031894	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031895	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031896	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031897	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00031898	MIMAT0000752	hsa-miR-328-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000752		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031899	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00031900	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031901	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031902	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031903	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031904	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031905	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00031906	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031907	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031908	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031909	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031910	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031911	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031912	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031913	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031914	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031915	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031916	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031917	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00031918	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031919	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00031920	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031921	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00031922	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00031923	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031924	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00031925	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031926	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031927	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031928	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031929	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00031930	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00031931	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031932	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031933	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031934	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031935	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031936	MIMAT0000753	hsa-miR-342-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000753	hsa-miR-342	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00031937	MIMAT0000754	hsa-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000754	hsa-miR-337	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031938	MIMAT0000754	hsa-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000754	hsa-miR-337	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031939	MIMAT0000754	hsa-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000754	hsa-miR-337	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031940	MIMAT0000754	hsa-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000754	hsa-miR-337	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031941	MIMAT0000754	hsa-miR-337-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000754	hsa-miR-337	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031942	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00031943	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031944	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031945	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031946	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031947	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031948	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031949	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031950	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031951	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031952	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00031953	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031954	MIMAT0000755	hsa-miR-323a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000755	"hsa-miR-323, hsa-miR-323-3p "	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00031955	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031956	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	24937531	Circulating	Plasma	qRT-PCR	"Quantitative RT-PCR validation confirmed the significant up-regulation of miR-326 (P = .004) and down-regulation of let-7a (P < .001) and let-7f (P = .003). Notably, an inverse negative correlation was found between circulating miR-326 and its putative target adiponectin (p = -0.479, P = .009).  "
RLID00031957	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031958	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031959	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031960	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031961	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031962	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031963	MIMAT0000756	hsa-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000756		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00031964	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031965	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00031966	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00031967	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031968	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00031969	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031970	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00031971	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031972	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00031973	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00031974	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00031975	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031976	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031977	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00031978	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00031979	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00031980	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00031981	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031982	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00031983	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031984	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00031985	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00031986	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031987	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00031988	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031989	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031990	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00031991	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031992	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00031993	MIMAT0000757	hsa-miR-151a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000757	"hsa-miR-151, hsa-miR-151-3p "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00031994	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00031995	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00031996	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00031997	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00031998	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00031999	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032000	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032001	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032002	MIMAT0000758	hsa-miR-135b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000758	hsa-miR-135b	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032003	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032004	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032005	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032006	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032007	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032008	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032009	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032010	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032011	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032012	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	19951903	Microvesicle	Plasma	qRT-PCR|Microarray	"We found several miRNAs whose expression was consistently up-regulated in blood microvesicles samples from IBS patients with increased membrane permeability compared to controls (Figure 2A-lower, left panel). Three up-regulated miRNAs with a p<0.001 were identified: miR-142-3p, miRNA-29a and miR-148b (Figure 2A-lower, left panel). "
RLID00032013	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00032014	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032015	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032016	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032017	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032018	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032019	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032020	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032021	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032022	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00032023	MIMAT0000759	hsa-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000759	hsa-miR-148b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032024	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032025	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032026	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032027	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032028	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032029	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032030	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032031	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032032	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032033	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032034	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032035	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032036	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032037	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032038	MIMAT0000760	hsa-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000760	hsa-miR-331	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032039	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032040	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032041	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032042	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032043	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032044	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032045	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032046	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032047	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032048	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032049	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032050	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032051	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00032052	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032053	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032054	MIMAT0000761	hsa-miR-324-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000761		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032055	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032056	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032057	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032058	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032059	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032060	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032061	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032062	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032063	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00032064	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032065	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032066	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032067	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032068	MIMAT0000762	hsa-miR-324-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000762		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032069	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032070	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032071	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032072	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032073	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032074	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032075	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032076	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032077	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00032078	MIMAT0000763	hsa-miR-338-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000763	hsa-miR-338	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032079	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032080	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032081	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032082	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032083	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032084	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032085	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032086	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032087	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032088	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032089	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032090	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032091	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032092	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032093	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032094	MIMAT0000764	hsa-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000764	hsa-miR-339	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032095	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032096	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032097	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00032098	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032099	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032100	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032101	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032102	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032103	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032104	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00032105	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032106	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032107	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032108	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032109	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032110	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	22529849	Exosome	T cell|B cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032111	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032112	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032113	MIMAT0000765	hsa-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000765	hsa-miR-335	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00032114	MIMAT0000766	mmu-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000766	mmu-miR-335	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00032115	MIMAT0000766	mmu-miR-335-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000766	mmu-miR-335	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00032116	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032117	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032118	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	21924071	Circulating	Plasma	Microarray	"MiR-296-5p (Fold change 0.47, P = 0.013) and miR-133b (Fold change 0.57, P = 0.033) were consistently down-regulated in the patient plasma, whereas let-7e (Fold change 1.62, P = 0.009) and hcmv-miR-UL112 (Fold change 2.72, P = 0.004), one human cytomegalovirus encoded microRNAs, were up-regulated in the patient samples.  "
RLID00032119	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032120	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032121	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032122	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032123	MIMAT0000770	hsa-miR-133b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000770		miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032124	MIMAT0000771	hsa-miR-325	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000771		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032125	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032126	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032127	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032128	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032129	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032130	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032131	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032132	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032133	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032134	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032135	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032136	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032137	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032138	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032139	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032140	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032141	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032142	MIMAT0000772	hsa-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000772	hsa-miR-345	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032143	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00032144	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032145	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032146	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032147	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032148	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032149	MIMAT0000773	hsa-miR-346	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000773		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032150	MIMAT0000774	rno-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000774	rno-let-7a	miRNA	Rattus norvegicus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032151	MIMAT0000774	rno-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000774	rno-let-7a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032152	MIMAT0000775	rno-let-7b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000775	rno-let-7b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032153	MIMAT0000776	rno-let-7c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000776	rno-let-7c	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032154	MIMAT0000777	rno-let-7e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000777	rno-let-7e	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032155	MIMAT0000781	rno-miR-9a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000781	rno-miR-9	miRNA	Rattus norvegicus	19465924	Synapse	Hippocampus	In situ hybridization|Northern blot	"The observed enrichment of several miRNAs in RNA preparations from synaptosomes was validated for selected candidates by Northern blot analysis (Fig. 2A). To monitor the subcellular localization of miRNAs identified in our screen, we performed in situ hybridization (ISH) in rat hippocampal neurons at 18 days in vitro (DIV) (Fig. 2B), using probes for miR-9, miR-218, miR-138 and miR-124 as a control (Fig. 2A, Suppl. Table 1). Data are collected from Figure 2. "
RLID00032156	MIMAT0000783	rno-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000783	rno-miR-10b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032157	MIMAT0000784	rno-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000784	rno-miR-15b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032158	MIMAT0000784	rno-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000784	rno-miR-15b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032159	MIMAT0000784	rno-miR-15b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000784	rno-miR-15b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032160	MIMAT0000785	rno-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000785	rno-miR-16	miRNA	Rattus norvegicus	21435393	Microvesicle	Serum	RT-PCR	"By using RT-PCR and specific forward/reverse primers these microRNAs were all detected in microvesicles, that had been released from primary and differentiated rat adipocytes after 6 and 24h incubation, respectively, as well as in microvesicles from rat serum(Fig. 6; shown only for miR-16, miR-27a, miR-146b and miR-222). "
RLID00032161	MIMAT0000785	rno-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000785	rno-miR-16	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032162	MIMAT0000785	rno-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000785	rno-miR-16	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032163	MIMAT0000785	rno-miR-16-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000785	rno-miR-16	miRNA	Rattus norvegicus	22529849	Exosome	Adipocytes	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032164	MIMAT0000787	rno-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000787	"rno-miR-18, rno-miR-18a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032165	MIMAT0000787	rno-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000787	"rno-miR-18, rno-miR-18a "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032166	MIMAT0000787	rno-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000787	"rno-miR-18, rno-miR-18a "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032167	MIMAT0000787	rno-miR-18a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000787	"rno-miR-18, rno-miR-18a "	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032168	MIMAT0000788	rno-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000788	rno-miR-19b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032169	MIMAT0000788	rno-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000788	rno-miR-19b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032170	MIMAT0000788	rno-miR-19b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000788	rno-miR-19b	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032171	MIMAT0000789	rno-miR-19a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000789	rno-miR-19a	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032172	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032173	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00032174	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032175	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032176	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032177	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	23978520	Microvesicle	NRK-52E cell	qRT-PCR|In situ hybridization	"These results demonstrate that tubular cells can secrete miR-21 and deliver it into recipient tubules by microvesicles, where the exogenous miR-21 can target PTEN protein and enhance Akt signaling in recipient cells.  "
RLID00032178	MIMAT0000790	rno-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000790	rno-miR-21	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032179	MIMAT0000791	rno-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000791	rno-miR-22	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032180	MIMAT0000791	rno-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000791	rno-miR-22	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032181	MIMAT0000791	rno-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000791	rno-miR-22	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032182	MIMAT0000791	rno-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000791	rno-miR-22	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032183	MIMAT0000791	rno-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000791	rno-miR-22	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032184	MIMAT0000792	rno-miR-23a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000792	rno-miR-23a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032185	MIMAT0000793	rno-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000793	rno-miR-23b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032186	MIMAT0000793	rno-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000793	rno-miR-23b	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032187	MIMAT0000793	rno-miR-23b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000793	rno-miR-23b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032188	MIMAT0000794	rno-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000794	rno-miR-24	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032189	MIMAT0000794	rno-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000794	rno-miR-24	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032190	MIMAT0000794	rno-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000794	rno-miR-24	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032191	MIMAT0000794	rno-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000794	rno-miR-24	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032192	MIMAT0000795	rno-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000795	rno-miR-25	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032193	MIMAT0000795	rno-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000795	rno-miR-25	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032194	MIMAT0000795	rno-miR-25-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000795	rno-miR-25	miRNA	Rattus norvegicus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032195	MIMAT0000796	rno-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000796	rno-miR-26a	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032196	MIMAT0000796	rno-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000796	rno-miR-26a	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032197	MIMAT0000796	rno-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000796	rno-miR-26a	miRNA	Rattus norvegicus	17592044	Dendrite	Hippocampus	In situ hybridization|RT-PCR	"Dendritic miRNAs appeared punctate by in situ hybridization (Fig. 4), a pattern typical of many dendritic mRNA populations.  Fogure 4: miRNAs appear granular by in situ hybridization in cultured hippocampal neurons. (A) rno-miR-26a. (B) High power of rno-miR-26a puncta; (C) rno-miR-92; (D) rno-let-7d; and (E) rno-124a. Images were acquired using a confocal microscope. (A,C,D,E) Scale bar, 50 um; (B) scale bar, 5  um. "
RLID00032198	MIMAT0000796	rno-miR-26a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000796	rno-miR-26a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032199	MIMAT0000797	rno-miR-26b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000797	rno-miR-26b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032200	MIMAT0000798	rno-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000798	rno-miR-27b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032201	MIMAT0000799	rno-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000799	rno-miR-27a	miRNA	Rattus norvegicus	21435393	Microvesicle	Serum	RT-PCR	"By using RT-PCR and specific forward/reverse primers these microRNAs were all detected in microvesicles, that had been released from primary and differentiated rat adipocytes after 6 and 24h incubation, respectively, as well as in microvesicles from rat serum(Fig. 6; shown only for miR-16, miR-27a, miR-146b and miR-222). "
RLID00032202	MIMAT0000799	rno-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000799	rno-miR-27a	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032203	MIMAT0000799	rno-miR-27a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000799	rno-miR-27a	miRNA	Rattus norvegicus	22529849	Exosome	Adipocytes	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032204	MIMAT0000801	rno-miR-29b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000801		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032205	MIMAT0000802	rno-miR-29a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000802	rno-miR-29a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032206	MIMAT0000804	rno-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000804	rno-miR-30c	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032207	MIMAT0000804	rno-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000804	rno-miR-30c	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032208	MIMAT0000804	rno-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000804	rno-miR-30c	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032209	MIMAT0000804	rno-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000804	rno-miR-30c	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032210	MIMAT0000805	rno-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000805	rno-miR-30e	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032211	MIMAT0000805	rno-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000805	rno-miR-30e	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032212	MIMAT0000805	rno-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000805	rno-miR-30e	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032213	MIMAT0000805	rno-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000805	rno-miR-30e	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032214	MIMAT0000806	rno-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000806	rno-miR-30b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032215	MIMAT0000806	rno-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000806	rno-miR-30b	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032216	MIMAT0000807	rno-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000807	rno-miR-30d	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032217	MIMAT0000807	rno-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000807	rno-miR-30d	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032218	MIMAT0000807	rno-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000807	rno-miR-30d	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032219	MIMAT0000807	rno-miR-30d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000807	rno-miR-30d	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032220	MIMAT0000808	rno-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000808	"rno-miR-30a-5p, rno-miR-30a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032221	MIMAT0000808	rno-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000808	"rno-miR-30a-5p, rno-miR-30a "	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032222	MIMAT0000810	rno-miR-31a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000810	rno-miR-31	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032223	MIMAT0000810	rno-miR-31a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000810	rno-miR-31	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032224	MIMAT0000813	rno-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000813	rno-miR-34b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032225	MIMAT0000813	rno-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000813	rno-miR-34b	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032226	MIMAT0000813	rno-miR-34b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000813	rno-miR-34b	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032227	MIMAT0000814	rno-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000814	rno-miR-34c	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032228	MIMAT0000814	rno-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000814	rno-miR-34c	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032229	MIMAT0000814	rno-miR-34c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000814	rno-miR-34c	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032230	MIMAT0000815	rno-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000815	rno-miR-34a	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032231	MIMAT0000815	rno-miR-34a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000815	rno-miR-34a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032232	MIMAT0000816	rno-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000816	"rno-miR-92, rno-miR-92a "	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032233	MIMAT0000816	rno-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000816	"rno-miR-92, rno-miR-92a "	miRNA	Rattus norvegicus	17592044	Dendrite	Hippocampus	In situ hybridization|RT-PCR	"Dendritic miRNAs appeared punctate by in situ hybridization (Fig. 4), a pattern typical of many dendritic mRNA populations.  Fogure 4: miRNAs appear granular by in situ hybridization in cultured hippocampal neurons. (A) rno-miR-26a. (B) High power of rno-miR-26a puncta; (C) rno-miR-92; (D) rno-let-7d; and (E) rno-124a. Images were acquired using a confocal microscope. (A,C,D,E) Scale bar, 50 um; (B) scale bar, 5  um. "
RLID00032234	MIMAT0000817	rno-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000817	rno-miR-93	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032235	MIMAT0000817	rno-miR-93-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000817	rno-miR-93	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032236	MIMAT0000819	rno-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000819	rno-miR-98	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032237	MIMAT0000819	rno-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000819	rno-miR-98	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00032238	MIMAT0000819	rno-miR-98-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000819	rno-miR-98	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032239	MIMAT0000820	rno-miR-99a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000820	rno-miR-99a	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032240	MIMAT0000821	rno-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000821	rno-miR-99b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032241	MIMAT0000821	rno-miR-99b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000821	rno-miR-99b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032242	MIMAT0000822	rno-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000822	rno-miR-100	miRNA	Rattus norvegicus	25297646	Circulating	Plasma	qRT-PCR|Microarray	"In plasma, miRNA upregulation was observed for miR-133a and miR-133b following PH and SL, whereas miR-100 and miR-466c were similarly downregulated following anesthesia and surgery. "
RLID00032243	MIMAT0000822	rno-miR-100-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000822	rno-miR-100	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032244	MIMAT0000823	rno-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000823	"rno-miR-101, rno-miR-101a "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032245	MIMAT0000823	rno-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000823	"rno-miR-101, rno-miR-101a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032246	MIMAT0000823	rno-miR-101a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000823	"rno-miR-101, rno-miR-101a "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032247	MIMAT0000824	rno-miR-103-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000824	rno-miR-103	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032248	MIMAT0000824	rno-miR-103-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000824	rno-miR-103	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032249	MIMAT0000825	rno-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000825	rno-miR-106b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032250	MIMAT0000825	rno-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000825	rno-miR-106b	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032251	MIMAT0000825	rno-miR-106b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000825	rno-miR-106b	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032252	MIMAT0000826	rno-miR-107-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000826	rno-miR-107	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032253	MIMAT0000826	rno-miR-107-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000826	rno-miR-107	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032254	MIMAT0000827	rno-miR-122-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000827	"rno-miR-122a, rno-miR-122 "	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032255	MIMAT0000828	rno-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000828	"rno-miR-124a, rno-miR-124 "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032256	MIMAT0000828	rno-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000828	"rno-miR-124a, rno-miR-124 "	miRNA	Rattus norvegicus	17592044	Dendrite	Hippocampus	In situ hybridization|RT-PCR	"Dendritic miRNAs appeared punctate by in situ hybridization (Fig. 4), a pattern typical of many dendritic mRNA populations.  Fogure 4: miRNAs appear granular by in situ hybridization in cultured hippocampal neurons. (A) rno-miR-26a. (B) High power of rno-miR-26a puncta; (C) rno-miR-92; (D) rno-let-7d; and (E) rno-124a. Images were acquired using a confocal microscope. (A,C,D,E) Scale bar, 50 um; (B) scale bar, 5  um. "
RLID00032257	MIMAT0000828	rno-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000828	"rno-miR-124a, rno-miR-124 "	miRNA	Rattus norvegicus	19465924	Synapse	Hippocampus	In situ hybridization|Northern blot	"The observed enrichment of several miRNAs in RNA preparations from synaptosomes was validated for selected candidates by Northern blot analysis (Fig. 2A). To monitor the subcellular localization of miRNAs identified in our screen, we performed in situ hybridization (ISH) in rat hippocampal neurons at 18 days in vitro (DIV) (Fig. 2B), using probes for miR-9, miR-218, miR-138 and miR-124 as a control (Fig. 2A, Suppl. Table 1). Data are collected from Figure 2. "
RLID00032258	MIMAT0000828	rno-miR-124-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000828	"rno-miR-124a, rno-miR-124 "	miRNA	Rattus norvegicus	20584895	Cell body	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032259	MIMAT0000829	rno-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000829	rno-miR-125a	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	In situ hybridization	"MiR-199a-3p and miR-125a-5p appeared more concentrated in the nucleoplasm and cytoplasm compared with the nucleolus; their hybridization pattern more closely resembled that of let-7a, a microRNA that earlier in situ hybridization experiments had shown not to be concentrated in the nucleolus (Fig. 3; Politz et al. 2006). "
RLID00032260	MIMAT0000829	rno-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000829	rno-miR-125a	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	In situ hybridization	"MiR-199a-3p and miR-125a-5p appeared more concentrated in the nucleoplasm and cytoplasm compared with the nucleolus; their hybridization pattern more closely resembled that of let-7a, a microRNA that earlier in situ hybridization experiments had shown not to be concentrated in the nucleolus (Fig. 3; Politz et al. 2006). "
RLID00032261	MIMAT0000829	rno-miR-125a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000829	rno-miR-125a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032262	MIMAT0000830	rno-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000830	rno-miR-125b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032263	MIMAT0000830	rno-miR-125b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000830	rno-miR-125b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032264	MIMAT0000833	rno-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000833	rno-miR-127	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032265	MIMAT0000833	rno-miR-127-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000833	rno-miR-127	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032266	MIMAT0000834	rno-miR-128-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000834	"rno-miR-128a, rno-miR-128 "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032267	MIMAT0000836	rno-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000836	rno-miR-130a	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032268	MIMAT0000836	rno-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000836	rno-miR-130a	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032269	MIMAT0000836	rno-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000836	rno-miR-130a	miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00032270	MIMAT0000836	rno-miR-130a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000836	rno-miR-130a	miRNA	Rattus norvegicus	19106625	Mitochondrion	livers	qRT-PCR|Microarray	"To further define whether the miRNAs were present within the mitochondria, we used deoxycholic acid (DCA) to induce opening of the mitochondrial megapore channel33 and induction of the mitochondria permeability transition (MPT) in the isolated mitochondria.This disruption of mitochondrial integrity resulted in a significant loss of miRNAs by RT-PCR in the DCA treated mitochondria relative to the control vehicle group. The release of miR-130a and b, miR-320 and miR-494 was about 50% and that of miR-140 almost 80%. "
RLID00032271	MIMAT0000837	rno-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000837	rno-miR-130b	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032272	MIMAT0000837	rno-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000837	rno-miR-130b	miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00032273	MIMAT0000837	rno-miR-130b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000837	rno-miR-130b	miRNA	Rattus norvegicus	19106625	Mitochondrion	livers	qRT-PCR|Microarray	"To further define whether the miRNAs were present within the mitochondria, we used deoxycholic acid (DCA) to induce opening of the mitochondrial megapore channel33 and induction of the mitochondria permeability transition (MPT) in the isolated mitochondria.This disruption of mitochondrial integrity resulted in a significant loss of miRNAs by RT-PCR in the DCA treated mitochondria relative to the control vehicle group. The release of miR-130a and b, miR-320 and miR-494 was about 50% and that of miR-140 almost 80%. "
RLID00032274	MIMAT0000838	rno-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000838	rno-miR-132	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032275	MIMAT0000838	rno-miR-132-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000838	rno-miR-132	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00032276	MIMAT0000839	rno-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000839	rno-miR-133a	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032277	MIMAT0000839	rno-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000839	rno-miR-133a	miRNA	Rattus norvegicus	25092230	Circulating	Plasma	Microarray	"From the above results, miRNAs were selected as candidate plasma miRNA biomarkers as follows: miR-208 (rno-miR- 208a-3p) for cardiotoxicity; miR-1 (rno-miR-1-3p), miR-133a (rno-miR-133a-3p), miR-133a* (rno-miR-133a-5p), and miR-133b (rno-miR-133b-3p) for shared cardiotoxicity and skeletal muscle toxicity; and miR- 206 (rno-miR-206-3p) for skeletal muscle toxicity. "
RLID00032278	MIMAT0000839	rno-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000839	rno-miR-133a	miRNA	Rattus norvegicus	25297646	Circulating	Plasma	qRT-PCR|Microarray	"In plasma, miRNA upregulation was observed for miR-133a and miR-133b following PH and SL, whereas miR-100 and miR-466c were similarly downregulated following anesthesia and surgery. "
RLID00032279	MIMAT0000839	rno-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000839	rno-miR-133a	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032280	MIMAT0000840	rno-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000840	rno-miR-134	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032281	MIMAT0000840	rno-miR-134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000840	rno-miR-134	miRNA	Rattus norvegicus	16421561	Dendrite	Hippocampus 	In situ hybridization	"Here we show that a brain-specific microRNA, miR-134, is localized to the synaptodendritic compartment of rat hippocampal neurons and negatively regulates the size of dendritic spines �postsynapticsites of excitatory synaptic transmission.  A substantial fraction of the dendritic miR-134 was found to partially colocalize with synapsin immunostaining, indicating that miR-134 is present near synaptic sites on dendrites (Fig. 1d, lower panel and inset at higher magnification). "
RLID00032282	MIMAT0000844	rno-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000844	rno-miR-138	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032283	MIMAT0000844	rno-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000844	rno-miR-138	miRNA	Rattus norvegicus	19465924	Dendrite	Hippocampus	In situ hybridization|Northern blot	"One of the identified miRNAs, miR-138, is highly enriched in the brain, localized within dendrites and negatively regulates the size of dendritic spines in rat hippocampal neurons.   The observed enrichment of several miRNAs in RNA preparations from synaptosomes was validated for selected candidates by Northern blot analysis (Fig. 2A).   To monitor the subcellular localization of miRNAs identified in our screen, we performed in situ hybridization (ISH) in rat hippocampal neurons at 18 days in vitro (DIV) (Fig. 2B), using probes for miR-9, miR-218, miR-138 and miR-124 as a control (Fig. 2A, Suppl. Table 1). "
RLID00032284	MIMAT0000844	rno-miR-138-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000844	rno-miR-138	miRNA	Rattus norvegicus	25919946	Dendrite	DRG neurons	PCR	MiRNAs-150 and -138 have been shown to be localize to dendrites.
RLID00032285	MIMAT0000849	rno-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000849	rno-miR-143	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032286	MIMAT0000849	rno-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000849	rno-miR-143	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032287	MIMAT0000851	rno-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000851	rno-miR-145	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00032288	MIMAT0000852	rno-miR-146a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000852	"rno-miR-146, rno-miR-146a "	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032289	MIMAT0000853	rno-miR-150-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000853	rno-miR-150	miRNA	Rattus norvegicus	25919946	Dendrite	DRG neurons	PCR	MiRNAs-150 and -138 have been shown to be localize to dendrites.
RLID00032290	MIMAT0000854	rno-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000854	rno-miR-152	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032291	MIMAT0000854	rno-miR-152-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000854	rno-miR-152	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032292	MIMAT0000856	rno-miR-154-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000856	rno-miR-154	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032293	MIMAT0000857	rno-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000857	rno-miR-181c	miRNA	Rattus norvegicus	22518031	Mitochondrion	Heart 	qRT-PCR|Microarray 	"We find that miR-181c is encoded in the nucleus, assembled in the cytoplasm, and finally translocated into the mitochondria of cardiac myocytes. "
RLID00032294	MIMAT0000857	rno-miR-181c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000857	rno-miR-181c	miRNA	Rattus norvegicus	22518031	Mitochondrion	Heart 	qRT-PCR	"We validated our microarray data using qPCR. 12S rRNA, a mitochondrial gene product 1, served as our internal control. We confirmed that miR-181c was predominantly localized to the mitochondrial fraction; its expression in the mitochondrial fraction was similar to that in the total heart fraction (Fig. 2A). In addition, fluorescence in situ hybridization (FISH) (Fig. 2C) shows co-localization of miR-181c with the mitochondrial marker, mitoTracker red. We also examined miR-181c expression in both cytosolic and mitochondrial fractions (Fig. 2B, left panel), using qPCR and found that miR-181c was enriched primarily in the mitochondrial fraction. We evaluated several other miRNAs as negative controls for mitochondrial localization, and miR-1192 data are included in Fig. 2B (right panel). We used 5S rRNA as an internal control for these sets of qPCR data, as it is known that this gene is present in both the cytosol and mitochondrial fractions 18. Data are collected from Figure 2. "
RLID00032295	MIMAT0000858	rno-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000858	rno-miR-181a	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032296	MIMAT0000858	rno-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000858	rno-miR-181a	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032297	MIMAT0000859	rno-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000859	rno-miR-181b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032298	MIMAT0000859	rno-miR-181b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000859	rno-miR-181b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032299	MIMAT0000860	rno-miR-183-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000860	rno-miR-183	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032300	MIMAT0000861	rno-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000861		miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032301	MIMAT0000862	rno-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000862	rno-miR-185	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032302	MIMAT0000862	rno-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000862	rno-miR-185	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032303	MIMAT0000862	rno-miR-185-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000862	rno-miR-185	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032304	MIMAT0000863	rno-miR-186-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000863	rno-miR-186	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032305	MIMAT0000865	rno-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000865		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032306	MIMAT0000865	rno-miR-190a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000865		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032307	MIMAT0000866	rno-miR-191a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000866	rno-miR-191	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032308	MIMAT0000866	rno-miR-191a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000866	rno-miR-191	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032309	MIMAT0000866	rno-miR-191a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000866	rno-miR-191	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032310	MIMAT0000867	rno-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000867	rno-miR-192	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032311	MIMAT0000867	rno-miR-192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000867	rno-miR-192	miRNA	Rattus norvegicus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032312	MIMAT0000868	rno-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000868	rno-miR-193-3p	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032313	MIMAT0000868	rno-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000868	rno-miR-193-3p	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032314	MIMAT0000871	rno-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000871	rno-miR-196a	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032315	MIMAT0000871	rno-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000871	rno-miR-196a	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032316	MIMAT0000871	rno-miR-196a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000871	rno-miR-196a	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00032317	MIMAT0000872	rno-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000872	rno-miR-199a	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032318	MIMAT0000876	rno-miR-203a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000876	rno-miR-203	miRNA	Rattus norvegicus	23682678	Circulating	Serum	qRT-PCR|Microarray	"Generally,there were 25 up-regulated and seven down-regulated miRNAs between serum of ASH and control groups as well as 20 up-regulated and 14 down-regulated miRNAs between liver tissues of ASH and control groups (Table 2). Data are collected from Table 2. "
RLID00032319	MIMAT0000877	rno-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000877	rno-miR-204	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032320	MIMAT0000877	rno-miR-204-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000877	rno-miR-204	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032321	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	17135348	Cytoplasm	Myogenic cell	In situ hybridization	"These results suggest that miR-206 may associate both with nascent ribosomes in the nucleolus and with exported, functional ribosomes in the cytoplasm. "
RLID00032322	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	25092230	Circulating	Plasma	Microarray	"From the above results, miRNAs were selected as candidate plasma miRNA biomarkers as follows: miR-208 (rno-miR- 208a-3p) for cardiotoxicity; miR-1 (rno-miR-1-3p), miR-133a (rno-miR-133a-3p), miR-133a* (rno-miR-133a-5p), and miR-133b (rno-miR-133b-3p) for shared cardiotoxicity and skeletal muscle toxicity; and miR- 206 (rno-miR-206-3p) for skeletal muscle toxicity. "
RLID00032323	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	17135348	Nucleolus	Myogenic cell	In situ hybridization	"These results suggest that miR-206 may associate both with nascent ribosomes in the nucleolus and with exported, functional ribosomes in the cytoplasm. "
RLID00032324	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	17135348	Ribosome	Myogenic cell	In situ hybridization	"These results suggest that miR-206 may associate both with nascent ribosomes in the nucleolus and with exported, functional ribosomes in the cytoplasm. "
RLID00032325	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032326	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	20584895	Cell body	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032327	MIMAT0000879	rno-miR-206-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000879	rno-miR-206	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032328	MIMAT0000881	rno-miR-210-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000881	rno-miR-210	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032329	MIMAT0000883	rno-miR-212-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000883	rno-miR-212	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032330	MIMAT0000885	rno-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000885	rno-miR-214	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032331	MIMAT0000885	rno-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000885	rno-miR-214	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032332	MIMAT0000885	rno-miR-214-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000885	rno-miR-214	miRNA	Rattus norvegicus	23682678	Circulating	Serum	qRT-PCR|Microarray	"Generally,there were 25 up-regulated and seven down-regulated miRNAs between serum of ASH and control groups as well as 20 up-regulated and 14 down-regulated miRNAs between liver tissues of ASH and control groups (Table 2). Data are collected from Table 2. "
RLID00032333	MIMAT0000888	rno-miR-218a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000888	"rno-miR-218, rno-miR-218a "	miRNA	Rattus norvegicus	19465924	Synapse	Hippocampus	In situ hybridization|Northern blot	"The observed enrichment of several miRNAs in RNA preparations from synaptosomes was validated for selected candidates by Northern blot analysis (Fig. 2A). To monitor the subcellular localization of miRNAs identified in our screen, we performed in situ hybridization (ISH) in rat hippocampal neurons at 18 days in vitro (DIV) (Fig. 2B), using probes for miR-9, miR-218, miR-138 and miR-124 as a control (Fig. 2A, Suppl. Table 1). Data are collected from Figure 2. "
RLID00032334	MIMAT0000888	rno-miR-218a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000888	"rno-miR-218, rno-miR-218a "	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032335	MIMAT0000890	rno-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000890	rno-miR-221	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032336	MIMAT0000890	rno-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000890	rno-miR-221	miRNA	Rattus norvegicus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032337	MIMAT0000890	rno-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000890	rno-miR-221	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032338	MIMAT0000890	rno-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000890	rno-miR-221	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032339	MIMAT0000891	rno-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000891	rno-miR-222	miRNA	Rattus norvegicus	21435393	Microvesicle	Serum	RT-PCR	"By using RT-PCR and specific forward/reverse primers these microRNAs were all detected in microvesicles, that had been released from primary and differentiated rat adipocytes after 6 and 24h incubation, respectively, as well as in microvesicles from rat serum(Fig. 6; shown only for miR-16, miR-27a, miR-146b and miR-222). "
RLID00032340	MIMAT0000891	rno-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000891	rno-miR-222	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032341	MIMAT0000891	rno-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000891	rno-miR-222	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032342	MIMAT0000891	rno-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000891	rno-miR-222	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032343	MIMAT0000891	rno-miR-222-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000891	rno-miR-222	miRNA	Rattus norvegicus	22529849	Exosome	Adipocytes	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032344	MIMAT0000893	rno-miR-290	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000893		miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00032345	MIMAT0000894	rno-miR-291a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000894	rno-miR-291-5p	miRNA	Rattus norvegicus	23713256	Circulating	Blood	RT-PCR	The RT-PCR result of the expression of miR-291a-5p with the peak time efficiency on day 7 showed that the expressions of miR-291a-5p in the peripheral blood and the liver tissue were basically identical.
RLID00032346	MIMAT0000896	rno-miR-292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000896		miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00032347	MIMAT0000898	rno-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000898	"rno-miR-296, rno-miR-296* "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032348	MIMAT0000899	rno-miR-297	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000899		miRNA	Rattus norvegicus	20584895	Cell body	Sympathetic neurons	Microarray	"However, a number of miRNAs were observed that were significantly enriched in the axons compared with the cell bodies, while others were enriched or present only in the cell bodies. For example, miR-204, miR-221, miR-15b, and miR-16 are characterized by the former pattern, while miR-297, miR-206, and miR-124a are examples of the latter pattern. "
RLID00032349	MIMAT0000899	rno-miR-297	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000899		miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032350	MIMAT0000900	rno-miR-298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000900	rno-miR-298	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032351	MIMAT0000900	rno-miR-298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000900	rno-miR-298	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032352	MIMAT0000902	rno-miR-300-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000902	rno-miR-300	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032353	MIMAT0000903	rno-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000903	rno-miR-320	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032354	MIMAT0000903	rno-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000903	rno-miR-320	miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00032355	MIMAT0000903	rno-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000903	rno-miR-320	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032356	MIMAT0000903	rno-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000903	rno-miR-320	miRNA	Rattus norvegicus	19106625	Mitochondrion	livers	qRT-PCR|Microarray	"To further define whether the miRNAs were present within the mitochondria, we used deoxycholic acid (DCA) to induce opening of the mitochondrial megapore channel33 and induction of the mitochondria permeability transition (MPT) in the isolated mitochondria.This disruption of mitochondrial integrity resulted in a significant loss of miRNAs by RT-PCR in the DCA treated mitochondria relative to the control vehicle group. The release of miR-130a and b, miR-320 and miR-494 was about 50% and that of miR-140 almost 80%. "
RLID00032357	MIMAT0000903	rno-miR-320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000903	rno-miR-320	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032358	MIMAT0000996	ebv-miR-BHRF1-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000996	ebv-miR-BHRF1-2*	miRNA	Human herpesvirus 4	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032359	MIMAT0001075	hsa-miR-384	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001075		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032360	MIMAT0001075	hsa-miR-384	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001075		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032361	MIMAT0001076	mmu-miR-384-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001076	mmu-miR-384	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032362	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032363	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032364	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032365	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032366	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032367	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032368	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032369	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032370	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032371	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00032372	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032373	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032374	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032375	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032376	MIMAT0001080	hsa-miR-196b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001080	hsa-miR-196b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032377	MIMAT0001090	mmu-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001090	mmu-miR-409	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032378	MIMAT0001090	mmu-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001090	mmu-miR-409	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00032379	MIMAT0001091	mmu-miR-410-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001091	mmu-miR-410	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032380	MIMAT0001092	mmu-miR-376b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001092	mmu-miR-376b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032381	MIMAT0001095	mmu-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001095	mmu-miR-370	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032382	MIMAT0001095	mmu-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001095	mmu-miR-370	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00032383	MIMAT0001095	mmu-miR-370-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001095	mmu-miR-370	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00032384	MIMAT0001320	rno-miR-421-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001320	rno-miR-421	miRNA	Rattus norvegicus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00032385	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032386	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032387	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032388	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032389	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032390	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032391	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032392	MIMAT0001339	hsa-miR-422a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001339		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032393	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	21098710	Circulating	Serum	qRT-PCR	"By selecting miRNAs that have 3-fold higher expression in HBV compared with control serum, we identified total of 13 upregulated miRNAs, including miR-375, miR-92a, miR-10a, miR-223, miR-423, miR-23b/a, miR-342-3p, miR-99a, miR-122a, miR-125b, miR-150, and let-7c. As shown in Figure 2, the upregulation of these 13 miRNA expressions in the serum of HBV cases, compared with those of controls, was largely consistent when detected by Solexa in pooled samples and qRT-PCR in individual samples. Data are collected from Figure 2. "
RLID00032394	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032395	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032396	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032397	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032398	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032399	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032400	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032401	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032402	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032403	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032404	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00032405	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032406	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032407	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032408	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032409	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032410	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032411	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032412	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032413	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032414	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032415	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032416	MIMAT0001340	hsa-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001340	hsa-miR-423	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00032417	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032418	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032419	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032420	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032421	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032422	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00032423	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032424	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032425	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032426	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032427	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032428	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032429	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032430	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032431	MIMAT0001341	hsa-miR-424-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001341	hsa-miR-424	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00032432	MIMAT0001342	mmu-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001342	"mmu-miR-425, mmu-miR-425* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00032433	MIMAT0001342	mmu-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001342	"mmu-miR-425, mmu-miR-425* "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00032434	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032435	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032436	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032437	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032438	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032439	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032440	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00032441	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032442	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032443	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032444	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032445	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032446	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00032447	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032448	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032449	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032450	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032451	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00032452	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032453	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032454	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00032455	MIMAT0001343	hsa-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001343	"hsa-miR-425, hsa-miR-425-3p, hsa-miR-425* "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032456	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032457	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032458	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032459	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032460	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032461	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032462	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00032463	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032464	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032465	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032466	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032467	MIMAT0001412	hsa-miR-18b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001412	hsa-miR-18b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032468	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032469	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032470	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032471	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032472	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032473	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032474	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032475	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032476	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032477	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032478	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032479	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032480	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032481	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00032482	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032483	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00032484	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032485	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032486	MIMAT0001413	hsa-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001413	hsa-miR-20b	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032487	MIMAT0001419	mmu-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001419	"mmu-miR-433-5p, mmu-miR-433* "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032488	MIMAT0001419	mmu-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001419	"mmu-miR-433-5p, mmu-miR-433* "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00032489	MIMAT0001419	mmu-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001419	"mmu-miR-433-5p, mmu-miR-433* "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00032490	MIMAT0001421	mmu-miR-434-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001421		miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00032491	MIMAT0001422	mmu-miR-434-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001422		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032492	MIMAT0001422	mmu-miR-434-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001422		miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00032493	MIMAT0001422	mmu-miR-434-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001422		miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00032494	MIMAT0001532	hsa-miR-448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001532		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032495	MIMAT0001532	hsa-miR-448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001532		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032496	MIMAT0001532	hsa-miR-448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001532		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032497	MIMAT0001532	hsa-miR-448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001532		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032498	MIMAT0001532	hsa-miR-448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001532		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00032499	MIMAT0001536	hsa-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001536		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032500	MIMAT0001536	hsa-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001536		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032501	MIMAT0001536	hsa-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001536		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00032502	MIMAT0001536	hsa-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001536		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032503	MIMAT0001536	hsa-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001536		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032504	MIMAT0001537	mmu-miR-429-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001537	mmu-miR-429	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00032505	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	23424776	Circulating	Blood	qRT-PCR|Microarray	"Five miRNAs (let-7c, miR-16, miR- 449, miR-181a and miR-181b) were found to exhibit similar expression patterns (p < 0.05) in peripheral blood when compared to data obtained by using bone marrow aspirates from MM patients in other studies.  "
RLID00032506	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032507	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032508	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032509	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032510	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032511	MIMAT0001541	hsa-miR-449a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001541	hsa-miR-449	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032512	MIMAT0001542	mmu-miR-449a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001542	"mmu-miR-449, mmu-miR-449a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032513	MIMAT0001545	hsa-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001545	"hsa-miR-450, hsa-miR-450a "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032514	MIMAT0001545	hsa-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001545	"hsa-miR-450, hsa-miR-450a "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032515	MIMAT0001545	hsa-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001545	"hsa-miR-450, hsa-miR-450a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032516	MIMAT0001545	hsa-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001545	"hsa-miR-450, hsa-miR-450a "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032517	MIMAT0001546	mmu-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001546	"mmu-miR-450, mmu-miR-450a-5p, mmu-miR-450a "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032518	MIMAT0001546	mmu-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001546	"mmu-miR-450, mmu-miR-450a-5p, mmu-miR-450a "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032519	MIMAT0001547	rno-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001547	"rno-miR-450, rno-miR-450a "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032520	MIMAT0001547	rno-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001547	"rno-miR-450, rno-miR-450a "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032521	MIMAT0001547	rno-miR-450a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001547	"rno-miR-450, rno-miR-450a "	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00032522	MIMAT0001577	hcmv-miR-UL112-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001577	"hcv-miR-UL112-1, hcmv-miR-UL112-1 "	miRNA	Human herpesvirus 5	21924071	Circulating	Plasma	Microarray	"MiR-296-5p (Fold change 0.47, P = 0.013) and miR-133b (Fold change 0.57, P = 0.033) were consistently down-regulated in the patient plasma, whereas let-7e (Fold change 1.62, P = 0.009) and hcmv-miR-UL112 (Fold change 2.72, P = 0.004), one human cytomegalovirus encoded microRNAs, were up-regulated in the patient samples.  "
RLID00032523	MIMAT0001578	hcmv-miR-UL148D	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001578	"hcv-miR-UL148D-1, hcmv-miR-UL148D-1 "	miRNA	Human herpesvirus 5	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032524	MIMAT0001618	hsa-miR-191-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001618	hsa-miR-191*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032525	MIMAT0001618	hsa-miR-191-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001618	hsa-miR-191*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032526	MIMAT0001618	hsa-miR-191-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001618	hsa-miR-191*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032527	MIMAT0001618	hsa-miR-191-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001618	hsa-miR-191*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032528	MIMAT0001618	hsa-miR-191-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001618	hsa-miR-191*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032529	MIMAT0001620	hsa-miR-200a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001620	hsa-miR-200a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032530	MIMAT0001620	hsa-miR-200a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001620	hsa-miR-200a*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032531	MIMAT0001620	hsa-miR-200a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001620	hsa-miR-200a*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032532	MIMAT0001620	hsa-miR-200a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001620	hsa-miR-200a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032533	MIMAT0001621	hsa-miR-369-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001621		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032534	MIMAT0001621	hsa-miR-369-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001621		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032535	MIMAT0001621	hsa-miR-369-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001621		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032536	MIMAT0001621	hsa-miR-369-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001621		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032537	MIMAT0001621	hsa-miR-369-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001621		miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00032538	MIMAT0001625	hsa-miR-431-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001625	hsa-miR-431	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032539	MIMAT0001625	hsa-miR-431-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001625	hsa-miR-431	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032540	MIMAT0001625	hsa-miR-431-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001625	hsa-miR-431	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032541	MIMAT0001625	hsa-miR-431-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001625	hsa-miR-431	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032542	MIMAT0001625	hsa-miR-431-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001625	hsa-miR-431	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032543	MIMAT0001626	rno-miR-431	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001626		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00032544	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00032545	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00032546	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00032547	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032548	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032549	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032550	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032551	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032552	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00032553	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032554	MIMAT0001627	hsa-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001627		miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032555	MIMAT0001628	rno-miR-433-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001628	rno-miR-433	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00032556	MIMAT0001629	hsa-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001629		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032557	MIMAT0001629	hsa-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001629		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032558	MIMAT0001629	hsa-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001629		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032559	MIMAT0001629	hsa-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001629		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032560	MIMAT0001629	hsa-miR-329-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001629		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00032561	MIMAT0001630	hsa-miR-323b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001630	hsa-miR-453	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00032562	MIMAT0001630	hsa-miR-323b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001630	hsa-miR-453	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032563	MIMAT0001630	hsa-miR-323b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001630	hsa-miR-453	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032564	MIMAT0001630	hsa-miR-323b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001630	hsa-miR-453	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032565	MIMAT0001630	hsa-miR-323b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001630	hsa-miR-453	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032566	MIMAT0001630	hsa-miR-323b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001630	hsa-miR-453	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032567	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032568	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00032569	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032570	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032571	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032572	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032573	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00032574	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032575	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032576	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23169280	Circulating	Serum	Microarray	"Table 2 miRNAs detected in pooled patient and control samples, as detected by Agilent Human miRNA microarrays. All of these showed potential as biomarkers as the levels of miRNAs varied between the patient and control groups. The expression levels of six of these miRNAs (in bold) were verified using TaqMan qRT–PCR. Three miRNAs (miR-720, miR-1246 and miR-1308) chosen for further analysis in individual patient samples. TaqMan qRT–PCR assays for the remaining three miRNAs were not available or were unreliable. Data are collected from Table 2. "
RLID00032577	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032578	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032579	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00032580	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	25330373	Extracellular vesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00032581	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032582	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032583	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032584	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032585	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	24633190	Circulating	Plasma	RT-PCR	We also selected 1 miRNA (miR-150-5p) from these 3 mildly up-regulated miRNAs that expressed >= 50 copies in at least one group. The expression levels and the related functions of 8 selected miRNAs are shown in Table 2. Data are collected from Table 2.
RLID00032586	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032587	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032588	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032589	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032590	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00032591	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032592	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	24130905	Circulating	Plasma	RT-PCR	"Overall expression levels of circulating miRNAs: most miRNAs from the designated list were successfully detected (with Ct values between 18 and 35) in virtually all samples. The highest signal was detected for miR-451, -223, -15a, -486-5p, -16, and -21, which is in agreement with literature data "
RLID00032593	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00032594	MIMAT0001631	hsa-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001631	hsa-miR-451	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00032595	MIMAT0001632	mmu-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001632	mmu-miR-451	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032596	MIMAT0001632	mmu-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001632	mmu-miR-451	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00032597	MIMAT0001632	mmu-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001632	mmu-miR-451	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032598	MIMAT0001632	mmu-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001632	mmu-miR-451	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00032599	MIMAT0001632	mmu-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001632	mmu-miR-451	miRNA	Mus musculus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032600	MIMAT0001632	mmu-miR-451a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001632	mmu-miR-451	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00032601	MIMAT0001633	rno-miR-451-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001633	rno-miR-451	miRNA	Rattus norvegicus	18766170	Circulating	Serum	qRT-PCR	"We also showed that miRNA let-7a, miR-21, miR-223, miR-451, miR-24, and miR-20a were detected in the serum of rats (Ra.S), mice (Mo.S), calves (Ca.S), bovine fetuses (FBS), and horses (Ho.S) (Figure 1B). Data are collected from Figure 1B. "
RLID00032602	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032603	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032604	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032605	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032606	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032607	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032608	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032609	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032610	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032611	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032612	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032613	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032614	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032615	MIMAT0001635	hsa-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001635	hsa-miR-452	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032616	MIMAT0001636	hsa-miR-452-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001636	hsa-miR-452*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032617	MIMAT0001637	mmu-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001637	mmu-miR-452	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032618	MIMAT0001637	mmu-miR-452-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001637	mmu-miR-452	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00032619	MIMAT0001638	hsa-miR-409-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001638		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032620	MIMAT0001638	hsa-miR-409-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001638		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032621	MIMAT0001638	hsa-miR-409-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001638		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032622	MIMAT0001638	hsa-miR-409-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001638		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00032623	MIMAT0001638	hsa-miR-409-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001638		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032624	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032625	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032626	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032627	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032628	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032629	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032630	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032631	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032632	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032633	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032634	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032635	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00032636	MIMAT0001639	hsa-miR-409-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0001639		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00032637	MIMAT0002104	mmu-miR-463-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002104	"mmu-miR-463, mmu-miR-463* "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00032638	MIMAT0002107	mmu-miR-466a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002107	mmu-miR-466	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00032639	MIMAT0002108	mmu-miR-467a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002108	"mmu-miR-467, mmu-miR-467a, mmu-miR-467a*, mmu-miR-467a-1*, mmu-miR-467a* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00032640	MIMAT0002109	mmu-miR-468-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002109	mmu-miR-468	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032641	MIMAT0002111	mmu-miR-470-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002111	mmu-miR-470	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00032642	MIMAT0002118	ssc-miR-106a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002118		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032643	MIMAT0002119	ssc-miR-122	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002119	ssc-miR-122a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032644	MIMAT0002120	ssc-miR-125b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002120		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032645	MIMAT0002123	ssc-miR-145-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002123	ssc-miR-145	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032646	MIMAT0002124	ssc-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002124	ssc-miR-148a	miRNA	Sus scrofa	25158130	Extracellular vesicle	Mesenchymal stem cell	Next-generation sequencing	"RNA-seq generated reads for at least 386 annotated miRNAs, but only miR148a, miR532-5p, miR378, and let-7f were enriched in EVs compared to MSCs. "
RLID00032647	MIMAT0002124	ssc-miR-148a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002124	ssc-miR-148a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032648	MIMAT0002125	ssc-miR-15b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002125		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032649	MIMAT0002126	ssc-miR-181b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002126		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032650	MIMAT0002127	ssc-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002127		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032651	MIMAT0002133	ssc-miR-23a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002133		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032652	MIMAT0002134	ssc-miR-24-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002134	ssc-miR-24	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032653	MIMAT0002135	ssc-miR-26a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002135		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032654	MIMAT0002137	ssc-miR-29b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002137		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032655	MIMAT0002139	ssc-miR-323	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002139		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032656	MIMAT0002140	ssc-miR-326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002140		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032657	MIMAT0002141	ssc-miR-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002141		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032658	MIMAT0002144	ssc-miR-181c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002144		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032659	MIMAT0002145	ssc-miR-183	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002145		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032660	MIMAT0002146	ssc-miR-205	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002146		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032661	MIMAT0002148	ssc-miR-27a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002148		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032662	MIMAT0002151	ssc-let-7c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002151		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032663	MIMAT0002152	ssc-let-7f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002152		miRNA	Sus scrofa	25158130	Extracellular vesicle	Mesenchymal stem cell	Next-generation sequencing	"RNA-seq generated reads for at least 386 annotated miRNAs, but only miR148a, miR532-5p, miR378, and let-7f were enriched in EVs compared to MSCs.  "
RLID00032664	MIMAT0002152	ssc-let-7f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002152		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032665	MIMAT0002153	ssc-let-7i	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002153		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032666	MIMAT0002154	ssc-miR-103	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002154		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032667	MIMAT0002155	ssc-miR-107	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002155		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032668	MIMAT0002156	ssc-miR-124a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002156		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032669	MIMAT0002157	ssc-miR-128	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002157	ssc-miR-128a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032670	MIMAT0002159	ssc-miR-139-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002159	ssc-miR-139	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032671	MIMAT0002161	ssc-miR-18a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002161	ssc-miR-18	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032672	MIMAT0002162	ssc-miR-186	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002162		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032673	MIMAT0002164	ssc-miR-204	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002164		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032674	MIMAT0002165	ssc-miR-21	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002165		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032675	MIMAT0002166	ssc-miR-29c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002166		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032676	MIMAT0002167	ssc-miR-30c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002167	ssc-miR-30c	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032677	MIMAT0002168	ssc-miR-9-1	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002168		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032678	MIMAT0002169	ssc-miR-9-2	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002169		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00032679	MIMAT0002170	hsa-miR-412-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002170		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032680	MIMAT0002170	hsa-miR-412-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002170		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032681	MIMAT0002171	hsa-miR-410-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002171		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032682	MIMAT0002171	hsa-miR-410-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002171		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032683	MIMAT0002171	hsa-miR-410-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002171		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032684	MIMAT0002171	hsa-miR-410-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002171		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032685	MIMAT0002171	hsa-miR-410-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002171		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032686	MIMAT0002172	hsa-miR-376b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002172	hsa-miR-376b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032687	MIMAT0002172	hsa-miR-376b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002172	hsa-miR-376b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032688	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	24961598	Circulating	Plasma	qRT-PCR	"This is the first report of circulating miR biomarkers in LVAD patients. We demonstrate the feasibility of this approach, report the potential for miR-483-3p and miR-1202, respectively, to monitor and predict response to LVAD therapy, and propose further work to study these hypotheses and elucidate roles for miR-483-3p and miR-1202 in clinical practice and in underlying biological processes. "
RLID00032689	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032690	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00032691	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032692	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032693	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032694	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032695	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032696	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00032697	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032698	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00032699	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032700	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032701	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00032702	MIMAT0002173	hsa-miR-483-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002173	hsa-miR-483	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032703	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00032704	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032705	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032706	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032707	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032708	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032709	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032710	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032711	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032712	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032713	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032714	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032715	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032716	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00032717	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032718	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00032719	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032720	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032721	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032722	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032723	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	24865854	Circulating	Plasma	qRT-PCR|Next-generation sequcencing	"Further exploration of their levels in the plasma of CAD patient and control cases, only circulating miR-361-5p and miR-484 were more abundant in CAD cases by RT-qPCR (Fig. 2D). Levels of circulating miR-140-5p showed no different between healthy and disease population (Fig. 2D). Moreover, levels of miR-342-3p, miR-125b-5p, miR-34a-5p, miR-103a-3p, and miR-125a-5p were even reduced significantly in patient circulation (Fig. 2D). "
RLID00032724	MIMAT0002174	hsa-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002174		miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR|In situ hybridization	"Through in situ hybridisation, we have localised these miRNAs, including miR-191 and miR-484, in the nucleolus of a diversity of human and rodent cell lines.  Four cleolar miRNAs; miR191, miR-484, miR-574-3p and miR-193b, were tested in our ISH experiments, and all four miRNAs exhibit strong nucleolar localisation (Figure 2A).  "
RLID00032725	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032726	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032727	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00032728	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032729	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032730	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032731	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00032732	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00032733	MIMAT0002175	hsa-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002175		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00032734	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00032735	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00032736	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032737	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032738	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032739	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032740	MIMAT0002176	hsa-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002176		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032741	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00032742	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	20194856	Circulating	Serum	Next-generation sequencing	"Endogenous circulating miRNAs are stable, are well protected from RNases, and remain stable even after being subjected to harsh conditions. Eleven serum miRNAs were found to be altered more than five-fold by Solexa sequencing between longer-survival and shorter-survival groups, and levels of four miRNAs (ie, miR-486, miR-30d, miR-1 and miR-501) were significantly associated with overall survival. "
RLID00032743	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00032744	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032745	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032746	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032747	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	24981880	Circulating	Serum	qRT-PCR	"Results from recent studies revealed that circulating miRNAs are also potential diagnostic biomarkers and prognostic factors in diabetes. The results of qRT-PCR assessment revealed low serum levels of miR-23a, let-7i, miR-486, miR-96, miR-186, miR-191, miR-192, and miR-146a in T2D. "
RLID00032748	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032749	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032750	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032751	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032752	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032753	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032754	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032755	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00032756	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032757	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032758	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032759	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00032760	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00032761	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032762	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032763	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	25793394	Cytoplasm	GC cell	In situ hybridization	miR-486-5p was mainly located in the cytoplasm of GC cells and neighboring normal tissues.
RLID00032764	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032765	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032766	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00032767	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	24130905	Circulating	Plasma	RT-PCR	"Overall expression levels of circulating miRNAs: most miRNAs from the designated list were successfully detected (with Ct values between 18 and 35) in virtually all samples. The highest signal was detected for miR-451, -223, -15a, -486-5p, -16, and -21, which is in agreement with literature data "
RLID00032768	MIMAT0002177	hsa-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002177	hsa-miR-486	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00032769	MIMAT0002178	hsa-miR-487a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002178	hsa-miR-487	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032770	MIMAT0002178	hsa-miR-487a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002178	hsa-miR-487	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032771	MIMAT0002178	hsa-miR-487a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002178	hsa-miR-487	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032772	MIMAT0002178	hsa-miR-487a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002178	hsa-miR-487	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032773	MIMAT0002193	kshv-miR-K12-3-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002193	kshv-miR-K12-3	miRNA	Human herpesvirus 8	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032774	MIMAT0002194	kshv-miR-K12-3-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002194	kshv-miR-K12-3*	miRNA	Human herpesvirus 8	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032775	MIMAT0002805	hsa-miR-489-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002805		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00032776	MIMAT0002805	hsa-miR-489-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002805		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032777	MIMAT0002805	hsa-miR-489-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002805		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032778	MIMAT0002806	hsa-miR-490-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002806	hsa-miR-490	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032779	MIMAT0002806	hsa-miR-490-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002806	hsa-miR-490	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032780	MIMAT0002806	hsa-miR-490-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002806	hsa-miR-490	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032781	MIMAT0002807	hsa-miR-491-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002807	hsa-miR-491	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032782	MIMAT0002807	hsa-miR-491-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002807	hsa-miR-491	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032783	MIMAT0002807	hsa-miR-491-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002807	hsa-miR-491	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032784	MIMAT0002807	hsa-miR-491-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002807	hsa-miR-491	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032785	MIMAT0002808	hsa-miR-511-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002808		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032786	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032787	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032788	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032789	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032790	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032791	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032792	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032793	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032794	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032795	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032796	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032797	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032798	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032799	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032800	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032801	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032802	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table4. Forty Most Highly Expressed miRNAs of Exosome I, Exosome II and WS. Data are collected from Table 4. "
RLID00032803	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032804	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032805	MIMAT0002809	hsa-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002809	hsa-miR-146b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00032806	MIMAT0002810	hsa-miR-202-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002810	hsa-miR-202*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032807	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032808	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032809	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032810	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032811	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032812	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032813	MIMAT0002811	hsa-miR-202-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002811	hsa-miR-202	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032814	MIMAT0002812	hsa-miR-492	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002812		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032815	MIMAT0002812	hsa-miR-492	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002812		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032816	MIMAT0002812	hsa-miR-492	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002812		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032817	MIMAT0002813	hsa-miR-493-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002813	"hsa-miR-493, hsa-miR-493-5p, hsa-miR-493* "	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00032818	MIMAT0002813	hsa-miR-493-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002813	"hsa-miR-493, hsa-miR-493-5p, hsa-miR-493* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032819	MIMAT0002813	hsa-miR-493-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002813	"hsa-miR-493, hsa-miR-493-5p, hsa-miR-493* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032820	MIMAT0002813	hsa-miR-493-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002813	"hsa-miR-493, hsa-miR-493-5p, hsa-miR-493* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032821	MIMAT0002813	hsa-miR-493-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002813	"hsa-miR-493, hsa-miR-493-5p, hsa-miR-493* "	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032822	MIMAT0002813	hsa-miR-493-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002813	"hsa-miR-493, hsa-miR-493-5p, hsa-miR-493* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032823	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032824	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032825	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00032826	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032827	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032828	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032829	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032830	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032831	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032832	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00032833	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032834	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032835	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032836	MIMAT0002814	hsa-miR-432-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002814	hsa-miR-432	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00032837	MIMAT0002815	hsa-miR-432-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002815	hsa-miR-432*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032838	MIMAT0002815	hsa-miR-432-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002815	hsa-miR-432*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032839	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00032840	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032841	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032842	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00032843	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032844	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032845	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032846	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032847	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00032848	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032849	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032850	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	RT-PCR|Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00032851	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00032852	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032853	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032854	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00032855	MIMAT0002816	hsa-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002816		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032856	MIMAT0002817	hsa-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002817	hsa-miR-495	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032857	MIMAT0002817	hsa-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002817	hsa-miR-495	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032858	MIMAT0002817	hsa-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002817	hsa-miR-495	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032859	MIMAT0002817	hsa-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002817	hsa-miR-495	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032860	MIMAT0002817	hsa-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002817	hsa-miR-495	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032861	MIMAT0002817	hsa-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002817	hsa-miR-495	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00032862	MIMAT0002818	hsa-miR-496	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002818		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032863	MIMAT0002818	hsa-miR-496	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002818		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032864	MIMAT0002818	hsa-miR-496	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002818		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032865	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032866	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032867	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032868	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00032869	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00032870	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032871	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032872	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032873	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032874	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032875	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032876	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032877	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032878	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032879	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032880	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032881	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00032882	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032883	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00032884	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032885	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032886	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032887	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032888	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR|In situ hybridization	"Four nucleolar miRNAs; miR191, miR-484, miR-574-3p and miR-193b, were tested in our ISH experiments, and all four miRNAs exhibit strong nucleolar localisation (Figure 2A).  "
RLID00032889	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032890	MIMAT0002819	hsa-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002819	hsa-miR-193b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032891	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032892	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00032893	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00032894	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032895	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032896	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00032897	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032898	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00032899	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00032900	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032901	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00032902	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032903	MIMAT0002820	hsa-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002820	hsa-miR-497	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00032904	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032905	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032906	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032907	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00032908	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00032909	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032910	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00032911	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00032912	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032913	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00032914	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032915	MIMAT0002821	hsa-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002821		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00032916	MIMAT0002822	hsa-miR-512-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002822		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032917	MIMAT0002822	hsa-miR-512-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002822		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032918	MIMAT0002823	hsa-miR-512-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002823		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032919	MIMAT0002823	hsa-miR-512-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002823		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032920	MIMAT0002824	hsa-miR-498	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002824		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032921	MIMAT0002824	hsa-miR-498	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002824		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032922	MIMAT0002824	hsa-miR-498	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002824		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00032923	MIMAT0002824	hsa-miR-498	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002824		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032924	MIMAT0002824	hsa-miR-498	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002824		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032925	MIMAT0002824	hsa-miR-498	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002824		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032926	MIMAT0002825	hsa-miR-520e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002825		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032927	MIMAT0002825	hsa-miR-520e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002825		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032928	MIMAT0002826	hsa-miR-515-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002826		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032929	MIMAT0002826	hsa-miR-515-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002826		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032930	MIMAT0002826	hsa-miR-515-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002826		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032931	MIMAT0002826	hsa-miR-515-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002826		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00032932	MIMAT0002826	hsa-miR-515-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002826		miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032933	MIMAT0002827	hsa-miR-515-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002827		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032934	MIMAT0002827	hsa-miR-515-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002827		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032935	MIMAT0002828	hsa-miR-519e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002828	hsa-miR-519e*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032936	MIMAT0002828	hsa-miR-519e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002828	hsa-miR-519e*	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032937	MIMAT0002828	hsa-miR-519e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002828	hsa-miR-519e*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032938	MIMAT0002829	hsa-miR-519e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002829	hsa-miR-519e	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032939	MIMAT0002830	hsa-miR-520f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002830		miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00032940	MIMAT0002830	hsa-miR-520f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002830		miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032941	MIMAT0002831	hsa-miR-519c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002831	hsa-miR-526c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032942	MIMAT0002831	hsa-miR-519c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002831	hsa-miR-526c	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032943	MIMAT0002832	hsa-miR-519c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002832	hsa-miR-519c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032944	MIMAT0002833	hsa-miR-520a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002833	hsa-miR-520a*	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032945	MIMAT0002833	hsa-miR-520a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002833	hsa-miR-520a*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032946	MIMAT0002834	hsa-miR-520a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002834	hsa-miR-520a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032947	MIMAT0002834	hsa-miR-520a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002834	hsa-miR-520a	miRNA	Homo sapiens	25017274	Circulating	Serum	qRT-PCR	"The expression of four miRNAs (miR-1233, miR-520, miR-210, miR-144) was validated by quantitative real-time polymerase chain reaction analysis. MiR-1233 was the most overexpressed in the serum of women who later developed sPE. Circulating miRNAs deserve further investigation in order to explore their potential role in the pathogenesis of preeclampsia. In particular, miR-1233 might represent a potential marker of early sPE. "
RLID00032948	MIMAT0002835	hsa-miR-526b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002835	hsa-miR-526b	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032949	MIMAT0002835	hsa-miR-526b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002835	hsa-miR-526b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032950	MIMAT0002835	hsa-miR-526b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002835	hsa-miR-526b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032951	MIMAT0002836	hsa-miR-526b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002836	hsa-miR-526b*	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032952	MIMAT0002836	hsa-miR-526b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002836	hsa-miR-526b*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032953	MIMAT0002837	hsa-miR-519b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002837	hsa-miR-519b	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032954	MIMAT0002838	hsa-miR-525-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002838	hsa-miR-525	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032955	MIMAT0002838	hsa-miR-525-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002838	hsa-miR-525	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032956	MIMAT0002838	hsa-miR-525-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002838	hsa-miR-525	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032957	MIMAT0002839	hsa-miR-525-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002839	hsa-miR-525*	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032958	MIMAT0002839	hsa-miR-525-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002839	hsa-miR-525*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032959	MIMAT0002840	hsa-miR-523-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002840	hsa-miR-523	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032960	MIMAT0002840	hsa-miR-523-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002840	hsa-miR-523	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032961	MIMAT0002840	hsa-miR-523-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002840	hsa-miR-523	miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00032962	MIMAT0002840	hsa-miR-523-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002840	hsa-miR-523	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00032963	MIMAT0002840	hsa-miR-523-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002840	hsa-miR-523	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032964	MIMAT0002841	hsa-miR-518f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002841	hsa-miR-518f*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032965	MIMAT0002841	hsa-miR-518f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002841	hsa-miR-518f*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032966	MIMAT0002842	hsa-miR-518f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002842	hsa-miR-518f	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032967	MIMAT0002842	hsa-miR-518f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002842	hsa-miR-518f	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032968	MIMAT0002842	hsa-miR-518f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002842	hsa-miR-518f	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032969	MIMAT0002843	hsa-miR-520b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002843		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032970	MIMAT0002843	hsa-miR-520b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002843		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032971	MIMAT0002843	hsa-miR-520b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002843		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032972	MIMAT0002844	hsa-miR-518b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002844		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032973	MIMAT0002844	hsa-miR-518b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002844		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032974	MIMAT0002844	hsa-miR-518b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002844		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00032975	MIMAT0002845	hsa-miR-526a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002845		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032976	MIMAT0002845	hsa-miR-526a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002845		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032977	MIMAT0002845	hsa-miR-526a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002845		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032978	MIMAT0002846	hsa-miR-520c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002846	hsa-miR-520c	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032979	MIMAT0002846	hsa-miR-520c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002846	hsa-miR-520c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032980	MIMAT0002846	hsa-miR-520c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002846	hsa-miR-520c	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00032981	MIMAT0002847	hsa-miR-518c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002847	hsa-miR-518c*	miRNA	Homo sapiens	20145944	Circulating	Saliva	RT-PCR|Microarray	"Also the miRNAs, miR-583, miR-518c*, and miR-208b identified by microarray analysis as candidate markers for saliva and miR-617 for vaginal secretion, demonstrated a strong discordance between microarray and TaqMan data (Electronic supplementary materials, Fig. 2).  "
RLID00032982	MIMAT0002847	hsa-miR-518c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002847	hsa-miR-518c*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00032983	MIMAT0002847	hsa-miR-518c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002847	hsa-miR-518c*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032984	MIMAT0002847	hsa-miR-518c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002847	hsa-miR-518c*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00032985	MIMAT0002848	hsa-miR-518c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002848	hsa-miR-518c	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032986	MIMAT0002848	hsa-miR-518c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002848	hsa-miR-518c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032987	MIMAT0002849	hsa-miR-524-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002849	hsa-miR-524*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032988	MIMAT0002849	hsa-miR-524-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002849	hsa-miR-524*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00032989	MIMAT0002851	hsa-miR-517-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002851	hsa-miR-517*	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032990	MIMAT0002851	hsa-miR-517-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002851	hsa-miR-517*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032991	MIMAT0002852	hsa-miR-517a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002852	hsa-miR-517a	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00032992	MIMAT0002852	hsa-miR-517a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002852	hsa-miR-517a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032993	MIMAT0002852	hsa-miR-517a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002852	hsa-miR-517a	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00032994	MIMAT0002852	hsa-miR-517a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002852	hsa-miR-517a	miRNA	Homo sapiens	22529849	Exosome	Placenta	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00032995	MIMAT0002854	hsa-miR-521	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002854		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00032996	MIMAT0002854	hsa-miR-521	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002854		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032997	MIMAT0002855	hsa-miR-520d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002855	hsa-miR-520d*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032998	MIMAT0002856	hsa-miR-520d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002856	hsa-miR-520d	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00032999	MIMAT0002857	hsa-miR-517b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002857	hsa-miR-517b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033000	MIMAT0002858	hsa-miR-520g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002858		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033001	MIMAT0002859	hsa-miR-516b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002859	"hsa-miR-516-5p, hsa-miR-516b "	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033002	MIMAT0002859	hsa-miR-516b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002859	"hsa-miR-516-5p, hsa-miR-516b "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033003	MIMAT0002859	hsa-miR-516b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002859	"hsa-miR-516-5p, hsa-miR-516b "	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033004	MIMAT0002859	hsa-miR-516b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002859	"hsa-miR-516-5p, hsa-miR-516b "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033005	MIMAT0002860	hsa-miR-516b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002860	"hsa-miR-516-3p, hsa-miR-516b*, hsa-miR-516a-3p, hsa-miR-516b*, hsa-miR-516a-3p, hsa-miR-516b* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033006	MIMAT0002861	hsa-miR-518e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002861	hsa-miR-518e	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00033007	MIMAT0002861	hsa-miR-518e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002861	hsa-miR-518e	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033008	MIMAT0002862	hsa-miR-527	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002862		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033009	MIMAT0002862	hsa-miR-527	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002862		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033010	MIMAT0002862	hsa-miR-527	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002862		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033011	MIMAT0002862	hsa-miR-527	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002862		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033012	MIMAT0002863	hsa-miR-518a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002863	hsa-miR-518a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033013	MIMAT0002864	hsa-miR-518d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002864	hsa-miR-518d	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033014	MIMAT0002864	hsa-miR-518d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002864	hsa-miR-518d	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033015	MIMAT0002864	hsa-miR-518d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002864	hsa-miR-518d	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033016	MIMAT0002866	hsa-miR-517c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002866	hsa-miR-517c	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00033017	MIMAT0002866	hsa-miR-517c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002866	hsa-miR-517c	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033018	MIMAT0002866	hsa-miR-517c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002866	hsa-miR-517c	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033019	MIMAT0002866	hsa-miR-517c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002866	hsa-miR-517c	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033020	MIMAT0002867	hsa-miR-520h	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002867		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033021	MIMAT0002868	hsa-miR-522-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002868	hsa-miR-522	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033022	MIMAT0002868	hsa-miR-522-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002868	hsa-miR-522	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033023	MIMAT0002868	hsa-miR-522-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002868	hsa-miR-522	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033024	MIMAT0002869	hsa-miR-519a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002869	hsa-miR-519a	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00033025	MIMAT0002869	hsa-miR-519a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002869	hsa-miR-519a	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033026	MIMAT0002870	hsa-miR-499a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002870	"hsa-miR-499, hsa-miR-499-5p "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033027	MIMAT0002870	hsa-miR-499a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002870	"hsa-miR-499, hsa-miR-499-5p "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033028	MIMAT0002870	hsa-miR-499a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002870	"hsa-miR-499, hsa-miR-499-5p "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033029	MIMAT0002870	hsa-miR-499a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002870	"hsa-miR-499, hsa-miR-499-5p "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033030	MIMAT0002870	hsa-miR-499a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002870	"hsa-miR-499, hsa-miR-499-5p "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033031	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033032	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033033	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033034	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00033035	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033036	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033037	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033038	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033039	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033040	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033041	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00033042	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033043	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033044	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033045	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033046	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033047	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033048	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033049	MIMAT0002871	hsa-miR-500a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002871	"hsa-miR-500, hsa-miR-500*, hsa-miR-500a* "	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033050	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	20194856	Circulating	Serum	Next-generation sequencing	"Endogenous circulating miRNAs are stable, are well protected from RNases, and remain stable even after being subjected to harsh conditions. Eleven serum miRNAs were found to be altered more than five-fold by Solexa sequencing between longer-survival and shorter-survival groups, and levels of four miRNAs (ie, miR-486, miR-30d, miR-1 and miR-501) were significantly associated with overall survival. "
RLID00033051	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033052	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033053	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033054	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033055	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033056	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033057	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033058	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033059	MIMAT0002872	hsa-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002872	hsa-miR-501	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00033060	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033061	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033062	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033063	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033064	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033065	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033066	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033067	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033068	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033069	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00033070	MIMAT0002873	hsa-miR-502-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002873	hsa-miR-502	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00033071	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033072	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033073	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033074	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033075	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033076	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033077	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033078	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033079	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033080	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033081	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033082	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033083	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033084	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033085	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033086	MIMAT0002874	hsa-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002874	hsa-miR-503	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033087	MIMAT0002875	hsa-miR-504-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002875		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00033088	MIMAT0002875	hsa-miR-504-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002875		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033089	MIMAT0002875	hsa-miR-504-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002875		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033090	MIMAT0002875	hsa-miR-504-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002875		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033091	MIMAT0002875	hsa-miR-504-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002875		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033092	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033093	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	23938262	Circulating	Plasma	RT-PCR|Microarray	"Plasma-based circulating MicroRNA biomarkers for Parkinson's disease. We identified 9 pairs of PD-predictive classifiers using k-TSP analysis and 13 most differentially-expressed miRNAs by SAM. A combination of both data sets produced a panel of PD-predictive biomarkers: k-TSP1 (miR-1826/miR-450b-3p), miR-626, and miR-505, and achieved the highest predictive power of 91% sensitivity, 100% specificity, 100% positive predicted value, and 88% negative predicted value in the replication set. However, low predictive values were shown in the validation set. "
RLID00033094	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00033095	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033096	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00033097	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033098	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033099	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033100	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033101	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033102	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033103	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033104	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033105	MIMAT0002876	hsa-miR-505-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002876	hsa-miR-505	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033106	MIMAT0002877	hsa-miR-513a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002877	"hsa-miR-513, hsa-miR-513-5p "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033107	MIMAT0002877	hsa-miR-513a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002877	"hsa-miR-513, hsa-miR-513-5p "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033108	MIMAT0002877	hsa-miR-513a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002877	"hsa-miR-513, hsa-miR-513-5p "	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033109	MIMAT0002877	hsa-miR-513a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002877	"hsa-miR-513, hsa-miR-513-5p "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033110	MIMAT0002877	hsa-miR-513a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002877	"hsa-miR-513, hsa-miR-513-5p "	miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00033111	MIMAT0002877	hsa-miR-513a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002877	"hsa-miR-513, hsa-miR-513-5p "	miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00033112	MIMAT0002878	hsa-miR-506-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002878	hsa-miR-506	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033113	MIMAT0002879	hsa-miR-507	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002879		miRNA	Homo sapiens	20145944	Circulating	Semen	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00033114	MIMAT0002879	hsa-miR-507	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002879		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033115	MIMAT0002880	hsa-miR-508-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002880	hsa-miR-508	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00033116	MIMAT0002880	hsa-miR-508-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002880	hsa-miR-508	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033117	MIMAT0002881	hsa-miR-509-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002881	hsa-miR-509	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033118	MIMAT0002881	hsa-miR-509-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002881	hsa-miR-509	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033119	MIMAT0002882	hsa-miR-510-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002882		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033120	MIMAT0002882	hsa-miR-510-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002882		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033121	MIMAT0002883	hsa-miR-514a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002883	hsa-miR-514	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033122	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033123	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033124	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033125	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033126	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033127	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00033128	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00033129	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033130	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033131	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033132	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033133	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033134	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033135	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033136	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033137	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033138	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033139	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033140	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033141	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033142	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00033143	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033144	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033145	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033146	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033147	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033148	MIMAT0002888	hsa-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002888	hsa-miR-532	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00033149	MIMAT0002889	mmu-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002889	mmu-miR-532	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033150	MIMAT0002889	mmu-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002889	mmu-miR-532	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033151	MIMAT0002889	mmu-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002889	mmu-miR-532	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00033152	MIMAT0002890	hsa-miR-299-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002890		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033153	MIMAT0002890	hsa-miR-299-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002890		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033154	MIMAT0002890	hsa-miR-299-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002890		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033155	MIMAT0002890	hsa-miR-299-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002890		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033156	MIMAT0002891	hsa-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002891	hsa-miR-18a*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033157	MIMAT0002891	hsa-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002891	hsa-miR-18a*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033158	MIMAT0002891	hsa-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002891	hsa-miR-18a*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033159	MIMAT0002891	hsa-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002891	hsa-miR-18a*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00033160	MIMAT0002891	hsa-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002891	hsa-miR-18a*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033161	MIMAT0002891	hsa-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0002891	hsa-miR-18a*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033162	MIMAT0003112	mmu-miR-489-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003112	mmu-miR-489	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033163	MIMAT0003112	mmu-miR-489-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003112	mmu-miR-489	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033164	MIMAT0003114	rno-miR-383-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003114	rno-miR-383	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033165	MIMAT0003115	rno-miR-207	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003115		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033166	MIMAT0003115	rno-miR-207	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003115		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033167	MIMAT0003117	rno-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003117	rno-miR-361	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033168	MIMAT0003117	rno-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003117	rno-miR-361	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033169	MIMAT0003117	rno-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003117	rno-miR-361	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033170	MIMAT0003119	rno-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003119	rno-miR-224	miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033171	MIMAT0003119	rno-miR-224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003119	rno-miR-224	miRNA	Rattus norvegicus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00033172	MIMAT0003125	rno-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003125	rno-miR-1	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033173	MIMAT0003125	rno-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003125	rno-miR-1	miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033174	MIMAT0003125	rno-miR-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003125	rno-miR-1	miRNA	Rattus norvegicus	25092230	Circulating	Plasma	Microarray	"From the above results, miRNAs were selected as candidate plasma miRNA biomarkers as follows: miR-208 (rno-miR- 208a-3p) for cardiotoxicity; miR-1 (rno-miR-1-3p), miR-133a (rno-miR-133a-3p), miR-133a* (rno-miR-133a-5p), and miR-133b (rno-miR-133b-3p) for shared cardiotoxicity and skeletal muscle toxicity; and miR- 206 (rno-miR-206-3p) for skeletal muscle toxicity. "
RLID00033175	MIMAT0003126	rno-miR-133b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003126	rno-miR-133b	miRNA	Rattus norvegicus	25092230	Circulating	Plasma	Microarray	"From the above results, miRNAs were selected as candidate plasma miRNA biomarkers as follows: miR-208 (rno-miR- 208a-3p) for cardiotoxicity; miR-1 (rno-miR-1-3p), miR-133a (rno-miR-133a-3p), miR-133a* (rno-miR-133a-5p), and miR-133b (rno-miR-133b-3p) for shared cardiotoxicity and skeletal muscle toxicity; and miR- 206 (rno-miR-206-3p) for skeletal muscle toxicity. "
RLID00033176	MIMAT0003126	rno-miR-133b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003126	rno-miR-133b	miRNA	Rattus norvegicus	25297646	Circulating	Plasma	qRT-PCR|Microarray	"In plasma, miRNA upregulation was observed for miR-133a and miR-133b following PH and SL, whereas miR-100 and miR-466c were similarly downregulated following anesthesia and surgery. "
RLID00033177	MIMAT0003126	rno-miR-133b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003126	rno-miR-133b	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033178	MIMAT0003127	mmu-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003127		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033179	MIMAT0003127	mmu-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003127		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033180	MIMAT0003127	mmu-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003127		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033181	MIMAT0003127	mmu-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003127		miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00033182	MIMAT0003130	mmu-miR-486a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003130	mmu-miR-486-5p	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033183	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033184	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033185	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033186	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033187	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033188	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033189	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033190	MIMAT0003150	hsa-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003150	hsa-miR-455	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00033191	MIMAT0003151	mmu-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003151	"mmu-miR-422b, mmu-miR-378, mmu-miR-378-3p "	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033192	MIMAT0003151	mmu-miR-378a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003151	"mmu-miR-422b, mmu-miR-378, mmu-miR-378-3p "	miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00033193	MIMAT0003153	rno-miR-24-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003153	"rno-miR-189, rno-miR-24-1* "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033194	MIMAT0003161	hsa-miR-493-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003161	"hsa-miR-493-3p, hsa-miR-493 "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033195	MIMAT0003161	hsa-miR-493-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003161	"hsa-miR-493-3p, hsa-miR-493 "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033196	MIMAT0003161	hsa-miR-493-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003161	"hsa-miR-493-3p, hsa-miR-493 "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033197	MIMAT0003161	hsa-miR-493-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003161	"hsa-miR-493-3p, hsa-miR-493 "	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00033198	MIMAT0003161	hsa-miR-493-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003161	"hsa-miR-493-3p, hsa-miR-493 "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033199	MIMAT0003161	hsa-miR-493-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003161	"hsa-miR-493-3p, hsa-miR-493 "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033200	MIMAT0003163	hsa-miR-539-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003163	hsa-miR-539	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033201	MIMAT0003163	hsa-miR-539-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003163	hsa-miR-539	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033202	MIMAT0003163	hsa-miR-539-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003163	hsa-miR-539	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033203	MIMAT0003164	hsa-miR-544a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003164	hsa-miR-544	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033204	MIMAT0003165	hsa-miR-545-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003165	hsa-miR-545	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033205	MIMAT0003165	hsa-miR-545-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003165	hsa-miR-545	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033206	MIMAT0003165	hsa-miR-545-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003165	hsa-miR-545	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033207	MIMAT0003166	mmu-miR-546	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003166		miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033208	MIMAT0003171	mmu-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003171		miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033209	MIMAT0003171	mmu-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003171		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033210	MIMAT0003172	mmu-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003172		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033211	MIMAT0003172	mmu-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003172		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033212	MIMAT0003173	mmu-miR-547-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003173	mmu-miR-547	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033213	MIMAT0003176	rno-miR-539-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003176	rno-miR-539	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033214	MIMAT0003176	rno-miR-539-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003176	rno-miR-539	miRNA	Rattus norvegicus	23682678	Circulating	Serum	qRT-PCR|Microarray	"Generally,there were 25 up-regulated and seven down-regulated miRNAs between serum of ASH and control groups as well as 20 up-regulated and 14 down-regulated miRNAs between liver tissues of ASH and control groups (Table 2). Data are collected from Table 2. "
RLID00033215	MIMAT0003177	rno-miR-541-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003177	rno-miR-541	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033216	MIMAT0003179	rno-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003179		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033217	MIMAT0003179	rno-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003179		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033218	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033219	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033220	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033221	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033222	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00033223	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033224	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033225	MIMAT0003180	hsa-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003180		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00033226	MIMAT0003181	mmu-miR-367-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003181	mmu-miR-367	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033227	MIMAT0003182	mmu-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003182	mmu-miR-494	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033228	MIMAT0003182	mmu-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003182	mmu-miR-494	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033229	MIMAT0003183	mmu-miR-376c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003183	mmu-miR-376c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033230	MIMAT0003187	mmu-miR-20b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003187	mmu-miR-20b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033231	MIMAT0003188	mmu-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003188	mmu-miR-503	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033232	MIMAT0003188	mmu-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003188	mmu-miR-503	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033233	MIMAT0003188	mmu-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003188	mmu-miR-503	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033234	MIMAT0003189	mmu-miR-291b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003189		miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033235	MIMAT0003192	rno-miR-379-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003192	rno-miR-379	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033236	MIMAT0003193	rno-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003193	rno-miR-494	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033237	MIMAT0003193	rno-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003193	rno-miR-494	miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033238	MIMAT0003193	rno-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003193	rno-miR-494	miRNA	Rattus norvegicus	19106625	Mitochondrion	livers	qRT-PCR|Microarray	"Interestingly, miR-494 appears to be significantly enriched in mitochondria as its abundance in total RNA increased with purification as measured by qRT-PCR.  To further define whether the miRNAs were present within the mitochondria, we used deoxycholic acid (DCA) to induce opening of the mitochondrial megapore channel33 and induction of the mitochondria permeability transition (MPT) in the isolated mitochondria.This disruption of mitochondrial integrity resulted in a significant loss of miRNAs by RT-PCR in the DCA treated mitochondria relative to the control vehicle group. The release of miR-130a and b, miR-320 and miR-494 was ~50% and that of miR-140 almost 80%. "
RLID00033239	MIMAT0003193	rno-miR-494-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003193	rno-miR-494	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Five miRNAs, miR-340-5p, miR-351, miR-494, miR-664, and let-7e, were significantly concentrated (two- to eightfold) in the nucleolus compared with the nucleoplasm and/or the cytoplasm (Fig. 2A; Supplemental Table 1). "
RLID00033240	MIMAT0003196	rno-miR-376b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003196	rno-miR-376b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033241	MIMAT0003199	rno-miR-381-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003199	rno-miR-381	miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033242	MIMAT0003200	rno-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003200	rno-miR-487b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033243	MIMAT0003200	rno-miR-487b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003200	rno-miR-487b	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033244	MIMAT0003201	rno-miR-382-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003201	rno-miR-382	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033245	MIMAT0003203	rno-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003203	rno-miR-485	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033246	MIMAT0003203	rno-miR-485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003203	rno-miR-485	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033247	MIMAT0003205	rno-miR-409a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003205	rno-miR-409-3p	miRNA	Rattus norvegicus	20584895	Axon	Sympathetic neurons	Microarray	"Microarray expression profiling revealed that axons of rat sympathetic neurons contain a large, heterogeneous population of miRNAs (Supplemental Table S1): Several of these miRNAs are highly expressed in these neurons. A listing of miRNAs that are most abundant and/or enriched in the axon is provided in Table 1. Data are collected from Table S1. "
RLID00033248	MIMAT0003208	rno-miR-374-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003208	rno-miR-374	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00033249	MIMAT0003209	rno-miR-363-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003209	"rno-miR-363-5p, rno-miR-363* "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033250	MIMAT0003213	rno-miR-503-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003213		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033251	MIMAT0003214	hsa-miR-551a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003214		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033252	MIMAT0003217	hsa-miR-554	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003217		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033253	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00033254	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00033255	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033256	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033257	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033258	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00033259	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033260	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033261	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033262	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033263	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033264	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033265	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033266	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033267	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033268	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033269	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	25420022	Exosome	Cerebrospinal fluid	Next-generation sequencing	Table 1: Reads from next generation sequencing of vesicle RNA isolated from CSF (less than 2 years) and aligned to the human genome. Data are collected from Table 1.
RLID00033270	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033271	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033272	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033273	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033274	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033275	MIMAT0003218	hsa-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003218	hsa-miR-92b	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033276	MIMAT0003219	hsa-miR-555	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003219		miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00033277	MIMAT0003220	hsa-miR-556-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003220	hsa-miR-556	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033278	MIMAT0003221	hsa-miR-557	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003221		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033279	MIMAT0003221	hsa-miR-557	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003221		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033280	MIMAT0003221	hsa-miR-557	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003221		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033281	MIMAT0003221	hsa-miR-557	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003221		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033282	MIMAT0003221	hsa-miR-557	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003221		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033283	MIMAT0003221	hsa-miR-557	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003221		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033284	MIMAT0003225	hsa-miR-561-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003225	hsa-miR-561	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033285	MIMAT0003227	hsa-miR-563	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003227		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033286	MIMAT0003227	hsa-miR-563	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003227		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00033287	MIMAT0003228	hsa-miR-564	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003228		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033288	MIMAT0003228	hsa-miR-564	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003228		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033289	MIMAT0003228	hsa-miR-564	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003228		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033290	MIMAT0003228	hsa-miR-564	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003228		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033291	MIMAT0003228	hsa-miR-564	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003228		miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00033292	MIMAT0003233	hsa-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003233	hsa-miR-551b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033293	MIMAT0003233	hsa-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003233	hsa-miR-551b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033294	MIMAT0003233	hsa-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003233	hsa-miR-551b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033295	MIMAT0003233	hsa-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003233	hsa-miR-551b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033296	MIMAT0003233	hsa-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003233	hsa-miR-551b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033297	MIMAT0003236	hsa-miR-571	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003236		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033298	MIMAT0003237	hsa-miR-572	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003237		miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00033299	MIMAT0003237	hsa-miR-572	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003237		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033300	MIMAT0003237	hsa-miR-572	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003237		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033301	MIMAT0003238	hsa-miR-573	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003238		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033302	MIMAT0003238	hsa-miR-573	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003238		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00033303	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00033304	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033305	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033306	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033307	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033308	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033309	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00033310	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033311	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033312	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033313	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033314	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033315	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	24373621	Circulating	Plasma	qRT-PCR	"Unsupervised clustering of the expression profiles using the six most regulated miRNAs (miR-425-5p, miR-21-5p, miR-106b-5p, miR-590-5p, miR-574-3p, miR-885-3p) significantly (p = 0.012) separated plasma samples collected prior to treatment from plasma samples collected after two days of radiochemotherapy. "
RLID00033316	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033317	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033318	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033319	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033320	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033321	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033322	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00033323	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033324	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033325	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033326	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033327	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033328	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033329	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033330	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR|In situ hybridization	"Four nucleolar miRNAs; miR191, miR-484, miR-574-3p and miR-193b, were tested in our ISH experiments, and all four miRNAs exhibit strong nucleolar localisation (Figure 2A).  "
RLID00033331	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033332	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033333	MIMAT0003239	hsa-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003239	hsa-miR-574	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033334	MIMAT0003240	hsa-miR-575	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003240		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033335	MIMAT0003240	hsa-miR-575	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003240		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033336	MIMAT0003240	hsa-miR-575	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003240		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033337	MIMAT0003240	hsa-miR-575	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003240		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033338	MIMAT0003240	hsa-miR-575	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003240		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00033339	MIMAT0003241	hsa-miR-576-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003241	hsa-miR-576	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033340	MIMAT0003241	hsa-miR-576-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003241	hsa-miR-576	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033341	MIMAT0003241	hsa-miR-576-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003241	hsa-miR-576	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033342	MIMAT0003241	hsa-miR-576-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003241	hsa-miR-576	miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00033343	MIMAT0003241	hsa-miR-576-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003241	hsa-miR-576	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033344	MIMAT0003241	hsa-miR-576-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003241	hsa-miR-576	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033345	MIMAT0003242	hsa-miR-577	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003242		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033346	MIMAT0003242	hsa-miR-577	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003242		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033347	MIMAT0003243	hsa-miR-578	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003243		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033348	MIMAT0003245	hsa-miR-580-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003245		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033349	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033350	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033351	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033352	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00033353	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033354	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033355	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033356	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033357	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033358	MIMAT0003247	hsa-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003247	hsa-miR-582	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033359	MIMAT0003248	hsa-miR-583	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003248		miRNA	Homo sapiens	20145944	Circulating	Saliva	RT-PCR|Microarray	"Also the miRNAs, miR-583, miR-518c*, and miR-208b identified by microarray analysis as candidate markers for saliva and miR-617 for vaginal secretion, demonstrated a strong discordance between microarray and TaqMan data (Electronic supplementary materials, Fig. 2).  "
RLID00033360	MIMAT0003248	hsa-miR-583	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003248		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033361	MIMAT0003248	hsa-miR-583	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003248		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033362	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033363	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033364	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033365	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033366	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033367	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00033368	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033369	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033370	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033371	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033372	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033373	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033374	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033375	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033376	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033377	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033378	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	22529849	Exosome	HCC cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033379	MIMAT0003249	hsa-miR-584-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003249	hsa-miR-584	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033380	MIMAT0003250	hsa-miR-585-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003250		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033381	MIMAT0003250	hsa-miR-585-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003250		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033382	MIMAT0003251	hsa-miR-548a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003251	hsa-miR-548a	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033383	MIMAT0003251	hsa-miR-548a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003251	hsa-miR-548a	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033384	MIMAT0003256	hsa-miR-589-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003256	"hsa-miR-589, hsa-miR-589* "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033385	MIMAT0003256	hsa-miR-589-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003256	"hsa-miR-589, hsa-miR-589* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033386	MIMAT0003256	hsa-miR-589-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003256	"hsa-miR-589, hsa-miR-589* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033387	MIMAT0003257	hsa-miR-550a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003257	"hsa-miR-550, hsa-miR-550*, hsa-miR-550a* "	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033388	MIMAT0003257	hsa-miR-550a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003257	"hsa-miR-550, hsa-miR-550*, hsa-miR-550a* "	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033389	MIMAT0003257	hsa-miR-550a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003257	"hsa-miR-550, hsa-miR-550*, hsa-miR-550a* "	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00033390	MIMAT0003257	hsa-miR-550a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003257	"hsa-miR-550, hsa-miR-550*, hsa-miR-550a* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033391	MIMAT0003257	hsa-miR-550a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003257	"hsa-miR-550, hsa-miR-550*, hsa-miR-550a* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033392	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033393	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033394	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033395	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	24373621	Circulating	Plasma	qRT-PCR	"Unsupervised clustering of the expression profiles using the six most regulated miRNAs (miR-425-5p, miR-21-5p, miR-106b-5p, miR-590-5p, miR-574-3p, miR-885-3p) significantly (p = 0.012) separated plasma samples collected prior to treatment from plasma samples collected after two days of radiochemotherapy. "
RLID00033396	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033397	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00033398	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033399	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033400	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033401	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033402	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033403	MIMAT0003258	hsa-miR-590-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003258	hsa-miR-590	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033404	MIMAT0003260	hsa-miR-592	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003260		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033405	MIMAT0003260	hsa-miR-592	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003260		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033406	MIMAT0003261	hsa-miR-593-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003261	"hsa-miR-593, hsa-miR-593* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033407	MIMAT0003261	hsa-miR-593-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003261	"hsa-miR-593, hsa-miR-593* "	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033408	MIMAT0003263	hsa-miR-595	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003263		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033409	MIMAT0003263	hsa-miR-595	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003263		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033410	MIMAT0003263	hsa-miR-595	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003263		miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00033411	MIMAT0003263	hsa-miR-595	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003263		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033412	MIMAT0003264	hsa-miR-596	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003264		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00033413	MIMAT0003265	hsa-miR-597-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003265		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033414	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033415	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00033416	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033417	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033418	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00033419	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00033420	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033421	MIMAT0003266	hsa-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003266		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033422	MIMAT0003269	hsa-miR-601	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003269		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033423	MIMAT0003269	hsa-miR-601	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003269		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033424	MIMAT0003269	hsa-miR-601	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003269		miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00033425	MIMAT0003270	hsa-miR-602	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003270		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033426	MIMAT0003270	hsa-miR-602	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003270		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033427	MIMAT0003270	hsa-miR-602	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003270		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00033428	MIMAT0003270	hsa-miR-602	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003270		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00033429	MIMAT0003270	hsa-miR-602	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003270		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033430	MIMAT0003271	hsa-miR-603	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003271		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033431	MIMAT0003271	hsa-miR-603	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003271		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033432	MIMAT0003271	hsa-miR-603	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003271		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033433	MIMAT0003271	hsa-miR-603	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003271		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033434	MIMAT0003271	hsa-miR-603	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003271		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033435	MIMAT0003273	hsa-miR-605-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003273		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033436	MIMAT0003276	hsa-miR-608	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003276		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033437	MIMAT0003276	hsa-miR-608	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003276		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033438	MIMAT0003277	hsa-miR-609	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003277		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033439	MIMAT0003278	hsa-miR-610	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003278		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033440	MIMAT0003278	hsa-miR-610	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003278		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033441	MIMAT0003279	hsa-miR-611	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003279		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033442	MIMAT0003280	hsa-miR-612	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003280		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033443	MIMAT0003280	hsa-miR-612	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003280		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033444	MIMAT0003280	hsa-miR-612	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003280		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00033445	MIMAT0003280	hsa-miR-612	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003280		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033446	MIMAT0003281	hsa-miR-613	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003281		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033447	MIMAT0003282	hsa-miR-614	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003282		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033448	MIMAT0003283	hsa-miR-615-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003283	hsa-miR-615	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033449	MIMAT0003283	hsa-miR-615-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003283	hsa-miR-615	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033450	MIMAT0003283	hsa-miR-615-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003283	hsa-miR-615	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033451	MIMAT0003283	hsa-miR-615-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003283	hsa-miR-615	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033452	MIMAT0003283	hsa-miR-615-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003283	hsa-miR-615	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033453	MIMAT0003284	hsa-miR-616-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003284	"hsa-miR-616, hsa-miR-616* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033454	MIMAT0003286	hsa-miR-617	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003286		miRNA	Homo sapiens	20145944	Circulating	Vaginal secretion	RT-PCR|Microarray	"Also the miRNAs, miR-583, miR-518c*, and miR-208b identified by microarray analysis as candidate markers for saliva and miR-617 for vaginal secretion, demonstrated a strong discordance between microarray and TaqMan data (Electronic supplementary materials, Fig. 2).  "
RLID00033455	MIMAT0003286	hsa-miR-617	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003286		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033456	MIMAT0003286	hsa-miR-617	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003286		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033457	MIMAT0003286	hsa-miR-617	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003286		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033458	MIMAT0003287	hsa-miR-618	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003287		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033459	MIMAT0003287	hsa-miR-618	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003287		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033460	MIMAT0003288	hsa-miR-619-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003288		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033461	MIMAT0003290	hsa-miR-621	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003290		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00033462	MIMAT0003290	hsa-miR-621	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003290		miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033463	MIMAT0003291	hsa-miR-622	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003291		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033464	MIMAT0003292	hsa-miR-623	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003292		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033465	MIMAT0003292	hsa-miR-623	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003292		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033466	MIMAT0003293	hsa-miR-624-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003293	"hsa-miR-624, hsa-miR-624* "	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033467	MIMAT0003293	hsa-miR-624-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003293	"hsa-miR-624, hsa-miR-624* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033468	MIMAT0003293	hsa-miR-624-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003293	"hsa-miR-624, hsa-miR-624* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033469	MIMAT0003294	hsa-miR-625-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003294	hsa-miR-625	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033470	MIMAT0003294	hsa-miR-625-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003294	hsa-miR-625	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033471	MIMAT0003294	hsa-miR-625-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003294	hsa-miR-625	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00033472	MIMAT0003294	hsa-miR-625-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003294	hsa-miR-625	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033473	MIMAT0003294	hsa-miR-625-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003294	hsa-miR-625	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033474	MIMAT0003295	hsa-miR-626	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003295		miRNA	Homo sapiens	23938262	Circulating	Plasma	RT-PCR|Microarray	"Plasma-based circulating MicroRNA biomarkers for Parkinson's disease. We identified 9 pairs of PD-predictive classifiers using k-TSP analysis and 13 most differentially-expressed miRNAs by SAM. A combination of both data sets produced a panel of PD-predictive biomarkers: k-TSP1 (miR-1826/miR-450b-3p), miR-626, and miR-505, and achieved the highest predictive power of 91% sensitivity, 100% specificity, 100% positive predicted value, and 88% negative predicted value in the replication set. However, low predictive values were shown in the validation set. "
RLID00033475	MIMAT0003295	hsa-miR-626	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003295		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00033476	MIMAT0003296	hsa-miR-627-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003296		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033477	MIMAT0003296	hsa-miR-627-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003296		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033478	MIMAT0003296	hsa-miR-627-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003296		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033479	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033480	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033481	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033482	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	24352417	Circulating	Blood platelet	Next-generation sequencing	"Platelets in both groups demonstrated miRNA expression profiles comparable to previously published data. The statistical analysis unveiled a signature of only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques. "
RLID00033483	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033484	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033485	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033486	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033487	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033488	MIMAT0003297	hsa-miR-628-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003297	hsa-miR-628	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033489	MIMAT0003298	hsa-miR-629-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003298	"hsa-miR-629, hsa-miR-629* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033490	MIMAT0003298	hsa-miR-629-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003298	"hsa-miR-629, hsa-miR-629* "	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033491	MIMAT0003298	hsa-miR-629-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003298	"hsa-miR-629, hsa-miR-629* "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033492	MIMAT0003298	hsa-miR-629-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003298	"hsa-miR-629, hsa-miR-629* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033493	MIMAT0003298	hsa-miR-629-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003298	"hsa-miR-629, hsa-miR-629* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033494	MIMAT0003299	hsa-miR-630	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003299		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033495	MIMAT0003299	hsa-miR-630	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003299		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033496	MIMAT0003299	hsa-miR-630	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003299		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033497	MIMAT0003300	hsa-miR-631	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003300		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033498	MIMAT0003300	hsa-miR-631	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003300		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033499	MIMAT0003301	hsa-miR-33b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003301	hsa-miR-33b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033500	MIMAT0003301	hsa-miR-33b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003301	hsa-miR-33b	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033501	MIMAT0003301	hsa-miR-33b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003301	hsa-miR-33b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033502	MIMAT0003301	hsa-miR-33b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003301	hsa-miR-33b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033503	MIMAT0003301	hsa-miR-33b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003301	hsa-miR-33b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033504	MIMAT0003301	hsa-miR-33b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003301	hsa-miR-33b	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00033505	MIMAT0003302	hsa-miR-632	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003302		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033506	MIMAT0003304	hsa-miR-634	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003304		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033507	MIMAT0003304	hsa-miR-634	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003304		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033508	MIMAT0003304	hsa-miR-634	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003304		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033509	MIMAT0003304	hsa-miR-634	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003304		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033510	MIMAT0003306	hsa-miR-636	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003306		miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00033511	MIMAT0003306	hsa-miR-636	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003306		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033512	MIMAT0003306	hsa-miR-636	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003306		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033513	MIMAT0003306	hsa-miR-636	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003306		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033514	MIMAT0003306	hsa-miR-636	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003306		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033515	MIMAT0003307	hsa-miR-637	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003307		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033516	MIMAT0003307	hsa-miR-637	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003307		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033517	MIMAT0003307	hsa-miR-637	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003307		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033518	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033519	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033520	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033521	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033522	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	22997154	Circulating	Plasma	Microarray	"Co-transfection with HBV replicative constructs suggested that let-7f, miR-939 and miR-638 can modulate HBV replication. Therefore, we propose that the miRNA profile constitutes a novel circulating marker that can help to predict response to IFN treatment in CHB patients. "
RLID00033523	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033524	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	23169280	Circulating	Serum	Microarray	"Table 2 miRNAs detected in pooled patient and control samples, as detected by Agilent Human miRNA microarrays. All of these showed potential as biomarkers as the levels of miRNAs varied between the patient and control groups. The expression levels of six of these miRNAs (in bold) were verified using TaqMan qRT–PCR. Three miRNAs (miR-720, miR-1246 and miR-1308) chosen for further analysis in individual patient samples. TaqMan qRT–PCR assays for the remaining three miRNAs were not available or were unreliable. Data are collected from Table 2. "
RLID00033525	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033526	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033527	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00033528	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	25394686	Exosome	Hepatocellular cancer cell	qRT-PCR	"These data suggest that SMPD3 plays an important role in the release of a number of microRNAs, including miR-638, and that microRNAs accumulated in cells following the inhibition of exosome membrane formation by GW4869. "
RLID00033529	MIMAT0003308	hsa-miR-638	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003308		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00033530	MIMAT0003309	hsa-miR-639	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003309		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033531	MIMAT0003310	hsa-miR-640	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003310		miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00033532	MIMAT0003310	hsa-miR-640	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003310		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033533	MIMAT0003311	hsa-miR-641	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003311		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033534	MIMAT0003311	hsa-miR-641	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003311		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033535	MIMAT0003311	hsa-miR-641	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003311		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033536	MIMAT0003312	hsa-miR-642a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003312	"hsa-miR-642, hsa-miR-642a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033537	MIMAT0003312	hsa-miR-642a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003312	"hsa-miR-642, hsa-miR-642a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033538	MIMAT0003312	hsa-miR-642a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003312	"hsa-miR-642, hsa-miR-642a "	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033539	MIMAT0003312	hsa-miR-642a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003312	"hsa-miR-642, hsa-miR-642a "	miRNA	Homo sapiens	20668554	Microvesicle	Liver stem cell	qRT-PCR	Table 4: Selectively expressed miRNAs from HLSC MVs and their cells of origin. Data are collected from Table 4.
RLID00033540	MIMAT0003313	hsa-miR-643	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003313		miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033541	MIMAT0003313	hsa-miR-643	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003313		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033542	MIMAT0003315	hsa-miR-645	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003315		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033543	MIMAT0003316	hsa-miR-646	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003316		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033544	MIMAT0003316	hsa-miR-646	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003316		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033545	MIMAT0003316	hsa-miR-646	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003316		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033546	MIMAT0003316	hsa-miR-646	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003316		miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033547	MIMAT0003316	hsa-miR-646	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003316		miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033548	MIMAT0003317	hsa-miR-647	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003317		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033549	MIMAT0003317	hsa-miR-647	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003317		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033550	MIMAT0003318	hsa-miR-648	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003318		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033551	MIMAT0003318	hsa-miR-648	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003318		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033552	MIMAT0003319	hsa-miR-649	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003319		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033553	MIMAT0003319	hsa-miR-649	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003319		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033554	MIMAT0003320	hsa-miR-650	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003320		miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033555	MIMAT0003321	hsa-miR-651-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003321		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033556	MIMAT0003321	hsa-miR-651-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003321		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033557	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033558	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033559	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00033560	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00033561	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033562	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00033563	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033564	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033565	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033566	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033567	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033568	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033569	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033570	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033571	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033572	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033573	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033574	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033575	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033576	MIMAT0003322	hsa-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003322	hsa-miR-652	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033577	MIMAT0003324	hsa-miR-661	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003324		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033578	MIMAT0003325	hsa-miR-662	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003325		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033579	MIMAT0003325	hsa-miR-662	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003325		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033580	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00033581	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033582	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033583	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033584	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033585	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033586	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033587	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033588	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033589	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033590	MIMAT0003326	hsa-miR-663a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003326	hsa-miR-663	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033591	MIMAT0003327	hsa-miR-449b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003327	hsa-miR-449b	miRNA	Homo sapiens	22529849	Exosome	Renal carcinomas cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033592	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033593	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00033594	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033595	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033596	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033597	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033598	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00033599	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033600	MIMAT0003329	hsa-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003329	hsa-miR-411	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033601	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033602	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033603	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033604	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033605	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033606	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00033607	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033608	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033609	MIMAT0003330	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033610	MIMAT0003331	hsa-miR-655-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003331		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033611	MIMAT0003333	hsa-miR-549a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003333	hsa-miR-549	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033612	MIMAT0003335	hsa-miR-657	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003335		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033613	MIMAT0003336	hsa-miR-658	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003336		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033614	MIMAT0003336	hsa-miR-658	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003336		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033615	MIMAT0003336	hsa-miR-658	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003336		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033616	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033617	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033618	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033619	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033620	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033621	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033622	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033623	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00033624	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033625	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033626	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033627	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033628	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033629	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033630	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033631	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033632	MIMAT0003338	hsa-miR-660-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003338	hsa-miR-660	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033633	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033634	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033635	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	24456939	Circulating	Gastric juice	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00033636	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033637	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00033638	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033639	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033640	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00033641	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033642	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033643	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033644	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033645	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033646	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033647	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033648	MIMAT0003339	hsa-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003339		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033649	MIMAT0003340	hsa-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003340		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033650	MIMAT0003340	hsa-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003340		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033651	MIMAT0003340	hsa-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003340		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033652	MIMAT0003340	hsa-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003340		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033653	MIMAT0003340	hsa-miR-542-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003340		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033654	MIMAT0003344	sv40-miR-S1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003344		miRNA	Simian virus 40	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033655	MIMAT0003378	rno-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003378	"rno-miR-378, rno-miR-378* "	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033656	MIMAT0003378	rno-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003378	"rno-miR-378, rno-miR-378* "	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033657	MIMAT0003378	rno-miR-378a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003378	"rno-miR-378, rno-miR-378* "	miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033658	MIMAT0003382	rno-miR-664-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003382	rno-miR-664	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00033659	MIMAT0003382	rno-miR-664-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003382	rno-miR-664	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Five miRNAs, miR-340-5p, miR-351, miR-494, miR-664, and let-7e, were significantly concentrated (two- to eightfold) in the nucleolus compared with the nucleoplasm and/or the cytoplasm (Fig. 2A; Supplemental Table 1). "
RLID00033660	MIMAT0003383	rno-miR-497-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003383	rno-miR-497	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00033661	MIMAT0003385	hsa-miR-363-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003385	hsa-miR-363*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033662	MIMAT0003385	hsa-miR-363-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003385	hsa-miR-363*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033663	MIMAT0003385	hsa-miR-363-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003385	hsa-miR-363*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033664	MIMAT0003385	hsa-miR-363-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003385	hsa-miR-363*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033665	MIMAT0003386	hsa-miR-376a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003386	hsa-miR-376a*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033666	MIMAT0003386	hsa-miR-376a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003386	hsa-miR-376a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033667	MIMAT0003389	hsa-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003389		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033668	MIMAT0003389	hsa-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003389		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033669	MIMAT0003389	hsa-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003389		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033670	MIMAT0003389	hsa-miR-542-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003389		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033671	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033672	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033673	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033674	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033675	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033676	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033677	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	24373621	Circulating	Plasma	qRT-PCR	"Unsupervised clustering of the expression profiles using the six most regulated miRNAs (miR-425-5p, miR-21-5p, miR-106b-5p, miR-590-5p, miR-574-3p, miR-885-3p) significantly (p = 0.012) separated plasma samples collected prior to treatment from plasma samples collected after two days of radiochemotherapy. "
RLID00033678	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033679	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033680	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033681	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033682	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033683	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033684	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033685	MIMAT0003393	hsa-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003393	"hsa-miR-425-5p, hsa-miR-425 "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00033686	MIMAT0003409	mmu-miR-467a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003409	"mmu-miR-467*, mmu-miR-467a "	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00033687	MIMAT0003409	mmu-miR-467a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003409	"mmu-miR-467*, mmu-miR-467a "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033688	MIMAT0003450	mmu-miR-488-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003450	"mmu-miR-488*, mmu-miR-488 "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033689	MIMAT0003453	mmu-miR-497a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003453	mmu-miR-497-5p	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033690	MIMAT0003454	mmu-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003454	mmu-miR-423	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033691	MIMAT0003454	mmu-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003454	mmu-miR-423	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033692	MIMAT0003454	mmu-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003454	mmu-miR-423	miRNA	Mus musculus	23897634	Cell body	Neuron ball cultures	Fluorescence in situ hybridization	Data are collected from Table 2: Cell Body-Enriched miRNAs.
RLID00033693	MIMAT0003455	mmu-miR-679-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003455	mmu-miR-679	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033694	MIMAT0003456	mmu-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003456	mmu-miR-495	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033695	MIMAT0003456	mmu-miR-495-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003456	mmu-miR-495	miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00033696	MIMAT0003457	mmu-miR-680	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003457		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033697	MIMAT0003457	mmu-miR-680	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003457		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033698	MIMAT0003457	mmu-miR-680	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003457		miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00033699	MIMAT0003459	mmu-miR-682	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003459		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033700	MIMAT0003459	mmu-miR-682	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003459		miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00033701	MIMAT0003460	mmu-miR-449c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003460	"mmu-miR-449b, mmu-miR-449c "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033702	MIMAT0003461	mmu-miR-683	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003461		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033703	MIMAT0003469	mmu-miR-690	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003469		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033704	MIMAT0003469	mmu-miR-690	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003469		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033705	MIMAT0003469	mmu-miR-690	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003469		miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00033706	MIMAT0003469	mmu-miR-690	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003469		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033707	MIMAT0003471	mmu-miR-692	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003471		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00033708	MIMAT0003475	mmu-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003475	mmu-miR-146b	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033709	MIMAT0003475	mmu-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003475	mmu-miR-146b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033710	MIMAT0003475	mmu-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003475	mmu-miR-146b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033711	MIMAT0003478	mmu-miR-467b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003478	"mmu-miR-467b, mmu-miR-467b* "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033712	MIMAT0003479	mmu-miR-669c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003479	mmu-miR-669c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033713	MIMAT0003483	mmu-miR-696	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003483		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033714	MIMAT0003485	mmu-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003485	"mmu-miR-455, mmu-miR-455-5p, mmu-miR-455* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033715	MIMAT0003485	mmu-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003485	"mmu-miR-455, mmu-miR-455-5p, mmu-miR-455* "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033716	MIMAT0003486	mmu-miR-491-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003486	mmu-miR-491	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033717	MIMAT0003490	mmu-miR-700-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003490	mmu-miR-700	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033718	MIMAT0003493	mmu-miR-703	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003493		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033719	MIMAT0003493	mmu-miR-703	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003493		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033720	MIMAT0003494	mmu-miR-704	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003494		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033721	MIMAT0003495	mmu-miR-705	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003495		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033722	MIMAT0003495	mmu-miR-705	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003495		miRNA	Mus musculus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033723	MIMAT0003495	mmu-miR-705	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003495		miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00033724	MIMAT0003496	mmu-miR-706	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003496		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033725	MIMAT0003496	mmu-miR-706	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003496		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033726	MIMAT0003498	mmu-miR-708-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003498	"mmu-miR-708, mmu-miR-708* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033727	MIMAT0003499	mmu-miR-709	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003499		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033728	MIMAT0003499	mmu-miR-709	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003499		miRNA	Mus musculus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033729	MIMAT0003499	mmu-miR-709	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003499		miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00033730	MIMAT0003499	mmu-miR-709	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003499		miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00033731	MIMAT0003501	mmu-miR-711	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003501		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00033732	MIMAT0003501	mmu-miR-711	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003501		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033733	MIMAT0003501	mmu-miR-711	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003501		miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00033734	MIMAT0003502	mmu-miR-712-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003502	mmu-miR-712	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033735	MIMAT0003502	mmu-miR-712-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003502	mmu-miR-712	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033736	MIMAT0003507	mmu-miR-500-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003507	mmu-miR-500	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00033737	MIMAT0003507	mmu-miR-500-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003507	mmu-miR-500	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033738	MIMAT0003507	mmu-miR-500-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003507	mmu-miR-500	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033739	MIMAT0003507	mmu-miR-500-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003507	mmu-miR-500	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00033740	MIMAT0003508	mmu-miR-501-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003508	mmu-miR-501	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033741	MIMAT0003509	mmu-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003509	mmu-miR-501*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033742	MIMAT0003509	mmu-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003509	mmu-miR-501*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00033743	MIMAT0003512	mmu-miR-450b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003512	mmu-miR-450b*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033744	MIMAT0003515	mmu-miR-721	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003515		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033745	MIMAT0003515	mmu-miR-721	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003515		miRNA	Mus musculus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033746	MIMAT0003518	bta-miR-29a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003518		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033747	MIMAT0003522	bta-miR-148a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003522		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033748	MIMAT0003524	bta-miR-151-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003524	bta-miR-151	miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033749	MIMAT0003528	bta-miR-21-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003528	bta-miR-21	miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033750	MIMAT0003538	bta-miR-125a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003538		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033751	MIMAT0003548	bta-miR-31	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003548		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033752	MIMAT0003711	mmu-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003711	mmu-miR-652	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033753	MIMAT0003711	mmu-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003711	mmu-miR-652	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033754	MIMAT0003711	mmu-miR-652-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003711	mmu-miR-652	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033755	MIMAT0003727	mmu-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003727	"mmu-miR-374-5p, mmu-miR-374, mmu-miR-374-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033756	MIMAT0003730	mmu-miR-592-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003730	mmu-miR-592	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033757	MIMAT0003731	mmu-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003731	mmu-miR-671	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00033758	MIMAT0003733	mmu-miR-665-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003733	mmu-miR-665	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033759	MIMAT0003734	mmu-miR-667-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003734	mmu-miR-667	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033760	MIMAT0003735	mmu-miR-672-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003735	mmu-miR-672	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033761	MIMAT0003739	mmu-miR-673-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003739	mmu-miR-673	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033762	MIMAT0003740	mmu-miR-674-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003740	"mmu-miR-674-5p, mmu-miR-674 "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033763	MIMAT0003740	mmu-miR-674-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003740	"mmu-miR-674-5p, mmu-miR-674 "	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033764	MIMAT0003741	mmu-miR-674-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003741	"mmu-miR-674-3p, mmu-miR-674* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033765	MIMAT0003782	mmu-miR-676-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003782	mmu-miR-676	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033766	MIMAT0003782	mmu-miR-676-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003782	mmu-miR-676	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033767	MIMAT0003782	mmu-miR-676-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003782	mmu-miR-676	miRNA	Mus musculus	23897634	Axon	Neuron ball cultures	Fluorescence in situ hybridization	"We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)].We used LNA probes for FISH analyses to validate the localization of the above axon-enriched miRNAs shown to be associated with the RISC in vivo. FISH signals of miR-181a-1* (passenger strand of miR-181a-1) and miR-532, two axon-enriched miRNAs (Table 1), distributed as distinct granules in axons and growth cones as well as cell bodies in cultured cortical neurons [Fig. 3(A)]. Data are collected from Table 1. "
RLID00033768	MIMAT0003783	mmu-miR-615-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003783	mmu-miR-615	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033769	MIMAT0003792	bta-miR-15b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003792		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033770	MIMAT0003800	bta-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003800	bta-miR-345	miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033771	MIMAT0003810	bta-let-7d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003810		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033772	MIMAT0003815	bta-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003815		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033773	MIMAT0003816	bta-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003816		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033774	MIMAT0003819	bta-miR-191	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003819		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033775	MIMAT0003825	bta-miR-214	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003825		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033776	MIMAT0003827	bta-miR-23a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003827		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033777	MIMAT0003830	bta-miR-361	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003830		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033778	MIMAT0003831	bta-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003831	bta-miR-423	miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033779	MIMAT0003841	bta-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003841		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033780	MIMAT0003844	bta-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003844	bta-let-7a	miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033781	MIMAT0003879	hsa-miR-758-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003879	hsa-miR-758	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00033782	MIMAT0003879	hsa-miR-758-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003879	hsa-miR-758	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033783	MIMAT0003879	hsa-miR-758-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003879	hsa-miR-758	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033784	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00033785	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033786	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033787	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033788	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033789	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033790	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033791	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033792	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033793	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033794	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033795	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033796	MIMAT0003880	hsa-miR-671-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003880	hsa-miR-671	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033797	MIMAT0003881	hsa-miR-668-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003881		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033798	MIMAT0003881	hsa-miR-668-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003881		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033799	MIMAT0003882	hsa-miR-767-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003882		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033800	MIMAT0003882	hsa-miR-767-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003882		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033801	MIMAT0003882	hsa-miR-767-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003882		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033802	MIMAT0003882	hsa-miR-767-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003882		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033803	MIMAT0003882	hsa-miR-767-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003882		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033804	MIMAT0003883	hsa-miR-767-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003883		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033805	MIMAT0003883	hsa-miR-767-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003883		miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033806	MIMAT0003883	hsa-miR-767-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003883		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033807	MIMAT0003883	hsa-miR-767-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003883		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033808	MIMAT0003884	hsa-miR-454-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003884	"hsa-miR-454-5p, hsa-miR-454* "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033809	MIMAT0003884	hsa-miR-454-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003884	"hsa-miR-454-5p, hsa-miR-454* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033810	MIMAT0003884	hsa-miR-454-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003884	"hsa-miR-454-5p, hsa-miR-454* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033811	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033812	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033813	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033814	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00033815	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033816	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033817	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00033818	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033819	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033820	MIMAT0003885	hsa-miR-454-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003885	"hsa-miR-454-3p, hsa-miR-454 "	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033821	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033822	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033823	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033824	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033825	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033826	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033827	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033828	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033829	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033830	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033831	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033832	MIMAT0003886	hsa-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003886		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00033833	MIMAT0003887	hsa-miR-769-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003887		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033834	MIMAT0003887	hsa-miR-769-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003887		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033835	MIMAT0003887	hsa-miR-769-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003887		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033836	MIMAT0003887	hsa-miR-769-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003887		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033837	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00033838	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033839	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033840	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033841	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033842	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033843	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033844	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033845	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033846	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033847	MIMAT0003888	hsa-miR-766-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003888	hsa-miR-766	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033848	MIMAT0003890	mmu-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003890	mmu-miR-551b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033849	MIMAT0003892	mmu-miR-762	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003892		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033850	MIMAT0003892	mmu-miR-762	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003892		miRNA	Mus musculus	21862971	Nucleus	Liver cell	qRT-PCR|Microarray	Nuclear miRNA expression profile in C57BL/6J mouse liver as detected by miRNA microarray. Relative expression levels for the 50 miRNAs that exhibited a signal stronger than 2 000 detected on the microarray chip are shown in six columns corresponding to two groups of samples (cells and nuclei). Colors indicate relative signal intensity. The miRNA expression profile was sorted using a hierarchical clustering method (Cluster 3.0 software and Java TreeView). MiR-709 was specifically enriched in the nucleus. Data are collected from Table S1: Liver nucleus miRNA expression profile (top 44) validated via RT-qPCR.
RLID00033851	MIMAT0003893	mmu-miR-761	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003893		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00033852	MIMAT0003893	mmu-miR-761	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003893		miRNA	Mus musculus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033853	MIMAT0003896	mmu-miR-763	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003896		miRNA	Mus musculus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033854	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	20883153	Circulating	Plasma	qRT-PCR|Microarray	"In mild TBI patients (GCS score >=12), miR-765 levels were unchanged, while the plasma levels of miR-92a and miR-16 were significantly increased within the first 24h of injury compared to healthy volunteers, and had AUC values of 0.78 and 0.82, respectively. "
RLID00033855	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00033856	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033857	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033858	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033859	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00033860	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033861	MIMAT0003945	hsa-miR-765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003945		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00033862	MIMAT0003948	hsa-miR-770-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003948		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033863	MIMAT0003948	hsa-miR-770-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003948		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033864	MIMAT0004089	mdo-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004089		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033865	MIMAT0004090	mdo-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004090		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033866	MIMAT0004090	mdo-miR-10b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004090		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033867	MIMAT0004092	mdo-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004092		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033868	MIMAT0004092	mdo-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004092		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033869	MIMAT0004093	mdo-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004093		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033870	MIMAT0004113	mdo-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004113		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033871	MIMAT0004113	mdo-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004113		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033872	MIMAT0004119	mdo-miR-184-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004119		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033873	MIMAT0004127	mdo-miR-204	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004127		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033874	MIMAT0004138	mdo-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004138		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033875	MIMAT0004138	mdo-miR-375	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004138		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033876	MIMAT0004141	mdo-let-7a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004141		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033877	MIMAT0004143	mdo-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004143		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033878	MIMAT0004143	mdo-let-7i-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004143		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033879	MIMAT0004151	mdo-miR-141-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004151		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033880	MIMAT0004152	mdo-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004152		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033881	MIMAT0004152	mdo-miR-191-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004152		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033882	MIMAT0004154	mdo-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004154		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033883	MIMAT0004154	mdo-miR-181a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004154		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033884	MIMAT0004161	mdo-let-7f-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004161		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033885	MIMAT0004171	mdo-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004171		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033886	MIMAT0004171	mdo-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004171		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033887	MIMAT0004179	mdo-miR-25	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004179		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00033888	MIMAT0004186	mmu-miR-301b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004186	mmu-miR-301b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033889	MIMAT0004186	mmu-miR-301b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004186	mmu-miR-301b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033890	MIMAT0004187	mmu-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004187	mmu-miR-744	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00033891	MIMAT0004187	mmu-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004187	mmu-miR-744	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00033892	MIMAT0004187	mmu-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004187	mmu-miR-744	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033893	MIMAT0004187	mmu-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004187	mmu-miR-744	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00033894	MIMAT0004238	mmu-miR-743a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004238	"mmu-miR-743, mmu-miR-743a "	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00033895	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00033896	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033897	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033898	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00033899	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033900	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033901	MIMAT0004284	hsa-miR-675-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004284	hsa-miR-675	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00033902	MIMAT0004324	mmu-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004324	mmu-miR-181d	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00033903	MIMAT0004331	bta-let-7b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004331		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033904	MIMAT0004332	bta-let-7c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004332		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033905	MIMAT0004336	bta-miR-19a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004336		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033906	MIMAT0004337	bta-miR-19b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004337		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00033907	MIMAT0004450	hsa-miR-297	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004450		miRNA	Homo sapiens	22344312	Circulating	Serum	Microarray|qRT-PCR	"Serum micro-RNAs (miRNAs) can be used for the diagnosis and prognosis of various diseases. Using genome-wide scans, we sought to identify serum miRNAs that could be used as prognostic predictors for sepsis patients. We used microarray screens to identify differentially expressed serum miRNAs by comparing samples from 12 surviving and 12 nonsurviving sepsis patients. These differentially expressed serum miRNAs were validated by quantitative reverse transcriptase-polymerase chain reaction assays for 118 sepsis patients. The validated miRNAs along with sepsis patients' clinical indictors were analyzed in a multivariate logistic regression model. Microarray analysis showed that miR-297 and miR-574-5p were differentially expressed in sepsis survivors and nonsurvivors. Upon validation with 118 sepsis patients' samples, these two miRNA expressions were significantly different, with P < 0.001. miR-297 was more closely associated with survival from sepsis, whereas miR-574-5p was associated with death from sepsis. "
RLID00033908	MIMAT0004450	hsa-miR-297	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004450		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00033909	MIMAT0004481	hsa-let-7a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004481	hsa-let-7a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033910	MIMAT0004481	hsa-let-7a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004481	hsa-let-7a*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00033911	MIMAT0004481	hsa-let-7a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004481	hsa-let-7a*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033912	MIMAT0004481	hsa-let-7a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004481	hsa-let-7a*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033913	MIMAT0004481	hsa-let-7a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004481	hsa-let-7a*	miRNA	Homo sapiens	25330373	Extracellular vesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033914	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00033915	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033916	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033917	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033918	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033919	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033920	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033921	MIMAT0004482	hsa-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004482	hsa-let-7b*	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-134a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00033922	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033923	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033924	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033925	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00033926	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033927	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033928	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033929	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033930	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033931	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033932	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033933	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-137a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00033934	MIMAT0004484	hsa-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004484	hsa-let-7d*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033935	MIMAT0004485	hsa-let-7e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004485	hsa-let-7e*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033936	MIMAT0004485	hsa-let-7e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004485	hsa-let-7e*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00033937	MIMAT0004485	hsa-let-7e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004485	hsa-let-7e*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033938	MIMAT0004485	hsa-let-7e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004485	hsa-let-7e*	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00033939	MIMAT0004486	hsa-let-7f-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004486	hsa-let-7f-1*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033940	MIMAT0004486	hsa-let-7f-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004486	hsa-let-7f-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033941	MIMAT0004486	hsa-let-7f-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004486	hsa-let-7f-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033942	MIMAT0004486	hsa-let-7f-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004486	hsa-let-7f-1*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033943	MIMAT0004486	hsa-let-7f-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004486	hsa-let-7f-1*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033944	MIMAT0004486	hsa-let-7f-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004486	hsa-let-7f-1*	miRNA	Homo sapiens	25330373	Extracellular vesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00033945	MIMAT0004487	hsa-let-7f-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004487	hsa-let-7f-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033946	MIMAT0004488	hsa-miR-15a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004488	hsa-miR-15a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033947	MIMAT0004488	hsa-miR-15a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004488	hsa-miR-15a*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033948	MIMAT0004488	hsa-miR-15a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004488	hsa-miR-15a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033949	MIMAT0004488	hsa-miR-15a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004488	hsa-miR-15a*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033950	MIMAT0004489	hsa-miR-16-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004489	hsa-miR-16-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033951	MIMAT0004490	hsa-miR-19a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004490	hsa-miR-19a*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033952	MIMAT0004491	hsa-miR-19b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004491	hsa-miR-19b-1*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033953	MIMAT0004491	hsa-miR-19b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004491	hsa-miR-19b-1*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033954	MIMAT0004491	hsa-miR-19b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004491	hsa-miR-19b-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033955	MIMAT0004491	hsa-miR-19b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004491	hsa-miR-19b-1*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033956	MIMAT0004491	hsa-miR-19b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004491	hsa-miR-19b-1*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033957	MIMAT0004492	hsa-miR-19b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004492	hsa-miR-19b-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033958	MIMAT0004493	hsa-miR-20a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004493	hsa-miR-20a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033959	MIMAT0004493	hsa-miR-20a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004493	hsa-miR-20a*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033960	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033961	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033962	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033963	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033964	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033965	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033966	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033967	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033968	MIMAT0004494	hsa-miR-21-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004494	hsa-miR-21*	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00033969	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00033970	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033971	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033972	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033973	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033974	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00033975	MIMAT0004495	hsa-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004495	hsa-miR-22*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033976	MIMAT0004496	hsa-miR-23a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004496	hsa-miR-23a*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033977	MIMAT0004496	hsa-miR-23a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004496	hsa-miR-23a*	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00033978	MIMAT0004496	hsa-miR-23a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004496	hsa-miR-23a*	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00033979	MIMAT0004496	hsa-miR-23a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004496	hsa-miR-23a*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033980	MIMAT0004497	hsa-miR-24-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004497	hsa-miR-24-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033981	MIMAT0004497	hsa-miR-24-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004497	hsa-miR-24-2*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033982	MIMAT0004497	hsa-miR-24-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004497	hsa-miR-24-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033983	MIMAT0004497	hsa-miR-24-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004497	hsa-miR-24-2*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033984	MIMAT0004498	hsa-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004498	hsa-miR-25*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00033985	MIMAT0004498	hsa-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004498	hsa-miR-25*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00033986	MIMAT0004498	hsa-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004498	hsa-miR-25*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033987	MIMAT0004498	hsa-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004498	hsa-miR-25*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033988	MIMAT0004498	hsa-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004498	hsa-miR-25*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00033989	MIMAT0004498	hsa-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004498	hsa-miR-25*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00033990	MIMAT0004499	hsa-miR-26a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004499	hsa-miR-26a-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033991	MIMAT0004499	hsa-miR-26a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004499	hsa-miR-26a-1*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00033992	MIMAT0004499	hsa-miR-26a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004499	hsa-miR-26a-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00033993	MIMAT0004499	hsa-miR-26a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004499	hsa-miR-26a-1*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033994	MIMAT0004499	hsa-miR-26a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004499	hsa-miR-26a-1*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00033995	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00033996	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00033997	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00033998	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00033999	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034000	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034001	MIMAT0004500	hsa-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004500	hsa-miR-26b*	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00034002	MIMAT0004501	hsa-miR-27a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004501	hsa-miR-27a*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034003	MIMAT0004501	hsa-miR-27a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004501	hsa-miR-27a*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034004	MIMAT0004501	hsa-miR-27a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004501	hsa-miR-27a*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00034005	MIMAT0004501	hsa-miR-27a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004501	hsa-miR-27a*	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034006	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034007	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034008	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034009	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034010	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034011	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00034012	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034013	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034014	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034015	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034016	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034017	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034018	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034019	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00034020	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034021	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034022	MIMAT0004502	hsa-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004502		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00034023	MIMAT0004503	hsa-miR-29a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004503	hsa-miR-29a*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00034024	MIMAT0004503	hsa-miR-29a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004503	hsa-miR-29a*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034025	MIMAT0004504	hsa-miR-31-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004504	hsa-miR-31*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034026	MIMAT0004505	hsa-miR-32-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004505	hsa-miR-32*	miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034027	MIMAT0004505	hsa-miR-32-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004505	hsa-miR-32*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034028	MIMAT0004506	hsa-miR-33a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004506	hsa-miR-33a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034029	MIMAT0004506	hsa-miR-33a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004506	hsa-miR-33a*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034030	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034031	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034032	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00034033	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034034	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034035	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034036	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034037	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034038	MIMAT0004507	hsa-miR-92a-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004507	hsa-miR-92a-1*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034039	MIMAT0004508	hsa-miR-92a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004508	hsa-miR-92a-2*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034040	MIMAT0004508	hsa-miR-92a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004508	hsa-miR-92a-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034041	MIMAT0004508	hsa-miR-92a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004508	hsa-miR-92a-2*	miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00034042	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034043	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034044	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034045	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034046	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034047	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00034048	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034049	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034050	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034051	MIMAT0004509	hsa-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004509	hsa-miR-93*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034052	MIMAT0004510	hsa-miR-96-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004510	hsa-miR-96*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034053	MIMAT0004511	hsa-miR-99a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004511	hsa-miR-99a*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034054	MIMAT0004511	hsa-miR-99a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004511	hsa-miR-99a*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034055	MIMAT0004511	hsa-miR-99a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004511	hsa-miR-99a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034056	MIMAT0004511	hsa-miR-99a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004511	hsa-miR-99a*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034057	MIMAT0004512	hsa-miR-100-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004512	hsa-miR-100*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034058	MIMAT0004513	hsa-miR-101-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004513	hsa-miR-101*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034059	MIMAT0004513	hsa-miR-101-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004513	hsa-miR-101*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034060	MIMAT0004513	hsa-miR-101-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004513	hsa-miR-101*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00034061	MIMAT0004513	hsa-miR-101-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004513	hsa-miR-101*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034062	MIMAT0004514	hsa-miR-29b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004514	hsa-miR-29b-1*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034063	MIMAT0004514	hsa-miR-29b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004514	hsa-miR-29b-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034064	MIMAT0004515	hsa-miR-29b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004515	hsa-miR-29b-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034065	MIMAT0004515	hsa-miR-29b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004515	hsa-miR-29b-2*	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00034066	MIMAT0004515	hsa-miR-29b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004515	hsa-miR-29b-2*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034067	MIMAT0004515	hsa-miR-29b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004515	hsa-miR-29b-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034068	MIMAT0004515	hsa-miR-29b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004515	hsa-miR-29b-2*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034069	MIMAT0004516	hsa-miR-105-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004516	hsa-miR-105*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034070	MIMAT0004516	hsa-miR-105-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004516	hsa-miR-105*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034071	MIMAT0004517	hsa-miR-106a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004517	hsa-miR-106a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034072	MIMAT0004517	hsa-miR-106a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004517	hsa-miR-106a*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034073	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034074	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034075	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034076	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034077	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034078	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034079	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034080	MIMAT0004518	hsa-miR-16-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004518	hsa-miR-16-2*	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034081	MIMAT0004521	mmu-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004521	mmu-miR-15b*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034082	MIMAT0004523	mmu-miR-29b-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004523	"mmu-miR-29b*, mmu-miR-29b-1* "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034083	MIMAT0004528	mmu-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004528		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034084	MIMAT0004528	mmu-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004528		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034085	MIMAT0004536	mmu-miR-151-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004536		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034086	MIMAT0004542	mmu-miR-191-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004542	mmu-miR-191*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034087	MIMAT0004543	hsa-miR-192-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004543	hsa-miR-192*	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034088	MIMAT0004544	mmu-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004544	"mmu-miR-193*, mmu-miR-193-5p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034089	MIMAT0004544	mmu-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004544	"mmu-miR-193*, mmu-miR-193-5p "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034090	MIMAT0004546	mmu-miR-202-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004546		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00034091	MIMAT0004548	hsa-miR-129-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004548	hsa-miR-129*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034092	MIMAT0004548	hsa-miR-129-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004548	hsa-miR-129*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034093	MIMAT0004548	hsa-miR-129-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004548	hsa-miR-129*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034094	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034095	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034096	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034097	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034098	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034099	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034100	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034101	MIMAT0004549	hsa-miR-148a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004549	hsa-miR-148a*	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034102	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034103	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034104	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034105	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034106	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034107	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034108	MIMAT0004550	hsa-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004550	hsa-miR-30c-2*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034109	MIMAT0004551	hsa-miR-30d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004551	hsa-miR-30d*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034110	MIMAT0004551	hsa-miR-30d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004551	hsa-miR-30d*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034111	MIMAT0004551	hsa-miR-30d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004551	hsa-miR-30d*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034112	MIMAT0004551	hsa-miR-30d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004551	hsa-miR-30d*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034113	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034114	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034115	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034116	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034117	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034118	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034119	MIMAT0004552	hsa-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004552		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034120	MIMAT0004553	hsa-miR-7-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004553	hsa-miR-7-1*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034121	MIMAT0004553	hsa-miR-7-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004553	hsa-miR-7-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034122	MIMAT0004553	hsa-miR-7-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004553	hsa-miR-7-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034123	MIMAT0004553	hsa-miR-7-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004553	hsa-miR-7-1*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034124	MIMAT0004553	hsa-miR-7-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004553	hsa-miR-7-1*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034125	MIMAT0004554	hsa-miR-7-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004554	hsa-miR-7-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034126	MIMAT0004555	hsa-miR-10a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004555	hsa-miR-10a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034127	MIMAT0004555	hsa-miR-10a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004555	hsa-miR-10a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034128	MIMAT0004555	hsa-miR-10a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004555	hsa-miR-10a*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034129	MIMAT0004555	hsa-miR-10a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004555	hsa-miR-10a*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034130	MIMAT0004555	hsa-miR-10a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004555	hsa-miR-10a*	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034131	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034132	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034133	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034134	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034135	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034136	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034137	MIMAT0004556	hsa-miR-10b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004556	hsa-miR-10b*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034138	MIMAT0004557	hsa-miR-34a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004557	hsa-miR-34a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034139	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034140	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034141	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034142	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034143	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034144	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034145	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034146	MIMAT0004558	hsa-miR-181a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004558	hsa-miR-181a-2*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034147	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034148	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034149	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034150	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034151	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034152	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034153	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034154	MIMAT0004559	hsa-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004559	hsa-miR-181c*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034155	MIMAT0004560	hsa-miR-183-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004560	hsa-miR-183*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034156	MIMAT0004560	hsa-miR-183-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004560	hsa-miR-183*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034157	MIMAT0004560	hsa-miR-183-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004560	hsa-miR-183*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034158	MIMAT0004560	hsa-miR-183-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004560	hsa-miR-183*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034159	MIMAT0004561	hsa-miR-187-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004561	hsa-miR-187*	miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00034160	MIMAT0004561	hsa-miR-187-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004561	hsa-miR-187*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034161	MIMAT0004561	hsa-miR-187-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004561	hsa-miR-187*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034162	MIMAT0004562	hsa-miR-196a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004562	hsa-miR-196a*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034163	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034164	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034165	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034166	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034167	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00034168	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034169	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034170	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034171	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034172	MIMAT0004563	hsa-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004563		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034173	MIMAT0004564	hsa-miR-214-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004564	hsa-miR-214*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034174	MIMAT0004564	hsa-miR-214-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004564	hsa-miR-214*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034175	MIMAT0004566	hsa-miR-218-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004566	hsa-miR-218-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034176	MIMAT0004567	hsa-miR-219a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004567		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034177	MIMAT0004567	hsa-miR-219a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004567		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034178	MIMAT0004568	hsa-miR-221-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004568	hsa-miR-221*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034179	MIMAT0004568	hsa-miR-221-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004568	hsa-miR-221*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034180	MIMAT0004568	hsa-miR-221-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004568	hsa-miR-221*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034181	MIMAT0004568	hsa-miR-221-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004568	hsa-miR-221*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034182	MIMAT0004568	hsa-miR-221-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004568	hsa-miR-221*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034183	MIMAT0004568	hsa-miR-221-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004568	hsa-miR-221*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034184	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034185	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034186	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034187	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034188	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034189	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034190	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034191	MIMAT0004570	hsa-miR-223-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004570	hsa-miR-223*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034192	MIMAT0004571	hsa-miR-200b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004571	hsa-miR-200b*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034193	MIMAT0004571	hsa-miR-200b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004571	hsa-miR-200b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034194	MIMAT0004576	mmu-miR-296-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004576		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034195	MIMAT0004576	mmu-miR-296-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004576		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00034196	MIMAT0004580	mmu-miR-34c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004580	mmu-miR-34c*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034197	MIMAT0004581	mmu-miR-34b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004581		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034198	MIMAT0004582	mmu-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004582	mmu-miR-106b*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034199	MIMAT0004582	mmu-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004582	mmu-miR-106b*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034200	MIMAT0004583	mmu-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004583	mmu-miR-130b*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034201	MIMAT0004583	mmu-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004583	mmu-miR-130b*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034202	MIMAT0004584	hsa-let-7g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004584	hsa-let-7g*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034203	MIMAT0004584	hsa-let-7g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004584	hsa-let-7g*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00034204	MIMAT0004584	hsa-let-7g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004584	hsa-let-7g*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034205	MIMAT0004584	hsa-let-7g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004584	hsa-let-7g*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034206	MIMAT0004584	hsa-let-7g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004584	hsa-let-7g*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034207	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034208	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034209	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00034210	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034211	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034212	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034213	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034214	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034215	MIMAT0004585	hsa-let-7i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004585	hsa-let-7i*	miRNA	Homo sapiens	21637849	Mitochondrion	Myoblast	In situ hybridization|qRT-PCR	"Other members of the let-7 familly, detected by RT-qPCR, had putative targets. These results suggested that some miRNA detected in the mitochondria like let-7 familly (let-7b, c, d, e, f, i) and mir-142a could be involved in a mitochondrial mRNA silencing regulation. "
RLID00034216	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034217	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034218	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034219	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00034220	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00034221	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034222	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034223	MIMAT0004586	hsa-miR-15b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004586	hsa-miR-15b*	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034224	MIMAT0004587	hsa-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004587	hsa-miR-23b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034225	MIMAT0004587	hsa-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004587	hsa-miR-23b*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034226	MIMAT0004587	hsa-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004587	hsa-miR-23b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034227	MIMAT0004587	hsa-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004587	hsa-miR-23b*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034228	MIMAT0004587	hsa-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004587	hsa-miR-23b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034229	MIMAT0004587	hsa-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004587	hsa-miR-23b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034230	MIMAT0004588	hsa-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004588	hsa-miR-27b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034231	MIMAT0004588	hsa-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004588	hsa-miR-27b*	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00034232	MIMAT0004588	hsa-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004588	hsa-miR-27b*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034233	MIMAT0004588	hsa-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004588	hsa-miR-27b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034234	MIMAT0004588	hsa-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004588	hsa-miR-27b*	miRNA	Homo sapiens	19002258	Microvesicle	Plasma	qRT-PCR	The filtered and normalized data were subjected to hierarchical cluster analysis comparing the miRNA expression profile between the PBMC and plasma microvesicles samples (Figure 3). Data are collectedf from figure 3: miRNA expression from peripheral blood microvesicles and PBMC.
RLID00034235	MIMAT0004588	hsa-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004588	hsa-miR-27b*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034236	MIMAT0004589	hsa-miR-30b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004589	hsa-miR-30b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034237	MIMAT0004589	hsa-miR-30b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004589	hsa-miR-30b*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034238	MIMAT0004589	hsa-miR-30b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004589	hsa-miR-30b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034239	MIMAT0004589	hsa-miR-30b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004589	hsa-miR-30b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00034240	MIMAT0004589	hsa-miR-30b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004589	hsa-miR-30b*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034241	MIMAT0004590	hsa-miR-122-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004590	hsa-miR-122*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034242	MIMAT0004590	hsa-miR-122-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004590	hsa-miR-122*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034243	MIMAT0004591	hsa-miR-124-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004591	hsa-miR-124*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034244	MIMAT0004591	hsa-miR-124-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004591	hsa-miR-124*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034245	MIMAT0004591	hsa-miR-124-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004591	hsa-miR-124*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034246	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034247	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034248	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00034249	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00034250	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034251	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034252	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034253	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034254	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034255	MIMAT0004592	hsa-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004592	hsa-miR-125b-1*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034256	MIMAT0004593	hsa-miR-130a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004593	hsa-miR-130a*	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00034257	MIMAT0004593	hsa-miR-130a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004593	hsa-miR-130a*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034258	MIMAT0004594	hsa-miR-132-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004594	hsa-miR-132*	miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00034259	MIMAT0004594	hsa-miR-132-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004594	hsa-miR-132*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034260	MIMAT0004594	hsa-miR-132-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004594	hsa-miR-132*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034261	MIMAT0004594	hsa-miR-132-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004594	hsa-miR-132*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034262	MIMAT0004594	hsa-miR-132-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004594	hsa-miR-132*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034263	MIMAT0004595	hsa-miR-135a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004595	hsa-miR-135a*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034264	MIMAT0004595	hsa-miR-135a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004595	hsa-miR-135a*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034265	MIMAT0004595	hsa-miR-135a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004595	hsa-miR-135a*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034266	MIMAT0004595	hsa-miR-135a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004595	hsa-miR-135a*	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034267	MIMAT0004595	hsa-miR-135a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004595	hsa-miR-135a*	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034268	MIMAT0004596	hsa-miR-138-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004596	hsa-miR-138-2*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034269	MIMAT0004596	hsa-miR-138-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004596	hsa-miR-138-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034270	MIMAT0004596	hsa-miR-138-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004596	hsa-miR-138-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034271	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034272	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034273	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034274	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034275	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034276	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034277	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00034278	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034279	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034280	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034281	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034282	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034283	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034284	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034285	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00034286	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034287	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034288	MIMAT0004597	hsa-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004597		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034289	MIMAT0004598	hsa-miR-141-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004598	hsa-miR-141*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034290	MIMAT0004598	hsa-miR-141-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004598	hsa-miR-141*	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034291	MIMAT0004598	hsa-miR-141-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004598	hsa-miR-141*	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034292	MIMAT0004599	hsa-miR-143-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004599	hsa-miR-143*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034293	MIMAT0004599	hsa-miR-143-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004599	hsa-miR-143*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034294	MIMAT0004599	hsa-miR-143-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004599	hsa-miR-143*	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00034295	MIMAT0004599	hsa-miR-143-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004599	hsa-miR-143*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034296	MIMAT0004600	hsa-miR-144-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004600	hsa-miR-144*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034297	MIMAT0004600	hsa-miR-144-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004600	hsa-miR-144*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034298	MIMAT0004600	hsa-miR-144-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004600	hsa-miR-144*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034299	MIMAT0004600	hsa-miR-144-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004600	hsa-miR-144*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034300	MIMAT0004600	hsa-miR-144-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004600	hsa-miR-144*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034301	MIMAT0004600	hsa-miR-144-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004600	hsa-miR-144*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034302	MIMAT0004601	hsa-miR-145-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004601	hsa-miR-145*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034303	MIMAT0004601	hsa-miR-145-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004601	hsa-miR-145*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034304	MIMAT0004601	hsa-miR-145-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004601	hsa-miR-145*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034305	MIMAT0004601	hsa-miR-145-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004601	hsa-miR-145*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034306	MIMAT0004601	hsa-miR-145-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004601	hsa-miR-145*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034307	MIMAT0004601	hsa-miR-145-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004601	hsa-miR-145*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034308	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034309	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034310	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034311	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034312	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034313	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034314	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00034315	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034316	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034317	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034318	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034319	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00034320	MIMAT0004602	hsa-miR-125a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004602		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034321	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034322	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034323	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00034324	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034325	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034326	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034327	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00034328	MIMAT0004603	hsa-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004603	hsa-miR-125b-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034329	MIMAT0004604	hsa-miR-127-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004604		miRNA	Homo sapiens	22798503	Circulating	Serum	qRT-PCR	"Our stem-loop RT-MGB qPCR in plasma and tissue samples from healthy individuals and patients with colon cancer presented in Table IV show that out of the 15 selected miRNAs exhibiting preferential expression and which have been shown to be related to colon carcinogenesis; nine of them (miR-7, miR-17-3p, miR-20a, miR-21, miR-92a, miR-96, miR-183, miR196a and miR-214) exhibited increased expression in plasma (and also in tissues) of patients with CRC, and that later TNM carcinoma stages had a more increased expression than did adenomas. On the other hand, six of the selected miRNAs (miR-124, miR-127-5p, miR-138, miR-143, miR-146a and miR-222) were reduced in expression in plasma (and also in tissues) of patients with CRC, the reduction becoming more pronounced during progression from early to later TNM carcinoma stages. "
RLID00034330	MIMAT0004604	hsa-miR-127-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004604		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034331	MIMAT0004604	hsa-miR-127-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004604		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034332	MIMAT0004604	hsa-miR-127-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004604		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034333	MIMAT0004605	hsa-miR-129-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004605	hsa-miR-129-3p	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034334	MIMAT0004605	hsa-miR-129-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004605	hsa-miR-129-3p	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034335	MIMAT0004605	hsa-miR-129-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004605	hsa-miR-129-3p	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034336	MIMAT0004605	hsa-miR-129-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004605	hsa-miR-129-3p	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034337	MIMAT0004605	hsa-miR-129-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004605	hsa-miR-129-3p	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034338	MIMAT0004606	hsa-miR-136-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004606	hsa-miR-136*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034339	MIMAT0004606	hsa-miR-136-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004606	hsa-miR-136*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034340	MIMAT0004606	hsa-miR-136-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004606	hsa-miR-136*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034341	MIMAT0004606	hsa-miR-136-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004606	hsa-miR-136*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034342	MIMAT0004606	hsa-miR-136-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004606	hsa-miR-136*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034343	MIMAT0004606	hsa-miR-136-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004606	hsa-miR-136*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034344	MIMAT0004607	hsa-miR-138-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004607	hsa-miR-138-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034345	MIMAT0004607	hsa-miR-138-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004607	hsa-miR-138-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034346	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00034347	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034348	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034349	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034350	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00034351	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034352	MIMAT0004609	hsa-miR-149-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004609	hsa-miR-149*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034353	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034354	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034355	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034356	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00034357	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034358	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034359	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034360	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034361	MIMAT0004610	hsa-miR-150-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004610	hsa-miR-150*	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034362	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	20145944	Circulating	Blood	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00034363	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034364	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034365	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034366	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034367	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034368	MIMAT0004611	hsa-miR-185-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004611	hsa-miR-185*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034369	MIMAT0004612	hsa-miR-186-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004612	hsa-miR-186*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034370	MIMAT0004613	hsa-miR-188-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004613		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034371	MIMAT0004613	hsa-miR-188-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004613		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034372	MIMAT0004613	hsa-miR-188-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004613		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034373	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034374	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034375	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034376	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034377	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034378	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034379	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034380	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034381	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034382	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034383	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034384	MIMAT0004614	hsa-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004614		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034385	MIMAT0004615	hsa-miR-195-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004615	hsa-miR-195*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034386	MIMAT0004615	hsa-miR-195-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004615	hsa-miR-195*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034387	MIMAT0004615	hsa-miR-195-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004615	hsa-miR-195*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034388	MIMAT0004620	mmu-let-7a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004620	"mmu-let-7a*, mmu-let-7a-1* "	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00034389	MIMAT0004622	mmu-let-7c-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004622	mmu-let-7c-1*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034390	MIMAT0004625	mmu-miR-16-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004625	"mmu-miR-16*, mmu-miR-16-1* "	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034391	MIMAT0004626	mmu-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004626	mmu-miR-18a*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034392	MIMAT0004626	mmu-miR-18a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004626	mmu-miR-18a*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034393	MIMAT0004627	mmu-miR-20a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004627	mmu-miR-20a*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034394	MIMAT0004628	mmu-miR-21a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004628	"mmu-miR-21*, mmu-miR-21-3p "	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00034395	MIMAT0004629	mmu-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004629	mmu-miR-22*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034396	MIMAT0004629	mmu-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004629	mmu-miR-22*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00034397	MIMAT0004629	mmu-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004629	mmu-miR-22*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034398	MIMAT0004630	mmu-miR-26b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004630	mmu-miR-26b*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034399	MIMAT0004631	mmu-miR-29a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004631	mmu-miR-29a*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034400	MIMAT0004636	mmu-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004636	mmu-miR-93*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034401	MIMAT0004640	mmu-miR-325-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004640	mmu-miR-325	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034402	MIMAT0004640	mmu-miR-325-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004640	mmu-miR-325	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00034403	MIMAT0004642	mmu-miR-330-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004642	mmu-miR-330	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034404	MIMAT0004643	mmu-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004643		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034405	MIMAT0004643	mmu-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004643		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034406	MIMAT0004644	mmu-miR-337-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004644		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034407	MIMAT0004646	rno-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004646	rno-miR-338*	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00034408	MIMAT0004647	mmu-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004647		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034409	MIMAT0004648	rno-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004648		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034410	MIMAT0004649	mmu-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004649		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034411	MIMAT0004650	rno-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004650		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00034412	MIMAT0004650	rno-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004650		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Five miRNAs, miR-340-5p, miR-351, miR-494, miR-664, and let-7e, were significantly concentrated (two- to eightfold) in the nucleolus compared with the nucleoplasm and/or the cytoplasm (Fig. 2A; Supplemental Table 1). "
RLID00034413	MIMAT0004651	mmu-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004651		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034414	MIMAT0004651	mmu-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004651		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034415	MIMAT0004651	mmu-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004651		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034416	MIMAT0004652	rno-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004652		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034417	MIMAT0004653	mmu-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004653		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034418	MIMAT0004653	mmu-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004653		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034419	MIMAT0004655	rno-miR-345-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004655		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034420	MIMAT0004656	mmu-miR-345-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004656		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034421	MIMAT0004661	mmu-miR-28a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004661	"mmu-miR-28*, mmu-miR-28-3p "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034422	MIMAT0004662	mmu-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004662		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034423	MIMAT0004663	mmu-miR-200c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004663	mmu-miR-200c*	miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00034424	MIMAT0004667	mmu-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004667	mmu-miR-199b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034425	MIMAT0004669	mmu-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004669	mmu-miR-125b-3p	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034426	MIMAT0004670	mmu-miR-7a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004670	"mmu-miR-7a*, mmu-miR-7a-1* "	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034427	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034428	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034429	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034430	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034431	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034432	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034433	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034434	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034435	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034436	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034437	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034438	MIMAT0004672	hsa-miR-106b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004672	hsa-miR-106b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034439	MIMAT0004673	hsa-miR-29c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004673	hsa-miR-29c*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034440	MIMAT0004673	hsa-miR-29c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004673	hsa-miR-29c*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034441	MIMAT0004673	hsa-miR-29c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004673	hsa-miR-29c*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034442	MIMAT0004673	hsa-miR-29c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004673	hsa-miR-29c*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034443	MIMAT0004673	hsa-miR-29c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004673	hsa-miR-29c*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034444	MIMAT0004674	hsa-miR-30c-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004674	hsa-miR-30c-1*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034445	MIMAT0004674	hsa-miR-30c-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004674	hsa-miR-30c-1*	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034446	MIMAT0004674	hsa-miR-30c-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004674	hsa-miR-30c-1*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034447	MIMAT0004674	hsa-miR-30c-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004674	hsa-miR-30c-1*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034448	MIMAT0004674	hsa-miR-30c-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004674	hsa-miR-30c-1*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034449	MIMAT0004675	hsa-miR-219a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004675		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034450	MIMAT0004675	hsa-miR-219a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004675		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034451	MIMAT0004675	hsa-miR-219a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004675		miRNA	Homo sapiens	22094284	Circulating	serum	qRT-PCR|RNA-seq	"When compared with family schizophrenia patients, circulating miR-219-2-3p, miR-92a, miR-346, let-7g and miR-17 were significantly higher in sporadic schizophrenia ( p < 0.001, Fig. 4 ). On contrary,  miR-181b  and  miR-195  were  significantlydown-regulated in sporadic  schizophrenia  compared  with  family schizophrenia patients ( p < 0.001), miR-1308 was slightly lower in sporadic schizophrenia compared family schizophrenia patients (0.05 < p < 0.001), and miR-103 was highly consistent between sporadic schizophrenia and family schizophrenia  patients ( p > 0.05). These data indicate that there is a close relationship between levels of circulating miRNAs and schizophrenia patients whether they have the family history or not. "
RLID00034452	MIMAT0004675	hsa-miR-219a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004675		miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00034453	MIMAT0004675	hsa-miR-219a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004675		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034454	MIMAT0004676	hsa-miR-34b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004676	hsa-miR-34b	miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00034455	MIMAT0004676	hsa-miR-34b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004676	hsa-miR-34b	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034456	MIMAT0004676	hsa-miR-34b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004676	hsa-miR-34b	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034457	MIMAT0004676	hsa-miR-34b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004676	hsa-miR-34b	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034458	MIMAT0004677	hsa-miR-34c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004677		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034459	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034460	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034461	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034462	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034463	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034464	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034465	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034466	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034467	MIMAT0004678	hsa-miR-99b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004678	hsa-miR-99b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034468	MIMAT0004679	hsa-miR-296-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004679		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034469	MIMAT0004680	hsa-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004680	hsa-miR-130b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034470	MIMAT0004680	hsa-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004680	hsa-miR-130b*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034471	MIMAT0004680	hsa-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004680	hsa-miR-130b*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034472	MIMAT0004680	hsa-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004680	hsa-miR-130b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034473	MIMAT0004680	hsa-miR-130b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004680	hsa-miR-130b*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034474	MIMAT0004681	hsa-miR-26a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004681	hsa-miR-26a-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034475	MIMAT0004681	hsa-miR-26a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004681	hsa-miR-26a-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034476	MIMAT0004681	hsa-miR-26a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004681	hsa-miR-26a-2*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034477	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	22675530	Circulating	Serum	qRT-PCR	Low levels of cell-free circulating miR-361-3p and miR-625* as blood-based markers for discriminating malignant from benign lung tumors.
RLID00034478	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034479	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034480	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034481	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034482	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034483	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034484	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034485	MIMAT0004682	hsa-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004682		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034486	MIMAT0004683	hsa-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004683		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034487	MIMAT0004683	hsa-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004683		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034488	MIMAT0004683	hsa-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004683		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034489	MIMAT0004683	hsa-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004683		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034490	MIMAT0004683	hsa-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004683		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034491	MIMAT0004684	mmu-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004684		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034492	MIMAT0004684	mmu-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004684		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034493	MIMAT0004684	mmu-miR-362-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004684		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034494	MIMAT0004686	hsa-miR-367-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004686	hsa-miR-367*	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034495	MIMAT0004686	hsa-miR-367-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004686	hsa-miR-367*	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034496	MIMAT0004687	hsa-miR-371a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004687	hsa-miR-371-5p	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034497	MIMAT0004687	hsa-miR-371a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004687	hsa-miR-371-5p	miRNA	Homo sapiens	24259014	Circulating	Serum	Microarray	"Elevated Serum Level of MicroRNA (miRNA)-200c nd miRNA-371-5p in Children with Kawasaki Disease. Two miRNAs, miR-200c and miR-371-5p, were differentially expressed between children with and without KD (Fig.2). Both miRNAs were significantly upregulated in the KD group compared with the control group (p=0.032 in both). "
RLID00034498	MIMAT0004687	hsa-miR-371a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004687	hsa-miR-371-5p	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034499	MIMAT0004687	hsa-miR-371a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004687	hsa-miR-371-5p	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034500	MIMAT0004687	hsa-miR-371a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004687	hsa-miR-371-5p	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034501	MIMAT0004689	hsa-miR-377-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004689	hsa-miR-377*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034502	MIMAT0004689	hsa-miR-377-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004689	hsa-miR-377*	miRNA	Homo sapiens	24352417	Circulating	Blood platelet	Next-generation sequencing	"Platelets in both groups demonstrated miRNA expression profiles comparable to previously published data. The statistical analysis unveiled a signature of only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques. "
RLID00034503	MIMAT0004689	hsa-miR-377-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004689	hsa-miR-377*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034504	MIMAT0004690	hsa-miR-379-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004690	hsa-miR-379*	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00034505	MIMAT0004690	hsa-miR-379-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004690	hsa-miR-379*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034506	MIMAT0004690	hsa-miR-379-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004690	hsa-miR-379*	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034507	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034508	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034509	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034510	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00034511	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034512	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034513	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034514	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034515	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034516	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034517	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00034518	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034519	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034520	MIMAT0004692	hsa-miR-340-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004692	hsa-miR-340	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034521	MIMAT0004693	hsa-miR-330-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004693		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034522	MIMAT0004693	hsa-miR-330-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004693		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034523	MIMAT0004693	hsa-miR-330-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004693		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034524	MIMAT0004693	hsa-miR-330-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004693		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034525	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034526	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034527	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034528	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034529	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034530	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034531	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034532	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034533	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034534	MIMAT0004694	hsa-miR-342-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004694		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034535	MIMAT0004695	hsa-miR-337-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004695		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034536	MIMAT0004695	hsa-miR-337-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004695		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034537	MIMAT0004695	hsa-miR-337-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004695		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034538	MIMAT0004696	hsa-miR-323a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004696	hsa-miR-323-5p	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034539	MIMAT0004696	hsa-miR-323a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004696	hsa-miR-323-5p	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034540	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034541	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034542	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034543	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034544	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00034545	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034546	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034547	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034548	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034549	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034550	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034551	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034552	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034553	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034554	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034555	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034556	MIMAT0004697	hsa-miR-151a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004697	hsa-miR-151-5p	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034557	MIMAT0004700	hsa-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004700		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034558	MIMAT0004700	hsa-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004700		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034559	MIMAT0004700	hsa-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004700		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034560	MIMAT0004700	hsa-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004700		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034561	MIMAT0004700	hsa-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004700		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034562	MIMAT0004700	hsa-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004700		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034563	MIMAT0004701	hsa-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004701		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034564	MIMAT0004701	hsa-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004701		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034565	MIMAT0004701	hsa-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004701		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034566	MIMAT0004701	hsa-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004701		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034567	MIMAT0004701	hsa-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004701		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034568	MIMAT0004701	hsa-miR-338-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004701		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034569	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034570	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034571	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034572	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034573	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034574	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034575	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034576	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034577	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034578	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034579	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00034580	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034581	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034582	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034583	MIMAT0004702	hsa-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004702		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00034584	MIMAT0004703	hsa-miR-335-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004703	hsa-miR-335*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034585	MIMAT0004703	hsa-miR-335-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004703	hsa-miR-335*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034586	MIMAT0004703	hsa-miR-335-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004703	hsa-miR-335*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034587	MIMAT0004705	rno-let-7b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004705	rno-let-7b*	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034588	MIMAT0004713	rno-miR-25-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004713	rno-miR-25*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034589	MIMAT0004728	rno-miR-124-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004728	rno-miR-124*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034590	MIMAT0004730	rno-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004730	rno-miR-125b-3p	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00034591	MIMAT0004730	rno-miR-125b-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004730	rno-miR-125b-3p	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034592	MIMAT0004734	rno-miR-138-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004734	"rno-miR-138*, rno-miR-138-1* "	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034593	MIMAT0004735	rno-miR-139-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004735		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00034594	MIMAT0004736	rno-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004736	rno-miR-193-5p	miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00034595	MIMAT0004738	rno-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004738		miRNA	Rattus norvegicus	19628621	Nucleoplasm	Myoblast	In situ hybridization	"MiR-199a-3p and miR-125a-5p appeared more concentrated in the nucleoplasm and cytoplasm compared with the nucleolus; their hybridization pattern more closely resembled that of let-7a, a microRNA that earlier in situ hybridization experiments had shown not to be concentrated in the nucleolus (Fig. 3; Politz et al. 2006). "
RLID00034596	MIMAT0004738	rno-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004738		miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	In situ hybridization	"MiR-199a-3p and miR-125a-5p appeared more concentrated in the nucleoplasm and cytoplasm compared with the nucleolus; their hybridization pattern more closely resembled that of let-7a, a microRNA that earlier in situ hybridization experiments had shown not to be concentrated in the nucleolus (Fig. 3; Politz et al. 2006). "
RLID00034597	MIMAT0004741	rno-miR-219a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004741		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034598	MIMAT0004745	mmu-miR-384-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004745		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034599	MIMAT0004745	mmu-miR-384-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004745		miRNA	Mus musculus	24381269	Axon	DRG neuron	qRT-PCR	"We only considered miRNAs with average CT (threshold cycle) values lower than 35, since a mature miRNA CT >35 is reported to be below the reliable detection limit (Chen et al., 2009). The axonal miRNAs were also ranked in order of abundance in axons (Fig. 2E; Table 1). Of the top 20 most abundant axonal miRNAs, only 11 were >1.5-fold enriched in axons, indicating that enrichment is not a simple reflection of abundance. Data are collected from Table 1. "
RLID00034600	MIMAT0004747	mmu-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004747	mmu-miR-411	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034601	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034602	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034603	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034604	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034605	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	24456939	Circulating	Serum	-	"In gastric cancer, several circulating miRNAs have been studied as potential diagnostic biomarkers by evaluating their amount in serum, plasma and gastric juice (Table 2). Data are collected from Table 2. "
RLID00034606	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034607	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034608	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00034609	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034610	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00034611	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00034612	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034613	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034614	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034615	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034616	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034617	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034618	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034619	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034620	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00034621	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034622	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034623	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	24937531	Exosome	Plasma	qRT-PCR	"For miRNome analysis, two homogeneous samples were created: one by pooling 2 μL of RNA from exosomes of diabetic patients and the other by pooling RNA from exosomes of control subjects. After reverse transcription (mirCURY LNA universal cDNA synthesis kit; Exiqon), the reaction was performed on a serum/plasma focus miRNA PCR panel 384 well (V1.R) (Exiqon) using the ABI 7900HT (Applied Biosystems). The most stable miRNAs (miR-425 and miR-423-5p) were identified by NormFinder and GeNorm, validated on each sample, and used as normalizators for circulating miRNAs. - See more at: http://press.endocrine.org/doi/10.1210/jc.2013-3843?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed&#sthash.kodyGYkk.dpuf "
RLID00034624	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034625	MIMAT0004748	hsa-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004748		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034626	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034627	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034628	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034629	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034630	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034631	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034632	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034633	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034634	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034635	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034636	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034637	MIMAT0004749	hsa-miR-424-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004749	hsa-miR-424*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034638	MIMAT0004750	mmu-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004750	mmu-miR-425	miRNA	Mus musculus	18410515	Synapse	ForeBrain	Microarray	Table 3: microRNAs most and least enriched in synaptoneurosomes as measured by microarray. Data are collected from Table 3.
RLID00034639	MIMAT0004751	hsa-miR-18b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004751	hsa-miR-18b*	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034640	MIMAT0004752	hsa-miR-20b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004752	hsa-miR-20b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034641	MIMAT0004752	hsa-miR-20b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004752	hsa-miR-20b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034642	MIMAT0004752	hsa-miR-20b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004752	hsa-miR-20b*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034643	MIMAT0004755	hcmv-miR-US25-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004755	hcmv-miR-US25-1*	miRNA	Human herpesvirus 5	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034644	MIMAT0004757	hsa-miR-431-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004757	hsa-miR-431*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034645	MIMAT0004757	hsa-miR-431-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004757	hsa-miR-431*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034646	MIMAT0004757	hsa-miR-431-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004757	hsa-miR-431*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034647	MIMAT0004757	hsa-miR-431-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004757	hsa-miR-431*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034648	MIMAT0004758	mmu-miR-463-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004758	mmu-miR-463	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034649	MIMAT0004759	mmu-miR-466a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004759		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034650	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034651	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034652	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034653	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00034654	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00034655	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00034656	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034657	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034658	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034659	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034660	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034661	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034662	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034663	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034664	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034665	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	22529849	Exosome	Liver carcinoma cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034666	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034667	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034668	MIMAT0004761	hsa-miR-483-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004761		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034669	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034670	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034671	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034672	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034673	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034674	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034675	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034676	MIMAT0004762	hsa-miR-486-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004762		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00034677	MIMAT0004763	hsa-miR-488-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004763	hsa-miR-488	miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00034678	MIMAT0004763	hsa-miR-488-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004763	hsa-miR-488	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034679	MIMAT0004763	hsa-miR-488-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004763	hsa-miR-488	miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034680	MIMAT0004763	hsa-miR-488-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004763	hsa-miR-488	miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034681	MIMAT0004763	hsa-miR-488-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004763	hsa-miR-488	miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034682	MIMAT0004764	hsa-miR-490-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004764		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034683	MIMAT0004764	hsa-miR-490-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004764		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034684	MIMAT0004766	hsa-miR-146b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004766		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034685	MIMAT0004766	hsa-miR-146b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004766		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034686	MIMAT0004766	hsa-miR-146b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004766		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034687	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034688	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034689	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034690	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00034691	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034692	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034693	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034694	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034695	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034696	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034697	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034698	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034699	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034700	MIMAT0004767	hsa-miR-193b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004767	hsa-miR-193b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034701	MIMAT0004770	hsa-miR-516a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004770		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034702	MIMAT0004773	hsa-miR-500a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004773	"hsa-miR-500, hsa-miR-500a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034703	MIMAT0004773	hsa-miR-500a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004773	"hsa-miR-500, hsa-miR-500a "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034704	MIMAT0004773	hsa-miR-500a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004773	"hsa-miR-500, hsa-miR-500a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034705	MIMAT0004773	hsa-miR-500a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004773	"hsa-miR-500, hsa-miR-500a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034706	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034707	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034708	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034709	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034710	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034711	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034712	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034713	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034714	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034715	MIMAT0004774	hsa-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004774		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034716	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034717	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034718	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034719	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034720	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034721	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034722	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00034723	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034724	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034725	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034726	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034727	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034728	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034729	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034730	MIMAT0004775	hsa-miR-502-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004775		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034731	MIMAT0004776	hsa-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004776	hsa-miR-505*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034732	MIMAT0004776	hsa-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004776	hsa-miR-505*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034733	MIMAT0004776	hsa-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004776	hsa-miR-505*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034734	MIMAT0004776	hsa-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004776	hsa-miR-505*	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00034735	MIMAT0004776	hsa-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004776	hsa-miR-505*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034736	MIMAT0004776	hsa-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004776	hsa-miR-505*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034737	MIMAT0004777	hsa-miR-513a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004777	hsa-miR-513-3p	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034738	MIMAT0004777	hsa-miR-513a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004777	hsa-miR-513-3p	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034739	MIMAT0004777	hsa-miR-513a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004777	hsa-miR-513-3p	miRNA	Homo sapiens	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00034740	MIMAT0004777	hsa-miR-513a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004777	hsa-miR-513-3p	miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034741	MIMAT0004778	hsa-miR-508-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004778		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00034742	MIMAT0004779	hsa-miR-509-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004779		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034743	MIMAT0004779	hsa-miR-509-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004779		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034744	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034745	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034746	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034747	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034748	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034749	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034750	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034751	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034752	MIMAT0004780	hsa-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004780		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034753	MIMAT0004781	mmu-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004781		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034754	MIMAT0004781	mmu-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004781		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034755	MIMAT0004781	mmu-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004781		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034756	MIMAT0004781	mmu-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004781		miRNA	Mus musculus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00034757	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00034758	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034759	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034760	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034761	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034762	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034763	MIMAT0004784	hsa-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004784		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034764	MIMAT0004785	hsa-miR-545-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004785	hsa-miR-545*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034765	MIMAT0004790	mmu-miR-503-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004790	mmu-miR-503*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034766	MIMAT0004792	hsa-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004792	hsa-miR-92b*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034767	MIMAT0004792	hsa-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004792	hsa-miR-92b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034768	MIMAT0004792	hsa-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004792	hsa-miR-92b*	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00034769	MIMAT0004792	hsa-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004792	hsa-miR-92b*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034770	MIMAT0004792	hsa-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004792	hsa-miR-92b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034771	MIMAT0004792	hsa-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004792	hsa-miR-92b*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034772	MIMAT0004794	hsa-miR-551b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004794	hsa-miR-551b*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034773	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	21258252	Circulating	Serum	qRT-PCR	The utility of miR-1254 and miR-574-5p serum-based biomarkers as minimally invasive screening and triage tools for subsequent diagnostic evaluation warrants additional validation.
RLID00034774	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	22344312	Circulating	Serum	Microarray|qRT-PCR	"Serum micro-RNAs (miRNAs) can be used for the diagnosis and prognosis of various diseases. Using genome-wide scans, we sought to identify serum miRNAs that could be used as prognostic predictors for sepsis patients. We used microarray screens to identify differentially expressed serum miRNAs by comparing samples from 12 surviving and 12 nonsurviving sepsis patients. These differentially expressed serum miRNAs were validated by quantitative reverse transcriptase-polymerase chain reaction assays for 118 sepsis patients. The validated miRNAs along with sepsis patients' clinical indictors were analyzed in a multivariate logistic regression model. Microarray analysis showed that miR-297 and miR-574-5p were differentially expressed in sepsis survivors and nonsurvivors. Upon validation with 118 sepsis patients' samples, these two miRNA expressions were significantly different, with P < 0.001. miR-297 was more closely associated with survival from sepsis, whereas miR-574-5p was associated with death from sepsis. "
RLID00034775	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034776	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034777	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00034778	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034779	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00034780	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	23169280	Circulating	Serum	Microarray	"Table 2 miRNAs detected in pooled patient and control samples, as detected by Agilent Human miRNA microarrays. All of these showed potential as biomarkers as the levels of miRNAs varied between the patient and control groups. The expression levels of six of these miRNAs (in bold) were verified using TaqMan qRT–PCR. Three miRNAs (miR-720, miR-1246 and miR-1308) chosen for further analysis in individual patient samples. TaqMan qRT–PCR assays for the remaining three miRNAs were not available or were unreliable. Data are collected from Table 2. "
RLID00034781	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034782	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034783	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034784	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034785	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	25330373	Extracellular vesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034786	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034787	MIMAT0004795	hsa-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004795		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034788	MIMAT0004796	hsa-miR-576-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004796		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034789	MIMAT0004796	hsa-miR-576-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004796		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034790	MIMAT0004796	hsa-miR-576-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004796		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034791	MIMAT0004797	hsa-miR-582-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004797		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034792	MIMAT0004797	hsa-miR-582-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004797		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034793	MIMAT0004797	hsa-miR-582-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004797		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034794	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034795	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034796	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034797	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034798	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034799	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034800	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034801	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034802	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034803	MIMAT0004799	hsa-miR-589-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004799	hsa-miR-589	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034804	MIMAT0004800	hsa-miR-550a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004800	"hsa-miR-550, hsa-miR-550a "	miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00034805	MIMAT0004800	hsa-miR-550a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004800	"hsa-miR-550, hsa-miR-550a "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034806	MIMAT0004800	hsa-miR-550a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004800	"hsa-miR-550, hsa-miR-550a "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034807	MIMAT0004800	hsa-miR-550a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004800	"hsa-miR-550, hsa-miR-550a "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034808	MIMAT0004801	hsa-miR-590-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004801		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034809	MIMAT0004801	hsa-miR-590-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004801		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034810	MIMAT0004801	hsa-miR-590-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004801		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034811	MIMAT0004801	hsa-miR-590-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004801		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034812	MIMAT0004802	hsa-miR-593-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004802	hsa-miR-593	miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034813	MIMAT0004803	hsa-miR-548a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004803		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034814	MIMAT0004804	hsa-miR-615-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004804		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034815	MIMAT0004804	hsa-miR-615-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004804		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034816	MIMAT0004804	hsa-miR-615-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004804		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034817	MIMAT0004804	hsa-miR-615-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004804		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034818	MIMAT0004806	hsa-miR-548c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004806		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034819	MIMAT0004806	hsa-miR-548c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004806		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034820	MIMAT0004806	hsa-miR-548c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004806		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00034821	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	22675530	Circulating	Serum	qRT-PCR	Low levels of cell-free circulating miR-361-3p and miR-625* as blood-based markers for discriminating malignant from benign lung tumors.
RLID00034822	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034823	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034824	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034825	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034826	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034827	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034828	MIMAT0004808	hsa-miR-625-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004808	hsa-miR-625*	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034829	MIMAT0004809	hsa-miR-628-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004809		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034830	MIMAT0004809	hsa-miR-628-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004809		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034831	MIMAT0004809	hsa-miR-628-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004809		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034832	MIMAT0004809	hsa-miR-628-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004809		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034833	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034834	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034835	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034836	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034837	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034838	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034839	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034840	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034841	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034842	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00034843	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034844	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034845	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00034846	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034847	MIMAT0004810	hsa-miR-629-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004810	hsa-miR-629	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034848	MIMAT0004811	hsa-miR-33b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004811	hsa-miR-33b*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034849	MIMAT0004812	hsa-miR-548d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004812		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034850	MIMAT0004813	hsa-miR-411-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004813	hsa-miR-411*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034851	MIMAT0004813	hsa-miR-411-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004813	hsa-miR-411*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034852	MIMAT0004813	hsa-miR-411-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004813	hsa-miR-411*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034853	MIMAT0004814	hsa-miR-654-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004814		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034854	MIMAT0004814	hsa-miR-654-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004814		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034855	MIMAT0004814	hsa-miR-654-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0003330	hsa-miR-654	miRNA	Homo sapiens	20668554	Microvesicle	MSC cell	qRT-PCR	Table 5: Selectively expressed miRNAs from MSC MVs and their cells of origin. Data are collected from Table 5.
RLID00034856	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00034857	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034858	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034859	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034860	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034861	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00034862	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034863	MIMAT0004819	hsa-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004819		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00034864	MIMAT0004820	mmu-miR-744-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004820	mmu-miR-744*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034865	MIMAT0004821	mmu-miR-671-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004821		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034866	MIMAT0004825	mmu-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004825		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034867	MIMAT0004825	mmu-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004825		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034868	MIMAT0004827	mmu-miR-297b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004827		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034869	MIMAT0004828	mmu-miR-708-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004828	mmu-miR-708	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034870	MIMAT0004857	mmu-miR-147-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004857	mmu-miR-147	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00034871	MIMAT0004859	mmu-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004859	mmu-miR-193b	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034872	MIMAT0004859	mmu-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004859	mmu-miR-193b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034873	MIMAT0004859	mmu-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004859	mmu-miR-193b	miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00034874	MIMAT0004859	mmu-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004859	mmu-miR-193b	miRNA	Mus musculus	21862971	Nucleus	Liver cell	Microarray	"Supplementary information, Figure S4 Screening for the target miRNAs of miR-709 in the nucleus via microarray assay (only top 44 miRNAs were showed). Data are collected from Figure S4. "
RLID00034875	MIMAT0004859	mmu-miR-193b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004859	mmu-miR-193b	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034876	MIMAT0004861	mmu-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004861	mmu-miR-877	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034877	MIMAT0004862	mmu-miR-877-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004862	mmu-miR-877*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034878	MIMAT0004862	mmu-miR-877-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004862	mmu-miR-877*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034879	MIMAT0004865	mmu-miR-297c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004865	mmu-miR-297c	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034880	MIMAT0004869	mmu-miR-421-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004869	mmu-miR-421	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034881	MIMAT0004869	mmu-miR-421-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004869	mmu-miR-421	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034882	MIMAT0004871	mmu-miR-465b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004871		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034883	MIMAT0004873	mmu-miR-465c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004873		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034884	MIMAT0004876	mmu-miR-466b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004876		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034885	MIMAT0004878	mmu-miR-466c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004878		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034886	MIMAT0004880	mmu-miR-466e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004880		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034887	MIMAT0004882	mmu-miR-466f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004882		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034888	MIMAT0004883	mmu-miR-466g	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004883		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034889	MIMAT0004884	mmu-miR-466h-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004884	mmu-miR-466h	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034890	MIMAT0004885	mmu-miR-467c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004885	mmu-miR-467c	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034891	MIMAT0004887	mmu-miR-467d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004887	mmu-miR-467d*	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034892	MIMAT0004889	mmu-miR-504-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004889	mmu-miR-504	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034893	MIMAT0004891	mmu-miR-509-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004891		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034894	MIMAT0004893	mmu-miR-574-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004893		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034895	MIMAT0004894	mmu-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004894		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034896	MIMAT0004894	mmu-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004894		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034897	MIMAT0004894	mmu-miR-574-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004894		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034898	MIMAT0004898	mmu-miR-654-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004898		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034899	MIMAT0004901	hsa-miR-298	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004901		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034900	MIMAT0004902	hsa-miR-891a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004902		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00034901	MIMAT0004902	hsa-miR-891a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004902		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00034902	MIMAT0004902	hsa-miR-891a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004902		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034903	MIMAT0004909	hsa-miR-450b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004909		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034904	MIMAT0004909	hsa-miR-450b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004909		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034905	MIMAT0004910	hsa-miR-450b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004910		miRNA	Homo sapiens	23938262	Circulating	Plasma	RT-PCR|Microarray	"Plasma-based circulating MicroRNA biomarkers for Parkinson's disease. We identified 9 pairs of PD-predictive classifiers using k-TSP analysis and 13 most differentially-expressed miRNAs by SAM. A combination of both data sets produced a panel of PD-predictive biomarkers: k-TSP1 (miR-1826/miR-450b-3p), miR-626, and miR-505, and achieved the highest predictive power of 91% sensitivity, 100% specificity, 100% positive predicted value, and 88% negative predicted value in the replication set. However, low predictive values were shown in the validation set. "
RLID00034906	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034907	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034908	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034909	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034910	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00034911	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034912	MIMAT0004911	hsa-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004911		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034913	MIMAT0004912	hsa-miR-890	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004912		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00034914	MIMAT0004917	hsa-miR-888-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004917	hsa-miR-888*	miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00034915	MIMAT0004917	hsa-miR-888-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004917	hsa-miR-888*	miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00034916	MIMAT0004918	hsa-miR-892b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004918		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034917	MIMAT0004918	hsa-miR-892b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004918		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034918	MIMAT0004918	hsa-miR-892b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004918		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00034919	MIMAT0004919	hsa-miR-541-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004919	hsa-miR-541*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034920	MIMAT0004919	hsa-miR-541-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004919	hsa-miR-541*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00034921	MIMAT0004919	hsa-miR-541-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004919	hsa-miR-541*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034922	MIMAT0004920	hsa-miR-541-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004920	hsa-miR-541	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00034923	MIMAT0004920	hsa-miR-541-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004920	hsa-miR-541	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034924	MIMAT0004920	hsa-miR-541-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004920	hsa-miR-541	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034925	MIMAT0004921	hsa-miR-889-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004921		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034926	MIMAT0004924	hsa-miR-876-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004924		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034927	MIMAT0004925	hsa-miR-876-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004925		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034928	MIMAT0004926	hsa-miR-708-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004926	hsa-miR-708	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034929	MIMAT0004926	hsa-miR-708-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004926	hsa-miR-708	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034930	MIMAT0004926	hsa-miR-708-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004926	hsa-miR-708	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034931	MIMAT0004926	hsa-miR-708-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004926	hsa-miR-708	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034932	MIMAT0004927	hsa-miR-708-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004927	hsa-miR-708*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034933	MIMAT0004927	hsa-miR-708-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004927	hsa-miR-708*	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00034934	MIMAT0004929	hsa-miR-190b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004929		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034935	MIMAT0004931	mmu-miR-466d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004931		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00034936	MIMAT0004933	mmu-miR-878-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004933		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034937	MIMAT0004934	mmu-miR-872-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004934	mmu-miR-872	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034938	MIMAT0004937	mmu-miR-875-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004937		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034939	MIMAT0004940	mmu-miR-511-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004940	mmu-miR-511	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00034940	MIMAT0004941	mmu-miR-544-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004941	mmu-miR-544	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034941	MIMAT0004942	mmu-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004942	mmu-miR-598	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00034942	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034943	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034944	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034945	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00034946	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00034947	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034948	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00034949	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034950	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034951	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00034952	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00034953	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034954	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034955	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034956	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034957	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034958	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034959	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034960	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034961	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00034962	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00034963	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034964	MIMAT0004945	hsa-miR-744-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004945	hsa-miR-744	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00034965	MIMAT0004946	hsa-miR-744-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004946	hsa-miR-744*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034966	MIMAT0004946	hsa-miR-744-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004946	hsa-miR-744*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034967	MIMAT0004946	hsa-miR-744-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004946	hsa-miR-744*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034968	MIMAT0004947	hsa-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004947		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00034969	MIMAT0004947	hsa-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004947		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034970	MIMAT0004947	hsa-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004947		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034971	MIMAT0004947	hsa-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004947		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00034972	MIMAT0004947	hsa-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004947		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034973	MIMAT0004947	hsa-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004947		miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00034974	MIMAT0004948	hsa-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004948		miRNA	Homo sapiens	19597549	Circulating	Serum	Microarray	"In a comparison of stages 3 and 4 prostate cancer sera and normal donor serum miRNA levels, we found that 15 miRNAs (miR-16, -92a, -103, -107, -197, -34b, -328, -485-3p, -486-5p, -92b, -574-3p, -636, -640, -766, -885-5p) were up-regulated in serum from prostate cancer patients compared to normal donor sera. "
RLID00034975	MIMAT0004948	hsa-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004948		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034976	MIMAT0004948	hsa-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004948		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00034977	MIMAT0004948	hsa-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004948		miRNA	Homo sapiens	24373621	Circulating	Plasma	qRT-PCR	"Unsupervised clustering of the expression profiles using the six most regulated miRNAs (miR-425-5p, miR-21-5p, miR-106b-5p, miR-590-5p, miR-574-3p, miR-885-3p) significantly (p = 0.012) separated plasma samples collected prior to treatment from plasma samples collected after two days of radiochemotherapy. "
RLID00034978	MIMAT0004948	hsa-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004948		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034979	MIMAT0004948	hsa-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004948		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034980	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00034981	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00034982	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034983	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00034984	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034985	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034986	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00034987	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00034988	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00034989	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034990	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00034991	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00034992	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00034993	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034994	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00034995	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00034996	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00034997	MIMAT0004949	hsa-miR-877-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004949	hsa-miR-877	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00034998	MIMAT0004950	hsa-miR-877-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004950	hsa-miR-877*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00034999	MIMAT0004950	hsa-miR-877-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004950	hsa-miR-877*	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035000	MIMAT0004951	hsa-miR-887-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004951		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035001	MIMAT0004951	hsa-miR-887-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004951		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035002	MIMAT0004952	hsa-miR-665	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004952		miRNA	Homo sapiens	21505438	Exosome	Primary dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035003	MIMAT0004952	hsa-miR-665	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004952		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035004	MIMAT0004952	hsa-miR-665	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004952		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035005	MIMAT0004952	hsa-miR-665	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004952		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035006	MIMAT0004952	hsa-miR-665	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004952		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035007	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035008	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035009	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035010	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035011	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035012	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035013	MIMAT0004953	hsa-miR-873-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004953	hsa-miR-873	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00035014	MIMAT0004954	hsa-miR-543	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004954		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035015	MIMAT0004954	hsa-miR-543	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004954		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035016	MIMAT0004954	hsa-miR-543	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004954		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035017	MIMAT0004954	hsa-miR-543	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004954		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035018	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035019	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035020	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035021	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035022	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035023	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035024	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035025	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035026	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035027	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00035028	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035029	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00035030	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035031	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035032	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035033	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035034	MIMAT0004955	hsa-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004955	hsa-miR-374b	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035035	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035036	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00035037	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035038	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035039	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035040	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035041	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035042	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035043	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035044	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00035045	MIMAT0004957	hsa-miR-760	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004957		miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00035046	MIMAT0004958	hsa-miR-301b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004958	hsa-miR-301b	miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00035047	MIMAT0004958	hsa-miR-301b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004958	hsa-miR-301b	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035048	MIMAT0004958	hsa-miR-301b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004958	hsa-miR-301b	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035049	MIMAT0004958	hsa-miR-301b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004958	hsa-miR-301b	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035050	MIMAT0004959	hsa-miR-216b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004959		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035051	MIMAT0004959	hsa-miR-216b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004959		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035052	MIMAT0004960	hsa-miR-208b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004960		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035053	MIMAT0004971	hsa-miR-921	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004971		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035054	MIMAT0004971	hsa-miR-921	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004971		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035055	MIMAT0004976	hsa-miR-933	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004976		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035056	MIMAT0004976	hsa-miR-933	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004976		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035057	MIMAT0004978	hsa-miR-935	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004978		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035058	MIMAT0004978	hsa-miR-935	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004978		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035059	MIMAT0004978	hsa-miR-935	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004978		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035060	MIMAT0004978	hsa-miR-935	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004978		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035061	MIMAT0004978	hsa-miR-935	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004978		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035062	MIMAT0004979	hsa-miR-936	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004979		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035063	MIMAT0004979	hsa-miR-936	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004979		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035064	MIMAT0004980	hsa-miR-937-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004980	hsa-miR-937	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035065	MIMAT0004980	hsa-miR-937-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004980	hsa-miR-937	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035066	MIMAT0004982	hsa-miR-939-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004982	hsa-miR-939	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035067	MIMAT0004982	hsa-miR-939-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004982	hsa-miR-939	miRNA	Homo sapiens	22997154	Circulating	Plasma	Microarray	"Co-transfection with HBV replicative constructs suggested that let-7f, miR-939 and miR-638 can modulate HBV replication. Therefore, we propose that the miRNA profile constitutes a novel circulating marker that can help to predict response to IFN treatment in CHB patients. "
RLID00035068	MIMAT0004982	hsa-miR-939-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004982	hsa-miR-939	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035069	MIMAT0004982	hsa-miR-939-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004982	hsa-miR-939	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035070	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035071	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035072	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00035073	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035074	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035075	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035076	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035077	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035078	MIMAT0004983	hsa-miR-940	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004983		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00035079	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035080	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035081	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035082	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035083	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035084	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035085	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035086	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035087	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035088	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035089	MIMAT0004984	hsa-miR-941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004984		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035090	MIMAT0004985	hsa-miR-942-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004985		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035091	MIMAT0004985	hsa-miR-942-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004985		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035092	MIMAT0004985	hsa-miR-942-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004985		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035093	MIMAT0004985	hsa-miR-942-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004985		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035094	MIMAT0004985	hsa-miR-942-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004985		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035095	MIMAT0004986	hsa-miR-943	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004986		miRNA	Homo sapiens	20145944	Circulating	Semen	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00035096	MIMAT0004986	hsa-miR-943	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004986		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035097	MIMAT0004986	hsa-miR-943	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004986		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035098	MIMAT0004986	hsa-miR-943	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004986		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00035099	MIMAT0004986	hsa-miR-943	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004986		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00035100	MIMAT0004987	hsa-miR-944	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004987		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035101	MIMAT0004987	hsa-miR-944	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0004987		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035102	MIMAT0005202	ppt-miR1073-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005202		miRNA	Physcomitrella patens	23749811	Chloroplast	Protonemata	RT-PCR	"From analysis of P. patens microRNA, miR1073 was predicted to target CuZn-SOD mRNAs. We noticed that two chloroplastic CuZn-SOD genes contain the miR1073 target sequence in the 3¡ä untranslated region; however, the cytosolic isozyme genes lack this sequence. In this study, we investigated the involvement of miR1073 in the expression of CuZn-SOD genes in P. patens. When protonemata of P. patens were cultured on a copper-depleted medium, SOD activity and mRNA levels of chloroplastic CuZn-SODs were decreased markedly. In contrast, cytosolic CuZn-SODs showed little or no change in mRNA levels or SOD activity. The precursor transcript and the mature form of miR1073 were induced by copper deficiency. The chloroplastic CuZn-SOD (PpCSD1) mRNA was cleaved at the miR1073 target site under copper deficiency. These results suggest that miR1073 is involved in the down-regulation of PpCSD1 expression. "
RLID00035103	MIMAT0005203	ppt-miR1073-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005203		miRNA	Physcomitrella patens	23749811	Chloroplast	Protonemata	RT-PCR	"From analysis of P. patens microRNA, miR1073 was predicted to target CuZn-SOD mRNAs. We noticed that two chloroplastic CuZn-SOD genes contain the miR1073 target sequence in the 3¡ä untranslated region; however, the cytosolic isozyme genes lack this sequence. In this study, we investigated the involvement of miR1073 in the expression of CuZn-SOD genes in P. patens. When protonemata of P. patens were cultured on a copper-depleted medium, SOD activity and mRNA levels of chloroplastic CuZn-SODs were decreased markedly. In contrast, cytosolic CuZn-SODs showed little or no change in mRNA levels or SOD activity. The precursor transcript and the mature form of miR1073 were induced by copper deficiency. The chloroplastic CuZn-SOD (PpCSD1) mRNA was cleaved at the miR1073 target site under copper deficiency. These results suggest that miR1073 is involved in the down-regulation of PpCSD1 expression. "
RLID00035104	MIMAT0005279	rno-miR-466c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005279	rno-miR-466c	miRNA	Rattus norvegicus	25297646	Circulating	Plasma	qRT-PCR|Microarray	"In plasma, miRNA upregulation was observed for miR-133a and miR-133b following PH and SL, whereas miR-100 and miR-466c were similarly downregulated following anesthesia and surgery. "
RLID00035105	MIMAT0005284	rno-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005284	rno-miR-874	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035106	MIMAT0005284	rno-miR-874-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005284	rno-miR-874	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00035107	MIMAT0005290	rno-miR-883-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005290	rno-miR-883	miRNA	Rattus norvegicus	22518031	Mitochondrion	Heart 	qRT-PCR	"We validated our microarray data using qPCR. 12S rRNA, a mitochondrial gene product 1, served as our internal control. We confirmed that miR-181c was predominantly localized to the mitochondrial fraction; its expression in the mitochondrial fraction was similar to that in the total heart fraction (Fig. 2A). In addition, fluorescence in situ hybridization (FISH) (Fig. 2C) shows co-localization of miR-181c with the mitochondrial marker, mitoTracker red. We also examined miR-181c expression in both cytosolic and mitochondrial fractions (Fig. 2B, left panel), using qPCR and found that miR-181c was enriched primarily in the mitochondrial fraction. We evaluated several other miRNAs as negative controls for mitochondrial localization, and miR-1192 data are included in Fig. 2B (right panel). We used 5S rRNA as an internal control for these sets of qPCR data, as it is known that this gene is present in both the cytosol and mitochondrial fractions 18. Data are collected from Figure 2. "
RLID00035108	MIMAT0005291	mmu-miR-582-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005291		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00035109	MIMAT0005293	mmu-miR-467e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005293	mmu-miR-467e	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035110	MIMAT0005300	rno-miR-182	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005300		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035111	MIMAT0005302	rno-miR-190b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005302	rno-miR-190b	miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00035112	MIMAT0005303	rno-miR-196c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005303	rno-miR-196c	miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00035113	MIMAT0005307	rno-miR-375-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005307	rno-miR-375	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00035114	MIMAT0005309	rno-miR-384-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005309		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035115	MIMAT0005312	rno-miR-411-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005312	rno-miR-411	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035116	MIMAT0005314	rno-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005314	rno-miR-425	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00035117	MIMAT0005314	rno-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005314	rno-miR-425	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035118	MIMAT0005315	rno-miR-434-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005315		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035119	MIMAT0005315	rno-miR-434-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005315		miRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00035120	MIMAT0005319	rno-miR-484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005319		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035121	MIMAT0005321	rno-miR-500-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005321	rno-miR-500	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035122	MIMAT0005321	rno-miR-500-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005321	rno-miR-500	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00035123	MIMAT0005322	rno-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005322		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00035124	MIMAT0005322	rno-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005322		miRNA	Rattus norvegicus	25562527	Mitochondrion	Hippocampus	qRT-PCR	"The levels of several mitochondria-associated miRNAs were found to increase following TBI. Among them, miR-155 and miR-223 levels were significantly elevated to 7.3 and 4.63 fold higher, respectively, in mitochondria fractions of injured relative to na?ve (uninjured) rats (Table 1). Data are collected from Table 1: Changes in mitochondria-associated and cytosolic miRNAs at 12 hr following TBI. "
RLID00035125	MIMAT0005323	rno-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005323		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035126	MIMAT0005324	rno-miR-598-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005324		miRNA	Rattus norvegicus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00035127	MIMAT0005325	rno-miR-598-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005325		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035128	MIMAT0005326	rno-miR-671	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005326		miRNA	Rattus norvegicus	19106625	Mitochondrion	Liver cell	qRT-PCR|Microarray	"We used a custom miRNA microarray system to survey miRNA expression at a genome-wide scale in the isolated mitochondria. The array had probes derived from rat (rno), mouse (mmu), or human (hsa) miRNAs. Using this array, 15 miRNA probes were identified that yielded signals significantly above background in each of the mitochondrial fractions and were also present following RNase treatment of the purified structures (Table 1). Data are collected from Table 1: miRNAs identified in RNA isolated from purified rat liver mitochondria "
RLID00035129	MIMAT0005331	rno-miR-708-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005331	rno-miR-708	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035130	MIMAT0005340	rno-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005340	rno-miR-92b	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035131	MIMAT0005439	mmu-let-7c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005439	mmu-let-7c-2*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035132	MIMAT0005440	mmu-miR-24-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005440	mmu-miR-24-2*	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00035133	MIMAT0005441	rno-miR-24-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005441	rno-miR-24-2*	miRNA	Rattus norvegicus	19628621	Cytoplasm	Myoblast	Microarray 	"Supplementary Table 1: This table contains data from a miRNA expression matrix for nucleolar (NO), nucleoplasmic (NU) and cytoplasmic (CY) fractions from L6 myoblasts. Data are collected from Table S1. "
RLID00035134	MIMAT0005442	rno-miR-30c-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005442	rno-miR-30c-2*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035135	MIMAT0005449	hsa-miR-523-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005449	hsa-miR-523*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035136	MIMAT0005450	hsa-miR-518e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005450	hsa-miR-518e*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035137	MIMAT0005450	hsa-miR-518e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005450	hsa-miR-518e*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035138	MIMAT0005451	hsa-miR-522-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005451	hsa-miR-522*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035139	MIMAT0005452	hsa-miR-519a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005452	hsa-miR-519a*	miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035140	MIMAT0005454	hsa-miR-519b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005454		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00035141	MIMAT0005454	hsa-miR-519b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005454		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035142	MIMAT0005455	hsa-miR-520c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005455		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035143	MIMAT0005456	hsa-miR-518d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005456		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035144	MIMAT0005457	hsa-miR-518a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005457		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00035145	MIMAT0005457	hsa-miR-518a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005457		miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00035146	MIMAT0005458	hsa-miR-1224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005458		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035147	MIMAT0005458	hsa-miR-1224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005458		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035148	MIMAT0005458	hsa-miR-1224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005458		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035149	MIMAT0005458	hsa-miR-1224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005458		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035150	MIMAT0005458	hsa-miR-1224-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005458		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00035151	MIMAT0005459	hsa-miR-1224-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005459		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035152	MIMAT0005572	hsa-miR-1225-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005572		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035153	MIMAT0005572	hsa-miR-1225-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005572		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035154	MIMAT0005573	hsa-miR-1225-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005573		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035155	MIMAT0005576	hsa-miR-1226-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005576	hsa-miR-1226*	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035156	MIMAT0005576	hsa-miR-1226-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005576	hsa-miR-1226*	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035157	MIMAT0005576	hsa-miR-1226-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005576	hsa-miR-1226*	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00035158	MIMAT0005577	hsa-miR-1226-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005577	hsa-miR-1226	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035159	MIMAT0005580	hsa-miR-1227-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005580	hsa-miR-1227	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035160	MIMAT0005580	hsa-miR-1227-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005580	hsa-miR-1227	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035161	MIMAT0005580	hsa-miR-1227-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005580	hsa-miR-1227	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035162	MIMAT0005580	hsa-miR-1227-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005580	hsa-miR-1227	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035163	MIMAT0005582	hsa-miR-1228-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005582	hsa-miR-1228*	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00035164	MIMAT0005582	hsa-miR-1228-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005582	hsa-miR-1228*	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035165	MIMAT0005582	hsa-miR-1228-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005582	hsa-miR-1228*	miRNA	Homo sapiens	25238238	Circulating	Serum	qRT-PCR	"Our study revealed that serum hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-26a-5p were potential circulating markers for HCC diagnosis. "
RLID00035166	MIMAT0005582	hsa-miR-1228-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005582	hsa-miR-1228*	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035167	MIMAT0005582	hsa-miR-1228-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005582	hsa-miR-1228*	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035168	MIMAT0005583	hsa-miR-1228-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005583	hsa-miR-1228	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035169	MIMAT0005583	hsa-miR-1228-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005583	hsa-miR-1228	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035170	MIMAT0005583	hsa-miR-1228-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005583	hsa-miR-1228	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035171	MIMAT0005583	hsa-miR-1228-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005583	hsa-miR-1228	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00035172	MIMAT0005584	hsa-miR-1229-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005584	hsa-miR-1229	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035173	MIMAT0005584	hsa-miR-1229-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005584	hsa-miR-1229	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035174	MIMAT0005584	hsa-miR-1229-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005584	hsa-miR-1229	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035175	MIMAT0005584	hsa-miR-1229-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005584	hsa-miR-1229	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035176	MIMAT0005586	hsa-miR-1231	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005586		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035177	MIMAT0005588	hsa-miR-1233-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005588	hsa-miR-1233	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035178	MIMAT0005588	hsa-miR-1233-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005588	hsa-miR-1233	miRNA	Homo sapiens	25017274	Circulating	Serum	qRT-PCR	"The expression of four miRNAs (miR-1233, miR-520, miR-210, miR-144) was validated by quantitative real-time polymerase chain reaction analysis. MiR-1233 was the most overexpressed in the serum of women who later developed sPE. Circulating miRNAs deserve further investigation in order to explore their potential role in the pathogenesis of preeclampsia. In particular, miR-1233 might represent a potential marker of early sPE. "
RLID00035179	MIMAT0005589	hsa-miR-1234-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005589	hsa-miR-1234	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035180	MIMAT0005589	hsa-miR-1234-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005589	hsa-miR-1234	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035181	MIMAT0005589	hsa-miR-1234-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005589	hsa-miR-1234	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00035182	MIMAT0005589	hsa-miR-1234-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005589	hsa-miR-1234	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00035183	MIMAT0005591	hsa-miR-1236-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005591	hsa-miR-1236	miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035184	MIMAT0005591	hsa-miR-1236-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005591	hsa-miR-1236	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035185	MIMAT0005592	hsa-miR-1237-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005592	hsa-miR-1237	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035186	MIMAT0005592	hsa-miR-1237-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005592	hsa-miR-1237	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035187	MIMAT0005593	hsa-miR-1238-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005593	hsa-miR-1238	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035188	MIMAT0005593	hsa-miR-1238-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005593	hsa-miR-1238	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035189	MIMAT0005593	hsa-miR-1238-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005593	hsa-miR-1238	miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00035190	MIMAT0005595	rno-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005595	rno-miR-146b	miRNA	Rattus norvegicus	21435393	Microvesicle	Serum	RT-PCR	"By using RT-PCR and specific forward/reverse primers these microRNAs were all detected in microvesicles, that had been released from primary and differentiated rat adipocytes after 6 and 24h incubation, respectively, as well as in microvesicles from rat serum(Fig. 6; shown only for miR-16, miR-27a, miR-146b and miR-222). "
RLID00035191	MIMAT0005595	rno-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005595	rno-miR-146b	miRNA	Rattus norvegicus	24553149	Circulating	Plasma	qRT-PCR|Microarray	"Microarray assay results showed a total of 36 differentially-expressed miRNAs, among which 15 miRNAs were considered as aberrantly expressed with a more than 2-fold change when calculating the ratio of fluorescence intense between the 2 groups. The elevated miRNAs included miR-290, miR-874, miR-292-5p, miR-327, miR-374, miR-98, miR-352, miR-132, miR-146b, and miR-196a. The down-regulated miRNAs included miR-145, miR-329, miR-375, miR-140*, and miR-29a. Validation of microarray assay by qRT-PCR showed similar results and the ΔΔCt value compared to the sham group are shown in Figure 1. "
RLID00035192	MIMAT0005595	rno-miR-146b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005595	rno-miR-146b	miRNA	Rattus norvegicus	22529849	Exosome	Adipocytes	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00035193	MIMAT0005596	rno-miR-551b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005596	rno-miR-551b	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035194	MIMAT0005788	hsa-miR-513b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005788		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035195	MIMAT0005789	hsa-miR-513c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005789	hsa-miR-513c	miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035196	MIMAT0005789	hsa-miR-513c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005789	hsa-miR-513c	miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035197	MIMAT0005790	osa-miR444a-3p.2	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005790	osa-miR444a.2	miRNA	Oryza sativa	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035198	MIMAT0005791	hsa-miR-1264	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005791		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035199	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035200	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035201	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035202	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00035203	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035204	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035205	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035206	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00035207	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035208	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035209	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00035210	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035211	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035212	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035213	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035214	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035215	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035216	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00035217	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035218	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035219	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035220	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035221	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00035222	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	24627568	Circulating	Plasma	qRT-PCR	"The plasma levels of miR-320b and miR-125b were significantly lower in patients with AMI when compared with controls, and these miRNAs may be involved in the pathogenesis of coronary heart disease. "
RLID00035223	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00035224	MIMAT0005792	hsa-miR-320b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005792		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035225	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035226	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035227	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035228	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00035229	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035230	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035231	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035232	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00035233	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035234	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035235	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035236	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035237	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035238	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035239	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035240	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035241	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035242	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035243	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00035244	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	22529849	Exosome	Ovarian	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00035245	MIMAT0005793	hsa-miR-320c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005793		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035246	MIMAT0005794	hsa-miR-1296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005794		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035247	MIMAT0005794	hsa-miR-1296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005794		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035248	MIMAT0005794	hsa-miR-1296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005794		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035249	MIMAT0005794	hsa-miR-1296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005794		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035250	MIMAT0005795	hsa-miR-1323	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005795		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035251	MIMAT0005795	hsa-miR-1323	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005795		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035252	MIMAT0005796	hsa-miR-1271-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005796	hsa-miR-1271	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035253	MIMAT0005796	hsa-miR-1271-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005796	hsa-miR-1271	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035254	MIMAT0005796	hsa-miR-1271-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005796	hsa-miR-1271	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035255	MIMAT0005796	hsa-miR-1271-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005796	hsa-miR-1271	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035256	MIMAT0005797	hsa-miR-1301-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005797		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035257	MIMAT0005797	hsa-miR-1301-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005797		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035258	MIMAT0005797	hsa-miR-1301-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005797		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035259	MIMAT0005797	hsa-miR-1301-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005797		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035260	MIMAT0005800	hsa-miR-1298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005800		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035261	MIMAT0005800	hsa-miR-1298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005800		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035262	MIMAT0005800	hsa-miR-1298-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005800		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035263	MIMAT0005823	hsa-miR-1178-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005823	hsa-miR-1178	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035264	MIMAT0005825	hsa-miR-1180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005825		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035265	MIMAT0005825	hsa-miR-1180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005825		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035266	MIMAT0005825	hsa-miR-1180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005825		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035267	MIMAT0005825	hsa-miR-1180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005825		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035268	MIMAT0005825	hsa-miR-1180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005825		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035269	MIMAT0005825	hsa-miR-1180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005825		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035270	MIMAT0005834	mmu-miR-466i-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005834	mmu-miR-466i	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035271	MIMAT0005837	mmu-miR-1187	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005837		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035272	MIMAT0005839	mmu-miR-669f-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005839	mmu-miR-669f	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035273	MIMAT0005844	mmu-miR-466f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005844		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035274	MIMAT0005846	mmu-miR-467f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005846		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035275	MIMAT0005846	mmu-miR-467f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005846		miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00035276	MIMAT0005855	mmu-miR-467h	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005855		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035277	MIMAT0005856	mmu-miR-1195	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005856		miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035278	MIMAT0005859	mmu-miR-1198-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005859	mmu-miR-1198	miRNA	Mus musculus	22031862	Exosome	Dendritic cell	Microarray	"Figure 1: miRNA in BMDC-derived immature and mature exosomes.  (A) Western blot analysis (top) of 1-mL density fractions from a continuous sucrose gradient used to purify BMDC exosomes. Exosomes, detected by their CD9 expression, were enriched in those fractions with characteristic exosome density. The digital gel (bottom), obtained with Agilent 2100 Bioanalyzer, shows the presence of miRNAs in the density fractions in which exosomes were present. One of 2 experiments is shown. (B) Digital gel (Agilent 2100 Bioanalyzer) showing the presence of similar levels of miRNAs isolated from exosomes treated (or not) with proteinase K and then incubated (or not) with RNase A. Results are representative of 2 independent experiments. (C) Analysis of miRNAs from BMDC exosomes showing intensity of expression of miRNAs against their rank position. Signals above the 2500 cutoff were considered positive. (D) Venn diagram with the numbers of miRNAs detected in immature and mature exosomes released by BMDCs. List with the miRNAs detected by Illumina miRNA Expression Array. In those cases were the probe did not resolve miRNAs differing at only 1 or 2 positions, miRNAs were listed in parentheses. Results are based on the miRNA profiling of 4 different samples of each type of exosomes. Data are collected from Figure 1. "
RLID00035279	MIMAT0005859	mmu-miR-1198-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005859	mmu-miR-1198	miRNA	Mus musculus	25159140	Exosome	Bone marrow Macrophage	qRT-PCR	"We profiled the miRNA transcriptome of BMDMs and their exo-macs, either UT (n = 3) or IL-4 treated (IL-4; n = 3), by low-density quantitative PCR (qPCR) arrays. A total of 178 (29%) of the 618 miRNAs present in the arrays were detected in at least two out of three biological replicates of both BMDMs and exo-macs (Table S1). "
RLID00035280	MIMAT0005863	hsa-miR-1200	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005863		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035281	MIMAT0005865	hsa-miR-1202	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005865		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00035282	MIMAT0005865	hsa-miR-1202	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005865		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035283	MIMAT0005865	hsa-miR-1202	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005865		miRNA	Homo sapiens	24961598	Circulating	Plasma	qRT-PCR	"This is the first report of circulating miR biomarkers in LVAD patients. We demonstrate the feasibility of this approach, report the potential for miR-483-3p and miR-1202, respectively, to monitor and predict response to LVAD therapy, and propose further work to study these hypotheses and elucidate roles for miR-483-3p and miR-1202 in clinical practice and in underlying biological processes. "
RLID00035284	MIMAT0005866	hsa-miR-1203	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005866		miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00035285	MIMAT0005866	hsa-miR-1203	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005866		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035286	MIMAT0005867	hsa-miR-663b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005867		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035287	MIMAT0005867	hsa-miR-663b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005867		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035288	MIMAT0005868	hsa-miR-1204	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005868		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035289	MIMAT0005874	hsa-miR-548e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005874		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035290	MIMAT0005874	hsa-miR-548e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005874		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035291	MIMAT0005874	hsa-miR-548e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005874		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035292	MIMAT0005875	hsa-miR-548j-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005875		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035293	MIMAT0005875	hsa-miR-548j-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005875		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035294	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035295	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035296	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035297	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035298	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035299	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035300	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00035301	MIMAT0005876	hsa-miR-1285-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005876	hsa-miR-1285	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00035302	MIMAT0005878	hsa-miR-1287-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005878		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035303	MIMAT0005878	hsa-miR-1287-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005878		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035304	MIMAT0005878	hsa-miR-1287-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005878		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035305	MIMAT0005878	hsa-miR-1287-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005878		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035306	MIMAT0005878	hsa-miR-1287-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005878		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035307	MIMAT0005878	hsa-miR-1287-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005878		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035308	MIMAT0005880	hsa-miR-1290	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005880		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035309	MIMAT0005880	hsa-miR-1290	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005880		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035310	MIMAT0005880	hsa-miR-1290	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005880		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035311	MIMAT0005880	hsa-miR-1290	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005880		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035312	MIMAT0005881	hsa-miR-1291	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005881		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035313	MIMAT0005881	hsa-miR-1291	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005881		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035314	MIMAT0005881	hsa-miR-1291	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005881		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035315	MIMAT0005882	hsa-miR-548k	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005882		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035316	MIMAT0005882	hsa-miR-548k	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005882		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035317	MIMAT0005882	hsa-miR-548k	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005882		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035318	MIMAT0005883	hsa-miR-1293	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005883		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035319	MIMAT0005883	hsa-miR-1293	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005883		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035320	MIMAT0005883	hsa-miR-1293	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005883		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035321	MIMAT0005883	hsa-miR-1293	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005883		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035322	MIMAT0005883	hsa-miR-1293	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005883		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035323	MIMAT0005884	hsa-miR-1294	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005884		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035324	MIMAT0005884	hsa-miR-1294	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005884		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035325	MIMAT0005884	hsa-miR-1294	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005884		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00035326	MIMAT0005887	hsa-miR-1299	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005887		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00035327	MIMAT0005889	hsa-miR-548l	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005889		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035328	MIMAT0005889	hsa-miR-548l	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005889		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035329	MIMAT0005892	hsa-miR-1304-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005892	hsa-miR-1304	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035330	MIMAT0005892	hsa-miR-1304-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005892	hsa-miR-1304	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035331	MIMAT0005892	hsa-miR-1304-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005892	hsa-miR-1304	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035332	MIMAT0005892	hsa-miR-1304-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005892	hsa-miR-1304	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00035333	MIMAT0005893	hsa-miR-1305	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005893		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035334	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035335	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035336	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00035337	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035338	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035339	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035340	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	23169280	Circulating	Serum	Microarray	"Table 2 miRNAs detected in pooled patient and control samples, as detected by Agilent Human miRNA microarrays. All of these showed potential as biomarkers as the levels of miRNAs varied between the patient and control groups. The expression levels of six of these miRNAs (in bold) were verified using TaqMan qRT–PCR. Three miRNAs (miR-720, miR-1246 and miR-1308) chosen for further analysis in individual patient samples. TaqMan qRT–PCR assays for the remaining three miRNAs were not available or were unreliable. Data are collected from Table 2. "
RLID00035341	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035342	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035343	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035344	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035345	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035346	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035347	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00035348	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035349	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035350	MIMAT0005898	hsa-miR-1246	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005898		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035351	MIMAT0005899	hsa-miR-1247-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005899	hsa-miR-1247	miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035352	MIMAT0005899	hsa-miR-1247-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005899	hsa-miR-1247	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035353	MIMAT0005899	hsa-miR-1247-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005899	hsa-miR-1247	miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035354	MIMAT0005899	hsa-miR-1247-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005899	hsa-miR-1247	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035355	MIMAT0005900	hsa-miR-1248	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005900		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035356	MIMAT0005901	hsa-miR-1249-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005901	hsa-miR-1249	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035357	MIMAT0005901	hsa-miR-1249-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005901	hsa-miR-1249	miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035358	MIMAT0005901	hsa-miR-1249-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005901	hsa-miR-1249	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035359	MIMAT0005902	hsa-miR-1250-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005902		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035360	MIMAT0005902	hsa-miR-1250-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005902		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035361	MIMAT0005902	hsa-miR-1250-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005902		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00035362	MIMAT0005903	hsa-miR-1251-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005903		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035363	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	21258252	Circulating	Serum	qRT-PCR	The utility of miR-1254 and miR-574-5p serum-based biomarkers as minimally invasive screening and triage tools for subsequent diagnostic evaluation warrants additional validation.
RLID00035364	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035365	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035366	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035367	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035368	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035369	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035370	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035371	MIMAT0005905	hsa-miR-1254	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005905		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035372	MIMAT0005906	hsa-miR-1255a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005906		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035373	MIMAT0005906	hsa-miR-1255a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005906		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035374	MIMAT0005906	hsa-miR-1255a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005906		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035375	MIMAT0005907	hsa-miR-1256	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005907		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035376	MIMAT0005908	hsa-miR-1257	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005908		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035377	MIMAT0005911	hsa-miR-1260a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005911	hsa-miR-1260	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035378	MIMAT0005911	hsa-miR-1260a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005911	hsa-miR-1260	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035379	MIMAT0005911	hsa-miR-1260a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005911	hsa-miR-1260	miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035380	MIMAT0005911	hsa-miR-1260a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005911	hsa-miR-1260	miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00035381	MIMAT0005914	hsa-miR-1262	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005914		miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00035382	MIMAT0005914	hsa-miR-1262	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005914		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035383	MIMAT0005914	hsa-miR-1262	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005914		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035384	MIMAT0005915	hsa-miR-1263	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005915		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035385	MIMAT0005920	hsa-miR-1266-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005920		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035386	MIMAT0005920	hsa-miR-1266-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005920		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035387	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035388	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035389	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035390	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035391	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035392	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035393	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035394	MIMAT0005922	hsa-miR-1268a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005922	hsa-miR-1268	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035395	MIMAT0005924	hsa-miR-1270	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005924		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035396	MIMAT0005924	hsa-miR-1270	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005924		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00035397	MIMAT0005924	hsa-miR-1270	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005924		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035398	MIMAT0005924	hsa-miR-1270	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005924		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035399	MIMAT0005925	hsa-miR-1272	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005925		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035400	MIMAT0005925	hsa-miR-1272	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005925		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035401	MIMAT0005926	hsa-miR-1273a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005926	hsa-miR-1273	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00035402	MIMAT0005928	hsa-miR-548h-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005928	hsa-miR-548h	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035403	MIMAT0005928	hsa-miR-548h-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005928	hsa-miR-548h	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035404	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035405	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035406	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035407	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035408	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035409	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	23940654	Nucleolus	HeLa cell	qRT-PCR	"Even under such stringent criteria, 11 miRNAs can be identified as miRNAs that are detectable in the nucleolus with very high levels of confidence (Figure 1D, Table S2). Since the detected nucleolar contents of many of these RNAs are very high, we termed these 11 miRNAs as nucleolar miRNAs. "
RLID00035410	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035411	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00035412	MIMAT0005929	hsa-miR-1275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005929		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035413	MIMAT0005930	hsa-miR-1276	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005930		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035414	MIMAT0005931	hsa-miR-302e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005931		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035415	MIMAT0005933	hsa-miR-1277-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005933	hsa-miR-1277	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035416	MIMAT0005936	hsa-miR-1278	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005936		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035417	MIMAT0005936	hsa-miR-1278	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005936		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035418	MIMAT0005939	hsa-miR-1281	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005939		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035419	MIMAT0005939	hsa-miR-1281	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005939		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035420	MIMAT0005941	hsa-miR-1284	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005941		miRNA	Homo sapiens	23056502	Exosome	Epidermal melanocyte	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035421	MIMAT0005943	hsa-miR-1292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005943	hsa-miR-1292	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035422	MIMAT0005943	hsa-miR-1292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005943	hsa-miR-1292	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035423	MIMAT0005943	hsa-miR-1292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005943	hsa-miR-1292	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035424	MIMAT0005943	hsa-miR-1292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005943	hsa-miR-1292	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035425	MIMAT0005943	hsa-miR-1292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005943	hsa-miR-1292	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035426	MIMAT0005943	hsa-miR-1292-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005943	hsa-miR-1292	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035427	MIMAT0005945	hsa-miR-1255b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005945	hsa-miR-1255b	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035428	MIMAT0005945	hsa-miR-1255b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005945	hsa-miR-1255b	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00035429	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035430	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035431	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035432	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035433	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035434	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035435	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035436	MIMAT0005948	hsa-miR-664a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005948	"hsa-miR-664*, hsa-miR-664-5p "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035437	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035438	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035439	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035440	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035441	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035442	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035443	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035444	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00035445	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035446	MIMAT0005949	hsa-miR-664a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005949	"hsa-miR-664, hsa-miR-664-3p "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035447	MIMAT0005950	hsa-miR-1306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005950	hsa-miR-1306	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035448	MIMAT0005950	hsa-miR-1306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005950	hsa-miR-1306	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035449	MIMAT0005950	hsa-miR-1306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005950	hsa-miR-1306	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035450	MIMAT0005950	hsa-miR-1306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005950	hsa-miR-1306	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035451	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035452	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035453	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035454	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035455	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035456	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035457	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035458	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035459	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035460	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035461	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035462	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035463	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035464	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035465	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035466	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	24918059	Nucleus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035467	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035468	MIMAT0005951	hsa-miR-1307-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005951	hsa-miR-1307	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035469	MIMAT0005953	hsa-miR-1322	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005953		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00035470	MIMAT0005955	hsa-miR-1197	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005955		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00035471	MIMAT0005955	hsa-miR-1197	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0005955		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035472	MIMAT0006018	ssc-miR-99b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006018		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035473	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035474	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035475	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035476	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035477	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035478	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	23077538	Microvesicle	Plasma	Next-generation sequencing	"To characterize the stability of secreted miRNAs in plasma, we selected eight plasma miRNAs with relatively high copy numbers detected by Solexa sequencing (Table S1).Data are collected from Table S1: Plasma miRNA level detected by Solexa Sequencing. Total miRNA copy number = 3780436. Only miRNAs with copy number >= 1500 were shown. "
RLID00035479	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035480	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S9. The expression level of all microRNAs that detected in the nuclear and cytoplasmic 18-30nt sRNA of 293T cell line. Table S5. The N/C values of all isomiRs. The isomiRs are shown only if it displayed a raw read count (non-normalized) more than 10 in at least one library. Data are collected from Table S5, S9. "
RLID00035481	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035482	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035483	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00035484	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035485	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035486	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	24918059	Cytoplasm	HeLa|MCF7	Microarray	Data are collected from supplementary Table S2. MiRNA reads in the subcellular fractions.
RLID00035487	MIMAT0006764	hsa-miR-320d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006764		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035488	MIMAT0006765	hsa-miR-1825	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006765		miRNA	Homo sapiens	23056502	Exosome	Malignant melanoma cell	Microarray	"To distinguish miRNA signatures between melanoma cell-derived exosomes and normal melanocyte-derived exosomes, we compared the miRNome in A375 and HEMa-LP exosomes. We identified 130 miRNAs upregulated and 98 miRNAs downregulated in A375 versus HEMa-LP exosomes (Table S6). Data are collected from table S6. "
RLID00035489	MIMAT0006767	hsa-miR-1827	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006767		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035490	MIMAT0006778	hsa-miR-516a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006778		miRNA	Homo sapiens	21505438	Exosome	B cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00035491	MIMAT0006778	hsa-miR-516a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006778		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035492	MIMAT0006786	ssc-miR-140-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006786	ssc-miR-140*	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035493	MIMAT0006789	hsa-miR-1468-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006789		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035494	MIMAT0006789	hsa-miR-1468-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006789		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00035495	MIMAT0006790	hsa-miR-675-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0006790	"hsa-miR-675b, hsa-miR-675* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035496	MIMAT0007347	hsa-miR-1469	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007347		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035497	MIMAT0007347	hsa-miR-1469	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007347		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035498	MIMAT0007347	hsa-miR-1469	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007347		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035499	MIMAT0007402	hsa-miR-103b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007402	hsa-miR-103-as	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035500	MIMAT0007402	hsa-miR-103b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007402	hsa-miR-103-as	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035501	MIMAT0007753	ssc-miR-15a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007753		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035502	MIMAT0007754	ssc-miR-16	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007754		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035503	MIMAT0007755	ssc-miR-17-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007755	ssc-miR-17	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035504	MIMAT0007756	ssc-miR-30b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007756	ssc-miR-30b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035505	MIMAT0007757	ssc-miR-34a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007757		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035506	MIMAT0007758	ssc-miR-130a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007758		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035507	MIMAT0007759	ssc-miR-185	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007759		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035508	MIMAT0007760	ssc-miR-199b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007760	ssc-miR-199b*	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035509	MIMAT0007761	ssc-miR-210	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007761		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035510	MIMAT0007762	ssc-miR-221-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007762	ssc-miR-221	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035511	MIMAT0007871	mmu-miR-1892	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007871		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035512	MIMAT0007872	mmu-miR-1906	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007872		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035513	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00035514	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035515	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035516	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035517	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035518	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035519	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035520	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035521	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035522	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035523	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035524	MIMAT0007881	hsa-miR-1908-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007881		miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00035525	MIMAT0007882	hsa-miR-1909-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007882	hsa-miR-1909*	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035526	MIMAT0007883	hsa-miR-1909-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007883	hsa-miR-1909	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035527	MIMAT0007883	hsa-miR-1909-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007883	hsa-miR-1909	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035528	MIMAT0007884	hsa-miR-1910-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007884		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035529	MIMAT0007885	hsa-miR-1911-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007885	hsa-miR-1911	miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035530	MIMAT0007885	hsa-miR-1911-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007885	hsa-miR-1911	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035531	MIMAT0007886	hsa-miR-1911-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007886	hsa-miR-1911*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035532	MIMAT0007887	hsa-miR-1912	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007887		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035533	MIMAT0007890	hsa-miR-1914-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007890	hsa-miR-1914*	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00035534	MIMAT0007892	hsa-miR-1915-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007892	hsa-miR-1915	miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00035535	MIMAT0007892	hsa-miR-1915-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007892	hsa-miR-1915	miRNA	Homo sapiens	23169280	Circulating	Serum	Microarray	"Table 2 miRNAs detected in pooled patient and control samples, as detected by Agilent Human miRNA microarrays. All of these showed potential as biomarkers as the levels of miRNAs varied between the patient and control groups. The expression levels of six of these miRNAs (in bold) were verified using TaqMan qRT–PCR. Three miRNAs (miR-720, miR-1246 and miR-1308) chosen for further analysis in individual patient samples. TaqMan qRT–PCR assays for the remaining three miRNAs were not available or were unreliable. Data are collected from Table 2. "
RLID00035536	MIMAT0007892	hsa-miR-1915-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007892	hsa-miR-1915	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035537	MIMAT0007892	hsa-miR-1915-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0007892	hsa-miR-1915	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035538	MIMAT0009196	hsa-miR-103a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009196	"hsa-miR-103-2*, hsa-miR-103a-2* "	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035539	MIMAT0009196	hsa-miR-103a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009196	"hsa-miR-103-2*, hsa-miR-103a-2* "	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035540	MIMAT0009196	hsa-miR-103a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009196	"hsa-miR-103-2*, hsa-miR-103a-2* "	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035541	MIMAT0009196	hsa-miR-103a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009196	"hsa-miR-103-2*, hsa-miR-103a-2* "	miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00035542	MIMAT0009196	hsa-miR-103a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009196	"hsa-miR-103-2*, hsa-miR-103a-2* "	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035543	MIMAT0009196	hsa-miR-103a-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009196	"hsa-miR-103-2*, hsa-miR-103a-2* "	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035544	MIMAT0009197	hsa-miR-205-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009197	hsa-miR-205*	miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00035545	MIMAT0009199	hsa-miR-365a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009199	hsa-miR-365*	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035546	MIMAT0009199	hsa-miR-365a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009199	hsa-miR-365*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035547	MIMAT0009199	hsa-miR-365a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009199	hsa-miR-365*	miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035548	MIMAT0009199	hsa-miR-365a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009199	hsa-miR-365*	miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035549	MIMAT0009199	hsa-miR-365a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009199	hsa-miR-365*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035550	MIMAT0009199	hsa-miR-365a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009199	hsa-miR-365*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035551	MIMAT0009201	hsa-miR-196b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009201	hsa-miR-196b*	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035552	MIMAT0009206	hsa-miR-2113	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009206		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035553	MIMAT0009218	bta-miR-106b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009218		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035554	MIMAT0009232	bta-miR-141	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009232		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035555	MIMAT0009233	bta-miR-143	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009233		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035556	MIMAT0009242	bta-miR-16a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009242		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035557	MIMAT0009270	bta-miR-223	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009270		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035558	MIMAT0009315	bta-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009315		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035559	MIMAT0009416	mmu-miR-1949	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009416		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035560	MIMAT0009447	hsa-miR-1972	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009447		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035561	MIMAT0009447	hsa-miR-1972	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009447		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035562	MIMAT0009448	hsa-miR-1973	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009448		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035563	MIMAT0009448	hsa-miR-1973	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009448		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035564	MIMAT0009448	hsa-miR-1973	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009448		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035565	MIMAT0009448	hsa-miR-1973	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009448		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray|RT-PCR	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035566	MIMAT0009451	hsa-miR-1976	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009451		miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00035567	MIMAT0009451	hsa-miR-1976	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0009451		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035568	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035569	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035570	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00035571	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035572	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035573	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00035574	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035575	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035576	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035577	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00035578	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035579	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035580	MIMAT0010133	hsa-miR-2110	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010133		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00035581	MIMAT0010185	ssc-miR-101	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010185	ssc-miR-101a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035582	MIMAT0010186	ssc-miR-133a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010186	ssc-miR-133a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035583	MIMAT0010187	ssc-miR-1	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010187	ssc-miR-1a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035584	MIMAT0010190	ssc-miR-146b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010190		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035585	MIMAT0010191	ssc-miR-181a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010191		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035586	MIMAT0010193	ssc-miR-30a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010193	ssc-miR-30a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035587	MIMAT0010195	hsa-let-7a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010195	hsa-let-7a-2*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035588	MIMAT0010195	hsa-let-7a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010195	hsa-let-7a-2*	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035589	MIMAT0010214	hsa-miR-151b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010214		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00035590	MIMAT0010214	hsa-miR-151b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010214		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035591	MIMAT0010214	hsa-miR-151b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010214		miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00035592	MIMAT0010251	hsa-miR-449c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010251	hsa-miR-449c	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00035593	MIMAT0010313	hsa-miR-762	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010313		miRNA	Homo sapiens	23169280	Circulating	Serum	Microarray	"Table 2 miRNAs detected in pooled patient and control samples, as detected by Agilent Human miRNA microarrays. All of these showed potential as biomarkers as the levels of miRNAs varied between the patient and control groups. The expression levels of six of these miRNAs (in bold) were verified using TaqMan qRT–PCR. Three miRNAs (miR-720, miR-1246 and miR-1308) chosen for further analysis in individual patient samples. TaqMan qRT–PCR assays for the remaining three miRNAs were not available or were unreliable. Data are collected from Table 2. "
RLID00035594	MIMAT0010313	hsa-miR-762	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010313		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035595	MIMAT0010313	hsa-miR-762	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0010313		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00035596	MIMAT0011159	hsa-miR-2115-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0011159	hsa-miR-2115*	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00035597	MIMAT0011160	hsa-miR-2116-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0011160	hsa-miR-2116	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035598	MIMAT0011212	mmu-miR-2136	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0011212		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035599	MIMAT0011777	hsa-miR-2277-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0011777	hsa-miR-2277	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00035600	MIMAT0011778	hsa-miR-2278	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0011778		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035601	MIMAT0012038	bta-miR-339b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012038		miRNA	Bos taurus	24614226	Extracellular vesicle	Luminal fluid	Next-generation sequencing	"This analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). his analysis found 81 conserved mature miRNAs in the ULF extracellular vesicle small RNA sequences, with 53 in common between cyclic and pregnant samples and 1 unique annotated miRNA (bta-miR-423) in the day 14 pregnant samples (Fig. 5). Data are collected from Figure 5. "
RLID00035602	MIMAT0012734	hsa-miR-711	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012734		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035603	MIMAT0012737	mdo-miR-148-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012737		miRNA	Monodelphis domestica	25417092	Exosome	Milk	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00035604	MIMAT0012751	mdo-miR-215	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012751		miRNA	Monodelphis domestica	25417092	Exosome	Serum	Next-generation sequencing	The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2).The ten most highly abundant miRNAs in milk at five lactation time points and blood serum samples at day 118 and 175 of lactation are summarized in (see Additional file 2). Data are collceted from Table S2.
RLID00035605	MIMAT0012771	mmu-miR-432	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012771		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00035606	MIMAT0012830	rno-miR-504	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012830		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035607	MIMAT0012852	rno-miR-667-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012852	rno-miR-667	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00035608	MIMAT0012951	eca-miR-101	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012951		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035609	MIMAT0012952	eca-miR-135b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012952		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035610	MIMAT0012959	eca-miR-197	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012959		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035611	MIMAT0012966	eca-miR-92b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012966		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035612	MIMAT0012986	eca-miR-23a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012986		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035613	MIMAT0012987	eca-miR-24	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0012987		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035614	MIMAT0013005	eca-miR-30b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013005		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035615	MIMAT0013021	eca-miR-132	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013021		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035616	MIMAT0013027	eca-miR-195	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013027		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035617	MIMAT0013029	eca-miR-21	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013029		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035618	MIMAT0013031	eca-miR-22	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013031		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035619	MIMAT0013049	eca-miR-192	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013049		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035620	MIMAT0013057	eca-miR-25	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013057		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035621	MIMAT0013060	eca-miR-93	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013060		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035622	MIMAT0013068	eca-miR-378	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013068		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035623	MIMAT0013078	eca-miR-135a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013078		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035624	MIMAT0013079	eca-miR-191a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013079	eca-miR-191	miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035625	MIMAT0013084	eca-miR-17	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013084		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035626	MIMAT0013087	eca-miR-19b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013087		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035627	MIMAT0013088	eca-miR-20a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013088		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035628	MIMAT0013089	eca-miR-92a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013089		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035629	MIMAT0013109	eca-miR-499-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013109		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035630	MIMAT0013113	eca-miR-23b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013113		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035631	MIMAT0013131	eca-miR-323-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013131		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035632	MIMAT0013158	eca-miR-433	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013158		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035633	MIMAT0013160	eca-miR-485-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013160		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035634	MIMAT0013178	eca-miR-181a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013178		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035635	MIMAT0013186	eca-miR-486-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013186		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035636	MIMAT0013190	eca-miR-215	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013190		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035637	MIMAT0013202	eca-miR-20b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013202		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035638	MIMAT0013205	eca-miR-223	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013205		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035639	MIMAT0013210	eca-miR-362-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013210		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035640	MIMAT0013216	eca-miR-421	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013216		miRNA	Equus caballus	22116803	Exosome	Follicular cell	qRT-PCR	TABLE 2: MicroRNAs enriched in microvesicle and exosome preparations obtained from follicular fluid. Data are collected from Table 2.
RLID00035641	MIMAT0013771	hsa-miR-449c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013771	hsa-miR-449c*	miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00035642	MIMAT0013802	hsa-miR-2861	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013802		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00035643	MIMAT0013864	ssc-miR-206	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013864		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035644	MIMAT0013865	ssc-let-7a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013865		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035645	MIMAT0013866	ssc-let-7e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013866		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035646	MIMAT0013867	ssc-let-7g	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013867		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035647	MIMAT0013868	ssc-miR-378	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013868		miRNA	Sus scrofa	25158130	Extracellular vesicle	Mesenchymal stem cell	Next-generation sequencing	"RNA-seq generated reads for at least 386 annotated miRNAs, but only miR148a, miR532-5p, miR378, and let-7f were enriched in EVs compared to MSCs. "
RLID00035648	MIMAT0013868	ssc-miR-378	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013868		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035649	MIMAT0013870	ssc-miR-29a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013870		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035650	MIMAT0013871	ssc-miR-30d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013871		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035651	MIMAT0013872	ssc-miR-30e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013872		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035652	MIMAT0013873	ssc-miR-30e-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013873		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035653	MIMAT0013874	ssc-miR-199a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013874		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035654	MIMAT0013875	ssc-miR-199a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013875		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035655	MIMAT0013876	ssc-miR-191	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013876		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035656	MIMAT0013877	ssc-miR-499-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013877	ssc-miR-499	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035657	MIMAT0013878	ssc-miR-320	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013878		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035658	MIMAT0013879	ssc-miR-143-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013879	ssc-miR-143	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035659	MIMAT0013880	ssc-miR-423-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013880		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035660	MIMAT0013881	ssc-miR-423-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013881		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035661	MIMAT0013882	ssc-miR-151-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013882		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035662	MIMAT0013883	ssc-miR-151-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013883		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035663	MIMAT0013884	ssc-miR-10a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013884	ssc-miR-10a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035664	MIMAT0013885	ssc-miR-10b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013885		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035665	MIMAT0013886	ssc-miR-486	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013886		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035666	MIMAT0013887	ssc-miR-152	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013887		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035667	MIMAT0013888	ssc-miR-181d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013888	ssc-miR-181d	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035668	MIMAT0013889	ssc-miR-27b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013889	ssc-miR-27b*	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035669	MIMAT0013890	ssc-miR-27b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013890	ssc-miR-27b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035670	MIMAT0013891	ssc-miR-340	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013891		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035671	MIMAT0013893	ssc-miR-23b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013893		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035672	MIMAT0013894	ssc-miR-193a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013894		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035673	MIMAT0013895	ssc-miR-193a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013895		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035674	MIMAT0013896	ssc-miR-99a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013896		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035675	MIMAT0013897	ssc-miR-125a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013897		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035676	MIMAT0013899	ssc-miR-345-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013899		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035677	MIMAT0013900	ssc-miR-345-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013900		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035678	MIMAT0013901	ssc-miR-148b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013901	ssc-miR-148b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035679	MIMAT0013902	ssc-miR-885-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013902		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035680	MIMAT0013903	ssc-miR-885-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013903		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035681	MIMAT0013904	ssc-miR-365-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013904	ssc-miR-365	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035682	MIMAT0013905	ssc-miR-98	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013905		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035683	MIMAT0013906	ssc-miR-664-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013906		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035684	MIMAT0013907	ssc-miR-664-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013907		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035685	MIMAT0013908	ssc-miR-92a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013908		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035686	MIMAT0013909	ssc-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013909	ssc-miR-92b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035687	MIMAT0013910	ssc-miR-192	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013910		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035688	MIMAT0013911	ssc-miR-100	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013911		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035689	MIMAT0013913	ssc-miR-374a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013913	ssc-miR-374a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035690	MIMAT0013914	ssc-miR-374a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013914	ssc-miR-374a*	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035691	MIMAT0013915	ssc-miR-374b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013915	ssc-miR-374b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035692	MIMAT0013916	ssc-miR-34c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013916		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035693	MIMAT0013917	ssc-miR-425-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013917		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035694	MIMAT0013918	ssc-miR-425-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013918		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035695	MIMAT0013919	ssc-miR-142-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013919	ssc-miR-142	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035696	MIMAT0013922	ssc-miR-130b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013922		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035697	MIMAT0013926	ssc-miR-497	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013926		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035698	MIMAT0013929	ssc-miR-331-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013929		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035699	MIMAT0013930	ssc-miR-331-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013930		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035700	MIMAT0013931	ssc-miR-504	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013931		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035701	MIMAT0013932	ssc-miR-127	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013932		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035702	MIMAT0013933	ssc-miR-361-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013933		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035703	MIMAT0013934	ssc-miR-361-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013934		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035704	MIMAT0013936	ssc-miR-1307	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013936		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035705	MIMAT0013937	ssc-miR-1306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013937		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035706	MIMAT0013938	ssc-miR-1306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013938		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035707	MIMAT0013939	ssc-miR-339-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013939	ssc-miR-339	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035708	MIMAT0013940	ssc-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013940		miRNA	Sus scrofa	25158130	Extracellular vesicle	Mesenchymal stem cell	Next-generation sequencing	"RNA-seq generated reads for at least 386 annotated miRNAs, but only miR148a, miR532-5p, miR378, and let-7f were enriched in EVs compared to MSCs. "
RLID00035709	MIMAT0013940	ssc-miR-532-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013940		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035710	MIMAT0013941	ssc-miR-532-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013941		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035711	MIMAT0013942	ssc-miR-222	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013942		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035712	MIMAT0013943	ssc-miR-676-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013943	ssc-miR-676	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035713	MIMAT0013944	ssc-miR-342	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013944		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035714	MIMAT0013947	ssc-miR-935	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013947		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035715	MIMAT0013949	ssc-miR-328	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013949		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035716	MIMAT0013950	ssc-miR-19b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013950		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035717	MIMAT0013951	ssc-miR-574	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013951		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035718	MIMAT0013952	ssc-miR-1839-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013952	ssc-miR-1839	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035719	MIMAT0013954	ssc-miR-1285	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013954		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035720	MIMAT0013956	ssc-miR-500	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013956		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035721	MIMAT0013957	ssc-miR-324	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013957		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035722	MIMAT0013958	ssc-miR-769-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013958	ssc-miR-769	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035723	MIMAT0013959	ssc-miR-129a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013959	ssc-miR-129a	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035724	MIMAT0013960	ssc-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013960	ssc-miR-455	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035725	MIMAT0013961	ssc-miR-505	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0013961		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00035726	MIMAT0014207	aae-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014207		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035727	MIMAT0014207	aae-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014207		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035728	MIMAT0014207	aae-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014207		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035729	MIMAT0014207	aae-miR-184	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014207		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035730	MIMAT0014208	aae-miR-275-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014208	aae-miR-275*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035731	MIMAT0014208	aae-miR-275-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014208	aae-miR-275*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035732	MIMAT0014208	aae-miR-275-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014208	aae-miR-275*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035733	MIMAT0014208	aae-miR-275-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014208	aae-miR-275*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035734	MIMAT0014209	aae-miR-275-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014209	aae-miR-275	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035735	MIMAT0014209	aae-miR-275-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014209	aae-miR-275	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035736	MIMAT0014209	aae-miR-275-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014209	aae-miR-275	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035737	MIMAT0014209	aae-miR-275-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014209	aae-miR-275	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035738	MIMAT0014211	aae-miR-277-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014211	aae-miR-277	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035739	MIMAT0014211	aae-miR-277-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014211	aae-miR-277	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035740	MIMAT0014211	aae-miR-277-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014211	aae-miR-277	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035741	MIMAT0014211	aae-miR-277-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014211	aae-miR-277	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035742	MIMAT0014212	aae-miR-9c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014212	aae-miR-9	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035743	MIMAT0014212	aae-miR-9c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014212	aae-miR-9	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035744	MIMAT0014212	aae-miR-9c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014212	aae-miR-9	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035745	MIMAT0014212	aae-miR-9c-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014212	aae-miR-9	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035746	MIMAT0014213	aae-miR-9c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014213	aae-miR-9*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035747	MIMAT0014213	aae-miR-9c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014213	aae-miR-9*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035748	MIMAT0014213	aae-miR-9c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014213	aae-miR-9*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035749	MIMAT0014213	aae-miR-9c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014213	aae-miR-9*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035750	MIMAT0014214	aae-miR-8-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014214	aae-miR-8*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035751	MIMAT0014214	aae-miR-8-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014214	aae-miR-8*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035752	MIMAT0014214	aae-miR-8-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014214	aae-miR-8*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035753	MIMAT0014214	aae-miR-8-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014214	aae-miR-8*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035754	MIMAT0014215	aae-miR-8-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014215	aae-miR-8	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035755	MIMAT0014215	aae-miR-8-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014215	aae-miR-8	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035756	MIMAT0014215	aae-miR-8-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014215	aae-miR-8	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035757	MIMAT0014215	aae-miR-8-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014215	aae-miR-8	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035758	MIMAT0014216	aae-miR-252-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014216	aae-miR-252	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035759	MIMAT0014216	aae-miR-252-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014216	aae-miR-252	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035760	MIMAT0014216	aae-miR-252-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014216	aae-miR-252	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035761	MIMAT0014218	aae-bantam-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014218		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035762	MIMAT0014218	aae-bantam-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014218		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035763	MIMAT0014218	aae-bantam-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014218		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035764	MIMAT0014218	aae-bantam-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014218		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035765	MIMAT0014219	aae-bantam-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014219		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035766	MIMAT0014219	aae-bantam-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014219		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035767	MIMAT0014219	aae-bantam-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014219		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035768	MIMAT0014219	aae-bantam-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014219		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035769	MIMAT0014220	aae-miR-71-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014220	aae-miR-71	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035770	MIMAT0014220	aae-miR-71-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014220	aae-miR-71	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035771	MIMAT0014220	aae-miR-71-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014220	aae-miR-71	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035772	MIMAT0014220	aae-miR-71-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014220	aae-miR-71	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035773	MIMAT0014221	aae-miR-71-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014221	aae-miR-71*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035774	MIMAT0014221	aae-miR-71-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014221	aae-miR-71*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035775	MIMAT0014221	aae-miR-71-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014221	aae-miR-71*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035776	MIMAT0014221	aae-miR-71-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014221	aae-miR-71*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035777	MIMAT0014223	aae-miR-276-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014223	aae-miR-276	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035778	MIMAT0014223	aae-miR-276-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014223	aae-miR-276	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035779	MIMAT0014223	aae-miR-276-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014223	aae-miR-276	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035780	MIMAT0014223	aae-miR-276-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014223	aae-miR-276	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035781	MIMAT0014224	aae-miR-317	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014224		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035782	MIMAT0014224	aae-miR-317	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014224		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035783	MIMAT0014224	aae-miR-317	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014224		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035784	MIMAT0014224	aae-miR-317	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014224		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035785	MIMAT0014226	aae-miR-2a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014226	aae-miR-2a	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035786	MIMAT0014226	aae-miR-2a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014226	aae-miR-2a	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035787	MIMAT0014226	aae-miR-2a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014226	aae-miR-2a	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035788	MIMAT0014226	aae-miR-2a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014226	aae-miR-2a	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035789	MIMAT0014227	aae-miR-998	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014227		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035790	MIMAT0014227	aae-miR-998	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014227		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035791	MIMAT0014227	aae-miR-998	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014227		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035792	MIMAT0014227	aae-miR-998	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014227		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035793	MIMAT0014228	aae-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014228	aae-miR-92a	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035794	MIMAT0014228	aae-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014228	aae-miR-92a	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035795	MIMAT0014228	aae-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014228	aae-miR-92a	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035796	MIMAT0014228	aae-miR-92a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014228	aae-miR-92a	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035797	MIMAT0014229	aae-miR-306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014229	aae-miR-306	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035798	MIMAT0014229	aae-miR-306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014229	aae-miR-306	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035799	MIMAT0014229	aae-miR-306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014229	aae-miR-306	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035800	MIMAT0014229	aae-miR-306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014229	aae-miR-306	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035801	MIMAT0014230	aae-miR-306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014230	aae-miR-306*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035802	MIMAT0014230	aae-miR-306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014230	aae-miR-306*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035803	MIMAT0014230	aae-miR-306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014230	aae-miR-306*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035804	MIMAT0014230	aae-miR-306-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014230	aae-miR-306*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035805	MIMAT0014231	aae-miR-281-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014231	aae-miR-281	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035806	MIMAT0014231	aae-miR-281-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014231	aae-miR-281	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035807	MIMAT0014231	aae-miR-281-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014231	aae-miR-281	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035808	MIMAT0014231	aae-miR-281-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014231	aae-miR-281	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035809	MIMAT0014232	aae-miR-281-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014232	aae-miR-281*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035810	MIMAT0014232	aae-miR-281-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014232	aae-miR-281*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035811	MIMAT0014232	aae-miR-281-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014232	aae-miR-281*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035812	MIMAT0014232	aae-miR-281-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014232	aae-miR-281*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035813	MIMAT0014233	aae-miR-1889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014233	aae-miR-1889*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035814	MIMAT0014233	aae-miR-1889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014233	aae-miR-1889*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035815	MIMAT0014233	aae-miR-1889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014233	aae-miR-1889*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035816	MIMAT0014233	aae-miR-1889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014233	aae-miR-1889*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035817	MIMAT0014234	aae-miR-1889-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014234	aae-miR-1889	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035818	MIMAT0014234	aae-miR-1889-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014234	aae-miR-1889	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035819	MIMAT0014234	aae-miR-1889-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014234	aae-miR-1889	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035820	MIMAT0014237	aae-miR-278-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014237	aae-miR-278	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035821	MIMAT0014237	aae-miR-278-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014237	aae-miR-278	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035822	MIMAT0014237	aae-miR-278-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014237	aae-miR-278	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035823	MIMAT0014237	aae-miR-278-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014237	aae-miR-278	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035824	MIMAT0014238	aae-miR-278-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014238	aae-miR-278*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035825	MIMAT0014238	aae-miR-278-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014238	aae-miR-278*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035826	MIMAT0014238	aae-miR-278-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014238	aae-miR-278*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035827	MIMAT0014238	aae-miR-278-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014238	aae-miR-278*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035828	MIMAT0014239	aae-miR-989	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014239		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035829	MIMAT0014239	aae-miR-989	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014239		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035830	MIMAT0014239	aae-miR-989	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014239		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035831	MIMAT0014239	aae-miR-989	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014239		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035832	MIMAT0014240	aae-miR-14	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014240		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035833	MIMAT0014240	aae-miR-14	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014240		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035834	MIMAT0014240	aae-miR-14	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014240		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035835	MIMAT0014240	aae-miR-14	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014240		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035836	MIMAT0014241	aae-miR-11-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014241	aae-miR-11*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035837	MIMAT0014241	aae-miR-11-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014241	aae-miR-11*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035838	MIMAT0014241	aae-miR-11-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014241	aae-miR-11*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035839	MIMAT0014242	aae-miR-11-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014242	aae-miR-11	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035840	MIMAT0014242	aae-miR-11-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014242	aae-miR-11	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035841	MIMAT0014242	aae-miR-11-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014242	aae-miR-11	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035842	MIMAT0014242	aae-miR-11-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014242	aae-miR-11	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035843	MIMAT0014243	aae-miR-190	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014243		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035844	MIMAT0014243	aae-miR-190	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014243		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035845	MIMAT0014243	aae-miR-190	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014243		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035846	MIMAT0014243	aae-miR-190	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014243		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035847	MIMAT0014244	aae-miR-1	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014244		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035848	MIMAT0014244	aae-miR-1	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014244		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035849	MIMAT0014245	aae-miR-34-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014245	aae-miR-34	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035850	MIMAT0014245	aae-miR-34-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014245	aae-miR-34	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035851	MIMAT0014245	aae-miR-34-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014245	aae-miR-34	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035852	MIMAT0014245	aae-miR-34-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014245	aae-miR-34	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035853	MIMAT0014246	aae-miR-34-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014246	aae-miR-34*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035854	MIMAT0014246	aae-miR-34-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014246	aae-miR-34*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035855	MIMAT0014246	aae-miR-34-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014246	aae-miR-34*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035856	MIMAT0014247	aae-miR-1890	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014247		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035857	MIMAT0014247	aae-miR-1890	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014247		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035858	MIMAT0014247	aae-miR-1890	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014247		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035859	MIMAT0014249	aae-miR-305-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014249	aae-miR-305	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035860	MIMAT0014249	aae-miR-305-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014249	aae-miR-305	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035861	MIMAT0014249	aae-miR-305-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014249	aae-miR-305	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035862	MIMAT0014249	aae-miR-305-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014249	aae-miR-305	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035863	MIMAT0014250	aae-miR-305-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014250	aae-miR-305*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035864	MIMAT0014250	aae-miR-305-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014250	aae-miR-305*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035865	MIMAT0014250	aae-miR-305-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014250	aae-miR-305*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035866	MIMAT0014250	aae-miR-305-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014250	aae-miR-305*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035867	MIMAT0014251	aae-miR-996	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014251		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035868	MIMAT0014251	aae-miR-996	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014251		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035869	MIMAT0014251	aae-miR-996	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014251		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035870	MIMAT0014251	aae-miR-996	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014251		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035871	MIMAT0014252	aae-miR-87	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014252		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035872	MIMAT0014252	aae-miR-87	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014252		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035873	MIMAT0014252	aae-miR-87	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014252		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035874	MIMAT0014252	aae-miR-87	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014252		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035875	MIMAT0014253	aae-miR-12-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014253	aae-miR-12	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035876	MIMAT0014253	aae-miR-12-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014253	aae-miR-12	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035877	MIMAT0014253	aae-miR-12-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014253	aae-miR-12	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035878	MIMAT0014253	aae-miR-12-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014253	aae-miR-12	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035879	MIMAT0014254	aae-miR-12-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014254	aae-miR-12*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035880	MIMAT0014254	aae-miR-12-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014254	aae-miR-12*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035881	MIMAT0014255	aae-miR-13-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014255	aae-miR-13*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035882	MIMAT0014255	aae-miR-13-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014255	aae-miR-13*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035883	MIMAT0014255	aae-miR-13-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014255	aae-miR-13*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035884	MIMAT0014255	aae-miR-13-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014255	aae-miR-13*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035885	MIMAT0014256	aae-miR-13-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014256	aae-miR-13	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035886	MIMAT0014256	aae-miR-13-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014256	aae-miR-13	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035887	MIMAT0014256	aae-miR-13-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014256	aae-miR-13	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035888	MIMAT0014256	aae-miR-13-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014256	aae-miR-13	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035889	MIMAT0014258	aae-miR-125-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014258	aae-miR-125	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035890	MIMAT0014258	aae-miR-125-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014258	aae-miR-125	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035891	MIMAT0014258	aae-miR-125-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014258	aae-miR-125	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035892	MIMAT0014260	aae-miR-308-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014260	aae-miR-308	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035893	MIMAT0014260	aae-miR-308-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014260	aae-miR-308	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035894	MIMAT0014264	aae-miR-1175-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014264	aae-miR-1175	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035895	MIMAT0014264	aae-miR-1175-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014264	aae-miR-1175	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035896	MIMAT0014265	aae-miR-1174	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014265		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035897	MIMAT0014265	aae-miR-1174	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014265		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035898	MIMAT0014268	aae-miR-965	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014268		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035899	MIMAT0014269	aae-miR-932-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014269	aae-miR-932*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035900	MIMAT0014270	aae-miR-932-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014270	aae-miR-932	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035901	MIMAT0014273	aae-miR-285	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014273		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035902	MIMAT0014273	aae-miR-285	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014273		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035903	MIMAT0014274	aae-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014274		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035904	MIMAT0014274	aae-miR-137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014274		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035905	MIMAT0014277	aae-miR-10	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014277		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035906	MIMAT0014277	aae-miR-10	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014277		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035907	MIMAT0014277	aae-miR-10	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014277		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035908	MIMAT0014279	aae-miR-283	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014279		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035909	MIMAT0014279	aae-miR-283	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014279		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035910	MIMAT0014279	aae-miR-283	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014279		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035911	MIMAT0014279	aae-miR-283	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014279		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035912	MIMAT0014280	aae-miR-988-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014280	aae-miR-988*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035913	MIMAT0014281	aae-miR-988-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014281	aae-miR-988	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035914	MIMAT0014281	aae-miR-988-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014281	aae-miR-988	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035915	MIMAT0014281	aae-miR-988-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014281	aae-miR-988	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035916	MIMAT0014281	aae-miR-988-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014281	aae-miR-988	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035917	MIMAT0014282	aae-miR-124	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014282		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035918	MIMAT0014282	aae-miR-124	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014282		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035919	MIMAT0014283	aae-miR-2940-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014283	aae-miR-2940	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035920	MIMAT0014283	aae-miR-2940-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014283	aae-miR-2940	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035921	MIMAT0014283	aae-miR-2940-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014283	aae-miR-2940	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035922	MIMAT0014283	aae-miR-2940-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014283	aae-miR-2940	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035923	MIMAT0014284	aae-miR-2940-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014284	aae-miR-2940*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035924	MIMAT0014284	aae-miR-2940-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014284	aae-miR-2940*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035925	MIMAT0014284	aae-miR-2940-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014284	aae-miR-2940*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035926	MIMAT0014284	aae-miR-2940-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014284	aae-miR-2940*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035927	MIMAT0014285	aae-miR-2765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014285		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035928	MIMAT0014285	aae-miR-2765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014285		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035929	MIMAT0014285	aae-miR-2765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014285		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035930	MIMAT0014285	aae-miR-2765	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014285		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035931	MIMAT0014286	aae-miR-2941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014286		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035932	MIMAT0014286	aae-miR-2941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014286		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035933	MIMAT0014286	aae-miR-2941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014286		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035934	MIMAT0014286	aae-miR-2941	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014286		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035935	MIMAT0014287	aae-miR-33	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014287		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035936	MIMAT0014288	aae-miR-279	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014288		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035937	MIMAT0014288	aae-miR-279	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014288		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035938	MIMAT0014288	aae-miR-279	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014288		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035939	MIMAT0014288	aae-miR-279	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014288		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035940	MIMAT0014289	aae-miR-263a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014289	aae-miR-263a	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035941	MIMAT0014289	aae-miR-263a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014289	aae-miR-263a	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035942	MIMAT0014289	aae-miR-263a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014289	aae-miR-263a	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035943	MIMAT0014289	aae-miR-263a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014289	aae-miR-263a	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035944	MIMAT0014290	aae-miR-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014290		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035945	MIMAT0014290	aae-miR-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014290		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035946	MIMAT0014290	aae-miR-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014290		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035947	MIMAT0014290	aae-miR-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014290		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035948	MIMAT0014291	aae-miR-100	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014291		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035949	MIMAT0014291	aae-miR-100	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014291		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035950	MIMAT0014291	aae-miR-100	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014291		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035951	MIMAT0014291	aae-miR-100	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014291		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035952	MIMAT0014292	aae-miR-970	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014292		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035953	MIMAT0014292	aae-miR-970	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014292		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035954	MIMAT0014292	aae-miR-970	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014292		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035955	MIMAT0014292	aae-miR-970	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014292		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035956	MIMAT0014293	aae-miR-210	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014293		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035957	MIMAT0014295	aae-miR-79-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014295	aae-miR-79*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035958	MIMAT0014297	aae-miR-1000	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014297		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035959	MIMAT0014297	aae-miR-1000	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014297		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035960	MIMAT0014299	aae-let-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014299		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035961	MIMAT0014299	aae-let-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014299		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035962	MIMAT0014299	aae-let-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014299		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035963	MIMAT0014299	aae-let-7	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014299		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035964	MIMAT0014306	aae-miR-2b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014306		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035965	MIMAT0014306	aae-miR-2b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014306		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035966	MIMAT0014306	aae-miR-2b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014306		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035967	MIMAT0014306	aae-miR-2b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014306		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035968	MIMAT0014307	aae-miR-219	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014307		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035969	MIMAT0014311	aae-miR-282-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014311	aae-miR-282	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035970	MIMAT0014311	aae-miR-282-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014311	aae-miR-282	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035971	MIMAT0014311	aae-miR-282-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014311	aae-miR-282	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035972	MIMAT0014313	aae-miR-286b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014313		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035973	MIMAT0014316	aae-miR-2945-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014316	aae-miR-2945	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035974	MIMAT0014316	aae-miR-2945-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014316	aae-miR-2945	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035975	MIMAT0014316	aae-miR-2945-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014316	aae-miR-2945	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035976	MIMAT0014316	aae-miR-2945-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014316	aae-miR-2945	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035977	MIMAT0014322	aae-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014322	aae-miR-92b	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035978	MIMAT0014322	aae-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014322	aae-miR-92b	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035979	MIMAT0014322	aae-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014322	aae-miR-92b	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035980	MIMAT0014322	aae-miR-92b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014322	aae-miR-92b	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035981	MIMAT0014323	aae-miR-9a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014323		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035982	MIMAT0014323	aae-miR-9a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014323		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035983	MIMAT0014324	aae-miR-9b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014324		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035984	MIMAT0014324	aae-miR-9b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014324		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035985	MIMAT0014324	aae-miR-9b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014324		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035986	MIMAT0014324	aae-miR-9b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014324		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035987	MIMAT0014325	aae-miR-2946	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014325		miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035988	MIMAT0014325	aae-miR-2946	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014325		miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035989	MIMAT0014325	aae-miR-2946	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014325		miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035990	MIMAT0014325	aae-miR-2946	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014325		miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00035991	MIMAT0014351	hsv2-miR-H7-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014351		miRNA	Human herpesvirus 2	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035992	MIMAT0014353	hsv2-miR-H10	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014353		miRNA	Human herpesvirus 2	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035993	MIMAT0014708	hsv2-miR-H25	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014708		miRNA	Human herpesvirus 2	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00035994	MIMAT0014901	mmu-miR-3090-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014901	mmu-miR-3090*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035995	MIMAT0014926	mmu-miR-344b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014926	mmu-miR-344b	miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00035996	MIMAT0014933	mmu-miR-3102-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014933	mmu-miR-3102*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00035997	MIMAT0014982	hsa-miR-3120-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014982	hsa-miR-3120	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00035998	MIMAT0014982	hsa-miR-3120-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014982	hsa-miR-3120	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00035999	MIMAT0014988	hsa-miR-3125	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014988		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036000	MIMAT0014989	hsa-miR-3126-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014989		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036001	MIMAT0014990	hsa-miR-3127-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014990	hsa-miR-3127	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036002	MIMAT0014995	hsa-miR-3130-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014995		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036003	MIMAT0014999	hsa-miR-378b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014999		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036004	MIMAT0014999	hsa-miR-378b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0014999		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036005	MIMAT0015005	hsa-miR-3137	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015005		miRNA	Homo sapiens	24352417	Circulating	Blood platelet	Next-generation sequencing	"Platelets in both groups demonstrated miRNA expression profiles comparable to previously published data. The statistical analysis unveiled a signature of only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques. "
RLID00036006	MIMAT0015006	hsa-miR-3138	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015006		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036007	MIMAT0015009	hsa-miR-548t-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015009	hsa-miR-548t	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036008	MIMAT0015010	hsa-miR-3141	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015010		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036009	MIMAT0015012	hsa-miR-3143	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015012		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036010	MIMAT0015027	hsa-miR-3074-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015027	hsa-miR-3074	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036011	MIMAT0015027	hsa-miR-3074-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015027	hsa-miR-3074	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036012	MIMAT0015028	hsa-miR-3154	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015028		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036013	MIMAT0015032	hsa-miR-3158-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015032	hsa-miR-3158	miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036014	MIMAT0015032	hsa-miR-3158-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015032	hsa-miR-3158	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036015	MIMAT0015032	hsa-miR-3158-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015032	hsa-miR-3158	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036016	MIMAT0015032	hsa-miR-3158-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015032	hsa-miR-3158	miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00036017	MIMAT0015034	hsa-miR-3160-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015034	hsa-miR-3160	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036018	MIMAT0015036	hsa-miR-3162-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015036	hsa-miR-3162	miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00036019	MIMAT0015036	hsa-miR-3162-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015036	hsa-miR-3162	miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036020	MIMAT0015041	hsa-miR-1260b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015041		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036021	MIMAT0015041	hsa-miR-1260b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015041		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036022	MIMAT0015041	hsa-miR-1260b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015041		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00036023	MIMAT0015041	hsa-miR-1260b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015041		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036024	MIMAT0015041	hsa-miR-1260b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015041		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036025	MIMAT0015043	hsa-miR-3168	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015043		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036026	MIMAT0015043	hsa-miR-3168	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015043		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036027	MIMAT0015044	hsa-miR-3169	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015044		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036028	MIMAT0015046	hsa-miR-3171	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015046		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036029	MIMAT0015050	hsa-miR-323b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015050		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036030	MIMAT0015050	hsa-miR-323b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015050		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036031	MIMAT0015051	hsa-miR-3174	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015051		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036032	MIMAT0015052	hsa-miR-3175	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015052		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036033	MIMAT0015053	hsa-miR-3176	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015053		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036034	MIMAT0015053	hsa-miR-3176	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015053		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036035	MIMAT0015054	hsa-miR-3177-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015054	hsa-miR-3177	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036036	MIMAT0015054	hsa-miR-3177-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015054	hsa-miR-3177	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036037	MIMAT0015055	hsa-miR-3178	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015055		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036038	MIMAT0015058	hsa-miR-3180-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015058		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036039	MIMAT0015061	hsa-miR-3181	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015061		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036040	MIMAT0015064	hsa-miR-3184-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015064	hsa-miR-3184	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036041	MIMAT0015064	hsa-miR-3184-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015064	hsa-miR-3184	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036042	MIMAT0015064	hsa-miR-3184-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015064	hsa-miR-3184	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036043	MIMAT0015065	hsa-miR-3185	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015065		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036044	MIMAT0015065	hsa-miR-3185	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015065		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036045	MIMAT0015066	hsa-miR-3065-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015066		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036046	MIMAT0015066	hsa-miR-3065-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015066		miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00036047	MIMAT0015066	hsa-miR-3065-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015066		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036048	MIMAT0015066	hsa-miR-3065-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015066		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036049	MIMAT0015066	hsa-miR-3065-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015066		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036050	MIMAT0015070	hsa-miR-3188	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015070		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036051	MIMAT0015070	hsa-miR-3188	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015070		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036052	MIMAT0015071	hsa-miR-3189-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015071	hsa-miR-3189	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036053	MIMAT0015072	hsa-miR-320e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015072		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036054	MIMAT0015072	hsa-miR-320e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015072		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036055	MIMAT0015072	hsa-miR-320e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015072		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036056	MIMAT0015073	hsa-miR-3190-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015073	"hsa-miR-3190-5p, hsa-miR-3190 "	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036057	MIMAT0015073	hsa-miR-3190-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015073	"hsa-miR-3190-5p, hsa-miR-3190 "	miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036058	MIMAT0015076	hsa-miR-3192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015076		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036059	MIMAT0015076	hsa-miR-3192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015076		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036060	MIMAT0015076	hsa-miR-3192-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015076		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036061	MIMAT0015078	hsa-miR-3194-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015078	hsa-miR-3194	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036062	MIMAT0015079	hsa-miR-3195	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015079		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036063	MIMAT0015080	hsa-miR-3196	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015080		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036064	MIMAT0015082	hsa-miR-3197	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015082		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036065	MIMAT0015082	hsa-miR-3197	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015082		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036066	MIMAT0015083	hsa-miR-3198	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015083		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036067	MIMAT0015085	hsa-miR-3200-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015085	hsa-miR-3200	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036068	MIMAT0015085	hsa-miR-3200-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015085	hsa-miR-3200	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036069	MIMAT0015085	hsa-miR-3200-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015085	hsa-miR-3200	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036070	MIMAT0015085	hsa-miR-3200-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015085	hsa-miR-3200	miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00036071	MIMAT0015086	hsa-miR-3201	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015086		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036072	MIMAT0015089	hsa-miR-3202	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015089		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036073	MIMAT0015090	hsa-miR-1273d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015090		miRNA	Homo sapiens	22427800	Exosome	Saliva	RT-PCR	The miRNAs tested in serum and saliva samples are shown in Table 1. These miRNAs were selected because they are either ubiquitously expressed or have been reported as biomarkers (Table 1). The relative concentration of these microRNAs was determined by calculating the difference of Ct values between the exosome samples and the exosome-depleted supernatant. A 1-unit difference in the Ct value between the miRNAs isolated from the exosomal pellet or supernatant represents a 2-fold difference in the amount of input miRNA. Data are collected from Table 1: List of miRNAs tested in serum and saliva samples.
RLID00036074	MIMAT0015090	hsa-miR-1273d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015090		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036075	MIMAT0015210	ssc-miR-24-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015210	ssc-miR-24*	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036076	MIMAT0015211	ssc-miR-28-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015211		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036077	MIMAT0015268	ssc-miR-17-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015268		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036078	MIMAT0015269	ssc-miR-30b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015269		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036079	MIMAT0015300	ssc-miR-30a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015300		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036080	MIMAT0015369	aae-miR-92a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015369	aae-miR-92a*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036081	MIMAT0015369	aae-miR-92a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015369	aae-miR-92a*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036082	MIMAT0015369	aae-miR-92a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015369	aae-miR-92a*	miRNA	Aedes aegypti	24759922	Nucleus	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036083	MIMAT0015371	aae-miR-1175-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015371	aae-miR-1175*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036084	MIMAT0015371	aae-miR-1175-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015371	aae-miR-1175*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036085	MIMAT0015372	aae-miR-263a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015372	aae-miR-263a*	miRNA	Aedes aegypti	24759922	Cytoplasm	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036086	MIMAT0015372	aae-miR-263a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015372	aae-miR-263a*	miRNA	Aedes aegypti	24759922	Nucleus	Aag2 cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036087	MIMAT0015372	aae-miR-263a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015372	aae-miR-263a*	miRNA	Aedes aegypti	24759922	Cytoplasm	Wolbachia-infected cell	Next-generation sequencing	"Globally, 71 different miRNAs in Aag2 cells were identified; 62 were detected in the nucleus and 66 in the cytoplasm (Table S1).  Data are collected from Table S1. "
RLID00036088	MIMAT0015375	hsv2-miR-H7-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015375		miRNA	Human herpesvirus 2	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036089	MIMAT0015378	hsa-miR-3065-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015378		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036090	MIMAT0015708	ssc-miR-744	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015708		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036091	MIMAT0015709	ssc-miR-22-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015709		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036092	MIMAT0015710	ssc-miR-22-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015710		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036093	MIMAT0015711	ssc-miR-363	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015711		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036094	MIMAT0015712	ssc-miR-299	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015712		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036095	MIMAT0015713	ssc-miR-338	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0015713		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036096	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036097	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036098	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036099	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036100	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036101	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036102	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036103	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036104	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036105	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036106	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036107	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036108	MIMAT0016847	hsa-miR-378c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016847		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036109	MIMAT0016852	hsa-miR-4298	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016852		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036110	MIMAT0016858	hsa-miR-4306	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016858		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036111	MIMAT0016880	hsa-miR-4259	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016880		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036112	MIMAT0016882	hsa-miR-4253	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016882		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036113	MIMAT0016888	hsa-miR-4326	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016888		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036114	MIMAT0016895	hsa-miR-2355-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016895	hsa-miR-2355	miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036115	MIMAT0016896	hsa-miR-4268	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016896		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036116	MIMAT0016896	hsa-miR-4268	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016896		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036117	MIMAT0016900	hsa-miR-4270	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016900		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036118	MIMAT0016905	hsa-miR-4275	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016905		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036119	MIMAT0016907	hsa-miR-4281	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016907		miRNA	Homo sapiens	23539611	Microvesicle	Seminal Plasma	Microarray	"MiRNAs shuttled by SMVs in seminal plasma are potent non-invasive biomarkers to evaluate defects originating from the different organs of the male reproductive tract, including the epididymis (Wang et al., 2011). In order to assess the reversibility of post-vasectomy miRNA sequelae, we investigated whether SMV miRNAs altered by vasectomy could be retrieved in SMVs from normospermic vasovasostomized donors. miRNA microarray profiling performed on SMVs from normal, vasectomized and vasovasostomized donors identified 313 miRNAs whose intensity was above the threshold of detection. Among these miRNAs, 293 were detected in samples from normal donors, 275 in vasectomized donors and 298 in vasovasostomized donors (Fig. 3, Supplementary data, Table SIV). Data are collected from Table S4. "
RLID00036120	MIMAT0016909	hsa-miR-4279	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016909		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036121	MIMAT0016909	hsa-miR-4279	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016909		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00036122	MIMAT0016913	hsa-miR-4285	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016913		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036123	MIMAT0016916	hsa-miR-4286	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016916		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036124	MIMAT0016916	hsa-miR-4286	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016916		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036125	MIMAT0016916	hsa-miR-4286	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016916		miRNA	Homo sapiens	22849433	Extracellular vesicle	HEK293T|HMEC-1|Mononuclear cell	Next-generation sequencing	"The total numbers of reads >15 bp matching each miRNA were calculated. These values were then normalized to number of reads per million mapped (RPMM) in each library, to enable direct comparison of expression levels. As a measure of the relative levels of expression of individual miRNAs in cells and EVs, the log (base two) of the ratio of the read number in EVs over that in cells was calculated (log2 (EV/cell)). The miRNA expression data for cells and EVs is presented in Additional file 1: Table S1. Data are collected from Table S1. "
RLID00036126	MIMAT0016919	hsa-miR-4292	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016919		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036127	MIMAT0016919	hsa-miR-4292	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016919		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036128	MIMAT0016921	hsa-miR-4290	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016921		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036129	MIMAT0016925	hsa-miR-500b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016925		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036130	MIMAT0016980	mmu-miR-23b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0016980	mmu-miR-23b*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00036131	MIMAT0017006	mmu-miR-143-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017006	mmu-miR-143*	miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00036132	MIMAT0017029	rno-miR-328a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017029	rno-miR-328a*	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036133	MIMAT0017031	rno-miR-329-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017031	rno-miR-329*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036134	MIMAT0017035	rno-miR-337-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017035	rno-miR-337*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036135	MIMAT0017048	mmu-miR-107-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017048	mmu-miR-107*	miRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The results showed that exosomes carry approxi-mately 121 miRNAs that have been found in all four experiments (Fig. 4 and see Supplementary Information, Table S5). Data are collected from Table S5. "
RLID00036136	MIMAT0017076	mmu-miR-363-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017076		miRNA	Mus musculus	23385731	Exosome	Serum	qRT-PCR|Microarray	Supplementary Table S2 List of 27 miRNAs coincidently up-regulated in sera and primary GCs of DCKO mice. Data are collected from Table S2.
RLID00036137	MIMAT0017086	rno-let-7a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017086	rno-let-7a-2*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036138	MIMAT0017109	rno-miR-93-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017109	rno-miR-93*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036139	MIMAT0017117	rno-miR-127-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017117	rno-miR-127*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036140	MIMAT0017119	rno-miR-128-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017119	rno-miR-128-2*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036141	MIMAT0017126	rno-miR-137-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017126	rno-miR-137*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036142	MIMAT0017137	rno-miR-181c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017137	rno-miR-181c*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036143	MIMAT0017184	rno-miR-365-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017184	rno-miR-365*	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036144	MIMAT0017198	rno-miR-501-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017198	rno-miR-501*	miRNA	Rattus norvegicus	25800054	Dendrite	Hippocampal and cortical neuron	qRT-PCR|In situ hybridization	"miR-501-3p expression is up-regulated locally in dendrites through the NMDAR subunit GluN2A, and this regulation is required for NMDA-induced suppression of GluA1 expression and long-lasting remodeling of dendritic spines.  Our further analysis of miR-501-3p shows that it is increased locally in dendrites after NMDAR activation and that this up-regulation of miR-501-3p is required for NMDAR-dependent inhibition of GluA1 expression, long-lasting spine shrinkage, and elimination.   These NMDA-induced changes were preserved in the CA1 neuropil of the slice in which cell bodies were removed before NMDA stimulation (Fig. 4, E-G), suggesting that miR-501-3p can repress GluA1 protein expression locally in dendrites.  "
RLID00036145	MIMAT0017205	rno-miR-133b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017205	rno-miR-133b*	miRNA	Rattus norvegicus	24324399	Nucleus	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036146	MIMAT0017226	rno-miR-505-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017226	rno-miR-505*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036147	MIMAT0017245	mmu-miR-760-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017245		miRNA	Mus musculus	20733615	Mitochondrion	Liver tissue	Microarray	Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Data are collected from Supplementary information Table S1 and Table S2.
RLID00036148	MIMAT0017307	rno-miR-434-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017307		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036149	MIMAT0017308	rno-miR-455-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017308	rno-miR-455*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036150	MIMAT0017317	rno-miR-770-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017317	rno-miR-770*	miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036151	MIMAT0017339	ssc-miR-199b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017339	ssc-miR-199b	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036152	MIMAT0017374	ssc-miR-143-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017374		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036153	MIMAT0017376	ssc-miR-365-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017376		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036154	MIMAT0017377	ssc-miR-92b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017377		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036155	MIMAT0017379	ssc-miR-196b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017379		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036156	MIMAT0017381	ssc-miR-339-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017381		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036157	MIMAT0017382	ssc-miR-676-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017382		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036158	MIMAT0017385	ssc-miR-1839-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017385		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036159	MIMAT0017392	hsa-miR-3200-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017392		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036160	MIMAT0017392	hsa-miR-3200-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017392		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036161	MIMAT0017811	rno-miR-344b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017811		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036162	MIMAT0017952	ssc-miR-296-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017952	ssc-miR-296	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036163	MIMAT0017955	ssc-miR-4331	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017955		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036164	MIMAT0017956	ssc-miR-382	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017956		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036165	MIMAT0017958	ssc-miR-362	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017958		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036166	MIMAT0017962	ssc-miR-4332	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017962		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036167	MIMAT0017966	ssc-miR-4334-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017966	ssc-miR-4334	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036168	MIMAT0017967	ssc-miR-1271	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017967		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036169	MIMAT0017981	hsa-miR-3605-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017981		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036170	MIMAT0017982	hsa-miR-3605-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017982		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036171	MIMAT0017982	hsa-miR-3605-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017982		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036172	MIMAT0017985	hsa-miR-3607-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017985		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036173	MIMAT0017988	hsa-miR-3611	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017988		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036174	MIMAT0017990	hsa-miR-3613-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017990		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036175	MIMAT0017991	hsa-miR-3613-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017991		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036176	MIMAT0017991	hsa-miR-3613-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017991		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036177	MIMAT0017991	hsa-miR-3613-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017991		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036178	MIMAT0017991	hsa-miR-3613-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017991		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036179	MIMAT0017991	hsa-miR-3613-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017991		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036180	MIMAT0017992	hsa-miR-3614-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017992		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036181	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036182	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036183	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036184	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036185	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036186	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036187	MIMAT0017994	hsa-miR-3615	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017994		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036188	MIMAT0017997	hsa-miR-3617-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0017997	hsa-miR-3617	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036189	MIMAT0018000	hsa-miR-23c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018000		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036190	MIMAT0018000	hsa-miR-23c	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018000		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036191	MIMAT0018001	hsa-miR-3620-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018001	hsa-miR-3620	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036192	MIMAT0018001	hsa-miR-3620-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018001	hsa-miR-3620	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036193	MIMAT0018065	hsa-miR-3646	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018065		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036194	MIMAT0018068	hsa-miR-3648	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018068		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036195	MIMAT0018071	hsa-miR-3651	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018071		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036196	MIMAT0018072	hsa-miR-3652	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018072		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036197	MIMAT0018073	hsa-miR-3653-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018073	hsa-miR-3653	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036198	MIMAT0018074	hsa-miR-3654	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018074		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036199	MIMAT0018074	hsa-miR-3654	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018074		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036200	MIMAT0018079	hsa-miR-1273e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018079		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00036201	MIMAT0018083	hsa-miR-3662	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018083		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036202	MIMAT0018083	hsa-miR-3662	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018083		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036203	MIMAT0018085	hsa-miR-3663-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018085		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036204	MIMAT0018087	hsa-miR-3665	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018087		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00036205	MIMAT0018089	hsa-miR-3667-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018089		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036206	MIMAT0018101	hsa-miR-3677-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018101	hsa-miR-3677	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036207	MIMAT0018101	hsa-miR-3677-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018101	hsa-miR-3677	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036208	MIMAT0018104	hsa-miR-3679-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018104		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036209	MIMAT0018114	hsa-miR-3686	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018114		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036210	MIMAT0018115	hsa-miR-3687	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018115		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036211	MIMAT0018115	hsa-miR-3687	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018115		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036212	MIMAT0018119	hsa-miR-3690	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018119		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036213	MIMAT0018182	hsa-miR-3908	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018182		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036214	MIMAT0018183	hsa-miR-3909	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018183		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036215	MIMAT0018183	hsa-miR-3909	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018183		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036216	MIMAT0018186	hsa-miR-3912-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018186		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036217	MIMAT0018189	hsa-miR-3915	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018189		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036218	MIMAT0018191	hsa-miR-3917	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018191		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036219	MIMAT0018191	hsa-miR-3917	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018191		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036220	MIMAT0018194	hsa-miR-3150b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018194	hsa-miR-3150b	miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036221	MIMAT0018204	hsa-miR-676-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018204	hsa-miR-676	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036222	MIMAT0018205	hsa-miR-3928-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018205		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036223	MIMAT0018356	hsa-miR-3940-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018356	hsa-miR-3940	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036224	MIMAT0018356	hsa-miR-3940-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018356	hsa-miR-3940	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036225	MIMAT0018379	ssc-miR-149	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018379		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036226	MIMAT0018382	ssc-miR-451	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018382		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036227	MIMAT0018925	hsa-miR-1268b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018925		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036228	MIMAT0018925	hsa-miR-1268b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018925		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036229	MIMAT0018926	hsa-miR-378d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018926		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036230	MIMAT0018926	hsa-miR-378d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018926		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036231	MIMAT0018926	hsa-miR-378d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018926		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036232	MIMAT0018926	hsa-miR-378d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018926		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036233	MIMAT0018926	hsa-miR-378d	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018926		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036234	MIMAT0018927	hsa-miR-378e	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018927		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036235	MIMAT0018932	hsa-miR-378f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018932		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036236	MIMAT0018932	hsa-miR-378f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018932		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036237	MIMAT0018932	hsa-miR-378f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018932		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036238	MIMAT0018933	hsa-miR-4420	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018933		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036239	MIMAT0018937	hsa-miR-378g	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018937		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036240	MIMAT0018937	hsa-miR-378g	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018937		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036241	MIMAT0018937	hsa-miR-378g	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018937		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036242	MIMAT0018944	hsa-miR-4429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018944		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036243	MIMAT0018944	hsa-miR-4429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018944		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036244	MIMAT0018949	hsa-miR-4433a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018949	hsa-miR-4433-3p	miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036245	MIMAT0018949	hsa-miR-4433a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018949	hsa-miR-4433-3p	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036246	MIMAT0018949	hsa-miR-4433a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018949	hsa-miR-4433-3p	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036247	MIMAT0018949	hsa-miR-4433a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018949	hsa-miR-4433-3p	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036248	MIMAT0018965	hsa-miR-4446-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018965		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036249	MIMAT0018965	hsa-miR-4446-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018965		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036250	MIMAT0018965	hsa-miR-4446-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018965		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036251	MIMAT0018965	hsa-miR-4446-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018965		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036252	MIMAT0018967	hsa-miR-4448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018967		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036253	MIMAT0018967	hsa-miR-4448	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018967		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00036254	MIMAT0018968	hsa-miR-4449	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018968		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036255	MIMAT0018976	hsa-miR-4454	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018976		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036256	MIMAT0018976	hsa-miR-4454	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018976		miRNA	Homo sapiens	25330373	Extracellular vesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036257	MIMAT0018980	hsa-miR-4458	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018980		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036258	MIMAT0018984	hsa-miR-378h	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018984		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036259	MIMAT0018985	hsa-miR-3135b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018985		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036260	MIMAT0018994	hsa-miR-4467	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018994		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036261	MIMAT0018994	hsa-miR-4467	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0018994		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036262	MIMAT0019000	hsa-miR-4473	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019000		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036263	MIMAT0019018	hsa-miR-4484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019018		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036264	MIMAT0019018	hsa-miR-4484	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019018		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036265	MIMAT0019022	hsa-miR-4488	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019022		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036266	MIMAT0019022	hsa-miR-4488	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019022		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036267	MIMAT0019022	hsa-miR-4488	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019022		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036268	MIMAT0019027	hsa-miR-4492	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019027		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036269	MIMAT0019032	hsa-miR-4497	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019032		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036270	MIMAT0019032	hsa-miR-4497	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019032		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036271	MIMAT0019032	hsa-miR-4497	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019032		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036272	MIMAT0019044	hsa-miR-4507	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019044		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036273	MIMAT0019045	hsa-miR-4508	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019045		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036274	MIMAT0019045	hsa-miR-4508	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019045		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036275	MIMAT0019045	hsa-miR-4508	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019045		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036276	MIMAT0019053	hsa-miR-4516	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019053		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036277	MIMAT0019054	hsa-miR-4517	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019054		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036278	MIMAT0019055	hsa-miR-4518	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019055		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036279	MIMAT0019058	hsa-miR-4521	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019058		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036280	MIMAT0019059	hsa-miR-1269b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019059		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036281	MIMAT0019064	hsa-miR-4525	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019064		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036282	MIMAT0019074	hsa-miR-378i	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019074		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036283	MIMAT0019074	hsa-miR-378i	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019074		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036284	MIMAT0019077	hsa-miR-1587	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019077		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036285	MIMAT0019198	hsa-miR-3120-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019198		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036286	MIMAT0019198	hsa-miR-3120-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019198		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036287	MIMAT0019208	hsa-miR-3074-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019208		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036288	MIMAT0019220	hsa-miR-3664-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019220		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036289	MIMAT0019337	hsa-miR-3960	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019337		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00036290	MIMAT0019337	hsa-miR-3960	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019337		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00036291	MIMAT0019691	hsa-miR-4634	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019691		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036292	MIMAT0019699	hsa-miR-4640-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019699		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036293	MIMAT0019708	hsa-miR-4646-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019708		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036294	MIMAT0019738	hsa-miR-4664-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019738		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036295	MIMAT0019772	hsa-miR-4685-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019772		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036296	MIMAT0019772	hsa-miR-4685-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019772		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036297	MIMAT0019775	hsa-miR-4687-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019775		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036298	MIMAT0019776	hsa-miR-1343-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019776		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036299	MIMAT0019813	hsa-miR-203b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019813	hsa-miR-3545-5p	miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036300	MIMAT0019814	hsa-miR-203b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019814	hsa-miR-3545-3p	miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036301	MIMAT0019819	hsa-miR-4712-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019819		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036302	MIMAT0019840	hsa-miR-451b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019840		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036303	MIMAT0019844	hsa-miR-4725-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019844		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036304	MIMAT0019845	hsa-miR-4726-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019845		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036305	MIMAT0019849	hsa-miR-4728-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019849		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036306	MIMAT0019855	hsa-miR-4732-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019855		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036307	MIMAT0019855	hsa-miR-4732-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019855		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036308	MIMAT0019855	hsa-miR-4732-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019855		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036309	MIMAT0019856	hsa-miR-4732-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019856		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036310	MIMAT0019856	hsa-miR-4732-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019856		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036311	MIMAT0019856	hsa-miR-4732-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019856		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036312	MIMAT0019856	hsa-miR-4732-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019856		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036313	MIMAT0019864	hsa-miR-3064-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019864		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036314	MIMAT0019868	hsa-miR-4739	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019868		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036315	MIMAT0019868	hsa-miR-4739	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019868		miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00036316	MIMAT0019876	hsa-miR-3591-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019876		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036317	MIMAT0019876	hsa-miR-3591-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019876		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036318	MIMAT0019878	hsa-miR-4745-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019878		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036319	MIMAT0019885	hsa-miR-4749-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019885		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036320	MIMAT0019887	hsa-miR-4750-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019887	hsa-miR-4750	miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036321	MIMAT0019903	hsa-miR-4758-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019903		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036322	MIMAT0019926	hsa-miR-4772-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019926		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036323	MIMAT0019949	hsa-miR-4785	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019949		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036324	MIMAT0019957	hsa-miR-4787-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019957		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036325	MIMAT0019964	hsa-miR-4792	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019964		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00036326	MIMAT0019965	hsa-miR-4793-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019965		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036327	MIMAT0019966	hsa-miR-4793-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019966		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036328	MIMAT0019976	hsa-miR-4799-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0019976		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036329	MIMAT0020362	ssc-miR-142-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020362		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036330	MIMAT0020363	ssc-miR-769-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020363		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036331	MIMAT0020366	ssc-miR-4334-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020366		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036332	MIMAT0020586	ssc-miR-129b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020586		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036333	MIMAT0020588	ssc-miR-190b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020588	ssc-miR-190	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036334	MIMAT0020590	ssc-miR-219a	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020590	ssc-miR-219	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036335	MIMAT0020591	ssc-miR-429	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020591		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036336	MIMAT0020592	ssc-miR-491	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020592		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036337	MIMAT0020596	ssc-miR-1343	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020596		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036338	MIMAT0020597	ssc-miR-2320-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020597	ssc-miR-2320	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036339	MIMAT0020598	ssc-miR-2320-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020598	ssc-miR-2320*	miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036340	MIMAT0020601	hsa-miR-1273f	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020601		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036341	MIMAT0020602	hsa-miR-1273g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020602	hsa-miR-1273g	miRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00036342	MIMAT0020925	hsa-miR-550a-3-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020925		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036343	MIMAT0020956	hsa-miR-4433a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020956	hsa-miR-4433-5p	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036344	MIMAT0020956	hsa-miR-4433a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020956	hsa-miR-4433-5p	miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036345	MIMAT0021021	hsa-miR-5001-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0021021		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036346	MIMAT0021044	hsa-miR-5010-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0021044		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036347	MIMAT0021044	hsa-miR-5010-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0021044		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036348	MIMAT0021120	hsa-miR-5189-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0021120		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036349	MIMAT0021120	hsa-miR-5189-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0021120		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036350	MIMAT0022255	hsa-miR-4524b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022255		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036351	MIMAT0022260	hsa-miR-5572	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022260		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036352	MIMAT0022265	hsa-miR-548ar-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022265		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036353	MIMAT0022272	hsa-miR-664b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022272	hsa-miR-644b-3p	miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036354	MIMAT0022286	hsa-miR-5585-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022286		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00036355	MIMAT0022303	hsa-miR-548av-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022303		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036356	MIMAT0022491	hsa-miR-5698	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022491		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036357	MIMAT0022494	hsa-miR-5701	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022494		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036358	MIMAT0022692	hsa-miR-181b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022692		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036359	MIMAT0022692	hsa-miR-181b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022692		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00036360	MIMAT0022692	hsa-miR-181b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022692		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In contrast to oncomirs, an miRNA that is involved in tumor-suppressing activities, is taken as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-223, which directly targeted Stathmin 1 to inhibit HCC growth, was only found in MVs of liver cancer cell line in our study (table 2). Data are collected from Table 2. "
RLID00036361	MIMAT0022693	hsa-miR-204-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022693		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036362	MIMAT0022693	hsa-miR-204-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022693		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036363	MIMAT0022695	hsa-miR-212-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022695		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00036364	MIMAT0022695	hsa-miR-212-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022695		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036365	MIMAT0022696	hsa-miR-301a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022696		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036366	MIMAT0022697	hsa-miR-382-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022697		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 1: Ten miRNAs differentially expressed in both tumor tissue and serum. Data are collected from Table 1.
RLID00036367	MIMAT0022697	hsa-miR-382-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022697		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036368	MIMAT0022698	hsa-miR-345-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022698		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036369	MIMAT0022700	hsa-miR-450a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022700		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036370	MIMAT0022700	hsa-miR-450a-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022700		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036371	MIMAT0022705	hsa-miR-539-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022705		miRNA	Homo sapiens	24904649	Circulating	Serum	Next-generation sequencing	Table 2: Inconsistent expression change of 28 miRNAs between tumor tissue and serum. Data are collected from Table 2.
RLID00036372	MIMAT0022705	hsa-miR-539-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022705		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036373	MIMAT0022705	hsa-miR-539-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022705		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036374	MIMAT0022708	hsa-miR-584-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022708		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036375	MIMAT0022708	hsa-miR-584-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022708		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036376	MIMAT0022709	hsa-miR-652-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022709		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036377	MIMAT0022711	hsa-miR-660-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022711		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036378	MIMAT0022711	hsa-miR-660-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022711		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036379	MIMAT0022717	hsa-miR-873-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022717		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036380	MIMAT0022717	hsa-miR-873-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022717		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036381	MIMAT0022717	hsa-miR-873-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022717		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036382	MIMAT0022717	hsa-miR-873-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022717		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036383	MIMAT0022717	hsa-miR-873-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022717		miRNA	Homo sapiens	24797360	Microvesicle	Cerebrospinal fluid	RNA-seq|miRDeep3	Table 1: Differentially expressed miRNAs detected in the cerebrospinal fluid (CSF). Data are collected from Table 1.
RLID00036384	MIMAT0022717	hsa-miR-873-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022717		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036385	MIMAT0022720	hsa-miR-1304-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022720		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036386	MIMAT0022720	hsa-miR-1304-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022720		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036387	MIMAT0022722	hsa-miR-548g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022722		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036388	MIMAT0022724	hsa-miR-1277-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022724		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036389	MIMAT0022725	hsa-miR-1255b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022725		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036390	MIMAT0022726	hsa-miR-1306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022726		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036391	MIMAT0022726	hsa-miR-1306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022726		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036392	MIMAT0022726	hsa-miR-1306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022726		miRNA	Homo sapiens	25349172	Exosome	Serum	Next-generation sequencing	"Deep sequencing of the exosomal RNA extracted from serum samples was performed and sequences were mapped to miRBase Exosomal miRNA biomarkers for Alzheimer's disease. Approximately half of the reads obtained (43%) from small RNA sequencing corresponded with miRNA sequences (Supplementary Table 1). Overall, the sample cohort mapped to 1419 known human miRNA sequences (Supplementary Table 2). Following normalisation of reads and performing ANOVA analyses, 17 miRNA were found to be significantly deregulated (Figure 1); 14 miRNA were found to be upregulated (hsa-miR-361-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-15a-5p, hsa-miR-143-3p, hsa-miR-335-5p, hsa-miR-106b-5p, hsa-miR-101-3p, hsa-miR-424-5p, hsa-miR-106a-5p, hsa-miR-18b-5p, hsa-miR-3065-5p, hsa-miR-20a-5p and hsa-miR-582-5p) and three miRNA were found to be downregulated (hsa-miR-1306-5p, hsa-miR-342-3p and 15b-3p; Table 2). Data are collected from Table 2. "
RLID00036393	MIMAT0022726	hsa-miR-1306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022726		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036394	MIMAT0022726	hsa-miR-1306-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022726		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036395	MIMAT0022727	hsa-miR-1307-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022727		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036396	MIMAT0022727	hsa-miR-1307-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022727		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036397	MIMAT0022727	hsa-miR-1307-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022727		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036398	MIMAT0022727	hsa-miR-1307-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022727		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036399	MIMAT0022727	hsa-miR-1307-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022727		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036400	MIMAT0022727	hsa-miR-1307-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022727		miRNA	Homo sapiens	24797360	Microvesicle	Serum	RNA-seq|miRDeep3	Table 2: Differentially expressed miRNAs detected in the serum (SER). Data are collected from Table 2.
RLID00036401	MIMAT0022731	hsa-miR-3184-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022731		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036402	MIMAT0022731	hsa-miR-3184-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022731		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036403	MIMAT0022733	hsa-miR-548x-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022733		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036404	MIMAT0022735	hsa-miR-374c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022735		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036405	MIMAT0022735	hsa-miR-374c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022735		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036406	MIMAT0022737	hsa-miR-550b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022737		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036407	MIMAT0022737	hsa-miR-550b-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022737		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036408	MIMAT0022739	hsa-miR-548aj-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022739		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036409	MIMAT0022741	hsa-miR-3529-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022741		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036410	MIMAT0022741	hsa-miR-3529-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022741		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036411	MIMAT0022741	hsa-miR-3529-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022741		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036412	MIMAT0022742	hsa-miR-1273g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022742		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036413	MIMAT0022742	hsa-miR-1273g-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022742		miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00036414	MIMAT0022833	hsa-miR-365b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022833		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036415	MIMAT0022834	hsa-miR-365b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022834		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036416	MIMAT0022834	hsa-miR-365b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022834		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036417	MIMAT0022834	hsa-miR-365b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022834		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036418	MIMAT0022834	hsa-miR-365b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022834		miRNA	Homo sapiens	25330373	Exosome	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036419	MIMAT0022834	hsa-miR-365b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022834		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036420	MIMAT0022834	hsa-miR-365b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022834		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036421	MIMAT0022838	hsa-miR-1185-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022838		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036422	MIMAT0022838	hsa-miR-1185-1-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022838		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036423	MIMAT0022842	hsa-miR-98-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022842		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036424	MIMAT0022842	hsa-miR-98-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022842		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00036425	MIMAT0022842	hsa-miR-98-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022842		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036426	MIMAT0022842	hsa-miR-98-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022842		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036427	MIMAT0022844	hsa-miR-216a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022844		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036428	MIMAT0022862	hsa-miR-381-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022862		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036429	MIMAT0022924	hsa-miR-495-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022924		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036430	MIMAT0022929	hsa-miR-758-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022929		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036431	MIMAT0022947	hsa-miR-1238-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022947		miRNA	Homo sapiens	23771658	Microvesicle	Hepatoma cell	qRT-PCR|Microarray	"In line with the difference in number of detectable miRNAs, the expression levels of these miRNAs also varied between MVs and cells. Statistical analysis of the 148 co-expressing miRNAs showed that 25 miRNAs were aberrantly elevated inMVs and 75 miRNAs were significantly elevated in cells with more than two folds change. Forty-eight miRNAs had the similar signal intensity in both groups (table 1). Data are collected from Table 1. "
RLID00036432	MIMAT0022957	ssc-miR-455-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022957		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036433	MIMAT0022967	hsa-miR-3620-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0022967		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036434	MIMAT0023712	hsa-miR-6087	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0023712		miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036435	MIMAT0023712	hsa-miR-6087	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0023712		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036436	MIMAT0023712	hsa-miR-6087	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0023712		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036437	MIMAT0024615	hsa-miR-6131	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0024615		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036438	MIMAT0024616	hsa-miR-6132	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0024616		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036439	MIMAT0025356	ssc-let-7d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025356		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036440	MIMAT0025357	ssc-let-7d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025357		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036441	MIMAT0025359	ssc-miR-20b	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025359		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036442	MIMAT0025483	hsa-miR-6513-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025483		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036443	MIMAT0025487	hsa-miR-6515-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025487		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036444	MIMAT0025487	hsa-miR-6515-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025487		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036445	MIMAT0025846	hsa-miR-6717-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025846		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036446	MIMAT0025853	hsa-miR-6722-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025853		miRNA	Homo sapiens	24683445	Exosome	Plasma	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036447	MIMAT0025854	hsa-miR-6722-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0025854		miRNA	Homo sapiens	24867291	Circulating	Aqueous humor 	Microarray	"There are three sources of extracellular miRNAs in the eye: tears, the vitreous humor, and the aqueous humor (AH). A receiver operating characteristic (ROC) analysis of the 11 up-regulated and 18 down-regulated miRNAs showed that they all had an area under the curve (AUC) greater than 0.74 (Figure 3b, c, and d). A hierarchal cluster analysis with these 29 miRNA markers showed a cluster composed only of glaucoma patients was formed (Figure 4). Data are collected from Figure 4: Cluster analysis of selected 29 miRNA markers for glaucoma. "
RLID00036448	MIMAT0026467	rno-miR-125b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026467		miRNA	Rattus norvegicus	24324399	Cytoplasm	Cortical cell|Hippocampal neuron	Microarray	"To determine expression levels of nuclear and cytoplasmic mature miRNAs, size-selected small RNA samples (3 nuclear and 3 cytoplasmic samples) were analyzed by miRNA microarrays (LCSciences), containing probes for 679 rat mature miRNAs (miRBase version 16). In total, we were able to detect 267 mature miRNAs which were common to both nucleus and cytoplasm (Table S1). Data are collected from Table S1. "
RLID00036449	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036450	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036451	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	21695135	Cytoplasm	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00036452	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00036453	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036454	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036455	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	25184951	Exosome	Esophageal cancer cell	Next-generation sequencing	"All known miRNAs in exosomes were detected at lower levels compared with their corresponding cells, whereas several novel miRNAs in exosomes were detected at higher levels compared with their corresponding cells.  Data are collected from Table 3. "
RLID00036456	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036457	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036458	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036459	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036460	MIMAT0026472	hsa-let-7c-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026472		miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00036461	MIMAT0026473	hsa-miR-95-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026473		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036462	MIMAT0026473	hsa-miR-95-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026473		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036463	MIMAT0026473	hsa-miR-95-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026473		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036464	MIMAT0026473	hsa-miR-95-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026473		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036465	MIMAT0026473	hsa-miR-95-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026473		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036466	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036467	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036468	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036469	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	24212760	Circulating	Serum	qRT-PCR	"Therefore, we investigated whether serum miR-210 could be a useful biomarker for the diagnosis and progression of CCC. "
RLID00036470	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036471	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	19289371	Exosome	Plasma	Microarray	Figure 1: Intensities for specific microRNAs derived from the tumor and exosomes isolated from the plasma of the patients. Data are collected from Figure 1.
RLID00036472	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00036473	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00036474	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036475	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036476	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	25017274	Circulating	Serum	qRT-PCR	"The expression of four miRNAs (miR-1233, miR-520, miR-210, miR-144) was validated by quantitative real-time polymerase chain reaction analysis. MiR-1233 was the most overexpressed in the serum of women who later developed sPE. Circulating miRNAs deserve further investigation in order to explore their potential role in the pathogenesis of preeclampsia. In particular, miR-1233 might represent a potential marker of early sPE. "
RLID00036477	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036478	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036479	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036480	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	20864815	Nucleus	Colon adenocarcinoma cell	Microarray	Table 2: Reported gene targets of nuclear-associated microRNAs. Data are collected from Table 2.
RLID00036481	MIMAT0026475	hsa-miR-210-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026475		miRNA	Homo sapiens	21363885	Nucleus	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00036482	MIMAT0026476	hsa-miR-215-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026476		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036483	MIMAT0026476	hsa-miR-215-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026476		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036484	MIMAT0026476	hsa-miR-215-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026476		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036485	MIMAT0026476	hsa-miR-215-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026476		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036486	MIMAT0026476	hsa-miR-215-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026476		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036487	MIMAT0026476	hsa-miR-215-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026476		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036488	MIMAT0026477	hsa-miR-128-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026477		miRNA	Homo sapiens	21363885	Cytoplasm	Neural progenitor cell	qRT-PCR|Microarray	The miRNAs with nuclear or cytoplasmic dominance are shown in Table 1 (complete data in Supplement 4).
RLID00036489	MIMAT0026477	hsa-miR-128-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026477		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00036490	MIMAT0026477	hsa-miR-128-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026477		miRNA	Homo sapiens	20976003	Exosome	Breast cancer cell	Microarray	"Because of the suggested roles of extracellular miRNAs in signaling and diagnosis, we investigated whether the intracellular and extracellular miRNA composition are the same. To answer this question, we performed microRNA microarray analyses of MCF7 cellular (c) and extracellular (x) RNAs (Figure 2A), and found that about 66% of the released miRNAs are at an abundance that closely reflects the cellular miRNA abundance (Figures 2B and 2C). This finding is in agreement with a model wherein most, but not all miRNAs are released passively by mass action. Data are collected from Figure 2. "
RLID00036491	MIMAT0026477	hsa-miR-128-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026477		miRNA	Homo sapiens	21505438	Exosome	Dendritic cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00036492	MIMAT0026477	hsa-miR-128-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026477		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036493	MIMAT0026477	hsa-miR-128-1-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026477		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036494	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036495	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036496	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036497	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036498	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036499	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036500	MIMAT0026478	hsa-miR-133a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026478		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036501	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036502	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036503	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036504	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00036505	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036506	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036507	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036508	MIMAT0026479	hsa-miR-152-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026479		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036509	MIMAT0026480	hsa-miR-153-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026480		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036510	MIMAT0026480	hsa-miR-153-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026480		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036511	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036512	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036513	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	21505438	Exosome	T cell	Microarray	Supplementary Data 1: Microarray analysis of exosomal miRNAs verses the miRNAs of their respective donor cells. Data are collected from Supplementary Data 1.
RLID00036514	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036515	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036516	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036517	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036518	MIMAT0026481	hsa-miR-134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026481		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036519	MIMAT0026483	hsa-miR-370-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026483		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036520	MIMAT0026483	hsa-miR-370-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026483		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036521	MIMAT0026483	hsa-miR-370-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026483		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036522	MIMAT0026483	hsa-miR-370-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026483		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036523	MIMAT0026483	hsa-miR-370-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026483		miRNA	Homo sapiens	22529849	Exosome	Ovarian tumor cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00036524	MIMAT0026484	hsa-miR-372-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026484		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036525	MIMAT0026484	hsa-miR-372-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026484		miRNA	Homo sapiens	25415674	Circulating	Plasma	Next-generation sequencing	"To determine the effects of CAD on the levels of circulating miRNAs, we performed miRNA profile analysis by deep sequencing using RNA isolated from 20 patients with CAD and 20 healthy controls. Two hundred ninety-six miRNAs were detected in the plasma of healthy individuals and 196 in patients with CAD. Among all the miRNAs detected, 173 miRNAs were found in both groups, only 123 miRNAs were detected in healthy individuals, while only 23 miRNAs were detected in patients with CAD. The levels of circulating miRNA profoundly differed between patients and healthy controls, as demonstrated in the scatter (Figure ?(Figure1).1). There were 53 miRNAs that showed more than 2-fold differential expression between groups. Detailed information of these miRNAs is listed in supplementary Table 2. "
RLID00036526	MIMAT0026484	hsa-miR-372-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026484		miRNA	Homo sapiens	24918059	Nucleolus	HeLa|MCF7	Microarray	Data are collected from supplementary Table S1.Top-ranking nucleolar miRNAs present in HeLa and MCF7 NCode arrays.
RLID00036527	MIMAT0026485	hsa-miR-383-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026485		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036528	MIMAT0026485	hsa-miR-383-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026485		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036529	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036530	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036531	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036532	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036533	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036534	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036535	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	RT-PCR|Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00036536	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00036537	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036538	MIMAT0026486	hsa-miR-328-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026486		miRNA	Homo sapiens	22529849	Exosome	PBMC	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00036539	MIMAT0026552	hcmv-miR-UL112-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026552		miRNA	Human herpesvirus 5	21690488	Circulating	Plasma	qRT-PCR	"The expressions of selected miRNAs (miR-296-5p, let-7e, and a human cytomegalovirus [HCMV]-encoded miRNA, hcmv-miR-UL112) were validated independently in plasma samples from 24 hypertensive patients and 22 control subjects. "
RLID00036540	MIMAT0026552	hcmv-miR-UL112-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026552		miRNA	Human herpesvirus 5	21924071	Circulating	Plasma	Microarray	"MiR-296-5p (Fold change 0.47, P = 0.013) and miR-133b (Fold change 0.57, P = 0.033) were consistently down-regulated in the patient plasma, whereas let-7e (Fold change 1.62, P = 0.009) and hcmv-miR-UL112 (Fold change 2.72, P = 0.004), one human cytomegalovirus encoded microRNAs, were up-regulated in the patient samples.  "
RLID00036541	MIMAT0026554	hsa-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026554		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036542	MIMAT0026554	hsa-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026554		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036543	MIMAT0026554	hsa-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026554		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036544	MIMAT0026554	hsa-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026554		miRNA	Homo sapiens	25323050	Circulating	serum	Next-generation sequencing	"Twenty seven candidate microRNAs were screened out from ONFH serum. Fifteen microRNAs, including miR-423-5p, miR-3960, miR-195-5p, miR-15b-3p and miR-1304-3p, were over-expressed. Twelve microRNAs, including miR-100-5p, miR-99a-5p, miR-532-5p, miR-140-5p, miR-10a-5p, miR-10b-5p, miR-181c-5p and miR-433, were under-expressed in ONFH serum compared with SLE controls and healthy controls (Fig. 3). Data are collected from Figure 3. "
RLID00036545	MIMAT0026554	hsa-miR-433-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026554		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036546	MIMAT0026555	hsa-miR-329-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026555		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036547	MIMAT0026555	hsa-miR-329-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026555		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036548	MIMAT0026557	hsa-miR-412-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026557		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036549	MIMAT0026557	hsa-miR-412-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026557		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036550	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036551	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036552	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	23666971	Circulating	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036553	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036554	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036555	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036556	MIMAT0026558	hsa-miR-410-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026558		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036557	MIMAT0026559	hsa-miR-487a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026559		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00036558	MIMAT0026559	hsa-miR-487a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026559		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036559	MIMAT0026605	hsa-miR-489-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026605		miRNA	Homo sapiens	25126405	Circulating	Serum	qRT-PCR	"Circulating miRNAs in the serum and plasma are remarkably stable and are suggested to have promise as noninvasive biomarkers for neurological and neurodevelopmental disorders. Thirteen miRNAs were differentially expressed in ASD individuals compared to the controls. MiR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. "
RLID00036560	MIMAT0026605	hsa-miR-489-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026605		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036561	MIMAT0026606	hsa-miR-511-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026606		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036562	MIMAT0026607	hsa-miR-494-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026607		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00036563	MIMAT0026607	hsa-miR-494-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026607		miRNA	Homo sapiens	23666971	Microvesicle	Follicular fluid	Microarray	"The TaqMan miRNA Array Card version 3.0, which includes 766 mature miRNAs, detected the presence of miRNAs in both the microvesicles and the supernatant. A total of 120 miRNAs (cycle threshold [Ct] <37) were found in the in microvesicles extracted from 8 mL fresh follicular fluid, and 82 miRNAs (Ct <37) were expressed in 500 uL supernatant (Table 2). Data are collected from Table 2. "
RLID00036564	MIMAT0026607	hsa-miR-494-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026607		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	RT-PCR|Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00036565	MIMAT0026608	hsa-miR-181d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026608		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036566	MIMAT0026608	hsa-miR-181d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026608		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036567	MIMAT0026608	hsa-miR-181d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026608		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036568	MIMAT0026608	hsa-miR-181d-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026608		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036569	MIMAT0026610	hsa-miR-519d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026610		miRNA	Homo sapiens	20729298	Circulating	Plasma	RT-PCR	Table 1. List of pregnancy-associated miRNAs in maternal plasma. Data are collected from Table 1.
RLID00036570	MIMAT0026610	hsa-miR-519d-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026610		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036571	MIMAT0026611	hsa-miR-520g-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026611		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036572	MIMAT0026612	hsa-miR-504-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026612		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036573	MIMAT0026612	hsa-miR-504-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026612		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036574	MIMAT0026612	hsa-miR-504-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026612		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036575	MIMAT0026613	hsa-miR-510-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026613		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036576	MIMAT0026614	hsa-miR-487b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026614		miRNA	Homo sapiens	25405200	Circulating	Serum	qRT-PCR	"Individual qRT-PCR results (expression level) of serum miRNA expression in macrosomia and controls is shown in Table 3, including has-miR-122, has-miR-192, has-miR-194, has-miR-296-5p, has-miR-376a, has-miR-487b, has-miR-505, has-miR-1262 "
RLID00036577	MIMAT0026614	hsa-miR-487b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026614		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036578	MIMAT0026614	hsa-miR-487b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026614		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036579	MIMAT0026614	hsa-miR-487b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026614		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036580	MIMAT0026616	hsa-miR-579-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026616		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036581	MIMAT0026616	hsa-miR-579-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026616		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036582	MIMAT0026616	hsa-miR-579-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026616		miRNA	Homo sapiens	20615901	Microvesicle	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00036583	MIMAT0026616	hsa-miR-579-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026616		miRNA	Homo sapiens	20615901	Exosome	A549|HepG2	Microarrays|RT-PCR	"These observations of miRNA distribution demonstrate that the miRNA export system in the cells must somehow be able to target specific miRNAs to specific extracellular structures, but does not exclusively channel specific miRNAs to a given fraction. There are, however, some miRNAs that are found in the supernatant almost to the exclusion of all other fractions (miR-219 in A549 culture medium, Figure 4b, for example). Another significant observation from this data is that even though we showed that the two cell lines studied here export a similar spectrum of miRNAs (Figure 1b) the distributions of miRNAs from the two cell lines demonstrate clear differences, as shown in Figure 4b and c. For example, miR-145 is present at very low levels in HepG2 derived microvesicles (Figure 4c), while the same miRNA is present at significant levels in both A549 derived microvesicles and exosomes (Figure 4b). On the other hand, there are some miRNAs, notably those that are almost uniformly distributed among the fractions, with the same distribution no matter which cell-line is the source. These observations certainly indicate the degree of complexity of this export system that will bear further investigation. Data are collected from Figure 4. "
RLID00036584	MIMAT0026616	hsa-miR-579-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026616		miRNA	Homo sapiens	22529849	Exosome	Epithelial cell	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00036585	MIMAT0026617	hsa-miR-580-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026617		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036586	MIMAT0026618	hsa-miR-585-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026618		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036587	MIMAT0026620	hsa-miR-598-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026620		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036588	MIMAT0026620	hsa-miR-598-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026620		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036589	MIMAT0026622	hsa-miR-619-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026622		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036590	MIMAT0026623	hsa-miR-627-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026623		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036591	MIMAT0026623	hsa-miR-627-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026623		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036592	MIMAT0026624	hsa-miR-651-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026624		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036593	MIMAT0026624	hsa-miR-651-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026624		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036594	MIMAT0026626	hsa-miR-655-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026626		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036595	MIMAT0026627	hsa-miR-656-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026627		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036596	MIMAT0026627	hsa-miR-656-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026627		miRNA	Homo sapiens	24683445	Exosome	Serum	Next-generation sequencing	"Exosomes are enriched with miRNA: Small RNA libraries of the samples described above were constructed for small RNA-seq by NGS. The number of miRNA identified in this study was 943 of 2,233 known mature miRNA from miRBase V.20. Mapping to Ensembl Release 74 was performed to identify other non-coding RNA such as tRNA, rRNA, small nucleolar RNA (snoRNA) and LincRNA. The average across all 3 samples was calculated to obtain a representative profile of biological diversity between patients (standard deviations of reads in Supplementary file) "
RLID00036597	MIMAT0026637	hsa-miR-1296-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026637		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036598	MIMAT0026637	hsa-miR-1296-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026637		miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036599	MIMAT0026637	hsa-miR-1296-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026637		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036600	MIMAT0026638	hsa-miR-1468-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026638		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036601	MIMAT0026639	hsa-miR-1301-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026639		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036602	MIMAT0026639	hsa-miR-1301-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026639		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036603	MIMAT0026639	hsa-miR-1301-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026639		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036604	MIMAT0026641	hsa-miR-1298-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026641		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036605	MIMAT0026641	hsa-miR-1298-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026641		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036606	MIMAT0026641	hsa-miR-1298-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026641		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036607	MIMAT0026717	hsa-miR-891a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026717		miRNA	Homo sapiens	20145944	Circulating	Semen	RT-PCR|Microarray	"Our results highlight four miRNA markers for blood identification (miR-20a, miR-106a, miR-185, and miR-144) and five for semen identification (miR-135a, miR-10a, miR-507, miR-943, and miR-891a). Of those, two miRNA markers for blood (miR-144 and miR-185) and two others for semen (miR-135a and miR-897a) are suggestive to be most useful for body fluid identification in future forensic applications, and the respective RT-PCR assays used here for their detection were highly sensitive, allowing the reliable marker detection from subpicogram amounts of total RNA. Our results proved the applicability of the miRNA approach for forensic body fluids identification.  "
RLID00036608	MIMAT0026717	hsa-miR-891a-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026717		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036609	MIMAT0026718	hsa-miR-874-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026718		miRNA	Homo sapiens	22262318	Circulating	Plasma	qRT-PCR	Table 1: The miRNAs the level of which were markedly decreased in post-operative plasma. Data are collected from Table 1.
RLID00036610	MIMAT0026718	hsa-miR-874-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026718		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036611	MIMAT0026718	hsa-miR-874-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026718		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036612	MIMAT0026718	hsa-miR-874-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026718		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036613	MIMAT0026718	hsa-miR-874-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026718		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036614	MIMAT0026719	hsa-miR-889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026719		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036615	MIMAT0026719	hsa-miR-889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026719		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036616	MIMAT0026719	hsa-miR-889-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026719		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036617	MIMAT0026721	hsa-miR-216b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026721		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036618	MIMAT0026721	hsa-miR-216b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026721		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036619	MIMAT0026722	hsa-miR-208b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026722		miRNA	Homo sapiens	20145944	Circulating	Saliva	RT-PCR|Microarray	"Also the miRNAs, miR-583, miR-518c*, and miR-208b identified by microarray analysis as candidate markers for saliva and miR-617 for vaginal secretion, demonstrated a strong discordance between microarray and TaqMan data (Electronic supplementary materials, Fig. 2).  "
RLID00036620	MIMAT0026722	hsa-miR-208b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026722		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036621	MIMAT0026722	hsa-miR-208b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026722		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S1. The expression profiles of serum miRNAs in non-survivors of sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S1.
RLID00036622	MIMAT0026734	hsa-miR-942-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026734		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036623	MIMAT0026734	hsa-miR-942-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026734		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036624	MIMAT0026735	hsa-miR-1180-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026735		miRNA	Homo sapiens	23525801	Circulating	Cerebrospinal fluid	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036625	MIMAT0026735	hsa-miR-1180-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026735		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036626	MIMAT0026735	hsa-miR-1180-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026735		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036627	MIMAT0026735	hsa-miR-1180-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026735		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036628	MIMAT0026735	hsa-miR-1180-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026735		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036629	MIMAT0026736	hsa-miR-548e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026736		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036630	MIMAT0026736	hsa-miR-548e-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026736		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036631	MIMAT0026737	hsa-miR-548j-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026737		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036632	MIMAT0026738	hsa-miR-1287-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026738		miRNA	Homo sapiens	23525801	Circulating	Serum	Next-generation sequencing|RT-PCR	"Next, we wanted to compare the miRNA identified in serum to miRNA present in CSF from the same subjects. We examined the miRNA profiles for five different subjects from whom both CSF and serum were collected (Supplemental Table 4). Data are collected from Table S4. "
RLID00036633	MIMAT0026740	hsa-miR-1250-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026740		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036634	MIMAT0026740	hsa-miR-1250-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026740		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036635	MIMAT0026740	hsa-miR-1250-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026740		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036636	MIMAT0026741	hsa-miR-1251-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026741		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036637	MIMAT0026742	hsa-miR-1266-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026742		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036638	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036639	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	19627513	Exosome	Saliva	Microarray	"For a more comprehensive assessment of exosomal miRNAs we ran two miRNA microarrays: one microarray was hybridized with microRNAs from parotid saliva against microRNAs from submandibular saliva from the same normal volunteer, and the second microarray was hybridized with miRNAs from parotid saliva from a normal volunteer against miRNAs from a Sjogren's syndrome patient saliva sample (Table 1). Data are collected from Table 1: list of the most highly expressed human microRNAs in parotid exosomes. "
RLID00036640	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036641	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036642	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	24468161	Exosome	Breast cancer cell	Microarray	"Figure 3: Differential gene expression in exosome-like vesicles. A) Hierarchical clustering was used to display miRNAs differentially expressed in each vesicle type. The extent of green (decreased fold change) or red (increased fold change) colors is directly proportional to the magnitude of differential expression of miRNAs. To perform these comparisons, probe sets whose target was not detected in any sample were eliminated from the data matrix. The data were grouped by type of exosome-like vesicles and members of each group were pooled, before a Student's t-test was used to identify those miRNAs that were expressed in a statistically significant manner (P < 0.05). B) miRNA profiles of the MDA-Exo versus MCF-Exo. Bars represent fold change of hybridization signals in MDA-Exo against MCF-Exo. Blue and red bars display relatively higher miRNA expressions in MDA-Exo and MCF-Exo, respectively. The miRNAs were quantified using the universal reference in equimolar concentrations and cross referenced with experimental data. Then the expression values were compared in two types of exosome-like vesicles (three independent experiments; P < 0.05). Data are collected from Figure 3. "
RLID00036643	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	21695135	Mitochondrion	HeLa cell	Microarray	"While 44 miRNAs showed a greater enrichment in the cytosolic Hy3-labeled RNA fraction, 13 miRNAs were significantly and reproducibly enriched in the mitochondrial Hy5-labeled RNA sample (ranging from 1.5- to 56-fold), namely hsa-miR-1973, hsa-miR-1275, hsa-miR-494, hsa-miR-513a-5p, hsa-miR-1246, hsa-miR-328, hsa-miR-1908, hsa-miR-1972, hsa-miR-1974, hsa-miR-1977, hsa-miR-638, hsa-miR-1978 and hsa-miR-1201 (Figure 5A). Data are collected from Figure 5. "
RLID00036644	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036645	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036646	MIMAT0026916	hsa-miR-1908-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0026916		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036647	MIMAT0027027	hsa-miR-3192-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027027		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036648	MIMAT0027027	hsa-miR-3192-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027027		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036649	MIMAT0027027	hsa-miR-3192-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027027		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036650	MIMAT0027027	hsa-miR-3192-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027027		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036651	MIMAT0027032	hsa-miR-500b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027032		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036652	MIMAT0027037	hsa-miR-3928-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027037		miRNA	Homo sapiens	23641832	Circulating	Serum	Next-generation sequencing	Additional file 2: Expression profile of serum miRNAs  in pooled sera from healthy controls and AMI patients by solexa sequencing technology. Data are collected from Additional file 2.
RLID00036653	MIMAT0027037	hsa-miR-3928-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027037		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036654	MIMAT0027037	hsa-miR-3928-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027037		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036655	MIMAT0027037	hsa-miR-3928-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027037		miRNA	Homo sapiens	22719975	Circulating	Serum	Next-generation sequencing	Table S2: Expression profiles of serum miRNAs in surviving sepsis patients (n=9) detected by Solexa sequencing. Data are collected from Table S2.
RLID00036656	MIMAT0027038	hsa-miR-1343-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027038		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036657	MIMAT0027088	hsa-miR-5189-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027088		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036658	MIMAT0027621	hsa-miR-6769b-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0027621		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036659	MIMAT0028143	ssc-miR-7134-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0028143		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036660	MIMAT0028144	ssc-miR-7134-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0028144		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036661	MIMAT0028149	ssc-miR-7137-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0028149		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036662	MIMAT0028150	ssc-miR-7137-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0028150		miRNA	Sus scrofa	24499489	Exosome	Milk	Next-generation sequencing	"In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). Data are collected from Additional file. "
RLID00036663	MIMAT0029782	hsa-miR-7641	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0029782		miRNA	Homo sapiens	25330373	Extracellular vesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036664	MIMAT0029894	mmu-miR-126b-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0029894		miRNA	Mus musculus	22965126	Exosome	Neuronal cell	Microarray	"In exosome preparations isolated from the same cells, we detected 157 (42%) specific miRNAs in both uninfected and prion-infected exosomes (Figure 2B and Supplementary Table S2). Data are collected from Table S2. "
RLID00036665	MIMAT0030019	hsa-miR-7704	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0030019		miRNA	Homo sapiens	25330373	Microvesicle	Colon Cancer Cell Line 	qRT-PCR|RNA-seq	"To assess whether some miRNAs are specifically sorted into EVs we conducted a miRNA-enrichment analysis for A33-Exos, EpCAM-Exos and sMVs. MiRNAs with <2 fold changes relative to CL miRNAs were filtered out, yielding 63 miRNAs for comparison (Table 2). Data are collected from Table 2. "
RLID00036666	MIMAT0031074	hsa-miR-450a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031074		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036667	MIMAT0031074	hsa-miR-450a-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031074		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036668	MIMAT0031095	hsa-miR-128-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031095		miRNA	Homo sapiens	18589210	Exosome	Serum	Microarray	Table 1:Association of microRNA with peripheral blood-derived tumor exosomes compared with microRNA isolated from their corresponding tumors. Data are collected from Table 1.
RLID00036669	MIMAT0031095	hsa-miR-128-2-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031095		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036670	MIMAT0031177	hsa-miR-7974	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031177		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036671	MIMAT0031178	hsa-miR-7975	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031178		miRNA	Homo sapiens	25242326	Exosome	B cell	Next-generation sequencing	"Although the miRNA distribution in exosomal fractions is clearly influenced by cellular miRNA abundance, we identified a subset of miRNAs that were discordantly distributed between cells and exosomes (false discovery rate [FDR] < 0.05; Tables S1B and S1C). "
RLID00036672	MIMAT0031890	hsa-miR-203a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031890		miRNA	Homo sapiens	22211110	Exosome	Breast milk	Next-generation sequencing	"Reads from mRNA and ribosome footprinting libraries were then remapped to this subset of mRNAs, allowing each read to map to two locations, allowing two mismatches in a 25-nt seed region, and enabling the best and strata options. Mapping details are provided in supplemental Table S1 with abundance and ribosome loading of each mRNA specified in supplemental Table S2. Data are collected from Table S2. "
RLID00036673	MIMAT0031890	hsa-miR-203a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031890		miRNA	Homo sapiens	23382797	Exosome	Brain tissue	Microarray	"We performed miRNA expression analysis using a FlexMAP3D instrument by (Luminex Corporation, Austin, TX) and a manufacturer's assay for 312 miRNA (Table S1). Data are collected from Table S1. "
RLID00036674	MIMAT0031890	hsa-miR-203a-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031890		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036675	MIMAT0031893	hsa-miR-181b-2-3p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0031893		miRNA	Homo sapiens	22058130	Nucleus	HeLa cell	Next-generation sequencing	"Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Data were collected from Supplementary file. "
RLID00036676	MIMAT0032029	hsa-miR-1249-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0032029		miRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"Because the abundance of most miRNAs is low in the exosomes, we defined detectable miRNAs as those that had at least one sequence per million mappable miRNA reads. Accordingly, we detected a total of 593 known miRNAs in the 14 libraries. In each individual library, the number of detectable known miRNAs varied from 380 to 474 with an average of 419 [see Additional file 2]. Data are collected from Additional file 2: Read counts of the miRNAs detected in the 14 libraries (normalized to read number per million mappable miRNA seqeuences). "
RLID00036677	MIMAT0032029	hsa-miR-1249-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0032029		miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036678	MIMAT0032116	hsa-miR-4485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0032116		miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036679	MIMAT0032116	hsa-miR-4485-5p	http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0032116		miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	The differential association of miRNA to mitochondria of both HEK293 and HeLa has been summarized in Table S3. Data are collected from Table S3: Pattern of miRNAs associated with mitochondria of HEK293 and HeLa.
RLID00036680	RLGI00001	hsa-novel_mir_36			miRNA	Homo sapiens	24577456	Circulating	Serum	Next-generation sequencing	The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. Table 2 has displayed the data.
RLID00036681	RLGI00002	hsa-pmiR-chr1-2130			miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036682	RLGI00003	hsa-pmiR-chr19-5802			miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036683	RLGI00004	hsa-pmiR-U2-snRNA			miRNA	Homo sapiens	25359176	Circulating	Serum	Next-generation sequencing	"In this study, we focused on examining global circulating miRNA profiles in serum samples from subjects with liver injury caused by accidental acetaminophen (APAP) overdose. Upon applying next generation high-throughput sequencing of small RNA libraries, we identified 36 miRNAs, including 3 novel miRNA-like small nuclear RNAs, which were enriched in the serum of APAP overdosed subjects. The location of the best hit for the sequences is shown in Supplementary Table 2. Data are collected from Table S2. "
RLID00036684	RLGI00005	gma-miR4422a			miRNA	Glycine max	21504877	Nucleus	Leaf	In situ hybridization	"Furthermore, localization studies showed that a novel soybean miRNA, miR4422a, was nuclear-localized. "
RLID00036685	RLGI00006	hcrsv-miR-H1-5p			miRNA	Hibiscus cannabinus	23155403	Nucleus	Seedling	RT-PCR|Northern blot	"The vir-miRNA (hcrsv-miR-H1-5p) was detected using TaqMan stem-loop real-time PCR, and by northern blot using DIG-end labeled probe in HCRSV-infected kenaf leaves. Finally, a novel nuclear localization signal (NLS) was discovered in p23 of HCRSV. "
RLID00036686	RLGI00007	hcrsv-miR-H1-5p			miRNA	Hibiscus chlorotic ringspot virus	23155403	Nucleus	Seedling	RT-PCR|Northern blot	"The vir-miRNA (hcrsv-miR-H1-5p) was detected using TaqMan stem-loop real-time PCR, and by northern blot using DIG-end labeled probe in HCRSV-infected kenaf leaves. Finally, a novel nuclear localization signal (NLS) was discovered in p23 of HCRSV. "
RLID00036687	RLGI00008	293m8-m0001			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036688	RLGI00009	293m8-m0002			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036689	RLGI00010	293m8-m0003			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036690	RLGI00011	293m8-m0004			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036691	RLGI00012	293m8-m0005			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036692	RLGI00013	293m8-m0006			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036693	RLGI00014	293m8-m0007			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036694	RLGI00015	293m8-m0008			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036695	RLGI00016	293m8-m0009			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036696	RLGI00017	293m8-m0010			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036697	RLGI00018	293m8-m0011			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036698	RLGI00019	293m8-m0012			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036699	RLGI00020	293m8-m0013			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036700	RLGI00021	293m8-m0014			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036701	RLGI00022	293m8-m0015			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036702	RLGI00023	293m8-m0016			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036703	RLGI00024	293m8-m0017			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036704	RLGI00025	293m8-m0018			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036705	RLGI00026	293m8-m0019			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036706	RLGI00027	293m8-m0020			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036707	RLGI00028	293m8-m0021			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036708	RLGI00029	293m8-m0022			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036709	RLGI00030	293m8-m0023			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036710	RLGI00031	293m8-m0024			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036711	RLGI00032	293m8-m0025			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036712	RLGI00033	293m8-m0026			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036713	RLGI00034	293m8-m0027			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036714	RLGI00035	293m8-m0028			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036715	RLGI00036	293m8-m0029			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036716	RLGI00037	293m8-m0030			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036717	RLGI00038	293m8-m0031			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036718	RLGI00039	293m8-m0032			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036719	RLGI00040	293m8-m0033			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036720	RLGI00041	293m8-m0034			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036721	RLGI00042	293m8-m0035			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036722	RLGI00043	293m8-m0036			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036723	RLGI00044	293m8-m0037			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036724	RLGI00045	293m8-m0038			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036725	RLGI00046	293m8-m0039			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036726	RLGI00047	293m8-m0040			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036727	RLGI00048	293m8-m0041			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036728	RLGI00049	293m8-m0042			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036729	RLGI00050	293m8-m0043			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036730	RLGI00051	293m8-m0044			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036731	RLGI00052	293m8-m0045			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036732	RLGI00053	293m8-m0046			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036733	RLGI00054	293m8-m0047			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036734	RLGI00055	293m8-m0048			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036735	RLGI00056	293m8-m0049			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036736	RLGI00057	293m8-m0050			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036737	RLGI00058	293m8-m0051			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036738	RLGI00059	293m8-m0052			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036739	RLGI00060	293m8-m0053			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036740	RLGI00061	293m8-m0054			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036741	RLGI00062	293m8-m0055			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036742	RLGI00063	293m8-m0056			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036743	RLGI00064	293m8-m0057			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036744	RLGI00065	293m8-m0058			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036745	RLGI00066	293m8-m0059			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036746	RLGI00067	293m8-m0060			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036747	RLGI00068	293m8-m0061			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036748	RLGI00069	293m8-m0062			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036749	RLGI00070	293m8-m0063			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036750	RLGI00071	293m8-m0064			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036751	RLGI00072	293m8-m0065			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036752	RLGI00073	293m8-m0066			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036753	RLGI00074	293m8-m0067			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036754	RLGI00075	293m8-m0068			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036755	RLGI00076	293m8-m0069			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036756	RLGI00077	293m8-m0070			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036757	RLGI00078	293m8-m0071			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036758	RLGI00079	293m8-m0072			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036759	RLGI00080	293m8-m0073			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036760	RLGI00081	293m8-m0074			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036761	RLGI00082	293m8-m0075			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036762	RLGI00083	293m8-m0076			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036763	RLGI00084	293m8-m0077			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036764	RLGI00085	293m8-m0078			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036765	RLGI00086	293m8-m0079			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036766	RLGI00087	293m8-m0080			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036767	RLGI00088	293m8-m0081			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036768	RLGI00089	293m8-m0082			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036769	RLGI00090	293m8-m0083			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036770	RLGI00091	293m8-m0084			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036771	RLGI00092	293m8-m0085			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036772	RLGI00093	293m8-m0086			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036773	RLGI00094	293m8-m0087			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036774	RLGI00095	293m8-m0088			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036775	RLGI00096	293m8-m0089			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036776	RLGI00097	293m8-m0090			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036777	RLGI00098	293m8-m0091			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036778	RLGI00099	293m8-m0092			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036779	RLGI00100	293m8-m0093			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036780	RLGI00101	293m8-m0094			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036781	RLGI00102	293m8-m0095			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036782	RLGI00103	293m8-m0096			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036783	RLGI00104	293m8-m0097			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036784	RLGI00105	293m8-m0098			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036785	RLGI00106	293m8-m0099			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036786	RLGI00107	293m8-m0100			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036787	RLGI00108	293m8-m0101			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036788	RLGI00109	293m8-m0102			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036789	RLGI00110	293m8-m0103			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036790	RLGI00111	293m8-m0104			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036791	RLGI00112	293m8-m0105			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036792	RLGI00113	293m8-m0106			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036793	RLGI00114	293m8-m0107			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036794	RLGI00115	293m8-m0108			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036795	RLGI00116	293m8-m0109			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036796	RLGI00117	293m8-m0110			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036797	RLGI00118	293m8-m0111			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036798	RLGI00119	293m8-m0112			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036799	RLGI00120	293m8-m0113			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036800	RLGI00121	293m8-m0114			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036801	RLGI00122	293m8-m0115			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036802	RLGI00123	293m8-m0116			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036803	RLGI00124	293m8-m0117			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036804	RLGI00125	293m8-m0118			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036805	RLGI00126	293m8-m0119			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036806	RLGI00127	293m8-m0120			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036807	RLGI00128	293m8-m0121			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036808	RLGI00129	293m8-m0122			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036809	RLGI00130	293m8-m0123			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036810	RLGI00131	293m8-m0124			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036811	RLGI00132	293m8-m0125			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036812	RLGI00133	293m8-m0126			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036813	RLGI00134	293m8-m0127			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036814	RLGI00135	293m8-m0128			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036815	RLGI00136	293m8-m0129			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036816	RLGI00137	293m8-m0130			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036817	RLGI00138	293m8-m0131			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036818	RLGI00139	293m8-m0132			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036819	RLGI00140	293m8-m0133			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036820	RLGI00141	293m8-m0134			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036821	RLGI00142	293m8-m0135			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036822	RLGI00143	293m8-m0136			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036823	RLGI00144	293m8-m0137			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036824	RLGI00145	293m8-m0138			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036825	RLGI00146	293m8-m0139			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036826	RLGI00147	293m8-m0140			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036827	RLGI00148	293m8-m0141			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036828	RLGI00149	293m8-m0142			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036829	RLGI00150	293m8-m0143			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036830	RLGI00151	293m8-m0144			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036831	RLGI00152	293m8-m0145			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036832	RLGI00153	293m8-m0146			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036833	RLGI00154	293m8-m0147			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036834	RLGI00155	293m8-m0148			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036835	RLGI00156	293m8-m0149			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036836	RLGI00157	293m8-m0150			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036837	RLGI00158	293m8-m0151			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036838	RLGI00159	293m8-m0152			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036839	RLGI00160	293m8-m0153			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036840	RLGI00161	293m8-m0154			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036841	RLGI00162	293m8-m0155			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036842	RLGI00163	293m8-m0156			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036843	RLGI00164	293m8-m0157			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036844	RLGI00165	293m8-m0158			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036845	RLGI00166	293m8-m0159			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036846	RLGI00167	293m8-m0160			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036847	RLGI00168	293m8-m0161			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036848	RLGI00169	293m8-m0162			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036849	RLGI00170	293m8-m0163			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036850	RLGI00171	293m8-m0164			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036851	RLGI00172	293m8-m0165			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036852	RLGI00173	293m8-m0166			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036853	RLGI00174	293m8-m0167			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036854	RLGI00175	293m8-m0168			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036855	RLGI00176	293m8-m0169			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036856	RLGI00177	293m8-m0170			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036857	RLGI00178	293m8-m0171			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036858	RLGI00179	293m8-m0172			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036859	RLGI00180	293m8-m0173			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036860	RLGI00181	293m8-m0174			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036861	RLGI00182	293m8-m0175			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036862	RLGI00183	293m8-m0176			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036863	RLGI00184	293m8-m0177			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036864	RLGI00185	293m8-m0178			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036865	RLGI00186	293m8-m0179			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036866	RLGI00187	293m8-m0180			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036867	RLGI00188	293m8-m0181			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036868	RLGI00189	293m8-m0182			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036869	RLGI00190	293m8-m0183			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036870	RLGI00191	293m8-m0184			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036871	RLGI00192	293m8-m0185			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036872	RLGI00193	293m8-m0186			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036873	RLGI00194	293m8-m0187			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036874	RLGI00195	293m8-m0188			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036875	RLGI00196	293m8-m0189			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036876	RLGI00197	293m8-m0190			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036877	RLGI00198	293m8-m0191			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036878	RLGI00199	293m8-m0192			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036879	RLGI00200	293m8-m0193			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036880	RLGI00201	293m8-m0194			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036881	RLGI00202	293m8-m0195			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036882	RLGI00203	293m8-m0196			miRNA	Homo sapiens	22984580	Mitochondrion	Eembryonic kidney cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036883	RLGI00204	HM3-m0001			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036884	RLGI00205	HM3-m0002			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036885	RLGI00206	HM3-m0003			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036886	RLGI00207	HM3-m0004			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036887	RLGI00208	HM3-m0005			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036888	RLGI00209	HM3-m0006			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036889	RLGI00210	HM3-m0007			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036890	RLGI00211	HM3-m0008			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036891	RLGI00212	HM3-m0009			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036892	RLGI00213	HM3-m0010			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036893	RLGI00214	HM3-m0011			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036894	RLGI00215	HM3-m0012			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036895	RLGI00216	HM3-m0013			miRNA	Homo sapiens	22984580	Mitochondrion	HeLa cell	Next-generation sequencing	"Reads were subsequently mapped to identify 4 395 094 and 3 676 525 reads that matched sequences in the mouse genome and miRBase in uninfected and prion-infected exosomes, respectively (Supplementary Table S4). Data are collected from Table S4: Putative novel miRNAs associated with mitochondria of HEK293 and HeLa.  "
RLID00036896	RLGI00217	hsa-miRPlus-A1031			miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036897	RLGI00218	hsa-miRPlus-C1087			miRNA	Homo sapiens	24460325	Exosome	K562 cell	Microarray	"Cluster analysis arranged samples and miRNAs into groups based on their expression levels, which allowed us to hypothesize the relationships between miRNAs and samples. Interestingly, 49 miRNAs were up regulated in exosomes as compared to K562 cells (Table 1), with both P-value of <= 0.05 and more than 1.5-fold changes. Data are collected from Table 1. Differentially Expressed miRNAs Between Exosomes and K562 Cells. "
RLID00036898	RLGI00219	hsa-miRPlus-C1089			miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036899	RLGI00220	hsa-miRPlus-D1033			miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036900	RLGI00221	hsa-miRPlus-D1046			miRNA	Homo sapiens	21637849	Mitochondrion	Skeletal muscular cell	In situ hybridization|qRT-PCR	"Table 4: List of microRNA significantly detected in the mitochondrial mRNA at three increasing mtRNA inputs (1, 5 and 35 uL). Table S3 List of microRNA significantly detected (Cp<35) in the mitochondrial mRNA at the two highest mtRNA inputs (5 and 35 uL). Data are collected from Table 4 and S3. "
RLID00036901	RLGI00222	novel-miR-01			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036902	RLGI00223	novel-miR-02			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036903	RLGI00224	novel-miR-03			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036904	RLGI00225	novel-miR-04			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036905	RLGI00226	novel-miR-05			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036906	RLGI00227	novel-miR-06			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036907	RLGI00228	novel-miR-07			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036908	RLGI00229	novel-miR-08			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036909	RLGI00230	novel-miR-09			miRNA	Mus musculus	23761296	Circulating	Serum	Next-generation sequencing	"In this way, we identified 39 putative novel miRNAs in the two libraries: 22 novel miRNAs in the lung tumor library and 17 in the normal adjacent lung tissue library. Nine novel miRNAs were shared by both libraries (Supplementary table S2). Data are collected from Table S2. "
RLID00036910	RLGI00231	csR-16sr-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data are shown in supplementary material.
RLID00036911	RLGI00232	csR-16sr-10			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036912	RLGI00233	csR-16sr-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036913	RLGI00234	csR-16sr-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036914	RLGI00235	csR-16sr-4			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036915	RLGI00236	csR-16sr-5			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036916	RLGI00237	csR-16sr-6			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036917	RLGI00238	csR-23sr-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036918	RLGI00239	csR-23sr-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036919	RLGI00240	csR-23sr-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036920	RLGI00241	csR-4.5sr-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036921	RLGI00242	csR-5sr-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036922	RLGI00243	csR-5sr-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036923	RLGI00244	csR-5sr-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036924	RLGI00245	csR-ig-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036925	RLGI00246	csR-ig-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036926	RLGI00247	csR-ig-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036927	RLGI00248	csR-ig-4			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036928	RLGI00249	csR-ig-5			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036929	RLGI00250	csR-ig-6			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036930	RLGI00251	csR-ig-7			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036931	RLGI00252	csR-mNDH-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036932	RLGI00253	csR-mPSB-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036933	RLGI00254	csR-mPSB-4			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036934	RLGI00255	csR-mPSB-5			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036935	RLGI00256	csR-mRPL-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036936	RLGI00257	csR-mYCF-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036937	RLGI00258	csR-mYCF-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036938	RLGI00259	csR-trnA-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036939	RLGI00260	csR-trnC-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036940	RLGI00261	csR-trnD-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036941	RLGI00262	csR-trnE-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036942	RLGI00263	csR-trnF-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036943	RLGI00264	csR-trnF-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036944	RLGI00265	csR-trnG-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036945	RLGI00266	csR-trnG-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036946	RLGI00267	csR-trnH-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036947	RLGI00268	csR-trnL-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036948	RLGI00269	csR-trnL-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036949	RLGI00270	csR-trnL-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036950	RLGI00271	csR-trnM-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036951	RLGI00272	csR-trnN-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036952	RLGI00273	csR-trnN-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036953	RLGI00274	csR-trnP-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036954	RLGI00275	csR-trnQ-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036955	RLGI00276	csR-trnS-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036956	RLGI00277	csR-trnT-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036957	RLGI00278	csR-trnV-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Microarray	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036958	RLGI00279	novel csRNA-1			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036959	RLGI00280	novel csRNA-2			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036960	RLGI00281	novel csRNA-3			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036961	RLGI00282	novel csRNA-4			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036962	RLGI00283	novel csRNA-5			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036963	RLGI00284	novel csRNA-6			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036964	RLGI00285	novel csRNA-7			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036965	RLGI00286	novel csRNA-8			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036966	RLGI00287	novel csRNA-9			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036967	RLGI00288	novel csRNA-10			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036968	RLGI00289	novel csRNA-11			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036969	RLGI00290	novel csRNA-12			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036970	RLGI00291	novel csRNA-13			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036971	RLGI00292	novel csRNA-14			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036972	RLGI00293	novel csRNA-15			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036973	RLGI00294	novel csRNA-16			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036974	RLGI00295	novel csRNA-17			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036975	RLGI00296	novel csRNA-18			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036976	RLGI00297	novel csRNA-19			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036977	RLGI00298	novel csRNA-20			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036978	RLGI00299	novel csRNA-21			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036979	RLGI00300	novel csRNA-22			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036980	RLGI00301	novel csRNA-23			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036981	RLGI00302	novel csRNA-24			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036982	RLGI00303	novel csRNA-25			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036983	RLGI00304	novel csRNA-26			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036984	RLGI00305	novel csRNA-27			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036985	RLGI00306	novel csRNA-28			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036986	RLGI00307	novel csRNA-29			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036987	RLGI00308	novel csRNA-30			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036988	RLGI00309	novel csRNA-31			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036989	RLGI00310	novel csRNA-32			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036990	RLGI00311	novel csRNA-33			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036991	RLGI00312	novel csRNA-34			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036992	RLGI00313	novel csRNA-35			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036993	RLGI00314	novel csRNA-36			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036994	RLGI00315	novel csRNA-37			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036995	RLGI00316	novel csRNA-38			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036996	RLGI00317	novel csRNA-39			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036997	RLGI00318	novel csRNA-40			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036998	RLGI00319	novel csRNA-41			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00036999	RLGI00320	novel csRNA-42			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00037000	RLGI00321	novel csRNA-43			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00037001	RLGI00322	novel csRNA-44			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00037002	RLGI00323	novel csRNA-45			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00037003	RLGI00324	novel csRNA-46			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00037004	RLGI00325	novel csRNA-47			csRNA	Brassica rapa subsp. Pekinensis	21639890	Chloroplast	Seedling	Next-generation sequencing	A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa). Data is shown in supplementary material.
RLID00037005	RLGI00326	ASAR6		Asynchronous replication and Autosomal RNA on chromosome 6	lncRNA	Homo sapiens	23593023	Nucleus	Skin fibroblast	In situ hybridization|RT-PCR	"ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. "
RLID00037006	RLGI00327	1/2-sbsRNA1			lncRNA	Homo sapiens	21307942	Cytoplasm	HeLa cell	qRT-PCR	"RT-semiquantitative (sq)PCR (Supplementary Fig. 2a) demonstrated that 1/2-sbsRNA1 is detected in cytoplasmic but not nuclear HeLa-cell fractions and is polyadenylated (Supplementary Fig. 2b,c).  "
RLID00037007	RLGI00328	alncRNA-EC1			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037008	RLGI00329	alncRNA-EC2			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037009	RLGI00330	alncRNA-EC3			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037010	RLGI00331	alncRNA-EC7			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037011	RLGI00332	ASncmtRNAs-1			lncRNA	Homo sapiens	21347712	Nucleus	Kidney	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037012	RLGI00332	ASncmtRNAs-1			lncRNA	Mus musculus	21347712	Nucleus	Testis	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037013	RLGI00333	ASncmtRNAs-2			lncRNA	Homo sapiens	21347712	Nucleus	Kidney	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037014	RLGI00333	ASncmtRNAs-2			lncRNA	Mus musculus	21347712	Nucleus	Testis	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037015	RLGI00334	Bsr			lncRNA	Rattus norvegicus	17507654	Cytoplasm	Fibroblast	In situ hybridization	"On drug treatments, a fraction of Bsr RNA relocalizes to the cytoplasm and associates with stress granules (SGs), but not with P-bodies, pointing to a potential link between SGs and the metabolism of ncRNA. Thus, Bsr might represent a novel type of nuclear-retained transcript. "
RLID00037016	RLGI00334	Bsr			lncRNA	Rattus norvegicus	10095072	Nucleus	Brain	In situ hybridization	None of the ORFs found in cDNA sequences is likely to be significant;Bsr RNA appears not to be polyadenylated at its 3'end;Bsr RNA was localized in the nucleus.
RLID00037017	RLGI00335	elncRNA-EC1			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037018	RLGI00335	elncRNA-EC3			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037019	RLGI00336	lincMKLN-1			lncRNA	Homo sapiens	19571010	Nucleus	HFF|HLF|HeLa cell	Fluorescence in situ hybridization	"Figure 3b: Subcellular localization analysis of lincRNAs by RNA FISH demonstrates localization of lincRNAs to the nucleus. Each panel represents the in situ hybridization of �0 fluorescently labeled DNA oligos with complementarity to the interrogated lincRNA. RNA FISH experiments were performed in male hFF for each represented lincRNA (XIST, HOTAIR, TUG-1, lincMKLN-1, lincFOXF1, and lincSFPQ), and also in female hLF for XIST (XX). White “speckles�indicate the subcellular localization of each lincRNA. The nuclear compartment is demarked by DAPI staining (purple). "
RLID00037020	RLGI00337	lincSFPQ			lncRNA	Homo sapiens	19571010	Nucleus	HFF|HLF|HeLa cell	Fluorescence in situ hybridization	"Figure 3b: Subcellular localization analysis of lincRNAs by RNA FISH demonstrates localization of lincRNAs to the nucleus. Each panel represents the in situ hybridization of �0 fluorescently labeled DNA oligos with complementarity to the interrogated lincRNA. RNA FISH experiments were performed in male hFF for each represented lincRNA (XIST, HOTAIR, TUG-1, lincMKLN-1, lincFOXF1, and lincSFPQ), and also in female hLF for XIST (XX). White “speckles�indicate the subcellular localization of each lincRNA. The nuclear compartment is demarked by DAPI staining (purple). "
RLID00037021	RLGI00337	lincSFPQ			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037022	RLGI00337	lincSFPQ			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037023	RLGI00337	lincSFPQ			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037024	RLGI00338	Delta-zein			mRNA	Oryza sativa	19508424	Endoplasmic reticulum	Endosperm	RT-PCR	"When the 10-kDa Delta-zein RNAs were mis-localized to the cisternal ER (Figure 2d), zein polypeptides were evident only in the PSVs (Figures 2e,f and 4b). These results indicate that the final site of deposition of 10-kDa Delta-zein within the endomembrane system is dependent on its RNA location to distinct cortical ER subdomains. "
RLID00037025	RLGI00338	Delta-zein			mRNA	Oryza sativa	19605415	Endoplasmic reticulum	Endosperm	RT-PCR	"Fig. 1 shows the schematic representation of the 10 kDa δ-zein transgenes containing various segments of the glutelin transcript sequences as well as their spatial distribution to the PB-ER and cisternal ER as viewed by in situ RT-PCR using the 10 kDa δ-zein-specific primers. In the absence of glutelin sequences, the 10 kDa δ-zein RNA is targeted to the PB-ER in transgenic rice endosperm cells (Hamada et al. 2003b). The presence of intact glutelin transcript sequences as part of the 3�UTR resulted in re-directing RNA targeting to the cisternal ER. "
RLID00037026	RLGI00339	ZNF2			lncRNA	Saccharomyces cerevisiae	26588844	Nucleus	Yeast	Fluorescence in situ hybridization	"Nonetheless, as expected for an mRNA, we observed ZNF2 transcripts in both the nucleus and the cytosol (Fig 7E and 7F). Interestingly, we observed a higher percentile of ZNF2 transcripts localized in the nuclei in the rze1Δ mutant (44.7% cytoplasmic: 55.2% nuclear distribution compared to that in the wild type (69.6% cytoplasmic: 30.4% nuclear distribution) (Fig 7G and S2 and S3 Tables). "
RLID00037027	RLGI00339	ZNF2			mRNA	Saccharomyces cerevisiae	26588844	Cytoplasm	Yeast	Fluorescence in situ hybridization	"Nonetheless, as expected for an mRNA, we observed ZNF2 transcripts in both the nucleus and the cytosol (Fig 7E and 7F). Interestingly, we observed a higher percentile of ZNF2 transcripts localized in the nuclei in the rze1Δ mutant (44.7% cytoplasmic: 55.2% nuclear distribution compared to that in the wild type (69.6% cytoplasmic: 30.4% nuclear distribution) (Fig 7G and S2 and S3 Tables). "
RLID00037028	RLGI00340	ZNF160			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037029	RLGI00341	ZF-1 			mRNA	Ascidian	17570671	Posterior	Embryo	Immunostaining	"We observed localization of ZF-1 mRNA, which is a type I postplasmic/PEM mRNA, as an indicator for PVC . In control MO-injected embryos, ZF-1 mRNA was localized close to the posterior pole at the four- and eight-cell stages in all cases (n = 12 and 19 for the four- and eight- cell  embryos,  respectively; Figures  4 A-4B 0 ,  white  arrows), whereas in embryos injected with Hr-PEM MO, ZF-1 mRNA was located more vegetally (92% and 100% of 13 and 14 cases at the four- and eight-cell stages, respectively; Figures  4 C-4D 0 ). "
RLID00037030	RLGI00341	ZF-1 			mRNA	Ascidian	17570671	Vegetal	Embryo	Immunostaining	"We observed localization of ZF-1 mRNA, which is a type I postplasmic/PEM mRNA, as an indicator for PVC . In control MO-injected embryos, ZF-1 mRNA was localized close to the posterior pole at the four- and eight-cell stages in all cases (n = 12 and 19 for the four- and eight- cell  embryos,  respectively; Figures  4 A-4B 0 ,  white  arrows), whereas in embryos injected with Hr-PEM MO, ZF-1 mRNA was located more vegetally (92% and 100% of 13 and 14 cases at the four- and eight-cell stages, respectively; Figures  4 C-4D 0 ). "
RLID00037031	RLGI00342	zein			mRNA	Oryza sativa	19508424	Endoplasmic reticulum	Endosperm	RT-PCR	"These hybrid GFP-zein RNAs (Figure 1, constructs 3 and 4) were distributed not only to the PB-ER but also to the cisternal ER. "
RLID00037032	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	7505061	Mitochondrion	Oocyte	-	Xlsirts are a family of interspersed repeat RNAs from Xenopus laevis that contain from 3 to 13 repeat units (each 79 to 81 nucleotides long) flanked by unique sequences. They are homologous to the mammalian Xist gene that is involved in X chromosome inactivation. Xlsirt RNA appears first in the mitochondrial cloud (Balbiani body) in stage 2 oocytes and is then translocated as island-like structures to the vegetal cortex at early stage 3 coincident with the localization of the germ plasm. Exogenous Xlsirt RNA injected into oocytes translocates to the location of the endogenous RNA at that particular stage.
RLID00037033	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	7505061	Vegetal	Oocyte	-	Xlsirts are a family of interspersed repeat RNAs from Xenopus laevis that contain from 3 to 13 repeat units (each 79 to 81 nucleotides long) flanked by unique sequences. They are homologous to the mammalian Xist gene that is involved in X chromosome inactivation. Xlsirt RNA appears first in the mitochondrial cloud (Balbiani body) in stage 2 oocytes and is then translocated as island-like structures to the vegetal cortex at early stage 3 coincident with the localization of the germ plasm. Exogenous Xlsirt RNA injected into oocytes translocates to the location of the endogenous RNA at that particular stage.
RLID00037034	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	7539356	Mitochondrion	Oocyte	In situ hybridization	"One of these, through which Xlsirts, Xcat2 and Xwnt11 are localized, involves transport during stages 1 and 2 of oogenesis via a region of the mitochondrial cloud that we call the message transport organizer or METRO. This pathway involved three steps, transport of RNA from the GV to the mitochondrial cloud, sorting of the RNAs to specific regions of the METRO, and translocation to and anchoring at the vegetal cortex. "
RLID00037035	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	8948579	Cytoplasm	Oocyte	In situ hybridization	During translocation through the cytoplasm Xlsirt and Xcat2 RNAs were detected associated with cytoplasmic particles of different morphologies.
RLID00037036	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	8948579	Mitochondrion	Oocyte	In situ hybridization	"In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud.  "
RLID00037037	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	8948579	Vegetal	Oocyte	In situ hybridization	"In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud.  "
RLID00037038	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	9545550	Mitochondrion	Oocyte	In situ hybridization	"To help distinguish between these alternatives, we made several constructs in which we linked the Xlsirts localization signals to various regions of the full-length Vg1 mRNA (Fig. 1) and tested the ability of the chimeric RNAs to move to the mitochondrial cloud in stage 1 oocytes. Fig. 2. Localization of endogenous and exogenous Xlsirts and Vg1 RNAs in oocytes. (A) Whole-mount in situ hybridization with Xlsirt RNA probe in late stage 1 oocytes. The arrow points to the endogenous Xlsirt RNA localized in the METRO region of the mitochondrial cloud. (C) Whole mount in situ hybridization with Vg1 RNA probe in late stage 1 oocytes, Vg1 RNA is dispersed in the oocyte cytoplasm and is excluded from the mitochondrial cloud (arrow). (D) Injected Vg1 RNA spreads throughout the cytoplasm and is excluded from the mitochondrial cloud in late stage 1 oocytes (arrow). (E) Stage 1 oocytes injected with Vg-Xlsirt chimeric RNA showing localization in the METRO region of the mitochondrial cloud (arrows). "
RLID00037039	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	9545550	Endoplasmic reticulum	Oocyte	In situ hybridization	Stage 3 oocyte showing endogenous Xlsirts (in situ hybridization) localized at the vegetal cortex (blue) at the leading edge of the wedge-shaped ER (red) (the arrow is pointing to the Xlsirts at the leading edge of the ER). Note that by stage 2 the ER is also uniformly distributed throughout the entire cortical region. Late stage 3 oocyte showing Xlsirts localized within the cortex (blue) and the remnants of the wedge containing ER (red).
RLID00037040	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	9545550	Vegetal	Oocyte	In situ hybridization	"To definitively demonstrate the co-localization of Vg1 mRNA with the wedge-shaped ER structure we performed in situ hybridization to identify the location of the Vg1 mRNA, and immunostaining with GRP-78 to identify the position of the ER. During stage 1, while Vg1 mRNA was dispersed throughout the cytoplasm, very little ER was associated with the cortex. (D) Stage 3 oocyte showing endogenous Xlsirts (in situ hybridization) localized at the vegetal cortex (blue) at the leading edge of the wedge-shaped ER (red) (the arrow is pointing to the Xlsirts at the leading edge of the ER). Note that by stage 2 the ER is also uniformly distributed throughout the entire cortical region. (E) Late stage 3 oocyte showing Xlsirts localized within the cortex (blue) and the remnants of the wedge containing ER (red). "
RLID00037041	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	9739112	Vegetal	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00037042	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	9739112	Mitochondrion	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00037043	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	9739112	Germ plasm	Oocyte	In situ hybridization	"We focused on Xlsirts, Xcat2, and Xwnt11 transcripts that are localized to the vegetal cortex through a region of the mitochondrial cloud called the messenger transport organizer (METRO) that also contains the nuage or germ plasm. At the ultrastructural level Xcat2 mRNA was detected on germinal granules while Xlsirts and Xwnt11 were associated with a fibrillar network of the germ plasm in stage-1 and stage-4 oocytes. "
RLID00037044	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00037045	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	11784096	Mitochondrion	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00037046	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	12676327	Vegetal	Oocyte	In situ hybridization	It is likely that the Xlsirt RNA at the cortex was heterogeneous population and that the individual Xlsirt RNAs were too rare to detect by this methodology.
RLID00037047	RLGI00343	Xlsirt			lncRNA	Xenopus laevis	19223445	Mitochondrion	Oocyte	Quantitative RNA localization assay	"Early RNAs, such as Xcat-2, Xlsirt, and Xwnt, become localized to a large subcellular structure called the Balbiani body or mitochondrial cloud. "
RLID00037048	RLGI00344	XLOC_012599			lncRNA	Homo sapiens	25630241	Cytoplasm	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037049	RLGI00345	XLOC_011950			lncRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037050	RLGI00345	XLOC_011950			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037051	RLGI00346	XLOC_011226			lncRNA	Homo sapiens	25630241	Cytoplasm	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037052	RLGI00346	XLOC_011226			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037053	RLGI00347	XLOC_011185			lncRNA	Homo sapiens	25630241	Cytoplasm	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037054	RLGI00347	XLOC_011185			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037055	RLGI00347	XLOC_011185			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037056	RLGI00348	XLOC_010514			lncRNA	Homo sapiens	25630241	Cytoplasm	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037057	RLGI00348	XLOC_010514			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037058	RLGI00349	XLOC_010017			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037059	RLGI00349	XLOC_010017			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037060	RLGI00349	XLOC_010017			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037061	RLGI00350	XLOC_009233			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037062	RLGI00351	XLOC_006922			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037063	RLGI00351	XLOC_006922			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037064	RLGI00351	XLOC_006922			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037065	RLGI00352	XLOC_005764			lncRNA	Homo sapiens	25630241	Nucleus	Foreskin fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037066	RLGI00352	XLOC_005764			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037067	RLGI00353	XLOC_004803			lncRNA	Homo sapiens	25630241	Cytoplasm	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037068	RLGI00353	XLOC_004803			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037069	RLGI00354	XLOC_003526			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037070	RLGI00354	XLOC_003526			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037071	RLGI00355	XLOC_002746			lncRNA	Homo sapiens	25630241	Cytoplasm	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037072	RLGI00355	XLOC_002746			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	qRT-PCR|Fluorescence in situ hybridization	"Figure 3: Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. Data are collected from Figure 3. "
RLID00037073	RLGI00355	XLOC_002746			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037074	RLGI00355	XLOC_002746			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037075	RLGI00356	XLOC_002094			lncRNA	Homo sapiens	25630241	Cytoplasm	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037076	RLGI00356	XLOC_002094			lncRNA	Homo sapiens	25630241	Nucleus	Lung fibroblast	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037077	RLGI00357	vGluT3			mRNA	Columba livia	25116931	Nucleus	Neuron|Retina	In situ hybridization	In situ hybridization revealed that the vGluT3 mRNA was expressed in neurons of the caudal linear nucleus (LC) of the brain and in amacrine cells of the inner nuclear layer of the retina. Double staining showed that the signals for the vGluT3 mRNA and serotonin colocalized in cells of the inner nuclear layer (Fig. 4E).
RLID00037078	RLGI00358	Val-TAC			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037079	RLGI00359	Val-GTG			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037080	RLGI00360	Val-GTA			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037081	RLGI00361	Val-CAC			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037082	RLGI00362	UsnRNAs			lncRNA	Homo sapiens	22855529	Nucleus	Hela cell	In situ hybridization	"Nuclear speckle-associated RNAs include uridine-rich small nuclear RNAs (UsnRNAs), 7SK RNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long ncRNA (lncRNA), and a population of uncharacterized poly(A)+ RNAs (Spector and Lamond, 2011 blue right-pointing triangle). "
RLID00037083	RLGI00363	UQCRB			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037084	RLGI00364	Ul			snRNA	Mus musculus	2967782	Nucleus	Oocyte|Embryo 	In situ hybridization	"In general Ul RNA transcripts appeared to be in both nuclear and cytoplasmic compartments, but when grain counts were carried out on larger photographs of blastocyst sections, the grain density was higher over the nuclei than over the cytoplasm.  "
RLID00037085	RLGI00364	Ul			snRNA	Mus musculus	2967782	Cytoplasm	Oocyte|Embryo 	In situ hybridization	"In general Ul RNA transcripts appeared to be in both nuclear and cytoplasmic compartments, but when grain counts were carried out on larger photographs of blastocyst sec- tions, the grain density was higher over the nuclei than over the cytoplasm.  "
RLID00037086	RLGI00365	UBE2V1			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037087	RLGI00366	U6			snRNA	Rattus norvegicus	25792744	Nucleus	Myocardium	qRT-PCR	"For both cytosolic isolation methods, immunoblotting showed enrichment of cytosolic proteins and depletion of nuclear/nucleolar proteins in cytosolic fractions, whereas qPCR demonstrated that the small ncRNAs 7SK and U6 were predominantly in the nuclear fraction (Fig. 1, E-H). "
RLID00037088	RLGI00367	U6			snRNA	Cricetulus griseus	16644724	Nucleus	Ovary cell	RT-PCR|Northern blot	"FIGURE 5. XBP1 mRNA splicing occurs in the cytoplasm. CHO/mXBP1ΔC(un)-d2EGFP reporter cells were treated with Tm for 4 h and then RNAs were isolated from total (T), nuclear (N), and cytoplasmic (C) fractions and used for RT-PCR analysis (A). To demonstrate the quality of the fractionation, nucleoplasmic (N) and cytoplasmic (C) RNAs were monitored by Northern blot analysis for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (B), tRNALys (C), and U6 small nuclear RNA (D). All RNAs shown were isolated from the same experiment. GADPH is shown as a loading control (E). The image of RNA stained with ethidium bromide in a formaldehyde/agarose gel demonstrates the quality of the RNA. N.B. indicates Northern blot. "
RLID00037089	RLGI00368	U6			snRNA	Mus musculus	18410515	Synapse	ForeBrain	qRT-PCR	"We noted that levels of all RNAs measured, including ribosomal 18S RNA, U6, CAMK2a and BC1, as well as mature microRNAs and their precursors, were lower in synaptosomes relative to that observed in synaptoneurosomes. "
RLID00037090	RLGI00369	U5			snRNA	Pisum sativum	2030967	Nucleus	Pea epicotyl tissue	Next-generation sequencing	"To identify the snRNA structural variants stably expressed in pea nuclei, we have constructed a cDNA library enriched in pea snRNAs. Initial screening of the cDNA library has led to the isolation of numerous Ul, U2, U4 and U5 snRNA clones. Sequence analysis of the clones has allowed us to demonstrate that four of the five snRNAs required for splicing are represented by sequence variants expressed in pea nuclei. "
RLID00037091	RLGI00370	U49			snoRNA	Zea mays	9664033	Nucleolus	Seed	In situ hybridization	"Fig. 2. Confocal images of maize root sections labelled with an antibody to fibrillarin (green) and by fluorescence in situ hybridization to each of the four novel snoRNAs (red). In each case the right hand panel shows the superimposition of the two labels. (A) U49 (box C/D) shows a similar pattern to fibrillarin, although the nucleolar cavity region is often labelled by the snoRNA probe (arrow). The coiled bodies are clearly labelled by anti-fibrillarin, but very weakly labelled by the snoRNA probe (arrowhead). (B) snoR1 (box C/D) shows a complementary labelling pattern to fibrillarin, and the nucleolar cavity is usually strongly labelled (arrow in red panel). The coiled bodies are not labelled by the snoRNA probe (arrowhead in green panel). (C) snoR2 (box H/ACA) labels a very similar region to fibrillarin, but the coiled bodies are not labelled (arrowhead in green panel). The nucleolar cavity is unlabelled by the snoRNA probe. (D) snoR3 (box C/D) shows a very similar labelling pattern to fibrillarin, but, again, the coiled bodies are unlabelled (arrowhead in green panel). Bar, 10um. Data are collected from Figure 2. "
RLID00037092	RLGI00371	U4			snRNA	Pisum sativum	2030967	Nucleus	Pea epicotyl tissue	Next-generation sequencing	"To identify the snRNA structural variants stably expressed in pea nuclei, we have constructed a cDNA library enriched in pea snRNAs. Initial screening of the cDNA library has led to the isolation of numerous Ul, U2, U4 and U5 snRNA clones. Sequence analysis of the clones has allowed us to demonstrate that four of the five snRNAs required for splicing are represented by sequence variants expressed in pea nuclei. "
RLID00037093	RLGI00372	U3			snoRNA	Solanum tuberosum	7816606	Nucleolus	Leaf|Ovule|Silk	In situ hybridization	Control in situ hybridisations were carried out using oligonucleotides complementary to plant Ul snRNA and U3 snoRNA sequences and showed specific labelling to the nucleoplasm and nucleoli respectively
RLID00037094	RLGI00373	U3			snoRNA	Zea mays	7816606	Nucleolus	Leaf|Ovule|Silk	In situ hybridization	Control in situ hybridisations were carried out using oligonucleotides complementary to plant Ul snRNA and U3 snoRNA sequences and showed specific labelling to the nucleoplasm and nucleoli respectively
RLID00037095	RLGI00374	U3			snoRNA	Olea europaea	9352223	Nucleus	Microsporocytes	In situ hybridization	"The presence of U3 snoRNA, as shown by in situ hybridization in nuclear bodies from plant material, is also evidence that these structures are coiled bodies. "
RLID00037096	RLGI00375	U2			snRNA	Pisum sativum	2030967	Nucleus	Pea epicotyl tissue	Next-generation sequencing	"To identify the snRNA structural variants stably expressed in pea nuclei, we have constructed a cDNA library enriched in pea snRNAs. Initial screening of the cDNA library has led to the isolation of numerous Ul, U2, U4 and U5 snRNA clones. Sequence analysis of the clones has allowed us to demonstrate that four of the five snRNAs required for splicing are represented by sequence variants expressed in pea nuclei. "
RLID00037097	RLGI00376	U2			snRNA	Human herpesvirus 4	1332043	Nucleus	Raji cell	In situ hybridization	"In contrast, use of the same technique indicated an exclusively nuclear location for cellular U2 RNA. "
RLID00037098	RLGI00377	U2			snRNA	Bos taurus	1571156	Nucleus	Oocyte	In situ hybridization	"The U2 antisense distribution was confined almost exclusively to the nuclei, since in embryo sections where a nucleus was not included in the plane of section (Fig. 2A; four-cell em- bryo, with only three nuclei in the plane of section), only a small number of silver grains in that region of the section were observed.  "
RLID00037099	RLGI00378	U2			snRNA	Allium cepa	22526497	Nucleus	Meristematic cell	Fluorescence in situ hybridization	"U2 snRNA was detected by in situ hybridisation. Although the overall signal intensity was weak, we were able to detect U2 snRNA which was localised at the chromatin periphery and in the condensed chromatin (Supplemental data Fig. S2b, c). "
RLID00037100	RLGI00378	U2			snRNA	Allium cepa	22526497	Nucleus	Meristematic cell	Fluorescence in situ hybridization	Fig.1f Localisation U2 snRNA. The bright spots are Cajal bodies (arrows). Diffuse staining of the nucleoplasm is also observed. Data are collected from Figure 1F.
RLID00037101	RLGI00379	U1			snoRNA	Solanum tuberosum	7816606	Nucleoplasm	Leaf|Ovule|Silk	In situ hybridization	Control in situ hybridisations were carried out using oligonucleotides complementary to plant Ul snRNA and U3 snoRNA sequences and showed specific labelling to the nucleoplasm and nucleoli respectively
RLID00037102	RLGI00380	U1			snoRNA	Zea mays	7816606	Nucleoplasm	Leaf|Ovule|Silk	In situ hybridization	Control in situ hybridisations were carried out using oligonucleotides complementary to plant Ul snRNA and U3 snoRNA sequences and showed specific labelling to the nucleoplasm and nucleoli respectively
RLID00037103	RLGI00381	U1			snRNA	Pisum sativum	2030967	Nucleus	Pea epicotyl tissue	Next-generation sequencing	"To identify the snRNA structural variants stably expressed in pea nuclei, we have constructed a cDNA library enriched in pea snRNAs. Initial screening of the cDNA library has led to the isolation of numerous Ul, U2, U4 and U5 snRNA clones. Sequence analysis of the clones has allowed us to demonstrate that four of the five snRNAs required for splicing are represented by sequence variants expressed in pea nuclei. "
RLID00037104	RLGI00382	tyrosine hydroxylase			mRNA	Rattus norvegicus	7753814	Axon	Hypothalamus	In situ hybridization	There is evidence to suggest that tyrosine hydroxylase mRNA is stored in the axons of magnocellular neurons in the internal zone of the median eminence and that this is transferred back into the perikaryon following the application of an acute osmotic stimulus.
RLID00037105	RLGI00383	Ty1			mRNA	Saccharomyces cerevisiae	24603646	Endoplasmic reticulum	Yeast	Northern blot	"The association of Ty1 RNA with SRP-RNC complexes and the presence of Gag in the ER lumen suggest that Gag is co-translationally translocated to the ER lumen. SRP directs nascent polypeptides to the ER lumen by binding to the SRP receptor and delivering the nascent peptides to the ER translocon, (Figure 1). Together, the results demonstrate that retrosomes are dynamic foci formed by the coalescence of Ty1 RNA translation complexes at the ER. "
RLID00037106	RLGI00383	Ty1			mRNA	Saccharomyces cerevisiae	24603646	Cytoplasm	Yeast	Northern blot	"Since Gag also associates with SRP-RNC complexes in the cytoplasm (Figure 4B), the most plausible scenario to explain these findings is that Gag, once it folds into a stable conformation in the ER lumen, is retrotranslocated to the cytoplasm, where it associates with Ty1 RNA on SRP-RNC complexes. "
RLID00037107	RLGI00384	tubulin			mRNA	Gallus gallus	2738094	Lamellipodium	Skeletal Myoblast|Fibroblast	Immunocytochemistry|In situ hybridization	"Conversely only 35 % of tubulin or vimentin messages were found in lamellipodia. Two cells, analyzed for hybridization to tubulin and vimentin mRNAs showed a perinuclear localization (65% of the messages), consistent with previous work cited above. "
RLID00037108	RLGI00384	tubulin			mRNA	Gallus gallus	3698103	Cytoplasm	Embryo blasts|Fibroblast	In situ hybridization	"Actin mRNA concentrations were highest at cell extremities, generally in lamellipodia, where grain densities were up to 16-fold higher than in areas near the nucleus. Vimentin mRNA, unlike actin mRNA, was distributed near the nucleus. Tubulin mRNA appeared most concentrated in the peripheral cytoplasm. These results demonstrate that cytoplasmic mRNAs are localized in specific, nonrandom cellular patterns and that localized concentrations of specific proteins may result from corresponding localization of their respective mRNAs. Hence, actin mRNA distribution may result in increased concentration of actin filaments in lamellipodia of motile cells. "
RLID00037109	RLGI00385	TUBBA4			mRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037110	RLGI00386	TRNY.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647887		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229472
RLID00037111	RLGI00387	TRNY.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647864		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229432
RLID00037112	RLGI00388	TRNY.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647912		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229427
RLID00037113	RLGI00389	TRNY	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647967		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229558
RLID00037114	RLGI00390	TRNW	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648076		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229594
RLID00037115	RLGI00390	TRNW	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647959		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229486
RLID00037116	RLGI00391	TRNV.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648057		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229384
RLID00037117	RLGI00392	TRNV.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647979		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229624
RLID00037118	RLGI00393	TRNV.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648036		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229578
RLID00037119	RLGI00394	TRNT.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647972		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229573
RLID00037120	RLGI00395	TRNT.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648017		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229560
RLID00037121	RLGI00396	TRNS.5	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647847		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229509
RLID00037122	RLGI00397	TRNS.4	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647917		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229471
RLID00037123	RLGI00398	TRNS.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648083		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229571
RLID00037124	RLGI00398	TRNS.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647954		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229435
RLID00037125	RLGI00400	TRNS.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648010		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229563
RLID00037126	RLGI00400	TRNS.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647856		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229426
RLID00037127	RLGI00402	TRNS.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648033		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229543
RLID00037128	RLGI00403	TRNR.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647971		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229648
RLID00037129	RLGI00404	TRNR.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647988		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229631
RLID00037130	RLGI00405	TRNR.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648032		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229545
RLID00037131	RLGI00406	TRNQ	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648030		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229540
RLID00037132	RLGI00406	TRNQ	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647922		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229488
RLID00037133	RLGI00408	TRNP	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647834		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229428
RLID00037134	RLGI00409	TRNN.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648012		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229647
RLID00037135	RLGI00410	TRNN.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647977		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229632
RLID00037136	RLGI00411	TRNN	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647945		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229431
RLID00037137	RLGI00412	TRNM.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647822		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229527
RLID00037138	RLGI00413	TRNM	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647994		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229579
RLID00037139	RLGI00414	TRNL.4	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648074		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229388
RLID00037140	RLGI00415	TRNL.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648002		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229636
RLID00037141	RLGI00416	TRNL.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648035		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229621
RLID00037142	RLGI00417	TRNL.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648013		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229574
RLID00037143	RLGI00418	TRNK.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647849		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229463
RLID00037144	RLGI00419	TRNK	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648066		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229537
RLID00037145	RLGI00420	TRNI.4	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648001		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229391
RLID00037146	RLGI00421	TRNI.3	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647976		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229382
RLID00037147	RLGI00422	TRNI.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648062		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229626
RLID00037148	RLGI00423	TRNI.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648088		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229618
RLID00037149	RLGI00424	TRNI	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647931		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229439
RLID00037150	RLGI00425	TRNH	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647964		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229535
RLID00037151	RLGI00426	TRNG.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648059		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229565
RLID00037152	RLGI00427	TRNG.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648058		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229544
RLID00037153	RLGI00428	TRNFM	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648005		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229566
RLID00037154	RLGI00429	TRNE	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648019		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229559
RLID00037155	RLGI00429	TRNE	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647892		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229473
RLID00037156	RLGI00431	TRND	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648009		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229557
RLID00037157	RLGI00431	TRND	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647861		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229500
RLID00037158	RLGI00431	TRND	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647861		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229500
RLID00037159	RLGI00434	TRNC	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648023		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229554
RLID00037160	RLGI00434	TRNC	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000647878		tRNA	Arabidopsis thaliana	22140109	Mitochondrion	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229429
RLID00037161	RLGI00436	tRNAVal-TAC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037162	RLGI00436	tRNAVal-TAC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037163	RLGI00438	tRNAVal-CAC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037164	RLGI00438	tRNAVal-CAC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037165	RLGI00440	tRNAVal-AAC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037166	RLGI00440	tRNAVal-AAC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037167	RLGI00442	tRNATyr-GTA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037168	RLGI00442	tRNATyr-GTA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037169	RLGI00444	tRNATrp-CCA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037170	RLGI00444	tRNATrp-CCA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037171	RLGI00446	tRNAThr-TGT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037172	RLGI00446	tRNAThr-TGT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037173	RLGI00448	tRNAThr-CGT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037174	RLGI00448	tRNAThr-CGT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037175	RLGI00450	tRNAThr-AGT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037176	RLGI00450	tRNAThr-AGT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037177	RLGI00452	tRNASer-TGA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037178	RLGI00452	tRNASer-TGA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037179	RLGI00454	tRNASer-GCT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037180	RLGI00454	tRNASer-GCT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037181	RLGI00456	tRNASer-CGA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037182	RLGI00456	tRNASer-CGA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037183	RLGI00458	tRNASer-AGA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037184	RLGI00458	tRNASer-AGA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037185	RLGI00460	tRNAPro-TGG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037186	RLGI00460	tRNAPro-TGG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037187	RLGI00462	tRNAPro-CGG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037188	RLGI00462	tRNAPro-CGG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037189	RLGI00464	tRNAPro-AGG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037190	RLGI00464	tRNAPro-AGG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037191	RLGI00466	tRNAPhe-GAA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037192	RLGI00466	tRNAPhe-GAA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037193	RLGI00468	tRNAMet-CAT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037194	RLGI00468	tRNAMet-CAT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037195	RLGI00470	tRNALys-TTT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037196	RLGI00470	tRNALys-TTT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037197	RLGI00472	tRNALys-CTT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037198	RLGI00472	tRNALys-CTT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037199	RLGI00474	tRNALeu-TAG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037200	RLGI00474	tRNALeu-TAG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037201	RLGI00476	tRNALeu-TAA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037202	RLGI00476	tRNALeu-TAA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037203	RLGI00478	tRNALeu-CAG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037204	RLGI00478	tRNALeu-CAG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037205	RLGI00480	tRNALeu-CAA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037206	RLGI00480	tRNALeu-CAA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037207	RLGI00482	tRNALeu-AAG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037208	RLGI00482	tRNALeu-AAG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037209	RLGI00484	tRNAIle-TAT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037210	RLGI00485	tRNAIle-AAT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037211	RLGI00485	tRNAIle-AAT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037212	RLGI00487	tRNAHis-GTG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037213	RLGI00487	tRNAHis-GTG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037214	RLGI00489	tRNAGly-TCC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037215	RLGI00489	tRNAGly-TCC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037216	RLGI00491	tRNAGly-GCC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037217	RLGI00491	tRNAGly-GCC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037218	RLGI00493	tRNAGly-CCC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037219	RLGI00493	tRNAGly-CCC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037220	RLGI00495	tRNAGlu-TTC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037221	RLGI00495	tRNAGlu-TTC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037222	RLGI00497	tRNAGlu-CTC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037223	RLGI00497	tRNAGlu-CTC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037224	RLGI00499	tRNA-GlnUUG			tRNA	Homo sapiens	21854988	Mitochondrion	-	qRT-PCR	"We found several nuclear-encoded tRNA species to be enriched within mitoplasts relative to mitochondrial preparations, including the previously detected tRNA-GlnUUG, an enrichment that was confirmed by qRT-PCR (Figure 3F,G). "
RLID00037225	RLGI00500	tRNAGln-TTG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037226	RLGI00500	tRNAGln-TTG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037227	RLGI00502	tRNAGln-CTG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037228	RLGI00502	tRNAGln-CTG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037229	RLGI00504	tRNA-derived_pseudogene			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037230	RLGI00504	tRNA-derived_pseudogene			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037231	RLGI00506	tRNACys-GCA			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037232	RLGI00506	tRNACys-GCA			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037233	RLGI00508	tRNAAsp-GTC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037234	RLGI00508	tRNAAsp-GTC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037235	RLGI00510	tRNAAsn-GTT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037236	RLGI00510	tRNAAsn-GTT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037237	RLGI00512	tRNAAsn-ATT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037238	RLGI00512	tRNAAsn-ATT			snoRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037239	RLGI00514	tRNAArg-TCT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037240	RLGI00514	tRNAArg-TCT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037241	RLGI00516	tRNAArg-TCG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037242	RLGI00516	tRNAArg-TCG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037243	RLGI00518	tRNAArg-CCT			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037244	RLGI00518	tRNAArg-CCT			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037245	RLGI00520	tRNAArg-CCG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037246	RLGI00520	tRNAArg-CCG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037247	RLGI00522	tRNAArg-ACG			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037248	RLGI00522	tRNAArg-ACG			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037249	RLGI00524	tRNAAla-TGC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037250	RLGI00524	tRNAAla-TGC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037251	RLGI00526	tRNAAla-CGC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037252	RLGI00526	tRNAAla-CGC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037253	RLGI00528	tRNAAla-AGC			tRNA	Homo sapiens	20498841	Nucleus	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037254	RLGI00528	tRNAAla-AGC			tRNA	Homo sapiens	20498841	Cytoplasm	Nasopharyngeal carcinoma cell	Next-generation sequencing	"Table S1: The N/C values of diverse sRNAs. sRNAs with raw read counts (non-normalized) more than 10 in at least one library were listed. N/C indicates the ratio of nuclear sRNA library count to cytoplasmic sRNA library count of each unique sequence. Nuclear and cytoplasmic indicate the read counts in the nuclear and cytoplasmic sRNA libraries, respectively. Read count of each sRNA were normalized to reads per million (RPM). Data are collected from Table S1. "
RLID00037255	RLGI00530	TRNA.2	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648024		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229381
RLID00037256	RLGI00531	TRNA.1	https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000648047		tRNA	Arabidopsis thaliana	22140109	Chloroplast	-	TAIR	Data are collected from TAIR database: https://www.arabidopsis.org/servlets/TairObject?type=locus&id=500229627
RLID00037257	RLGI00532	Tm-5			mRNA	Rattus norvegicus	8581312	Axon	Embryoneuron	In situ hybridization	Tm-5 mRNA is localized to the axonal pole of differentiating embryonic rat neurons.
RLID00037258	RLGI00533	TIGD1			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037259	RLGI00534	TDRD3			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037260	RLGI00535	SYS			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037261	RLGI00536	SYP			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037262	RLGI00537	SYE			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037263	RLGI00538	SUCLA2			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037264	RLGI00539	subunit A			mRNA	Manduca sexta	8786331	Ribosome	Epithelium	In situ hybridization	"In situ hybridization showed an even distribution of proteolipid mRNA throughout the cytosol in both cell types of the midgut (Fig. 2A), whereas subunit A mRNA was concentrated in the apical regions (Fig. 1A). Proteolipid mRNA distribution paralleled that of rough endoplasmic reticulum, whereas subunit A mRNA distribution paralleled that of free ribosomes: rough endoplasmic reticulum was abundant around the central nucleus but also extended into the entire cytosol, whereas free ribosomes were highly concentrated at the apical portion of the cell (Fig. 5A-C). In Malpighian tubules, however, subunit A mRNA (Fig. 3A) as well as the proteolipid mRNA (not shown) were evenly distributed. "
RLID00037265	RLGI00540	STI3			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037266	RLGI00541	SSUSB			mRNA	Lemna	12242353	Nucleus	Roots|Fronds	RNA Gel Blot	"While both small subunit genes encoding SSU1 and SSU5B were transcribed at comparable levels in root and frond nuclei, SSU1 mRNA accumulated to high levels in both roots and fronds in contrast to SSU5B mRNA, which was of very low abundance in the roots compared with the fronds. "
RLID00037267	RLGI00542	SSU1			mRNA	Lemna	12242353	Nucleus	Roots|Fronds	RNA Gel Blot	"While both small subunit genes encoding SSU1 and SSU5B were transcribed at comparable levels in root and frond nuclei, SSU1 mRNA accumulated to high levels in both roots and fronds in contrast to SSU5B mRNA, which was of very low abundance in the roots compared with the fronds. "
RLID00037268	RLGI00543	SSA			mRNA	Oryza sativa	19508424	Endoplasmic reticulum	Endosperm	RT-PCR	In situ RT-PCR using SSA-specific primers revealed that the distribution of SSA RNA was restricted solely to the cisternal ER (Figure 3a).
RLID00037269	RLGI00544	SRRP35			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037270	RLGI00545	s-rexs			mRNA	Rattus norvegicus	8793864	Axon	Cerebral cortex neuron	Subtractive hybridization	"In certain populations of adult brain neurons, most of s-rexs mRNA and a substantial amount of s-rexb mRNA are localized to the axonal pole of the cell body. "
RLID00037271	RLGI00546	s-rexb			mRNA	Rattus norvegicus	8793864	Axon	Cerebral cortex	Subtractive hybridization	"In certain populations of adult brain neurons, most of s-rexs mRNA and a substantial amount of s-rexb mRNA are localized to the axonal pole of the cell body. "
RLID00037272	RLGI00547	snoR3			snoRNA	Zea mays	9664033	Nucleolus	Seed	In situ hybridization	"Fig. 2. Confocal images of maize root sections labelled with an antibody to fibrillarin (green) and by fluorescence in situ hybridization to each of the four novel snoRNAs (red). In each case the right hand panel shows the superimposition of the two labels. (A) U49 (box C/D) shows a similar pattern to fibrillarin, although the nucleolar cavity region is often labelled by the snoRNA probe (arrow). The coiled bodies are clearly labelled by anti-fibrillarin, but very weakly labelled by the snoRNA probe (arrowhead). (B) snoR1 (box C/D) shows a complementary labelling pattern to fibrillarin, and the nucleolar cavity is usually strongly labelled (arrow in red panel). The coiled bodies are not labelled by the snoRNA probe (arrowhead in green panel). (C) snoR2 (box H/ACA) labels a very similar region to fibrillarin, but the coiled bodies are not labelled (arrowhead in green panel). The nucleolar cavity is unlabelled by the snoRNA probe. (D) snoR3 (box C/D) shows a very similar labelling pattern to fibrillarin, but, again, the coiled bodies are unlabelled (arrowhead in green panel). Bar, 10um. Data are collected from Figure 2. "
RLID00037273	RLGI00548	snoR2			snoRNA	Zea mays	9664033	Nucleolus	Seed	In situ hybridization	"Fig. 2. Confocal images of maize root sections labelled with an antibody to fibrillarin (green) and by fluorescence in situ hybridization to each of the four novel snoRNAs (red). In each case the right hand panel shows the superimposition of the two labels. (A) U49 (box C/D) shows a similar pattern to fibrillarin, although the nucleolar cavity region is often labelled by the snoRNA probe (arrow). The coiled bodies are clearly labelled by anti-fibrillarin, but very weakly labelled by the snoRNA probe (arrowhead). (B) snoR1 (box C/D) shows a complementary labelling pattern to fibrillarin, and the nucleolar cavity is usually strongly labelled (arrow in red panel). The coiled bodies are not labelled by the snoRNA probe (arrowhead in green panel). (C) snoR2 (box H/ACA) labels a very similar region to fibrillarin, but the coiled bodies are not labelled (arrowhead in green panel). The nucleolar cavity is unlabelled by the snoRNA probe. (D) snoR3 (box C/D) shows a very similar labelling pattern to fibrillarin, but, again, the coiled bodies are unlabelled (arrowhead in green panel). Bar, 10um. Data are collected from Figure 2. "
RLID00037274	RLGI00549	snoR1			snoRNA	Zea mays	9664033	Nucleolus	Seed	In situ hybridization	"Fig. 2. Confocal images of maize root sections labelled with an antibody to fibrillarin (green) and by fluorescence in situ hybridization to each of the four novel snoRNAs (red). In each case the right hand panel shows the superimposition of the two labels. (A) U49 (box C/D) shows a similar pattern to fibrillarin, although the nucleolar cavity region is often labelled by the snoRNA probe (arrow). The coiled bodies are clearly labelled by anti-fibrillarin, but very weakly labelled by the snoRNA probe (arrowhead). (B) snoR1 (box C/D) shows a complementary labelling pattern to fibrillarin, and the nucleolar cavity is usually strongly labelled (arrow in red panel). The coiled bodies are not labelled by the snoRNA probe (arrowhead in green panel). (C) snoR2 (box H/ACA) labels a very similar region to fibrillarin, but the coiled bodies are not labelled (arrowhead in green panel). The nucleolar cavity is unlabelled by the snoRNA probe. (D) snoR3 (box C/D) shows a very similar labelling pattern to fibrillarin, but, again, the coiled bodies are unlabelled (arrowhead in green panel). Bar, 10um. Data are collected from Figure 2. "
RLID00037275	RLGI00550	sno-lncRNA5			lncRNA	Homo sapiens	22959273	Nucleus	Human cell lines	In situ hybridization	"Figure 3. Nuclear Localization of snolncRNAs (A) Each PWS region sno-lncRNAexhibits strong nuclear accumulation in PA1 cells. RNA ISH (green) was performed with individual probes recognizing the internal sequence of each snolncRNA, or with pooled probes recognizing all PWS regionsno-lncRNAs (bottom right). Representative images are shown. DAPI is in blue and the white scale bar in all images denotes 10mm. (B) Sno-lncRNAs do not accumulate in either nucleoli or CBs. Costaining of sno-lncRNAs (green) and marker proteins for nucleoli (Nucleolin, red) and CBs (Coilin, red), respectively in H9 cells. Representative images are shown. (C) Sno-lncRNAs accumulate at a single chromosomal locus. Double FISH ofsno-lncRNAs (green) and its adjacent DNA region (red) in both PA1 and H9 cells. A single Z stack of representative images acquired with an Olympus IX70 DeltaVision Deconvolution System microscope is shown. (D) Total RNA from PA1 cells was separated into cytoplasmic (not shown), nuclear soluble, and nuclear insoluble fractions. Bar plots represent relative abundance of RNAs in the nuclear soluble and insoluble fractions as measured by RT-qPCR. Data are collected from Figure 3. "
RLID00037276	RLGI00551	sno-lncRNA4			lncRNA	Homo sapiens	22959273	Nucleus	Human cell lines	In situ hybridization	"Figure 3. Nuclear Localization of snolncRNAs (A) Each PWS region sno-lncRNAexhibits strong nuclear accumulation in PA1 cells. RNA ISH (green) was performed with individual probes recognizing the internal sequence of each snolncRNA, or with pooled probes recognizing all PWS regionsno-lncRNAs (bottom right). Representative images are shown. DAPI is in blue and the white scale bar in all images denotes 10mm. (B) Sno-lncRNAs do not accumulate in either nucleoli or CBs. Costaining of sno-lncRNAs (green) and marker proteins for nucleoli (Nucleolin, red) and CBs (Coilin, red), respectively in H9 cells. Representative images are shown. (C) Sno-lncRNAs accumulate at a single chromosomal locus. Double FISH ofsno-lncRNAs (green) and its adjacent DNA region (red) in both PA1 and H9 cells. A single Z stack of representative images acquired with an Olympus IX70 DeltaVision Deconvolution System microscope is shown. (D) Total RNA from PA1 cells was separated into cytoplasmic (not shown), nuclear soluble, and nuclear insoluble fractions. Bar plots represent relative abundance of RNAs in the nuclear soluble and insoluble fractions as measured by RT-qPCR. Data are collected from Figure 3. "
RLID00037277	RLGI00552	sno-lncRNA3			lncRNA	Homo sapiens	22959273	Nucleus	Human cell lines	In situ hybridization	"Figure 3. Nuclear Localization of snolncRNAs (A) Each PWS region sno-lncRNAexhibits strong nuclear accumulation in PA1 cells. RNA ISH (green) was performed with individual probes recognizing the internal sequence of each snolncRNA, or with pooled probes recognizing all PWS regionsno-lncRNAs (bottom right). Representative images are shown. DAPI is in blue and the white scale bar in all images denotes 10mm. (B) Sno-lncRNAs do not accumulate in either nucleoli or CBs. Costaining of sno-lncRNAs (green) and marker proteins for nucleoli (Nucleolin, red) and CBs (Coilin, red), respectively in H9 cells. Representative images are shown. (C) Sno-lncRNAs accumulate at a single chromosomal locus. Double FISH ofsno-lncRNAs (green) and its adjacent DNA region (red) in both PA1 and H9 cells. A single Z stack of representative images acquired with an Olympus IX70 DeltaVision Deconvolution System microscope is shown. (D) Total RNA from PA1 cells was separated into cytoplasmic (not shown), nuclear soluble, and nuclear insoluble fractions. Bar plots represent relative abundance of RNAs in the nuclear soluble and insoluble fractions as measured by RT-qPCR. Data are collected from Figure 3. "
RLID00037278	RLGI00553	sno-lncRNA2			lncRNA	Homo sapiens	22959273	Nucleus	Human cell lines	In situ hybridization	"Figure 3. Nuclear Localization of snolncRNAs (A) Each PWS region sno-lncRNAexhibits strong nuclear accumulation in PA1 cells. RNA ISH (green) was performed with individual probes recognizing the internal sequence of each snolncRNA, or with pooled probes recognizing all PWS regionsno-lncRNAs (bottom right). Representative images are shown. DAPI is in blue and the white scale bar in all images denotes 10mm. (B) Sno-lncRNAs do not accumulate in either nucleoli or CBs. Costaining of sno-lncRNAs (green) and marker proteins for nucleoli (Nucleolin, red) and CBs (Coilin, red), respectively in H9 cells. Representative images are shown. (C) Sno-lncRNAs accumulate at a single chromosomal locus. Double FISH ofsno-lncRNAs (green) and its adjacent DNA region (red) in both PA1 and H9 cells. A single Z stack of representative images acquired with an Olympus IX70 DeltaVision Deconvolution System microscope is shown. (D) Total RNA from PA1 cells was separated into cytoplasmic (not shown), nuclear soluble, and nuclear insoluble fractions. Bar plots represent relative abundance of RNAs in the nuclear soluble and insoluble fractions as measured by RT-qPCR. Data are collected from Figure 3. "
RLID00037279	RLGI00554	sno-lncRNA1			lncRNA	Homo sapiens	22959273	Nucleus	Human cell lines	In situ hybridization	"Figure 3. Nuclear Localization of snolncRNAs (A) Each PWS region sno-lncRNAexhibits strong nuclear accumulation in PA1 cells. RNA ISH (green) was performed with individual probes recognizing the internal sequence of each snolncRNA, or with pooled probes recognizing all PWS regionsno-lncRNAs (bottom right). Representative images are shown. DAPI is in blue and the white scale bar in all images denotes 10mm. (B) Sno-lncRNAs do not accumulate in either nucleoli or CBs. Costaining of sno-lncRNAs (green) and marker proteins for nucleoli (Nucleolin, red) and CBs (Coilin, red), respectively in H9 cells. Representative images are shown. (C) Sno-lncRNAs accumulate at a single chromosomal locus. Double FISH ofsno-lncRNAs (green) and its adjacent DNA region (red) in both PA1 and H9 cells. A single Z stack of representative images acquired with an Olympus IX70 DeltaVision Deconvolution System microscope is shown. (D) Total RNA from PA1 cells was separated into cytoplasmic (not shown), nuclear soluble, and nuclear insoluble fractions. Bar plots represent relative abundance of RNAs in the nuclear soluble and insoluble fractions as measured by RT-qPCR. Data are collected from Figure 3. "
RLID00037280	RLGI00555	SncmtRNA			lncRNA	Homo sapiens	21347712	Nucleolus	Kidney	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037281	RLGI00555	SncmtRNA			lncRNA	Mus musculus	21347712	Nucleolus	Testis	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037282	RLGI00555	SncmtRNA			lncRNA	Homo sapiens	21347712	Nucleus	Kidney	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037283	RLGI00555	SncmtRNA			lncRNA	Mus musculus	21347712	Nucleus	Testis	In situ hybridizationq|Electron microscopy	"In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. "
RLID00037284	RLGI00559	shlncRNA-EC6			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037285	RLGI00561	SCL6			mRNA	Arabidopsis thaliana	23622241	Ribosome	-	RT-PCR	"MiRNA target transcripts, such as AGO1, PHB, CSD2, SPL3, SCL6, and TCP4, showed a significant increase in membrane-bound polysomes (MBPs) association in the double mutant, whereas non-target transcripts such as UBQ5, eIF4A, ACTIN8, At2g01570, At5g28770, and At5g66770 were similarly distributed along membrane-bound polysomes (MBPs) fractions in wild type and amp1 lamp1 (Fig 6E). "
RLID00037286	RLGI00562	RkB DNA-binding protein			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00037287	RLGI00564	RZE1			lncRNA	Saccharomyces cerevisiae	26588844	Nucleus	Yeast	Fluorescence in situ hybridization	We therefore decided to examine the subcellular localization of RZE1 transcripts in the wild-type cells under a mating-inducing condition. We found that RZE1 was predominantly localized in the nucleus (29.3% cytoplasmic: 70.6% nuclear distribution; n = 514) (Fig 7H and S2 Table).
RLID00037288	RLGI00564	RZE1			mRNA	Saccharomyces cerevisiae	26588844	Cytoplasm	Yeast	Fluorescence in situ hybridization	We therefore decided to examine the subcellular localization of RZE1 transcripts in the wild-type cells under a mating-inducing condition. We found that RZE1 was predominantly localized in the nucleus (29.3% cytoplasmic: 70.6% nuclear distribution; n = 514) (Fig 7H and S2 Table).
RLID00037289	RLGI00566	RpVegT			mRNA	Rana pipiens	15515051	Vegetal	Oocyte	In situ hybridization	"As with RpDazl, RpVegT RNA was localized to a region of the cortex of the clear previtellogenic oocyte (Fig. 4c), although the localization was not as sharply delineated as for RpDazl(Fig. 4a). "
RLID00037290	RLGI00567	RPL34			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037291	RLGI00568	RPL12p			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037292	RLGI00569	RPL12m			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037293	RLGI00570	RPL12c			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037294	RLGI00571	RpDazl			mRNA	Rana pipiens	15515051	Vegetal	Oocyte	In situ hybridization	"To see whether this localization is conserved, the location of RpDazl RNA was examined by in situ hybridization. In full-grown oocytes, RpDazl RNA was localized to the vegetal cortex (Fig. 3a), as in X. laevis. Fig. 3. Whole mount in situ hybridization for RpDazl RNA. "
RLID00037295	RLGI00572	RNase P RNA			mRNA	Saccharomyces cerevisiae	20691904	Mitochondrion	Yeast	RT-PCR	"Figure 4: PNPASE Augments RNase P, 5S rRNA, and MRP RNA Import into Yeast Mitochondria. Data are collected from Figur 4. "
RLID00037296	RLGI00573	RH63320-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037297	RLGI00574	RH57802			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037298	RLGI00575	RH55307			mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037299	RLGI00576	RH53041			mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037300	RLGI00576	RH53041			mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037301	RLGI00578	RH49548			mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037302	RLGI00578	RH49548			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037303	RLGI00578	RH49548			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037304	RLGI00578	RH49548			mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037305	RLGI00582	RH48308			mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037306	RLGI00583	RH47707			mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037307	RLGI00583	RH47707			mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037308	RLGI00585	RH47344			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037309	RLGI00586	RH46030			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037310	RLGI00587	RH43693			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037311	RLGI00587	RH43693			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037312	RLGI00589	RH41467			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037313	RLGI00590	RH39561			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037314	RLGI00591	RH35946			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037315	RLGI00591	RH35946			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037316	RLGI00591	RH35946			mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037317	RLGI00594	RH34608			mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037318	RLGI00595	RH33996-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037319	RLGI00596	RH33270			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037320	RLGI00597	RH28486			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037321	RLGI00598	RH26018			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037322	RLGI00598	RH26018			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037323	RLGI00600	RH25742			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037324	RLGI00600	RH25742			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037325	RLGI00600	RH25742			mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037326	RLGI00603	RH25161			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037327	RLGI00604	RH19967			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037328	RLGI00605	RH19630			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037329	RLGI00606	RH19246			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037330	RLGI00607	RH18418			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037331	RLGI00607	RH18418			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037332	RLGI00609	RH13993			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037333	RLGI00611	RH13061			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037334	RLGI00611	RH13061			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037335	RLGI00611	RH13061			mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037336	RLGI00611	RH13161			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037337	RLGI00614	RH07382			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037338	RLGI00614	RH07382			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037339	RLGI00616	RH06493			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037340	RLGI00617	RH04454			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037341	RLGI00618	RH01124			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037342	RLGI00618	RH01124			mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037343	RLGI00620	RE74714			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037344	RLGI00621	RE72565			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037345	RLGI00622	RE61907			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037346	RLGI00623	RE53686			mRNA	Drosophila melanogaster	25838129	Anterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037347	RLGI00623	RE53686			mRNA	Drosophila melanogaster	25838129	Posterior	Follicle cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037348	RLGI00625	RE36972			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037349	RLGI00625	RE36972			mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037350	RLGI00627	RE36565			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037351	RLGI00628	RE31004			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037352	RLGI00629	RE29470			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037353	RLGI00629	RE29470			mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037354	RLGI00631	RE25729			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037355	RLGI00632	RE18879			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037356	RLGI00633	RE17905			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037357	RLGI00633	RE17905			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037358	RLGI00635	RE17686			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037359	RLGI00636	RE14971			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037360	RLGI00637	RE12750			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037361	RLGI00638	RE11569			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037362	RLGI00638	RE11569			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037363	RLGI00640	RE08153			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037364	RLGI00641	RaxOS			lncRNA	Mus musculus	15703187	Nucleus	Embryonic tissue	In situ hybridization|RT-PCR	"We detected the expression in adult retina (postnatal day 30, P30) of Six3OS, Six6OS, Otx2OS, CrxOS and RaxOS (Fig. 3 and data not shown). In general, these transcripts were all expressed at higher levels in the inner nuclear layer (INL) and in the ganglion cell layer (GCL).  "
RLID00037365	RLGI00642	RACK1			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037366	RLGI00643	RAB32			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037367	RLGI00644	psbA			mRNA	Nicotiana tabacum	8612593	Chloroplast	Tobacco	Gel mobility shift	PsbA mRNA is the most actively translated chloroplast transcript in vivo under light-grown conditions and fusion to lacZ mRNA renders the translation product soluble and eliminates possible effects of the 3'- UTR of psbA mRNA on translation initiation.
RLID00037368	RLGI00645	proteolipid			mRNA	Manduca sexta	8786331	Endoplasmic reticulum	Epithelium	In situ hybridization	"In situ hybridization showed an even distribution of proteolipid mRNA throughout the cytosol in both cell types of the midgut (Fig. 2A), whereas subunit A mRNA was concentrated in the apical regions (Fig. 1A). Proteolipid mRNA distribution paralleled that of rough endoplasmic reticulum, whereas subunit A mRNA distribution paralleled that of free ribosomes: rough endoplasmic reticulum was abundant around the central nucleus but also extended into the entire cytosol, whereas free ribosomes were highly concentrated at the apical portion of the cell (Fig. 5A-C). In Malpighian tubules, however, subunit A mRNA (Fig. 3A) as well as the proteolipid mRNA (not shown) were evenly distributed. "
RLID00037369	RLGI00645	proteolipid			mRNA	Manduca sexta	8786331	Cytosol	Epithelium	In situ hybridization	"In situ hybridization showed an even distribution of proteolipid mRNA throughout the cytosol in both cell types of the midgut (Fig. 2A), whereas subunit A mRNA was concentrated in the apical regions (Fig. 1A). Proteolipid mRNA distribution paralleled that of rough endoplasmic reticulum, whereas subunit A mRNA distribution paralleled that of free ribosomes: rough endoplasmic reticulum was abundant around the central nucleus but also extended into the entire cytosol, whereas free ribosomes were highly concentrated at the apical portion of the cell (Fig. 5A-C). In Malpighian tubules, however, subunit A mRNA (Fig. 3A) as well as the proteolipid mRNA (not shown) were evenly distributed. "
RLID00037370	RLGI00647	Prolamine			mRNA	Oryza sativa	14523246	Endoplasmic reticulum	Endosperm	RT-PCR	"Prolamine and glutelin RNAs are localized to two subdomains of the cortical endoplasmic reticulum (ER), the protein body ER and the cisternal ER, in developing rice seeds. "
RLID00037371	RLGI00647	prolamine			mRNA	Oryza sativa	11048726	Endoplasmic reticulum	Endosperm	RT-PCR	These results indicate that prolamine and glutelin RNAs are distributed on spatially distinct ER subdomains and that prolamine RNAs are localized specifically to the prolamine protein bodies.
RLID00037372	RLGI00649	pro alpha 2 collagen			mRNA	Mus musculus	2405055	Cytoplasm	Liver	In situ hybridization	"In normal mouse liver, pro α2 cob mRNA was detected in a subset of sinusoidal lining cells and was localized to the cytoplasm.  "
RLID00037373	RLGI00650	PPIAL4Fv2			mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037374	RLGI00650	PPIAL4Fv2			mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037375	RLGI00652	PPIAL4Fv1			mRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037376	RLGI00652	PPIAL4Fv1			mRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037377	RLGI00654	PPARbeta			mRNA	Homo sapiens	10195695	Cytoplasm	Skin	In situ hybridization	Fig. 5. Distribution of PPARbeta mRNA in normal human epidermis. Sections of normal human skin were analyzed by in situ hybridization with a digoxigenin-labeled antisense PPARb probe and an anti-digoxigenenin antibody. The highest level of PPARbeta mRNA expression was found in the upper spinous and granular layers as indicated by the prominent staining of the cytoplasm of cells in the suprabasal layers of the epidermis.
RLID00037378	RLGI00655	PPARbeta			mRNA	Rattus norvegicus	11036239	Cytoplasm	Purkinje cell	In situ hybridization	The in situ hybridization assays showed that PPARbeta transcripts were localized in the cytoplasm of the Purkinje cells. Fig. 4. In situ hybridization detection of PPARb mRNA in cerebellar sections.
RLID00037379	RLGI00656	piR-61648			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037380	RLGI00657	piR-60565			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037381	RLGI00658	piR-59293			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037382	RLGI00659	piR-57816			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037383	RLGI00660	piR-57142			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037384	RLGI00661	piR-55361			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037385	RLGI00662	piR-52207			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037386	RLGI00663	piR-48209			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037387	RLGI00664	piR-41405			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037388	RLGI00665	piR-39980			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037389	RLGI00666	piR-39858			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037390	RLGI00667	piR-38581			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037391	RLGI00668	piR-36095			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037392	RLGI00669	piR-35982			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037393	RLGI00670	piR-34896			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037394	RLGI00671	piR-33863			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037395	RLGI00672	piR-32679			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037396	RLGI00673	piR-31068			piRNA	Homo sapiens	23302638	Exosome	Saliva	Next-generation sequencing	"Table 5. Ten Most Highly Expressed piRNAs of Exosome I, Exosome II and WS. Data are collected from Table 5. "
RLID00037397	RLGI00674	piR-014923			piRNA	Homo sapiens	25376581	Exosome	Saliva	DDPCR	"To test the presence of piRNAs in exosomes, 2 highly expressed piRNAs (piR-001184 and piR-014923) were chosen for ddPCR analysis (Fig. 3C). Both piRNAs were identified in at least 2 individuals, which demonstrated predominant localization in exosomal RNA fractions. "
RLID00037398	RLGI00675	piR-001184			piRNA	Homo sapiens	25376581	Exosome	Saliva	DDPCR	"To test the presence of piRNAs in exosomes, 2 highly expressed piRNAs (piR-001184 and piR-014923) were chosen for ddPCR analysis (Fig. 3C). Both piRNAs were identified in at least 2 individuals, which demonstrated predominant localization in exosomal RNA fractions. "
RLID00037399	RLGI00676	PHLP			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037400	RLGI00677	PhCRT			mRNA	Petunia hybrida	25732863	Cytoplasm	Pollen tube	Fluorescence in situ hybridization	"In elongated tubes of different lengths, PhCRT mRNA was diffusely distributed throughout the cytoplasm of the tube shank, extending from the base to the subapical zone (Fig. 2c, d).  "
RLID00037401	RLGI00677	PhCRT			mRNA	Petunia hybrida	25732863	Ribosome	Pollen tube	Fluorescence in situ hybridization	"As germination proceeded, the hybridization and immunolabeling signals were prominent in the cytoplasm of outgrowing pollen tubes (Figs. 2b and 3b). By performing optical sectioning, we observed that PhCRT transcripts accumulated at the base of outgrowing tubes, where they formed rings or collars in the cortical cytoplasm (bracketed region and arrows in Fig. 2b-b' ). In elongated tubes of different lengths, PhCRT mRNA was diffusely distributed throughout the cytoplasm of the tube shank, extending from the base to the subapical zone (Fig. 2c, d). The above results led us to propose that the common sites of PhCRT mRNA, CRT, and 18S rRNA localization in germinating pollen and growing pollen tubes are enriched in ER membrane-bound ribosomes. Together, our results show that the regions in which PhCRT mRNA, CRT protein, and 18S rRNA are localized are also rich in RER. "
RLID00037402	RLGI00677	PhCRT			mRNA	Petunia hybrida	25732863	Endoplasmic reticulum	Pollen tube	Fluorescence in situ hybridization	"As germination proceeded, the hybridization and immunolabeling signals were prominent in the cytoplasm of outgrowing pollen tubes (Figs. 2b and 3b). By performing optical sectioning, we observed that PhCRT transcripts accumulated at the base of outgrowing tubes, where they formed rings or collars in the cortical cytoplasm (bracketed region and arrows in Fig. 2b-b' ). In elongated tubes of different lengths, PhCRT mRNA was diffusely distributed throughout the cytoplasm of the tube shank, extending from the base to the subapical zone (Fig. 2c, d). The above results led us to propose that the common sites of PhCRT mRNA, CRT, and 18S rRNA localization in germinating pollen and growing pollen tubes are enriched in ER membrane-bound ribosomes. Together, our results show that the regions in which PhCRT mRNA, CRT protein, and 18S rRNA are localized are also rich in RER. "
RLID00037403	RLGI00680	PH05			mRNA	Saccharomyces cerevisiae	8405926	Ribosome	Yeast	Northern blot	"Fig. 1. Segregation of secretory protein mRNA to membrane- bound ribosomes. Northern blot analysis with CYH2, PRC1 and PH05. DNA fragments from the genes CYH2, PRC1 and PH05 hybridized to a Northern blot of 1 ug poly(A)+-RNA from membrane-bound (MBP) and free polysomes (FP). Data are collected from Figure 1. "
RLID00037404	RLGI00681	per			mRNA	Ephestia kuehniella	25637625	Nucleus	Eye photoreceptors	In situ hybridization	"In contrast, a clear daily rhythm in the intensity of nuclear per mRNA expression was found in the eye photoreceptors (Figure 4B). "
RLID00037405	RLGI00682	PEM			mRNA	Ascidian	17570671	Centrosome	Embryo	Immunostaining	"Immunostaining showed that the protein is also present in the posterior cortex and the in centrosome-attracting body (CAB) and that the localization is extraction-resistant. Here we show that PEM of Ascidian  is required for correct orientation of early-cleavage planes and  subsequent unequal cell divisions because it repeatedly pulls a centrosome toward the posterior cortex and the CAB, respectively, where PEM mRNA and protein are localized. "
RLID00037406	RLGI00682	PEM			mRNA	Ascidian	17570671	Cell cortex	Embryo	Immunostaining	"Then, it is highly concentrated into the CAB during cleavages by the eight-cell stage. PEM mRNA is anchored to cortical ER and relocates together with cortical ER. "
RLID00037407	RLGI00682	PEM			mRNA	Ascidian	17570671	Vegetal	Embryo	Immunostaining	"In the unfertilized egg, it is distributed in a gradient, with the highest concentration at the vegetal pole. Just after fertilization, the first phase of ooplasmic movement brings PEM mRNA to the vegetal pole. "
RLID00037408	RLGI00685	PDH-E2			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037409	RLGI00686	PDH-E1-Alpha			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037410	RLGI00687	pA6			mRNA	Doryteuthis pealeii	9272637	Axon	Nervous|skeletal muscle	In situ hybridization	The axonal localization of pA6 mRNA was unequivocally established by in situ hybridization histochemistry.
RLID00037411	RLGI00688	oviduct			mRNA	Ovis aries	8579840	Apical	Ampulla oviduct	In situ hybridization	"The cellular location of the oviduct protein mRNA varied depending on the position of epithelial cells in longitudinal mucosal folds. In epithelial cells at the free margins of folds, the oviduct protein mRNA was contained predominantly in the apical cytoplasm, although specific reaction product was present in peri-nuclear regions (Fig. 2A). "
RLID00037412	RLGI00689	Nucleobindin precursor			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00037413	RLGI00691	nRCC			mRNA	Drosophila melanogaster	25565208	Mitochondrion	HEK293T 	Fluorescence in situ hybridization	"In HEK293T cells, the nRCC mRNAs homologous to those regulated by PINK1 in flies were found in highly purified mito (Figure 2A, B; S2A).  "
RLID00037414	RLGI00692	NNOS			mRNA	Rattus norvegicus	11020337	Nucleus	Brain	In situ hybridization	"NNOS mRNA was not found in the normal ND neurons, but was shown in the normal RN (red nucleus) neurons. The normal RN neurons displayed mild nNOS mRNA expression (Fig. 12a). "
RLID00037415	RLGI00693	NK-1			mRNA	Felis catus	10521569	Cytoplasm	ForeBrain	In situ hybridization	NK-1 mRNA was localized in the cytoplasm but not nuclei of cat forebrain neurons.
RLID00037416	RLGI00694	Neutral amino acid transporter			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00037417	RLGI00695	NEP			mRNA	Mus musculus	8026647	Cytoplasm	Enterocytes	In situ hybridization	"Interestingly, there was only one peak position for NEP mRNA which was located in the cytoplasm above the nucleus. "
RLID00037418	RLGI00696	NDM29			lncRNA	Homo sapiens	20581224	Cytoplasm	Neuroblastoma cell	Microarray	"The subcellular localization of NDM29 was then determined by real-time RT-PCR, measuring the amount of NDM29 RNA in the cytosolic and in the nuclear fractions of SKNBE2 cells. We found 71% of NDM29 RNA in the cytosol and 29% in the nucleus.  "
RLID00037419	RLGI00696	NDM29			lncRNA	Homo sapiens	20581224	Nucleus	Neuroblastoma cell	Microarray	"The subcellular localization of NDM29 was then determined by real-time RT-PCR, measuring the amount of NDM29 RNA in the cytosolic and in the nuclear fractions of SKNBE2 cells. We found 71% of NDM29 RNA in the cytosol and 29% in the nucleus.  "
RLID00037420	RLGI00698	ncHoxD4			lncRNA	Homo sapiens	23133536	Cytoplasm	Breast cancer cell	In situ hybridization	"RNA probes for ncHoxA1, ncHoxD4, and HOTAIR were created and found to create a dot-like pattern in the cytoplasm surrounding the nucleus upon in situ hybridization (Figure 1).  "
RLID00037421	RLGI00699	ncHoxA1			lncRNA	Homo sapiens	23133536	Cytoplasm	Breast cancer cell	In situ hybridization	"RNA probes for ncHoxA1, ncHoxD4, and HOTAIR were created and found to create a dot-like pattern in the cytoplasm surrounding the nucleus upon in situ hybridization (Figure 1).  "
RLID00037422	RLGI00700	NADP-ME			mRNA	Nicotiana tabacum	24484954	Chloroplast	Leaf	qRT-PCR	The amount of NADP-ME protein and transcription of mRNA for chloroplastic NADP-ME isoform were increased indicating their enhanced synthesis de novo.
RLID00037423	RLGI00701	nad9			mRNA	Solanum tuberosum	8614643	Mitochondrion	Tubers	In situ hybridization|Northern blot|RT-PCR	"Using two primer pairs that will either specifically amplify the larger transcript or amplify both the larger and the smaller transcripts in RT-PCR analyses it was found that the larger nad9 transcripts are partially edited, while the smaller transcripts are fully edited. Both the larger and the smaller transcripts were found to be associated with mitochondrial polysomes. "
RLID00037424	RLGI00702	Na+/Cl taurine transporter			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"In examining the relative distribution of mRNAs between the total and ER-associated RNA pools, mRNAs were categorized into three classes: mRNAs present in the ER-associated pool but below the limit of detection in total RNA (ER-membrane-enriched); mRNAs present in total RNA but absent in ER-associated RNA (cytosol-enriched); and mRNAs present in both pools, but enriched fourfold or greater in ER-associated RNA (ER membrane and cytosol; Fig. 5B; Table 2). In Table 2, 10 representative mRNAs from each class are listed. "
RLID00037425	RLGI00703	Na+ channel mRNA			mRNA	Rattus norvegicus	8833997	Cell body	GFL neuron	In situ hybridization	In situ hybridization with dissociated GFL neurons maintained in primary culture verified that Na+ channel mRNA is confined to the cell body.
RLID00037426	RLGI00707	mtlrRNA			rRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00037427	RLGI00707	mtlrRNA			rRNA	Xenopus laevis	11784096	Mitochondrion	Oocyte	In situ hybridization	"The fourth pattern included mtlrRNA and mtsrRNA that were present in the mitochondria and also in the cytoplasm (Table 1; Kloc et al., 2001b). "
RLID00037428	RLGI00707	mtlrRNA			rRNA	Xenopus laevis	11784096	Cytoplasm	Oocyte	In situ hybridization	"The fourth pattern included mtlrRNA and mtsrRNA that were present in the mitochondria and also in the cytoplasm (Table 1; Kloc et al., 2001b). "
RLID00037429	RLGI00707	mtsrRNA			rRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00037430	RLGI00707	mtsrRNA			rRNA	Xenopus laevis	11784096	Mitochondrion	Oocyte	In situ hybridization	"The fourth pattern included mtlrRNA and mtsrRNA that were present in the mitochondria and also in the cytoplasm (Table 1; Kloc et al., 2001b). "
RLID00037431	RLGI00707	mtsrRNA			rRNA	Xenopus laevis	11784096	Cytoplasm	Oocyte	In situ hybridization	"The fourth pattern included mtlrRNA and mtsrRNA that were present in the mitochondria and also in the cytoplasm (Table 1; Kloc et al., 2001b). "
RLID00037432	RLGI00710	MRPL16			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037433	RLGI00711	MRP RNA			mRNA	Saccharomyces cerevisiae	20691904	Mitochondrion	Yeast	RT-PCR	"Figure 4: PNPASE Augments RNase P, 5S rRNA, and MRP RNA Import into Yeast Mitochondria. Data are collected from Figur 4. "
RLID00037434	RLGI00712	MRAK088388			lncRNA	Rattus norvegicus	24702795	Cytoplasm	Lung tissue	qRT-PCR|In situ hybridization	"MRAK088388 and MRAK081523 were analysed as long-intergenic non-coding RNAs (lincRNAs), and identified as orthologues of mouse lncRNAs AK088388 and AK081523, respectively. qRT-PCR and in situ hybridization (ISH) showed that they were significantly up-regulated, and located in the cytoplasm of interstitial lung cells. "
RLID00037435	RLGI00713	MRAK081523			lncRNA	Rattus norvegicus	24702795	Cytoplasm	Lung tissue	qRT-PCR|In situ hybridization	"MRAK088388 and MRAK081523 were analysed as long-intergenic non-coding RNAs (lincRNAs), and identified as orthologues of mouse lncRNAs AK088388 and AK081523, respectively. qRT-PCR and in situ hybridization (ISH) showed that they were significantly up-regulated, and located in the cytoplasm of interstitial lung cells. "
RLID00037436	RLGI00714	MOCS2B			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037437	RLGI00715	MHM			lncRNA	Gallus gallus	22546690	Nucleus	Embryonic cell	In situ hybridizationq|Northern blot	"The long non-coding RNA, MHM, is localised in the nucleus of female chick embryos. "
RLID00037438	RLGI00716	MDH			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037439	RLGI00717	MAP2C			mRNA	Mus musculus	8647897	Cell body	Mature neuron	In situ hybridization	"Initially, each was detected in axons and dendrites, although tau persisted only in axons, whereas MAP2C and MAP2 were restricted to cell bodies and dendrites. "
RLID00037440	RLGI00717	MAP2C			mRNA	Mus musculus	8647897	Dendrite	Mature neuron	In situ hybridization	"Initially, each was detected in axons and dendrites, although tau persisted only in axons, whereas MAP2C and MAP2 were restricted to cell bodies and dendrites. "
RLID00037441	RLGI00719	macho 1			mRNA	Ascidian	14573512	Cell cortex	Eggs|Zygotes|Embryo	In situ hybridization	The postplasmic RNAs macho 1 and HrPEM were located on the cER network and could be detached from it. We also suggest that the RNAs segregate and concentrate in posterior blastomeres through compaction of the cER to form the CAB. 
RLID00037442	RLGI00720	Lys-AAG			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037443	RLGI00721	Lys-AAA			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037444	RLGI00722	Lys			tRNA	Cricetulus griseus	16644724	Nucleus	Ovary cell	RT-PCR|Northern blot	"FIGURE 5. XBP1 mRNA splicing occurs in the cytoplasm. CHO/mXBP1ΔC(un)-d2EGFP reporter cells were treated with Tm for 4 h and then RNAs were isolated from total (T), nuclear (N), and cytoplasmic (C) fractions and used for RT-PCR analysis (A). To demonstrate the quality of the fractionation, nucleoplasmic (N) and cytoplasmic (C) RNAs were monitored by Northern blot analysis for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (B), tRNALys (C), and U6 small nuclear RNA (D). All RNAs shown were isolated from the same experiment. GADPH is shown as a loading control (E). The image of RNA stained with ethidium bromide in a formaldehyde/agarose gel demonstrates the quality of the RNA. N.B. indicates Northern blot. "
RLID00037445	RLGI00722	Lys			tRNA	Cricetulus griseus	16644724	Cytoplasm	Ovary cell	RT-PCR|Northern blot	"FIGURE 5. XBP1 mRNA splicing occurs in the cytoplasm. CHO/mXBP1ΔC(un)-d2EGFP reporter cells were treated with Tm for 4 h and then RNAs were isolated from total (T), nuclear (N), and cytoplasmic (C) fractions and used for RT-PCR analysis (A). To demonstrate the quality of the fractionation, nucleoplasmic (N) and cytoplasmic (C) RNAs were monitored by Northern blot analysis for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (B), tRNALys (C), and U6 small nuclear RNA (D). All RNAs shown were isolated from the same experiment. GADPH is shown as a loading control (E). The image of RNA stained with ethidium bromide in a formaldehyde/agarose gel demonstrates the quality of the RNA. N.B. indicates Northern blot. "
RLID00037446	RLGI00724	LUAT			lncRNA	Mus musculus	24365181	Cytoplasm	Thymocytes 	Next-generation sequencing	"Assessment of subcellular localization of LUATs using recently published RNA-seq data obtained from fractionated chromatin-associated, nucleoplasmic and cytoplasmic transcripts (Bhatt et al.), showed that they remains mainly associated with the chromatin fraction (Additional file 5: Figure S3), "
RLID00037447	RLGI00724	LUAT			lncRNA	Mus musculus	24365181	Nucleoplasm	Thymocytes 	Next-generation sequencing	"Assessment of subcellular localization of LUATs using recently published RNA-seq data obtained from fractionated chromatin-associated, nucleoplasmic and cytoplasmic transcripts (Bhatt et al.), showed that they remains mainly associated with the chromatin fraction (Additional file 5: Figure S3), "
RLID00037448	RLGI00724	LUAT			lncRNA	Mus musculus	24365181	Nucleus	Thymocytes 	Next-generation sequencing	"Assessment of subcellular localization of LUATs using recently published RNA-seq data obtained from fractionated chromatin-associated, nucleoplasmic and cytoplasmic transcripts (Bhatt et al.), showed that they remains mainly associated with the chromatin fraction (Additional file 5: Figure S3), "
RLID00037449	RLGI00727	lnc-996			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037450	RLGI00727	lnc-996			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037451	RLGI00729	lnc-994			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037452	RLGI00729	lnc-994			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037453	RLGI00731	lnc-962			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037454	RLGI00731	lnc-962			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037455	RLGI00733	lnc-861			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037456	RLGI00733	lnc-861			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037457	RLGI00735	lnc-803			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037458	RLGI00735	lnc-803			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037459	RLGI00737	lnc-793			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037460	RLGI00737	lnc-793			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037461	RLGI00739	lnc-776			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037462	RLGI00739	lnc-776			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037463	RLGI00741	lnc-686b			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037464	RLGI00741	lnc-686b			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037465	RLGI00743	lnc-686a			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037466	RLGI00743	lnc-686a			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037467	RLGI00745	lnc-666			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037468	RLGI00745	lnc-666			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037469	RLGI00747	lnc-613			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037470	RLGI00747	lnc-613			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037471	RLGI00749	lnc-561			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037472	RLGI00749	lnc-561			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037473	RLGI00751	lnc-509			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037474	RLGI00751	lnc-509			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037475	RLGI00753	lnc-460			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037476	RLGI00753	lnc-460			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037477	RLGI00755	lnc-456b			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037478	RLGI00755	lnc-456b			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037479	RLGI00757	lnc-456a			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037480	RLGI00757	lnc-456a			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037481	RLGI00759	lnc-405			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037482	RLGI00759	lnc-405			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037483	RLGI00761	lnc-389			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037484	RLGI00761	lnc-389			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037485	RLGI00763	lnc-312b			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037486	RLGI00763	lnc-312b			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037487	RLGI00765	lnc-312a			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037488	RLGI00765	lnc-312a			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037489	RLGI00767	lnc-31			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037490	RLGI00767	lnc-31			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037491	RLGI00769	lnc-267			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037492	RLGI00769	lnc-267			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037493	RLGI00771	lnc-254			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037494	RLGI00771	lnc-254			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037495	RLGI00773	lnc-214			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037496	RLGI00773	lnc-214			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037497	RLGI00775	lnc-182			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037498	RLGI00775	lnc-182			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037499	RLGI00777	lnc-165			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037500	RLGI00777	lnc-165			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037501	RLGI00779	lnc-149			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037502	RLGI00779	lnc-149			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037503	RLGI00781	lnc-083			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037504	RLGI00781	lnc-083			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037505	RLGI00783	lnc-082			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037506	RLGI00783	lnc-082			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037507	RLGI00785	lnc-058			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037508	RLGI00785	lnc-058			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037509	RLGI00787	lnc-049			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037510	RLGI00787	lnc-049			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037511	RLGI00789	lnc-023			lncRNA	Mus musculus	25512605	Nucleus	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037512	RLGI00789	lnc-023			lncRNA	Mus musculus	25512605	Cytoplasm	C2C12 cell	qRT-PCR	"FIG 3: Subcellular distribution of the novel lncRNAs. Histograms show the quantifications of sqRT-PCR performed on RNA extracted from cytoplasmic (Cyt) and nuclear (N) fractions of myoblasts maintained under GM or DM (day 2) conditions. Results of a representative experiment are shown in Fig. S3 in the supplemental material. (A) Graphs show the cytoplasmic/nuclear partitioning of the lncRNAs, considering their expression conditions in GM or DM. The red shadow highlights the region of the graph occupied by lncRNAs with a bipartite subcellular distribution as defined by cytoplasmic/nuclear partitioning of control transcripts (see below). (B) Graphs show the quantification of the subcellular localization of control transcripts used to test the quality of the cytoplasmic/nuclear fractionation under GM or DM conditions: precursor (pre-Gapdh) and mature Gapdh mRNA, Rnu1-2 (U1) snRNA, and Snord55 (sno55). The red shadow defines the cytoplasmic/nuclear partition region in which no evident cytoplasmic/nuclear distribution can be assigned. Error bars represent standard deviations of data from multiple independent experiments. "
RLID00037513	RLGI00794	lincRNA-uc003opf.1			lncRNA	Homo sapiens	23872665	Cytoplasm	Esophageal squamous cell	qRT-PCR	"To determine the cellular localization of lincRNA-uc003opf.1, we fractionated ESCC cell lines into nuclear and cytoplasmic fractions. We can thoroughly separate nucleus from cytoplasm, as indicated by the results showing that GAPDH mRNA was exclusively detected in the cytoplasmic fraction, whereas the transcriptional level of nucleus-retained U6 was predominantly found in the nuclear fraction. For EC9706 cell line, qRT-PCR analysis revealed that (mean +/- SD) 40.3 +/- 17.3% lincRNA-uc003opf.1 was detected in the nuclear fraction, and 59.7 +/- 17.3% resided in the cytoplasm fraction. We got the similar results in TE-1 cell line that 39.7 +/- 9.5% and 60.3 +/- 9.5% lincRNA-uc003opf.1 were detected in the nuclear fraction and the cytoplasm fraction, respectively (Figure 1A).  "
RLID00037514	RLGI00794	lincRNA-uc003opf.1			lncRNA	Homo sapiens	23872665	Nucleus	Esophageal squamous cell	qRT-PCR	"To determine the cellular localization of lincRNA-uc003opf.1, we fractionated ESCC cell lines into nuclear and cytoplasmic fractions. We can thoroughly separate nucleus from cytoplasm, as indicated by the results showing that GAPDH mRNA was exclusively detected in the cytoplasmic fraction, whereas the transcriptional level of nucleus-retained U6 was predominantly found in the nuclear fraction. For EC9706 cell line, qRT-PCR analysis revealed that (mean +/- SD) 40.3 +/- 17.3% lincRNA-uc003opf.1 was detected in the nuclear fraction, and 59.7 +/- 17.3% resided in the cytoplasm fraction. We got the similar results in TE-1 cell line that 39.7 +/- 9.5% and 60.3 +/- 9.5% lincRNA-uc003opf.1 were detected in the nuclear fraction and the cytoplasm fraction, respectively (Figure 1A).  "
RLID00037515	RLGI00796	LD42239-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037516	RLGI00796	LD42239-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037517	RLGI00798	LD40851-dg			mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037518	RLGI00798	LD40851-dg			mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037519	RLGI00798	LD40851-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037520	RLGI00801	LD40851-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Oocyte	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037521	RLGI00801	LD40851-dg			mRNA	Drosophila melanogaster	25838129	Posterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037522	RLGI00803	LD26231-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037523	RLGI00803	LD26231-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037524	RLGI00805	lacZ			mRNA	Saccharomyces cerevisiae	15899876	Cellular bud	Yeast	In situ hybridization	Measurement of the percentage of budding yeast cells with bud-localized lacZ mRNA fused to wild-type or mutated localization elements.
RLID00037525	RLGI00806	kiss2			mRNA	Anoplopoma fimbria	26386183	Cytoplasm	Oocyte	In situ hybridization	"In situ hybridization revealed that kiss2 mRNA was localized to cytoplasm of perinucleolus stage oocytes, suggesting it could play a local role in oogenesis or could be synthesized and stored within oocytes as maternal mRNA. "
RLID00037526	RLGI00807	Kinesin			mRNA	Doryteuthis pealeii	8207422	Axon	Loligo pealii	In situ hybridization	Kinesin mRNA is a component of a select group of mRNAs present in the squid giant axon.
RLID00037527	RLGI00808	IVD			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037528	RLGI00809	InsP3receptor			mRNA	Rattus norvegicus	7773006	Dendrite	Neuron	In situ hybridization	"Table 1. As of 1994, mRNAs that have been localized within dendrites by in situ hybridization.  Data are collected from Table 1. "
RLID00037529	RLGI00810	inf5			mRNA	Drosophila melanogaster	25838129	Anterior	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037530	RLGI00811	inf195			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037531	RLGI00812	inf183			mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037532	RLGI00813	inf126			mRNA	Drosophila melanogaster	25838129	Cytoplasm	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037533	RLGI00813	inf126			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037534	RLGI00815	IDH			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037535	RLGI00816	Hsp90			mRNA	Mus musculus	12923260	Ribosome	B cell	S1 nuclease protection assays	"Oligonucleotide probes were designed to hybridize with mRNAs encoding representative members of three classes of protein: soluble (GAPDH, Hsp90, and LDH), ER resident membrane (Sec61a and calnexin), and ER resident lumenal (BiP, calreticulin, and GRP94). "
RLID00037536	RLGI00817	hSNF2a			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037537	RLGI00818	hsa-miRPlus_28993			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037538	RLGI00819	hsa-miRPlus_28575			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037539	RLGI00820	hsa-miRPlus_28431			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037540	RLGI00821	hsa-miRPlus_28232			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037541	RLGI00822	hsa-miRPlus_27839			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037542	RLGI00823	hsa-miRPlus_27564			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037543	RLGI00824	hsa-miRPlus_27561			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037544	RLGI00825	hsa-miRPlus_27560			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037545	RLGI00826	hsa-miRPlus_21472			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037546	RLGI00827	hsa-miRPlus_17952			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037547	RLGI00828	hsa-miRPlus_17945			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037548	RLGI00829	hsa-miRPlus_17921			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037549	RLGI00830	hsa-miRPlus_17900			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037550	RLGI00831	hsa-miRPlus_17896			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037551	RLGI00832	hsa-miRPlus_17890			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037552	RLGI00833	hsa-miRPlus_17869			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037553	RLGI00834	hsa-miRPlus_17865			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037554	RLGI00835	hsa-miRPlus_17861			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037555	RLGI00836	hsa-miRPlus_17832			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037556	RLGI00837	hsa-miRPlus_11201			miRNA	Homo sapiens	24009880	Exosome	Mast cell	Microarray	"In the exosomes, 116 microRNAs were identified and 134 microRNAs were identified in the donor HMC-1 cells (Fig. 3a and 3b, Table I and Additional Information, Table S16). Data are collected from Table 1. "
RLID00037557	RLGI00838	hsa-miRPIus_42526			miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00037558	RLGI00839	hsa-miRPIus_42487			miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00037559	RLGI00840	hsa-miRPIus_17858			miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00037560	RLGI00841	hsa-miRPIus_17848			miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00037561	RLGI00842	hsa-miRPIus_17841			miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00037562	RLGI00843	hsa-miRPIus_17824			miRNA	Homo sapiens	22529849	Exosome	Saliva	-	Table 1: Exosomal miRNAs as potential biomarkers and therapeutic targets. Data are collected from Table 1.
RLID00037563	RLGI00844	hsa-miR-BART18-3p			miRNA	Homo sapiens	24858071	Circulating	Serum	Microarray	"Prediction of targets of differentially expressed miRNA and function annotation in peripheral blood of GBM patients. To understand the potential functions of significantly differentially expressed miRNA in the GBM, and to further explore the function of these predicted target genes, we selected the most upregulated coherent 12 miRNAs (hsa-miR-4726-5p, hsa-miR-1255b-2-3p, hsa-miR-340-5p, hsa-miR-4275, hsa-miR-4712-3p, hsa-miR-576-5p, hsa-miR-1299, hsa-miR-4268, hsa-miR-3591-5p, hsa-miR-626, hsa-miR-BART18-3p, hsa-miR-3169), and the most downregulated coherent 8 miRNAs (hsa-miR-320b, hsa-let-7g-5p, hsa-miR-486-5p, hsa-miR-7-5p, hsa-miR-4524b-5p, hsa-miR-3171, hsa-miR-1246, hsa-miR-1273g-3p) to perform Gene Ontology analysis and pathway analysis. "
RLID00037564	RLGI00845	HrWnt-5 mRNA			mRNA	Xenopus laevis	9694628	Vegetal	Embryo	In situ hybridization	"HrWnt-5mRNA is present in the vegetal cortex in unfertilized eggs. After fertilization, HrWnt-5 mRNA movesto the equatorial region to form a crescent-like structure. after which the mRNA is concentrated inthe posteriormost region of the embryo. "
RLID00037565	RLGI00846	Hr-PEM1			mRNA	Ascidian	16207760	Cell cortex	Embryo	RT-PCR	"The Hr-PEM1 mRNA-rich region always coincided with the small cER-rich region (Fig. 8B, arrowheads). These observations indicate that POPK-1 is required for proper concentration and positioning of cER, and that it affects the mRNA distribution via cER movements. "
RLID00037566	RLGI00846	Hr-PEM1			mRNA	Ascidian	18062956	Cell cortex	Oocyte	In situ hybridization	We have previously shown that PEM-1 mRNA is associated with a network of rough cortical Endoplasmic Reticulum (cER) polarized along the animal-vegetal (a-v) axis forming a cER-mRNA domain in mature oocytes.
RLID00037567	RLGI00848	Hr-PEM			mRNA	Ascidian	17570671	Posterior	Embryo	Immunostaining	"Furthermore, detailed analysis of the Hr-PEM knockdown embryos revealed that Hr-PEM also controls orientation of the cleavage planes as early as at the second and third cleavages, which are almost equal in size, by attracting one centrosome to the posterior-vegetal region where Hr-PEM mRNA and the protein are localized. "
RLID00037568	RLGI00849	HrPEM			mRNA	Ascidian	14573512	Cell cortex	Eggs|Zygotes|Embryo	In situ hybridization	The postplasmic RNAs macho 1 and HrPEM were located on the cER network and could be detached from it. We also suggest that the RNAs segregate and concentrate in posterior blastomeres through compaction of the cER to form the CAB. 
RLID00037569	RLGI00850	HL05382-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037570	RLGI00851	Histone deacetylase			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037571	RLGI00852	Heme synthetase			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037572	RLGI00853	HDV RNA			mRNA	Homo sapiens	9622127	Nucleoplasm	Hepatoma cell	In situ hybridizationq|Microscopy	"The human hepatoma cell line Huh7 was stably transfected with wild-type HDV cDNA and the viral RNAs were localized by in situ hybridization and fluorescence confocal microscopy. HDV RNA is detected throughout the nucleoplasm, with additional concentration in focal structures closely associated with nuclear speckles or clusters of interchromatin granules. "
RLID00037573	RLGI00853	HDV RNA			mRNA	Homo sapiens	9622127	Nucleus	Hepatoma cell	In situ hybridizationq|Microscopy	"The human hepatoma cell line Huh7 was stably transfected with wild-type HDV cDNA and the viral RNAs were localized by in situ hybridization and fluorescence confocal microscopy. HDV RNA is detected throughout the nucleoplasm, with additional concentration in focal structures closely associated with nuclear speckles or clusters of interchromatin granules. "
RLID00037574	RLGI00855	HCRSV RNA			mRNA	Hibiscus cannabinus	23155403	Nucleus	Seedling	In situ hybridization	"Hibiscus chlorotic ringspot virus (HCRSV) RNA was detected in the nucleus of infected cells, as shown by fluorescent in situ hybridization.  "
RLID00037575	RLGI00856	HAC1p			mRNA	Homo sapiens	12923260	Endoplasmic reticulum	Jurkat cell	-	"The Hac1p mRNA, which displays noncanonical partitioning to the endoplasmic reticulum, is one useful example of an mRNA whose localization may serve important roles in metabolic regulation. "
RLID00037576	RLGI00857	H2			mRNA	Cavia porcellus	9284338	Axon	Brain	In situ hybridization	"In many brain areas, the distribution of the H2 receptor and its messenger RNAs appeared to parallel that known for histaminergic axons. "
RLID00037577	RLGI00858	GUS			mRNA	Oryza sativa	11048726	Endoplasmic reticulum	Endosperm	RT-PCR	"While GUS transcripts are localized to the PB-ER in GUS::prolamine plants (Fig. 3b), such a distribution pattern was not evident in GUS::glutelin plants (Fig. 3c). These results confirm the RNA signal dependence of prolamine RNA localization to the PB-ER. "
RLID00037578	RLGI00859	granzymeA			mRNA	Homo sapiens	2157676	Cytoplasm	LAK cell	In situ hybridization	The presence of PI and granzymeA mRNA in the cytoplasm was confirmed by in situ hybridization using specific antisense probes.
RLID00037579	RLGI00860	GPXR			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037580	RLGI00861	Gly-GGY			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037581	RLGI00862	Gly-GGG			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037582	RLGI00862	Gly-GGG			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037583	RLGI00864	Gly-GGC			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037584	RLGI00864	Gly-GGC			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037585	RLGI00866	Gly-GGA			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037586	RLGI00867	Gly-GCCv2			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037587	RLGI00868	Gly-GCCv1			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037588	RLGI00869	Gly-CCCv2			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037589	RLGI00869	Gly-CCCv2			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037590	RLGI00871	Gly-CCCv1			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037591	RLGI00871	Gly-CCCv1			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037592	RLGI00873	glutelin			mRNA	Oryza sativa	11048726	Endoplasmic reticulum	Endosperm	RT-PCR	These results indicate that prolamine and glutelin RNAs are distributed on spatially distinct ER subdomains and that prolamine RNAs are localized specifically to the prolamine protein bodies.
RLID00037593	RLGI00873	glutelin			mRNA	Oryza sativa	14523246	Endoplasmic reticulum	Endosperm	RT-PCR	"Prolamine and glutelin RNAs are localized to two subdomains of the cortical endoplasmic reticulum (ER), the protein body ER and the cisternal ER, in developing rice seeds. "
RLID00037594	RLGI00873	glutelin			mRNA	Oryza sativa	19605415	Endoplasmic reticulum	Endosperm	RT-PCR	"Fig. 1 shows the schematic representation of the 10 kDa delta-zein transgenes containing various segments of the glutelin transcript sequences as well as their spatial distribution to the PB-ER and cisternal ER as viewed by in situ RT-PCR using the 10 kDa delta-zein-specific primers. In the absence of glutelin sequences, the 10 kDa delta-zein RNA is targeted to the PB-ER in transgenic rice endosperm cells (Hamada et al. 2003b). The presence of intact glutelin transcript sequences as part of the 3�UTR resulted in re-directing RNA targeting to the cisternal ER. "
RLID00037595	RLGI00876	Glu-GAG			tRNA	Mus musculus	22821563	Extracellular vesicle	T cell	Next-generation sequencing	"In cellular RNA, we observed fragments located at the 5�or 3′end of the mature tRNA (Table 3). However, the most abundant tRNA hits in shuttle RNA were all located at the 5′end of mature tRNAs. Data are collected from Table 3: Most abundant tRNA fragments in cellular and shuttle RNA. "
RLID00037596	RLGI00877	Glu-GAG			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037597	RLGI00877	Glu-GAG			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037598	RLGI00879	Glu-GAA			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037599	RLGI00879	Glu-GAA			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037600	RLGI00881	Glu-CTCv2			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037601	RLGI00881	Glu-CTCv2			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037602	RLGI00883	Glu-CTCv1			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037603	RLGI00883	Glu-CTCv1			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037604	RLGI00885	Glu-CTC			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037605	RLGI00885	Glu-CTC			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037606	RLGI00887	GH-RBP			mRNA	Rattus norvegicus	8022524	Cytoplasm	Anterior pituitary	In situ hybridization	"RGH-RBP mRNA was readily identified in the cytoplasmic matrix, associated with the endoplasmic reticulum and the nucleus of the somatotrophs, the lactotrophs and the gonadotrophs. "
RLID00037607	RLGI00888	GH23462			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037608	RLGI00889	GH06646-dg			mRNA	Drosophila melanogaster	25838129	Nucleus	Embryo	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037609	RLGI00890	GGGGCC microsatellite repeat RNA			mRNA	Rattus norvegicus	26650351	Cell body	Spinal cord neuron	In situ hybridization	"We confirmed that iPSNs contained nuclear GGGGCC RNA foci, but also found that 78 ± 12% SD (carrier 1; n=25 neurons) and 75 ± 11% SD (carrier 2; n=23) of iPSNs that contained nuclear GGGGCC RNA foci also contained neuritic GGGGCC RNA particles by in situ hybridization (Figure 1A,L). The GGGGCC RNA particles were detected both proximally and distally at over 45 μm from the cell body in neurites and were, in some cases, lined up, consistent with possible association with a cytoskeletal track (Figure 1A-B). In addition, GGGGCC repeat RNA particles were detected in the cell body in nearly all iPSNs that also contained GGGGCC RNA nuclear foci (Figure 1C, also Almeida et al., 2013). "
RLID00037610	RLGI00890	GGGGCC microsatellite repeat RNA			mRNA	Rattus norvegicus	26650351	Nucleus	Spinal cord neuron	In situ hybridization	"We confirmed that iPSNs contained nuclear GGGGCC RNA foci, but also found that 78 ± 12% SD (carrier 1; n=25 neurons) and 75 ± 11% SD (carrier 2; n=23) of iPSNs that contained nuclear GGGGCC RNA foci also contained neuritic GGGGCC RNA particles by in situ hybridization (Figure 1A,L). The GGGGCC RNA particles were detected both proximally and distally at over 45 μm from the cell body in neurites and were, in some cases, lined up, consistent with possible association with a cytoskeletal track (Figure 1A-B). In addition, GGGGCC repeat RNA particles were detected in the cell body in nearly all iPSNs that also contained GGGGCC RNA nuclear foci (Figure 1C, also Almeida et al., 2013). "
RLID00037611	RLGI00892	gD			mRNA	Bovine herpesvirus 1	25529439	Cytoplasm	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00037612	RLGI00892	gD			mRNA	Bovine herpesvirus 1	25529439	Nucleus	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00037613	RLGI00894	gC			mRNA	Bovine herpesvirus 1	25529439	Cytoplasm	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00037614	RLGI00894	gC			mRNA	Bovine herpesvirus 1	25529439	Nucleus	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00037615	RLGI00896	gB			mRNA	Bovine herpesvirus 1	25529439	Cytoplasm	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00037616	RLGI00896	gB			mRNA	Bovine herpesvirus 1	25529439	Nucleus	COS-7 cell	qRT-PCR	"We demonstrated interactions of VP8 with bICP0, gB, gC and gD mRNAs by RNA-immunoprecipitation and qPCR, both in the nucleus and cytoplasm of COS-7 cells. "
RLID00037617	RLGI00898	GASS			lncRNA	Homo sapiens	25630241	Nucleus	Hela cell	Florescence micrograph	"Figure 2: LncRNAs exhibit a variety of cellular localization patterns. Florescence micrographs of representative expressing cells for each of 34 lncRNAs with a validated probe set. LncRNA-cell pairs are classified to cellular localization types I to V as described in the Methods (marked by their border color). Magenta stars mark five lncRNAs that are presented in two different cell types and two different classes (see same row for comparison). Scale bar, 5 um; when a scale bar is not specified, reference the scale bar within the top left image. Top panel: fraction of each classification for each type across the full set of 70 valid lncRNA-cell pairs imaged. Data are collected from Figure 2. "
RLID00037618	RLGI00899	GAPDH			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037619	RLGI00900	ferritin H chain mRNA			mRNA	Rattus norvegicus	10860832	Cell body	Hippocampus	In situ hybridization	"The ferritin H chain mRNA was found to be highly enriched in the synaptosomes. In situ hybridization for the ferritin H chain mRNA in the cultured dissociated neurons and in the hippocampal brain slices demonstrated its existence in the dendritic region.  These data clearly indicate the selective translocation of the ferritin H chain mRNA into the dendrites and suggested the local expression of ferritin at the synapse. Therefore, the mRNAs of the ferritin H chain are located in the cell bodies and in the dendrites of the dentate gyrus neurons. "
RLID00037620	RLGI00900	ferritin H chain mRNA			mRNA	Rattus norvegicus	10860832	Dendrite	Hippocampus	In situ hybridization	"The ferritin H chain mRNA was found to be highly enriched in the synaptosomes. In situ hybridization for the ferritin H chain mRNA in the cultured dissociated neurons and in the hippocampal brain slices demonstrated its existence in the dendritic region.  These data clearly indicate the selective translocation of the ferritin H chain mRNA into the dendrites and suggested the local expression of ferritin at the synapse. Therefore, the mRNAs of the ferritin H chain are located in the cell bodies and in the dendrites of the dentate gyrus neurons. "
RLID00037621	RLGI00902	FAK1			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037622	RLGI00903	ERAIm454-557			mRNA	Homo sapiens	26068456	Cytoplasm	MCF-7 cell 	RT-PCR	"In the acute ER stress condition, the spliced mRNA of both ERAIm454-557 and endogenous XBP1 was significantly increased in the cytoplasm but not in the nucleus.  "
RLID00037623	RLGI00904	elastase I			mRNA	Rattus norvegicus	6918221	Endoplasmic reticulum	Acinar cell	In situ hybridization	"The mRNA for elastase I is localized in the rough endoplasmic reticulum of acinar cells, as expected for the site of synthesis of an exocrine secretory enzyme. "
RLID00037624	RLGI00905	eIF4E1			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037625	RLGI00906	eEF1-Alpha			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037626	RLGI00907	EEF1A1			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037627	RLGI00908	ecNOS			mRNA	Rattus norvegicus	9290578	Cytoplasm	Vascular endothelial cell	In situ hybridization	In situ hybridization showed that ecNOS mRNA was expressed in the cytoplasm of vascular endothelial cells in control and endotoxin-treated rats.
RLID00037628	RLGI00909	EBER-2			mRNA	Human herpesvirus 4	1332043	Nucleus	Raji cell	In situ hybridization	"In situ hybridization of fluorescent oligodeoxynucleotides complementary to either EBER-1 or EBER-2 in Raji cells gave a strong pattern of staining, as illustrated in Fig. 1. Both probes revealed an essentially identical subcellular distribution for the two RNAs, with staining of both nucleus and cytoplasm. "
RLID00037629	RLGI00909	EBER-2			mRNA	Human herpesvirus 4	1332043	Cytoplasm	Raji cell	In situ hybridization	"In situ hybridization of fluorescent oligodeoxynucleotides complementary to either EBER-1 or EBER-2 in Raji cells gave a strong pattern of staining, as illustrated in Fig. 1. Both probes revealed an essentially identical subcellular distribution for the two RNAs, with staining of both nucleus and cytoplasm. "
RLID00037630	RLGI00911	EBER-1			mRNA	Human herpesvirus 4	1332043	Cytoplasm	Raji cell	In situ hybridization	"In situ hybridization of fluorescent oligodeoxynucleotides complementary to either EBER-1 or EBER-2 in Raji cells gave a strong pattern of staining, as illustrated in Fig. 1. Both probes revealed an essentially identical subcellular distribution for the two RNAs, with staining of both nucleus and cytoplasm. "
RLID00037631	RLGI00911	EBER-1			mRNA	Human herpesvirus 4	1332043	Nucleus	Raji cell	In situ hybridization	"In situ hybridization of fluorescent oligodeoxynucleotides complementary to either EBER-1 or EBER-2 in Raji cells gave a strong pattern of staining, as illustrated in Fig. 1. Both probes revealed an essentially identical subcellular distribution for the two RNAs, with staining of both nucleus and cytoplasm. "
RLID00037632	RLGI00913	E2			snoRNA	Rattus norvegicus	19628621	Nucleolus	Myoblast	qRT-PCR	"Thus, a known snoRNA, E2 (Mishra and Eliceiri 1997), was present at highest levels in the nucleolus-enriched fraction, while a Ro small RNA family member, Y1 RNA, was detected at highest levels in the cytoplasmic fraction, as expected for this known cytoplasm-concentrated RNA species (Fig. 1B;Hendrick et al. 1981). "
RLID00037633	RLGI00914	E19			mRNA	Rattus norvegicus	9724458	Axon	Olfactory	In situ hybridization	We had previous evidence that between E13 and E19 CGRP mRNA was present at the level of olfactory axons but the resolution of light-microscope in situ hybridization did not permit the axons to be distinguished from the closely apposed ensheathing cells
RLID00037634	RLGI00915	E13			mRNA	Rattus norvegicus	9724458	Axon	Olfactory	In situ hybridization	We had previous evidence that between E13 and E19 CGRP mRNA was present at the level of olfactory axons but the resolution of light-microscope in situ hybridization did not permit the axons to be distinguished from the closely apposed ensheathing cells
RLID00037635	RLGI00916	DPH4			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037636	RLGI00917	DHFR			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037637	RLGI00918	DECTIN-1			mRNA	Mus musculus	11491532	Dendrite	Dendritic cell	-	The DECTIN-1 gene is highly expressed at the mRNA level in dendritic cells and is not further up-regulated during the maturation of these cells with tumor necrosis factor-alpha.
RLID00037638	RLGI00919	cy-tRNA Phe			tRNA	Plasmodium falciparum	25391660	Cytoplasm	-	Northern blot	"We also show that cytoplasmic tRNA Cys and tRNA Phe are imported into the P. falciparum mitochondria, implying that the parasite mitochondria probably import charged tRNAs from the cytoplasmic pool.  Likewise, cy-tRNA Phe in charged (cy-Phe-tRNA Phe ) and uncharged forms was found in both cytoplasmic and organelle partitions (Figure 4E). This suggests the import of cy-Phe-tRNA Phe into the parasite mitochondria (Figure 4E). "
RLID00037639	RLGI00920	cy-tRNA Phe			tRNA	Plasmodium falciparum	25391660	Mitochondrion	-	Northern blot	"We also show that cytoplasmic tRNA Cys and tRNA Phe are imported into the P. falciparum mitochondria, implying that the parasite mitochondria probably import charged tRNAs from the cytoplasmic pool.  Likewise, cy-tRNA Phe in charged (cy-Phe-tRNA Phe ) and uncharged forms was found in both cytoplasmic and organelle partitions (Figure 4E). This suggests the import of cy-Phe-tRNA Phe into the parasite mitochondria (Figure 4E). "
RLID00037640	RLGI00921	cy-tRNA Cys			tRNA	Plasmodium falciparum	25391660	Cytoplasm	-	Northern blot	"We also show that cytoplasmic tRNA Cys and tRNA Phe are imported into the P. falciparum mitochondria, implying that the parasite mitochondria probably import charged tRNAs from the cytoplasmic pool. Our data show that cy-tRNA Cys was evident in both cellular and organelle RNA fractions, suggesting its presence in both cytoplasm and mitochondria (Figure 4B).  "
RLID00037641	RLGI00922	cy-tRNA Cys			tRNA	Plasmodium falciparum	25391660	Mitochondrion	-	Northern blot	"We also show that cytoplasmic tRNA Cys and tRNA Phe are imported into the P. falciparum mitochondria, implying that the parasite mitochondria probably import charged tRNAs from the cytoplasmic pool. Our data show that cy-tRNA Cys was evident in both cellular and organelle RNA fractions, suggesting its presence in both cytoplasm and mitochondria (Figure 4B).  "
RLID00037642	RLGI00923	Cytochrome p450			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037643	RLGI00924	CYP8B1			mRNA	Chlorocebus sabaeus	23271194	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"Note that only ALPP, and not CYP8B1 mRNA, is maintained on the ER after ribosomes are disassembled with puromycin or HHT (Figures 2-3).ote that only ALPP, and not CYP8B1 mRNA, is maintained on the ER after ribosomes are disassembled with puromycin or HHT (Figures 2-3). "
RLID00037644	RLGI00925	CYP8B1			mRNA	Chlorocebus sabaeus	23271194	Cytoplasm	COS-7 cell	Fluorescence in situ hybridization	"Our data clearly shows that for both ALPP and CYP8B1, about 60% of the cytoplasmic mRNA is associated with the ER. Since both of these mRNAs encode proteins that are processed in the ER-lumen, our results are consistent with the idea that such mRNAs are translated on the surface of the ER. "
RLID00037645	RLGI00928	CS			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037646	RLGI00929	cry			mRNA	Nicotiana tabacum	7632920	Cytoplasm	Protoplast	Northern blot	We provide evidence that this low cytoplasmic cry IA(b) mRNA level is not due to a rapid turnover but rather results from a marginal import flow of cry messenger into the cytoplasm.
RLID00037647	RLGI00930	Cox I			mRNA	Mus musculus	25847616	Mitochondrion	Liver	Next-generation sequencing|qRT-PCR	"MtDNA encoded Cox I, an RNA known to be localized within the mitochondrial matrix, served as a positive control.  "
RLID00037648	RLGI00931	Copia 837/947			mRNA	Drosophila melanogaster	17923096	Nucleus	Embryo	In situ hybridization	Table S6: Correlations in mRNA patterns and protein function/localization. Data are collected from Table S6.
RLID00037649	RLGI00932	Clytia Poc1			mRNA	Clytia hemisphaerica	21098654	Perinuclear	Gonads	In situ hybridization	"Within the oocyte, Poc1 mRNA appeared concentrated in a patchy distribution around the nucleus (=germinal vesicle). "
RLID00037650	RLGI00933	CLCK3			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037651	RLGI00934	CKCS2			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037652	RLGI00935	Ci-PEM1			mRNA	Ascidian	15923652	Cell cortex	Embryo	In situ hybridization	"The fluorescent signal for Ci-PEM1 RNAs colocalizes with this vegetal cER network (Fig. 2IIC1,C2) as described for Halocynthia (Sardet et al., 2003).  "
RLID00037653	RLGI00936	C-I 30			mRNA	Drosophila melanogaster	25565208	Mitochondrion	HEK293T 	Fluorescence in situ hybridization	"Mito localization of mammalian C-I 30 mRNA was further confirmed using the MS2-GFP/MS2-bs tagging system (Bertrand et al., 1998) (Fig. S2B, C). "
RLID00037654	RLGI00937	chr6.trna61-MetCAT			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037655	RLGI00938	chr5.trna5-ValAAC			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037656	RLGI00939	chr5.trna11-LysCTT			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037657	RLGI00940	chr17.trna28-CysGCA			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037658	RLGI00941	chr17.trna10-GlyTCC			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037659	RLGI00942	chr16.trna10-LysCTT			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037660	RLGI00943	chr13.trna3-GluTTC			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037661	RLGI00944	chr1.trna54-GluCTC			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037662	RLGI00945	chr1.trna33-GlyGCC			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037663	RLGI00946	chr1.trna124-GlyCCC			tRNA	Homo sapiens	24205503	Exosome	HeLa cell	Next-generation sequencing	Table 1: RNA representation in exosomes versus parental HeLa cells: top 10 RNA transcripts organized by RNA type. Values for cells and exosome preparations represent mean counts of mapped reads to reference transcripts from three replicate cell lysates. Accession numbers and gene symbols were obtained from NCBI RefSeq annotation. Data are collected from Table 1.
RLID00037664	RLGI00947	Cde2-related kinase			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray|Northern blot	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037665	RLGI00948	CDCH			mRNA	Lymnaea stagnalis	1431053	Lysosome	Neuropeptidergic  cell	In situ hybridization	"As was the case for the 28s rRNA sequences, CDCH mRNA was also found to be present in lysosomal structures. Gold label was also observed in the nucleus, mostly associated with heterochromatin, and some of these particles were localized in the vicinity of the nuclear membrane. "
RLID00037666	RLGI00948	CDCH			mRNA	Lymnaea stagnalis	1431053	Nucleus	Neuropeptidergic  cell	In situ hybridization	"Figure 2. Detection of CDCH mRNA in (a) a Lowicryl section and (b) an ultra-thin cryosection with digoxigenin-labeled 18-mer CDCH oligonucleotide. Most of the gold labels are associated with RER. M, mitochondrion; R, rough endoplasmic reticulum; N. nucleus. Bars = 0.5pm. Data are collected from Figure 2. "
RLID00037667	RLGI00948	CDCH			mRNA	Lymnaea stagnalis	1431053	Endoplasmic reticulum	Neuropeptidergic  cell	In situ hybridization	"Figure 2. Detection of CDCH mRNA in (a) a Lowicryl section and (b) an ultra-thin cryosection with digoxigenin-labeled 18-mer CDCH oligonucleotide. Most of the gold labels are associated with RER. M, mitochondrion; R, rough endoplasmic reticulum; N. nucleus. Bars = 0.5pm. Data are collected from Figure 2. "
RLID00037668	RLGI00948	CDCH			mRNA	Lymnaea stagnalis	1431053	Mitochondrion	Neuropeptidergic  cell	In situ hybridization	"Figure 2. Detection of CDCH mRNA in (a) a Lowicryl section and (b) an ultra-thin cryosection with digoxigenin-labeled 18-mer CDCH oligonucleotide. Most of the gold labels are associated with RER. M, mitochondrion; R, rough endoplasmic reticulum; N. nucleus. Bars = 0.5pm. Data are collected from Figure 2. "
RLID00037669	RLGI00948	CDCH			mRNA	Lymnaea stagnalis	8353303	Axon	Neuron	In situ hybridization	"Gold labeling was observed in secretion granules, and double labeling experiments showed that these granules also contain CDCH. This specific intragranular localization suggest that CDCH mRNA is transported through the axon and released by exocytosis in the haemolymph. "
RLID00037670	RLGI00953	CCM2			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037671	RLGI00954	CCDC2			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037672	RLGI00955	CaMKII-alpha			mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Nonstimulated rats: BDNF, TrkB, and CaMKII-beta mRNAs localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of dentate gyrus (DG) granule cells; CaMKII-a mRNA localized throughout the dendritic length in neurons of all hippocampal subfields.  In contrast, CaMKII-beta (Figs. 1C and 2D), BDNF (Figs. 1E and 2G), and TrkB mRNAs (Figs.1G and 2J) were localized in the soma and in the proximal dendrites of hippocampal pyramidal cells, and in the soma only of DG granule cells. "
RLID00037673	RLGI00956	CaMKII-beta			mRNA	Rattus norvegicus	12121312	Dendrite	Hippocampus	In situ hybridization	"Pilocarpine seizures: increased staining levels of CaMKII-alpha mRNA throughout the whole dendritic length in all hippocampal subfields; induction of CaMKII-beta, BDNF, and TrkB mRNAs dendritic targeting in CA1, CA3, and DG neurons.  Data provide evidence that BDNF, TrkB, and CaMKII-beta and -alpha mRNAs are accumulated in the dendrites of specific hippocampal neurons during pilocarpine seizures and kindling development. "
RLID00037674	RLGI00957	CaM I			mRNA	Rattus norvegicus	8833091	Dendrite	Brain	In situ hybridization	"In cerebral cortical neurons, the 4.0-kb CaM I mRNA was detected in apical dendrites at postnatal day (PD) 5 to 15.  Our results demonstrate that the 4.0-kb CaM I transcript is localized to apical dendrites of neurons during postnatal development of the rat brain.  Figure 4 illustrates the localization of the 4.0-kb CaM I mRNA in apical dendrites of pyramidal cortical neurons at PD 5 (Cx) and PD 15 (Cx, arrowheads). "
RLID00037675	RLGI00958	calreticulin (CRT)			mRNA	Petunia hybrida	14564059	Endoplasmic reticulum	Pollen tube	In situ hybridization	"The mRNA transcripts of the CRT gene were localized mainly on the surface of endoplasmic reticulum (ER) membranes, both in transmitting cells and in the tip cytoplasm of pollen tubes. "
RLID00037676	RLGI00958	calreticulin (CRT)			mRNA	Petunia hybrida	14564059	Cytoplasm	Pollen tube	In situ hybridization	"The mRNA transcripts of the CRT gene were localized mainly on the surface of endoplasmic reticulum (ER) membranes, both in transmitting cells and in the tip cytoplasm of pollen tubes. "
RLID00037677	RLGI00960	calreticulin (CRT)			mRNA	Hyacinthus orientalis	26354004	Endoplasmic reticulum	Embryo	Fluorescence in situ hybridization	"CRT mRNA and the protein localize mainly to the endoplasmic reticulum (ER) and Golgi compartments of the cells, which are involved in sexual reproduction events, such as those in sister synergids, the egg cell, the central cell, zygote and the developing endosperm. "
RLID00037678	RLGI00960	calreticulin (CRT)			mRNA	Hyacinthus orientalis	26354004	Golgi apparatus	Embryo	Fluorescence in situ hybridization	"CRT mRNA and the protein localize mainly to the endoplasmic reticulum (ER) and Golgi compartments of the cells, which are involved in sexual reproduction events, such as those in sister synergids, the egg cell, the central cell, zygote and the developing endosperm. "
RLID00037679	RLGI00960	calreticulin (CRT)			mRNA	Hyacinthus orientalis	26354004	Cytoplasm	Embryo	Fluorescence in situ hybridization	"The presence of CRT transcripts was still localized predominantly in the cytoplasm of investigated cells (Fig. 1e-g); however, few fluorescent spots were also observed around or within their nuclei (Fig. 1e, f, arrows) and nucleoli (Fig. 1e, f, arrowheads). "
RLID00037680	RLGI00960	calreticulin (CRT)			mRNA	Hyacinthus orientalis	26354004	Nucleus	Embryo	Fluorescence in situ hybridization	"The presence of CRT transcripts was still localized predominantly in the cytoplasm of investigated cells (Fig. 1e-g); however, few fluorescent spots were also observed around or within their nuclei (Fig. 1e, f, arrows) and nucleoli (Fig. 1e, f, arrowheads). "
RLID00037681	RLGI00960	calreticulin (CRT)			mRNA	Hyacinthus orientalis	26354004	Nucleolus	Embryo	Fluorescence in situ hybridization	"The presence of CRT transcripts was still localized predominantly in the cytoplasm of investigated cells (Fig. 1e-g); however, few fluorescent spots were also observed around or within their nuclei (Fig. 1e, f, arrows) and nucleoli (Fig. 1e, f, arrowheads). "
RLID00037682	RLGI00965	CagDazl			mRNA	Carassius auratus gibelio	19504540	Germ plasm	Oocyte	In situ hybridization	"In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. "
RLID00037683	RLGI00965	CagDazl			mRNA	Carassius auratus gibelio	19504540	Mitochondrion	Oocyte	In situ hybridization	"In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. "
RLID00037684	RLGI00967	C5T1			lncRNA	Homo sapiens	26673966	Nucleus	Huh7 cell	qRT-PCR	We also found the identified transcripts (C5T1lncRNA) to be highly enriched in the nucleus in contrast to their neighbouring coding C5 gene (Figure 2b).
RLID00037685	RLGI00968	C10/XFACS			mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00037686	RLGI00969	b-tubulin			mRNA	Rattus norvegicus	9322162	Dendrite	Neuron	In situ hybridization	"The mRNAs for b-tubulin, neurofilament 68, and F1/GAP43 were restricted to the region of the cell body and very proximal dendrites in most neurons.  "
RLID00037687	RLGI00969	b-tubulin			mRNA	Rattus norvegicus	9322162	Cell body	Neuron	In situ hybridization	"The mRNAs for b-tubulin, neurofilament 68, and F1/GAP43 were restricted to the region of the cell body and very proximal dendrites in most neurons.  "
RLID00037688	RLGI00971	btsz-2poly			mRNA	Drosophila melanogaster	14581614	Apical	Follicle cell	In situ hybridization	"When we examined btsz-2poly and btsz-2myc mRNA expression in follicle cells, we found that transcripts localized to the follicle cell apical plasma membrane in a manner indistinguishable from an untagged btsz-2 construct. "
RLID00037689	RLGI00972	btsz-2myc			mRNA	Drosophila melanogaster	14581614	Apical	Follicle cell	In situ hybridization	"When we examined btsz-2poly and btsz-2myc mRNA expression in follicle cells, we found that transcripts localized to the follicle cell apical plasma membrane in a manner indistinguishable from an untagged btsz-2 construct. "
RLID00037690	RLGI00973	bt884			mRNA	Nicotiana tabacum	7632920	Cytoplasm	Protoplast	Northern blot	"Based on a steady state level of about one transcript per cell, the nucleo-cytoplasmic flow rate of bt884 mRNA should be less than 1 transcript per 10h. "
RLID00037691	RLGI00973	bt884			mRNA	Nicotiana tabacum	7632920	Nucleus	Protoplast	Northern blot	"Based on a steady state level of about one transcript per cell, the nucleo-cytoplasmic flow rate of bt884 mRNA should be less than 1 transcript per 10h. "
RLID00037692	RLGI00975	box C/D			snoRNA	Rattus norvegicus	25792744	Cytoplasm	Myocardium	Next-generation sequencing|qRT-PCR	"RNA-sequencing analysis reveals that box C/D snoRNAs as a class are present in the cytoplasm, where their levels are dynamically regulated by NADPH oxidase. "
RLID00037693	RLGI00976	beta-F1-ATPase			mRNA	Rattus norvegicus	9065777	Cytoplasm	Hepatocytes	Electron microscopy|ISH	"In contrast, beta-F1-ATPase mRNA appears in rounded electron-dense clusters, often in close proximity to mitochondria.  "
RLID00037694	RLGI00977	bed			mRNA	Drosophila melanogaster	8895662	Anterior	Embryo	In situ hybridization	Bed mRNA is tightly localized to the anterior pole of the prospective embryo during oogenesis such that none is detectable elsewhere in the egg.
RLID00037695	RLGI00978	BC1			mRNA	Bos taurus	12654521	Dendrite	NG108-15 cell	Luciferase assay	"BC1 RNA is localized to dendritic domains as ribonucleoprotein particles, and it has been suggested to play a functional role in translational regulation of dendritic mRNAs. "
RLID00037696	RLGI00979	B7/Fingers			mRNA	Xenopus laevis	11784096	Germ plasm	Oocyte	In situ hybridization	"The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. "
RLID00037697	RLGI00980	ATP5p			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037698	RLGI00981	ATP5m			mRNA	Solanum tuberosum	20506035	Cytosol	Potato tuber	qRT-PCR	Table 1: Function and mitochondrial association of 17 cytosolic mRNAs. Data are collected from Table 1.
RLID00037699	RLGI00982	ATP synthase			mRNA	Rattus norvegicus	17785519	Axon	Dorsal root ganglia	qRT-PCR	Axonal mRNA levels for each of the 50 transcripts were determined using axonal RNA isolates for reverse transcription followed by quantitative PCR (qPCR). The qPCR results are detailed in Table I. These data show both ligand and transcript specificity for the regulation of axonal mRNA levels.
RLID00037700	RLGI00983	AteIF4E			mRNA	Arabidopsis thaliana	17662723	Chloroplast	Seedling	In situ hybridization|RT-PCR	"The disappearance of the exogenously added cpSRP43 protein and AteIF4E RNA after protease and RNase action, whereas the LseIF4E mRNA was still detectable, strongly suggests that it is located inside the chloroplast envelope. "
RLID00037701	RLGI00984	AT03385			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037702	RLGI00985	AT02159			mRNA	Drosophila melanogaster	25838129	Nucleus	Nurse cell	In situ hybridization	Data come from DOT (Dresden Ovary Table) database: http://tomancak-srv1.mpi-cbg.de/DOT/main.html
RLID00037703	RLGI00986	Asp-GAC			tRNA	Homo sapiens	25135963	Exosome	Serum	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037704	RLGI00986	Asp-GAC			tRNA	Homo sapiens	25135963	Exosome	Urine	Next-generation sequencing	"When summarizing total counts per sample type, we calculated mean raw counts per RNA-Seq library and then ranked them from high to low for miRNA, mRNA, ncRNA and tRNA categories. The top 12 are listed in table 1. Data are collected from Table 1: RNA representation in serum- and urine-derived exosomes: top 12 RNA transcripts organized by RNA type. Values represent mean counts of mapped reads to reference transcripts. "
RLID00037705	RLGI00988	aPKC			mRNA	Ascidian	16569661	Cytoplasm	Embryo	Northern blot	The aPKC mRNA is equally present in all cell lineages and is distributed ubiquitously throughout the cytoplasm of all blastomeres.
RLID00037706	RLGI00989	ANFR-C			mRNA	Rattus norvegicus	8745272	Cytoplasm	Pituitary gland	In situ hybridization	"Atrial Natriuretic Factor (ANF) action is mediated by highly selective and specific receptors. Three subtypes have been characterized and cloned: ANF receptor-A, -B and -C. These subtypes are all expressed in the anterior pituitary of the rat. In the present study, the mRNA for each subtype was detected by in situ hybridization. The amounts of ANFR-A and -B mRNA were found to be similar, and to be twice that of ANFR-C mRNA. At the ultrastructural level, the three types of ANFR mRNA were expressed in three anterior pituitary cell types, namely lactotrophs, corticotrophs, and gonadotrophs, identified by their hormonal content. No signal was revealed in somatotrophs or thyrotrophs. The different forms of mRNA were similar in terms of subcellular localization: in the cytoplasmic matrix and the nuclear euchromatin. These data indicate that the anterior pituitary is an important target tissue for ANF action. "
RLID00037707	RLGI00989	ANFR-C			mRNA	Rattus norvegicus	8745272	Nucleus	Pituitary gland	In situ hybridization	"Atrial Natriuretic Factor (ANF) action is mediated by highly selective and specific receptors. Three subtypes have been characterized and cloned: ANF receptor-A, -B and -C. These subtypes are all expressed in the anterior pituitary of the rat. In the present study, the mRNA for each subtype was detected by in situ hybridization. The amounts of ANFR-A and -B mRNA were found to be similar, and to be twice that of ANFR-C mRNA. At the ultrastructural level, the three types of ANFR mRNA were expressed in three anterior pituitary cell types, namely lactotrophs, corticotrophs, and gonadotrophs, identified by their hormonal content. No signal was revealed in somatotrophs or thyrotrophs. The different forms of mRNA were similar in terms of subcellular localization: in the cytoplasmic matrix and the nuclear euchromatin. These data indicate that the anterior pituitary is an important target tissue for ANF action. "
RLID00037708	RLGI00991	ANFR-B			mRNA	Rattus norvegicus	8745272	Cytoplasm	Pituitary gland	In situ hybridization	"Atrial Natriuretic Factor (ANF) action is mediated by highly selective and specific receptors. Three subtypes have been characterized and cloned: ANF receptor-A, -B and -C. These subtypes are all expressed in the anterior pituitary of the rat. In the present study, the mRNA for each subtype was detected by in situ hybridization. The amounts of ANFR-A and -B mRNA were found to be similar, and to be twice that of ANFR-C mRNA. At the ultrastructural level, the three types of ANFR mRNA were expressed in three anterior pituitary cell types, namely lactotrophs, corticotrophs, and gonadotrophs, identified by their hormonal content. No signal was revealed in somatotrophs or thyrotrophs. The different forms of mRNA were similar in terms of subcellular localization: in the cytoplasmic matrix and the nuclear euchromatin. These data indicate that the anterior pituitary is an important target tissue for ANF action. "
RLID00037709	RLGI00991	ANFR-B			mRNA	Rattus norvegicus	8745272	Nucleus	Pituitary gland	In situ hybridization	"Atrial Natriuretic Factor (ANF) action is mediated by highly selective and specific receptors. Three subtypes have been characterized and cloned: ANF receptor-A, -B and -C. These subtypes are all expressed in the anterior pituitary of the rat. In the present study, the mRNA for each subtype was detected by in situ hybridization. The amounts of ANFR-A and -B mRNA were found to be similar, and to be twice that of ANFR-C mRNA. At the ultrastructural level, the three types of ANFR mRNA were expressed in three anterior pituitary cell types, namely lactotrophs, corticotrophs, and gonadotrophs, identified by their hormonal content. No signal was revealed in somatotrophs or thyrotrophs. The different forms of mRNA were similar in terms of subcellular localization: in the cytoplasmic matrix and the nuclear euchromatin. These data indicate that the anterior pituitary is an important target tissue for ANF action. "
RLID00037710	RLGI00993	ANFR-A			mRNA	Rattus norvegicus	8745272	Cytoplasm	Pituitary gland	In situ hybridization	"Atrial Natriuretic Factor (ANF) action is mediated by highly selective and specific receptors. Three subtypes have been characterized and cloned: ANF receptor-A, -B and -C. These subtypes are all expressed in the anterior pituitary of the rat. In the present study, the mRNA for each subtype was detected by in situ hybridization. The amounts of ANFR-A and -B mRNA were found to be similar, and to be twice that of ANFR-C mRNA. At the ultrastructural level, the three types of ANFR mRNA were expressed in three anterior pituitary cell types, namely lactotrophs, corticotrophs, and gonadotrophs, identified by their hormonal content. No signal was revealed in somatotrophs or thyrotrophs. The different forms of mRNA were similar in terms of subcellular localization: in the cytoplasmic matrix and the nuclear euchromatin. These data indicate that the anterior pituitary is an important target tissue for ANF action. "
RLID00037711	RLGI00993	ANFR-A			mRNA	Rattus norvegicus	8745272	Nucleus	Pituitary gland	In situ hybridization	"Atrial Natriuretic Factor (ANF) action is mediated by highly selective and specific receptors. Three subtypes have been characterized and cloned: ANF receptor-A, -B and -C. These subtypes are all expressed in the anterior pituitary of the rat. In the present study, the mRNA for each subtype was detected by in situ hybridization. The amounts of ANFR-A and -B mRNA were found to be similar, and to be twice that of ANFR-C mRNA. At the ultrastructural level, the three types of ANFR mRNA were expressed in three anterior pituitary cell types, namely lactotrophs, corticotrophs, and gonadotrophs, identified by their hormonal content. No signal was revealed in somatotrophs or thyrotrophs. The different forms of mRNA were similar in terms of subcellular localization: in the cytoplasmic matrix and the nuclear euchromatin. These data indicate that the anterior pituitary is an important target tissue for ANF action. "
RLID00037712	RLGI00995	ALPP			mRNA	Chlorocebus sabaeus	23271194	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"Note that only ALPP, and not CYP8B1 mRNA, is maintained on the ER after ribosomes are disassembled with puromycin or HHT (Figures 2-3).ote that only ALPP, and not CYP8B1 mRNA, is maintained on the ER after ribosomes are disassembled with puromycin or HHT (Figures 2-3). "
RLID00037713	RLGI00995	ALPP			mRNA	Chlorocebus sabaeus	23271194	Cytoplasm	COS-7 cell	Fluorescence in situ hybridization	"Our data clearly shows that for both ALPP and CYP8B1, about 60% of the cytoplasmic mRNA is associated with the ER. Since both of these mRNAs encode proteins that are processed in the ER-lumen, our results are consistent with the idea that such mRNAs are translated on the surface of the ER. "
RLID00037714	RLGI00997	alpha-F1-ATPase			mRNA	Rattus norvegicus	9065777	Cytoplasm	Hepatocytes	Electron microscopy|ISH	Alpha-F1-ATPase mRNA is dispersed and scattered in the cytoplasm.
RLID00037715	RLGI00998	AKR7A5			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037716	RLGI00999	AF2			mRNA	Homo sapiens	24019514	Endoplasmic reticulum	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmids containing either ALPP, t-ftz, or the AF1, AF2 fusion constructs and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (Ctrl), puromycin (Puro), or HHT for 30 min and then extracted with either digitonin alone, or for puromycin-treated cells, with 20 mM EDTA. The cells were then fixed, stained for mRNA using specific FISH probes (ALPP probe for AF1, ftz probe for AF2), and imaged. FIGURE 2B: quantification of the fluorescence intensities of mRNA in the ER and nucleus.  Data are collected from Figure 2. "
RLID00037717	RLGI00999	AF2			mRNA	Homo sapiens	24019514	Nucleus	COS-7 cell	Fluorescence in situ hybridization	"COS-7 cells were transfected with plasmids containing either ALPP, t-ftz, or the AF1, AF2 fusion constructs and allowed to express mRNA for 18-24 h. The cells were then treated with DMSO (Ctrl), puromycin (Puro), or HHT for 30 min and then extracted with either digitonin alone, or for puromycin-treated cells, with 20 mM EDTA. The cells were then fixed, stained for mRNA using specific FISH probes (ALPP probe for AF1, ftz probe for AF2), and imaged. FIGURE 2B: quantification of the fluorescence intensities of mRNA in the ER and nucleus.  Data are collected from Figure 2. "
RLID00037718	RLGI01001	ADORA2BP			mRNA	Canis lupus familiaris	18845542	Pseudopodium	MSV-MDCK-INV cell	Microarray	"A cohort of 242 identified genes enriched 1.6-fold in the pseudopodial fraction is listed in Table 1 and functionally grouped. The number of genes/group is presented as a pie chart (Fig. 4B). Of particular interest is the abundance of proteins involved in signaling and protein translation. Indeed, a large number of pseudopod-enriched mRNAs encode ribosomal proteins (Table 1). TABLE 1: mRNAs enriched 1.6-fold in the pseudopodial fraction relative to cell body. Data are collected from Table 1. "
RLID00037719	RLGI01002	7SL			lncRNA	Mus musculus	26464439	Axon	Motoneuron	In situ hybridization|qRT-PCR	"In contrast, 7SL RNA was enriched in the axonal compared to the somatodendritic cytoplasm. Importantly, 7SL was readily detectable in motor axons which is in line with our whole transcriptome profiling data. "
RLID00037720	RLGI01003	7SK			snRNA	Rattus norvegicus	25792744	Nucleus	Myocardium	qRT-PCR	"For both cytosolic isolation methods, immunoblotting showed enrichment of cytosolic proteins and depletion of nuclear/nucleolar proteins in cytosolic fractions, whereas qPCR demonstrated that the small ncRNAs 7SK and U6 were predominantly in the nuclear fraction (Fig. 1, E-H). "
RLID00037721	RLGI01004	75S			mRNA	Chironomus	148971	Cytoplasm	Salivary gland cell	Electrophoretic analysis	"After a pulse of RNA precursor to the living animal, labeled Balbiani ring 75S RNA is found mainly in the cytoplasm located closer to the nuclear envelope, with smaller amounts toward the periphery of the cell. nuclear envelope, with smaller amounts toward the periphery of the cell. Thus the 75S RNA located closer to the nuclear envelope is the most recently exported 75S RNA. "
RLID00037722	RLGI01005	5S rRNA			rRNA	Saccharomyces cerevisiae	20691904	Mitochondrion	Yeast	RT-PCR	"Figure 4: PNPASE Augments RNase P, 5S rRNA, and MRP RNA Import into Yeast Mitochondria. Data are collected from Figur 4. "
RLID00037723	RLGI01006	28S			rRNA	Lymnaea stagnalis	1431053	Nucleolus	Neuropeptidergic  cell	In situ hybridization	"Figure 3. Detection of 28s rRNA in an ultra-thin cryosection with a digoxigenin- labeled plasmid probe, showing dense labeling of a nucleolus. N, nucleus; n=nucleolus. Bar = 0.5vm. Data are collected from Figure 3. "
RLID00037724	RLGI01006	28S			rRNA	Lymnaea stagnalis	1431053	Lysosome	Neuropeptidergic  cell	In situ hybridization	"Figure 4. Influence of fixation on the detection of 28s rRNA in ultra-thin cryosections of CDCs with a digoxigenin-labeled 28s oligonucleotide probe. (a) Localization of gold label in a lysosomal structure in addition to gold label associated with RER when tissue was fixed in 1% formaldehyde, 0.Wo glutaraldehyde. (b) Lysosomes were devoid of gold label after hybridization on formaldehyde-fixed tissue. L, lysosome; R, rough endoplasmic reticulum; N, nucleus. Bars = 0.5pm. Data are collected from Figure 4. "
RLID00037725	RLGI01009	26S RNA			mRNA	Gallus gallus	837448	Ribosome	Fibroblast	Radioactive labeling	"Here we show that during infection, the 26s RNA is found mainly in membrane-bound polysomes which synthesize all three virion structural proteins. "
RLID00037726	RLGI01010	18S			rRNA	Petunia hybrida	25732863	Cytoplasm	Pollen tube	Fluorescence in situ hybridization	"As germination proceeded, 18S rRNA preferentially accumulated in the cytoplasm of the outgrowing pollen tube (Fig. 4b).  "
RLID00037727	RLGI01010	18S			rRNA	Petunia hybrida	25732863	Ribosome	Pollen tube	Fluorescence in situ hybridization	"The above results led us to propose that the common sites of PhCRT mRNA, CRT, and 18S rRNA localization in germinating pollen and growing pollen tubes are enriched in ER membrane-bound ribosomes. Together, our results show that the regions in which PhCRT mRNA, CRT protein, and 18S rRNA are localized are also rich in RER. "
RLID00037728	RLGI01010	18S			rRNA	Petunia hybrida	25732863	Endoplasmic reticulum	Pollen tube	Fluorescence in situ hybridization	"The above results led us to propose that the common sites of PhCRT mRNA, CRT, and 18S rRNA localization in germinating pollen and growing pollen tubes are enriched in ER membrane-bound ribosomes. Together, our results show that the regions in which PhCRT mRNA, CRT protein, and 18S rRNA are localized are also rich in RER. "
RLID00037729	RLGI01013	18S			rRNA	Beta vulgaris	8718677	Cytoplasm	Pachytene meiocytes	In situ hybridization	"Both RNA-RNA and DNA-RNA hybridizations in sections of sugar beet anthers resulted in a very specific localization of 18 S rRNA fragments. Light microscopic observations showed that the most intense hybridization signal was visualized in the nucleoli, and less conspicuous labeling could be seen in the cytoplasm. Some labeling was also found in the nucleoplasm, whereas vacuoles and cell walls were clearly devoid of silverdeposits (Fig. 2A,B). "
RLID00037730	RLGI01013	18S			rRNA	Beta vulgaris	8718677	Nucleolus	Pachytene meiocytes	In situ hybridization	"Both RNA-RNA and DNA-RNA hybridizations in sections of sugar beet anthers resulted in a very specific localization of 18 S rRNA fragments. Light microscopic observations showed that the most intense hybridization signal was visualized in the nucleoli, and less conspicuous labeling could be seen in the cytoplasm. Some labeling was also found in the nucleoplasm, whereas vacuoles and cell walls were clearly devoid of silverdeposits (Fig. 2A,B). "
RLID00037731	RLGI01013	18S			rRNA	Beta vulgaris	8718677	Nucleoplasm	Pachytene meiocytes	In situ hybridization	"Both RNA-RNA and DNA-RNA hybridizations in sections of sugar beet anthers resulted in a very specific localization of 18 S rRNA fragments. Light microscopic observations showed that the most intense hybridization signal was visualized in the nucleoli, and less conspicuous labeling could be seen in the cytoplasm. Some labeling was also found in the nucleoplasm, whereas vacuoles and cell walls were clearly devoid of silverdeposits (Fig. 2A,B). "
RLID00037732	RLGI01016	16S			rRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00037733	RLGI01017	12S			rRNA	Homo sapiens	21854988	Mitochondrion	143B cell	Next-generation sequencing	"Table S2, Relating to Figure 2, (Sheet A) Expression of annotated mRNA, tRNA and rRNA in 143B cells whole mitochondria and mitoplast preparations determined by RNA sequencing (reads per million per kb), and expression levels relative to total mitochondrial gene expression, and ratio of sense/antisense transcription relative to each gene indicated. Data are collected from Figure 2. "
RLID00037734	RLGI01018	lincRNA-EC2			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037735	RLGI01019	lincRNA-EC4			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037736	RLGI01020	lincRNA-EC5			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037737	RLGI01021	lincRNA-EC8			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037738	RLGI01022	lincRNA-EC9			lncRNA	Mus musculus	24200680	Nucleus	Liver erythroid cell	qRT-PCR	We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Data are collected from Figure 6.
RLID00037739	RLGI01023	lncCyt b			lncRNA	Homo sapiens	22028365	Mitochondrion	HeLa cell	qRT-PCR|RNA-seq|Northern blot	"The regions of the mitochondrial genome complementary to the genes that encode ND5, ND6, and Cyt b mRNAs were found to have high levels of lncRNAs (Fig. 1B). "
RLID00037740	RLGI01024	lncND5			lncRNA	Homo sapiens	22028365	Mitochondrion	HeLa cell	qRT-PCR|RNA-seq|Northern blot	"The regions of the mitochondrial genome complementary to the genes that encode ND5, ND6, and Cyt b mRNAs were found to have high levels of lncRNAs (Fig. 1B). "
RLID00037741	RLGI01025	lncND6			lncRNA	Homo sapiens	22028365	Mitochondrion	HeLa cell	qRT-PCR|RNA-seq|Northern blot	"The regions of the mitochondrial genome complementary to the genes that encode ND5, ND6, and Cyt b mRNAs were found to have high levels of lncRNAs (Fig. 1B). "
RLID00037742	RLGI01026	lncRNA-LALR1			lncRNA	Mus musculus	23483581	Cytoplasm	Liver	In situ hybridization	The transcript of lncRNA-LALR1 was mainly located in the nucleus and cytoplasm of hepatocytes and was up-regulated at 18 hours after surgery.
RLID00037743	RLGI01027	lncRNA-hLALR1			lncRNA	Homo sapiens	23483581	Nucleus	Liver	In situ hybridization	The transcript of lncRNA-LALR1 was mainly located in the nucleus and cytoplasm of hepatocytes and was up-regulated at 18 hours after surgery.
RLID00037744	RLGI01028	lncRNA-LALR1			lncRNA	Mus musculus	23483581	Nucleus	Liver	In situ hybridization	The transcript of lncRNA-LALR1 was mainly located in the nucleus and cytoplasm of hepatocytes and was up-regulated at 18 hours after surgery.
RLID00037745	RLGI01030	CLCK3			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037746	RLGI01031	Cde2-related kinase			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037747	RLGI01032	hSNF2a			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037748	RLGI01033	Heme synthetase			mRNA	Homo sapiens	12923260	Ribosome	Jurkat cell	Microarray	"TABLE 2.Enrichment of mRNAs in free and ER-bound polysomes. Stratagene 1.2K human cDNA microarrays were screened with probes developed against either the total RNA pool or the ER-membrane-enriched RNA pool of Jurkat cells. Representative gene products enriched in the ER polysome fraction, free polysome fraction, or distributed between both pools are provided. For the latter, candidate gene products were selected on the basis of their noncanonical distribution on the ER-membrane-bound polysomes. The data are collected from Table 2. "
RLID00037749	RLGI01034	pair-rule			mRNA	Drosophila melanogaster	15852043	Apical	Embryo	-	"The best-characterized example is the PAIR-RULE mRNAs, which localize to the apical cytoplasm above the nuclei of D. melanogaster syncytial blastoderm embryos (FIG. 1c) "
RLID00037750	RLGI01035	PpCSD1			mRNA	Physcomitrella patens	23749811	Chloroplast	Protonemata	RT-PCR	"To examine the effect of copper deficiency on expression of CuZn-SOD genes, reverse transcription PCR (RT-PCR) was performed after culture for 30 d (Fig. 3). Copper deficiency resulted in the repression of two chloroplastic CuZn-SOD genes (PpCSD1 and PpCSD2), but did not affect the expression of two cytosolic CuZn-SOD genes (PpCSD3 and PpCSD4). Expression of the extracellular and chloroplastic Fe-SOD genes (PpFSD1 and PpFSD2) and the mitochondrial Mn-SOD gene (PpMSD) was unaffected by copper deficiency. Because the cytosolic PpFSD3 showed a degenerated gene structure, it seemed likely to be a pseudogene. However, its expression was strongly induced by copper deficiency. This observation will be discussed, along with the copper responsive cis-element, in the Discussion.  "
RLID00037751	RLGI01036	PpCSD2			mRNA	Physcomitrella patens	23749811	Chloroplast	Protonemata	RT-PCR	"To examine the effect of copper deficiency on expression of CuZn-SOD genes, reverse transcription PCR (RT-PCR) was performed after culture for 30 d (Fig. 3). Copper deficiency resulted in the repression of two chloroplastic CuZn-SOD genes (PpCSD1 and PpCSD2), but did not affect the expression of two cytosolic CuZn-SOD genes (PpCSD3 and PpCSD4). Expression of the extracellular and chloroplastic Fe-SOD genes (PpFSD1 and PpFSD2) and the mitochondrial Mn-SOD gene (PpMSD) was unaffected by copper deficiency. Because the cytosolic PpFSD3 showed a degenerated gene structure, it seemed likely to be a pseudogene. However, its expression was strongly induced by copper deficiency. This observation will be discussed, along with the copper responsive cis-element, in the Discussion.  "
RLID00037752	RLGI01037	PpCSD3			mRNA	Physcomitrella patens	23749811	Cytosol	Protonemata	RT-PCR	"To examine the effect of copper deficiency on expression of CuZn-SOD genes, reverse transcription PCR (RT-PCR) was performed after culture for 30 d (Fig. 3). Copper deficiency resulted in the repression of two chloroplastic CuZn-SOD genes (PpCSD1 and PpCSD2), but did not affect the expression of two cytosolic CuZn-SOD genes (PpCSD3 and PpCSD4). Expression of the extracellular and chloroplastic Fe-SOD genes (PpFSD1 and PpFSD2) and the mitochondrial Mn-SOD gene (PpMSD) was unaffected by copper deficiency. Because the cytosolic PpFSD3 showed a degenerated gene structure, it seemed likely to be a pseudogene. However, its expression was strongly induced by copper deficiency. This observation will be discussed, along with the copper responsive cis-element, in the Discussion.  "
RLID00037753	RLGI01038	PpCSD4			mRNA	Physcomitrella patens	23749811	Cytosol	Protonemata	RT-PCR	"To examine the effect of copper deficiency on expression of CuZn-SOD genes, reverse transcription PCR (RT-PCR) was performed after culture for 30 d (Fig. 3). Copper deficiency resulted in the repression of two chloroplastic CuZn-SOD genes (PpCSD1 and PpCSD2), but did not affect the expression of two cytosolic CuZn-SOD genes (PpCSD3 and PpCSD4). Expression of the extracellular and chloroplastic Fe-SOD genes (PpFSD1 and PpFSD2) and the mitochondrial Mn-SOD gene (PpMSD) was unaffected by copper deficiency. Because the cytosolic PpFSD3 showed a degenerated gene structure, it seemed likely to be a pseudogene. However, its expression was strongly induced by copper deficiency. This observation will be discussed, along with the copper responsive cis-element, in the Discussion.  "
RLID00037754	RLGI01039	PpFSD2			mRNA	Physcomitrella patens	23749811	Chloroplast	Protonemata	RT-PCR	"To examine the effect of copper deficiency on expression of CuZn-SOD genes, reverse transcription PCR (RT-PCR) was performed after culture for 30 d (Fig. 3). Copper deficiency resulted in the repression of two chloroplastic CuZn-SOD genes (PpCSD1 and PpCSD2), but did not affect the expression of two cytosolic CuZn-SOD genes (PpCSD3 and PpCSD4). Expression of the extracellular and chloroplastic Fe-SOD genes (PpFSD1 and PpFSD2) and the mitochondrial Mn-SOD gene (PpMSD) was unaffected by copper deficiency. Because the cytosolic PpFSD3 showed a degenerated gene structure, it seemed likely to be a pseudogene. However, its expression was strongly induced by copper deficiency. This observation will be discussed, along with the copper responsive cis-element, in the Discussion.  "
RLID00037755	RLGI01040	PpMSD			mRNA	Physcomitrella patens	23749811	Mitochondrion	Protonemata	RT-PCR	"To examine the effect of copper deficiency on expression of CuZn-SOD genes, reverse transcription PCR (RT-PCR) was performed after culture for 30 d (Fig. 3). Copper deficiency resulted in the repression of two chloroplastic CuZn-SOD genes (PpCSD1 and PpCSD2), but did not affect the expression of two cytosolic CuZn-SOD genes (PpCSD3 and PpCSD4). Expression of the extracellular and chloroplastic Fe-SOD genes (PpFSD1 and PpFSD2) and the mitochondrial Mn-SOD gene (PpMSD) was unaffected by copper deficiency. Because the cytosolic PpFSD3 showed a degenerated gene structure, it seemed likely to be a pseudogene. However, its expression was strongly induced by copper deficiency. This observation will be discussed, along with the copper responsive cis-element, in the Discussion.  "
RLID00037756	RLGI01041	Cox2 Divergent			lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037757	RLGI01041	Cox2 Divergent			lncRNA	Mus musculus	23898399	Cytoplasm	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037758	RLGI01042	Gp96 Convergent			lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037759	RLGI01042	Gp96 Convergent			lncRNA	Mus musculus	23898399	Cytoplasm	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037760	RLGI01043	H2-T23/24AS			lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037761	RLGI01043	H2-T23/24AS			lncRNA	Mus musculus	23898399	Cytoplasm	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037762	RLGI01044	Pbrm1 Convergent			lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037763	RLGI01045	"Scripture 16,612 "			lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037764	RLGI01046	"Scripture 60,588 "			lncRNA	Mus musculus	23898399	Nucleus	293T cell	qRT-PCR	"Gapdh was tested as a control and found to be evenly distributed between the nucleus and cytoplasm with little transcript found on the chromatin. Likewise, Cox2 Divergent, Gp96 Convergent, and H2-T23/24AS were evenly distributed between nucleus and cytoplasm. HoxA11AS was mostly nuclear with some transcript found in the cytoplasm, but not on the chromatin. Interestingly, Lethe, Pbrm1 Convergent, Scripture 16,612 and Scripture 60,588 were found mostly on the chromatin, with a smaller fraction in the nucleus. "
RLID00037765	U58494	U58494	http://www.ncbi.nlm.nih.gov/nuccore/U58494		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00037766	U58671	U58671	http://www.ncbi.nlm.nih.gov/nuccore/U58671		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00037767	X15624	X15624	http://www.ncbi.nlm.nih.gov/nuccore/X15624		lncRNA	Homo sapiens	23663360	Exosome	Plasma	Next-generation sequencing	"To annotate the exosomal RNA species that were not identified as miRNA transcripts, we first removed all the known miRNA sequences from the libraries and then mapped the remaining sequences to the human genome that had RNA annotations. Figure 5A shows the percentage of other small non-coding RNAs, tRNA, rRNA, small nuclear (snRNA), small nucleolar (snoRNA) and piwi-interacting RNA (piRNA) that were detected. The rRNA was the most common among them, accounting for 9.16% of all mappable counts, followed by piRNA (1.31%), tRNA (1.24%), snRNA (0.18%), and snoRNA (0.01%). Clearly, the exosomes contained relatively low levels of rRNA, which is in contrast to a typical eukaryotic cell where rRNA makes up at least 80% of the total RNA molecules. Interestingly, we also detected low levels of long RNA in the small RNA libraries. We detected 3.36% of long non-coding RNA (lncRNA), 1.36% of coding sequences (CDS), 0.54% of 3'untranslated region (UTR) and 0.21% of 5'UTR sequences [see Additional file 3]. Data are collected from Additional file 3: Top 20 RNAs in other RNA species (normalized to read number per million all mappable RNA seqeuences). "
RLID00037768	X53630	X53630	http://www.ncbi.nlm.nih.gov/nuccore/X53630		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00037769	X57780	X57780	http://www.ncbi.nlm.nih.gov/nuccore/X57780		mRNA	Mus musculus	22406755	Nucleus	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00037770	X96606	X96606	http://www.ncbi.nlm.nih.gov/nuccore/X96606		mRNA	Mus musculus	17486113	Exosome	Mast cell	Microarray	"The identified mRNA in exosomes was approximately 8% of the mRNA detected in the donor cells (16,000 mRNA; Fig. 3a-d; see Supplementary Information, Table S2, and see Accession numbers in Methods). Data are collected from Table S2. "
RLID00037771	Y14821	Y14821	http://www.ncbi.nlm.nih.gov/nuccore/Y14821		lncRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00037772	Y14822	Y14822	http://www.ncbi.nlm.nih.gov/nuccore/Y14822		mRNA	Mus musculus	22406755	Cytoplasm	Neuroblastoma cell	Microarray	"Array analysis revealed 499 lncRNAs that were significantly enriched in the cytoplasm and 191 in the nucleus. Intersection with lincRNAs and lncRNAs listed in lncRNAdb revealed a number of known and uncharacterized localizations of lncRNAs, including nuclear enrichment of Adapt33, Zfas1, and several other snoRNA host genes. Taken together, these results support the widespread trafficking of lncRNAs to different subcellular locations. All normalized stability and localization array data is available in Supplemental S2. "
RLID00037773	10984	KCNQ1OT1	http://www.ncbi.nlm.nih.gov/gene/?term=10984	"KCNQ1-AS2, KCNQ10T1, Kncq1, KvDMR1, KvLQT1-AS, LIT1, NCRNA00012"	lncRNA	Homo sapiens	17917697	Nucleus	NHFs(normal human fibroblast cell lines)	FISH	"We next performed RNA/DNA FISH on normal human lymphoblasts (NHF) and normal human fibroblasts (NHF, NHF2, NTI-4, TIG-1-20) to confirm the physiological state of LIT1 RNA in human cells. LIT1 RNA signals were observed in almost all interphase nuclei of the lymphoblast cell line (97% of interphase nuclei) and of four fibroblast cell lines."
RLID00037774	10984	KCNQ1OT1	http://www.ncbi.nlm.nih.gov/gene/?term=10984	"KCNQ1-AS2, KCNQ10T1, Kncq1, KvDMR1, KvLQT1-AS, LIT1, NCRNA00012"	lncRNA	Homo sapiens	17917697	Nucleus	CHO11P-8(Chinese hamster ovary hybrid cells) 	FISH	The RNA/DNA FISH shows that the LIT1 RNA signal co-localized with DNA in these CHO hybrid interphase nuclei. We detected a single LIT1 RNA signal in the nuclei of CHO11P-8 hybrid cells.
RLID00037775	100038448	Gm10840	http://www.ncbi.nlm.nih.gov/gene/?term=100038448		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037776	100042484	4732419C18Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100042484	Gm3866	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037777	100043309	4732414G09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=100043309		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037778	100043902	Six3os1	http://www.ncbi.nlm.nih.gov/gene/?term=100043902	"Rncr1, Six3os, D17Mgi26, E130112H22Rik"	lncRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037779	100503924	Fcor	http://www.ncbi.nlm.nih.gov/gene/?term=100503924	2400009B08Rik	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037780	100504593	Gm13431	http://www.ncbi.nlm.nih.gov/gene/?term=100504593		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037781	100526471	Mir3069	http://www.ncbi.nlm.nih.gov/gene/?term=100526471	"mir-3069, mmu-mir-3069"	miRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037782	100579148	Gm17409	http://www.ncbi.nlm.nih.gov/gene/?term=100579148		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037783	102640635	Gm26615	http://www.ncbi.nlm.nih.gov/gene/?term=102640635		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037784	103012	Firre	http://www.ncbi.nlm.nih.gov/gene/?term=103012	"AW048145, 5830467J12Rik, 6720401G13Rik"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037785	140795	P2ry14	http://www.ncbi.nlm.nih.gov/gene/?term=140795	"A330108O13Rik, Gpr105, P2Y14"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037786	15405	Hoxa9	http://www.ncbi.nlm.nih.gov/gene/?term=15405	"D6a9, Hox-1.7"	mRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037787	16201	Ilf3	http://www.ncbi.nlm.nih.gov/gene/?term=16201	"MBII-26, MPHOSPH4, NF90, NFAR"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037788	17263	Meg3	http://www.ncbi.nlm.nih.gov/gene/?term=17263	"Gtl2, R74756, R75394, AI425946, AW108224, D12Bwg1266e, 2900016C05Rik, 3110050O07Rik, 6330408G06Rik"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037789	17755	Map1b	http://www.ncbi.nlm.nih.gov/gene/?term=17755	"A230055D22, AI843217, LC1, MAP5, Mtap-5, Mtap1b, Mtap5"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037790	18484	Pam	http://www.ncbi.nlm.nih.gov/gene/?term=18484	PHM	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037791	19085	Prkar1b	http://www.ncbi.nlm.nih.gov/gene/?term=19085	"AI385716, RIbeta"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037792	19091	Prkg1	http://www.ncbi.nlm.nih.gov/gene/?term=19091	"AW125416, CGKI, Gm19690b, Prkgr1b, Prkg1"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037793	20238	Atxn1	http://www.ncbi.nlm.nih.gov/gene/?term=20238	"2900016G23Rik, Atx1, C85907, Gm10786, Sca1"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037794	207278	Fchsd2	http://www.ncbi.nlm.nih.gov/gene/?term=207278	"BC034086, R74866, Sh3md3, mKIAA0769"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037795	208941	Gm4755	http://www.ncbi.nlm.nih.gov/gene/?term=208941	F730043H23	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037796	210274	Shank2	http://www.ncbi.nlm.nih.gov/gene/?term=210274	"ProSAP1, mKIAA1022"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037797	210933	Adgrb3	http://www.ncbi.nlm.nih.gov/gene/?term=210933	"A830096D10Rik, Bai3"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037798	211712	Pcdh9	http://www.ncbi.nlm.nih.gov/gene/?term=211712		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037799	228012	Tlk1	http://www.ncbi.nlm.nih.gov/gene/?term=228012	4930545J15Rik	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037800	238161	Akap6	http://www.ncbi.nlm.nih.gov/gene/?term=238161	"AI482140, Akapalpha, Akapbeta, PRKA"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037801	23965	Tenm3	http://www.ncbi.nlm.nih.gov/gene/?term=23965	"2610100B16Rik, Odz1, Odz3, Ten-m3, mKIAA1455"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037802	268723	A830039N20Rik	http://www.ncbi.nlm.nih.gov/gene/?term=268723		lncRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037803	268755	Mir124a-1hg	http://www.ncbi.nlm.nih.gov/gene/?term=268755	"Rncr3, mir-3078, mir-124-1, A930011O12Rik"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037804	268906	LOC268906	http://www.ncbi.nlm.nih.gov/gene/?term=268906		mRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037805	30046	Zfp292	http://www.ncbi.nlm.nih.gov/gene/?term=30046	"5730450D02Rik, 5830493J20Rik, 9430062L07Rik, AI449016, Krox-10, Zfp-15, Zfp15, Zn-15, Zn-16, mKIAA0530"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037806	319622	Itpripl2	http://www.ncbi.nlm.nih.gov/gene/?term=319622	"C130081G24, E030018N11Rik"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037807	319982	5930430L01Rik	http://www.ncbi.nlm.nih.gov/gene/?term=319982		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037808	320019	Ptgs2os	http://www.ncbi.nlm.nih.gov/gene/?term=320019	7530420F21Rik	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037809	320138	A130050O07Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320138		unknown	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037810	320800	9230112E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=320800		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037811	329562	A530013C23Rik	http://www.ncbi.nlm.nih.gov/gene/?term=329562		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037812	330173	2610524H06Rik	http://www.ncbi.nlm.nih.gov/gene/?term=330173		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037813	330183	Gm16063	http://www.ncbi.nlm.nih.gov/gene/?term=330183	G630008E18	lncRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037814	384569	Nova2	http://www.ncbi.nlm.nih.gov/gene/?term=384569	Gm1424	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037815	433485	Syndig1	http://www.ncbi.nlm.nih.gov/gene/?term=433485	"AW123113, DSPC2, Gm14134, H2C20orf39, Tmem90b"	mRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037816	433966	5730422E09Rik	http://www.ncbi.nlm.nih.gov/gene/?term=433966		lncRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037817	434008	Tmem178b	http://www.ncbi.nlm.nih.gov/gene/?term=434008	"EG434008, Gm5567"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037818	434353	A330074K22Rik	http://www.ncbi.nlm.nih.gov/gene/?term=434353		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037819	50505	Ercc4	http://www.ncbi.nlm.nih.gov/gene/?term=50505	"AI606920, Xpf"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037820	50794	Klf13	http://www.ncbi.nlm.nih.gov/gene/?term=50794	"0610043C13Rik, 9430029L20Rik, Bteb3, FKLF-2, FKLF2, NSLP1, RFLAT-1, RFLAT1"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037821	52480	Snhg14	http://www.ncbi.nlm.nih.gov/gene/?term=52480	"Lncat, Pwcr1, Gm42386, Gm42387, Gm42388, Gm42389, Gm42390, Gm42391, Gm45921, AU018661, Ube3a-ATS, D7Ertd715e, U-Ube3a-ATS, lincRNA-EC50, C230091D08Rik"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037822	544874	LOC544874	http://www.ncbi.nlm.nih.gov/gene/?term=544874		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037823	625175	1700028E10Rik	http://www.ncbi.nlm.nih.gov/gene/?term=625175	"Gm6561, A630054D14"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037824	63830	Kcnq1ot1	http://www.ncbi.nlm.nih.gov/gene/?term=63830	"Lit1, Tssc8, Kvlqt1-as"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037825	66602	1700020I14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=66602	"Cyrano, AI451541, AI585852, AW538376, AW558897, 1190006L01Rik, 4933437I03Rik"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037826	66662	Fbxl12os	http://www.ncbi.nlm.nih.gov/gene/?term=66662	5730577I03Rik	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037827	68127	B230217C12Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68127	AI840637	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037828	68434	1010001N08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=68434	Gata6as	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037829	69077	Psmd11	http://www.ncbi.nlm.nih.gov/gene/?term=69077	"1700089D09Rik, 1810019E17Rik, 2610024G20Rik, 2810055C24Rik, C78232, P44.5, S9"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037830	69865	A1cf	http://www.ncbi.nlm.nih.gov/gene/?term=69865	"1810073H04Rik, ACF64, ACF65, ASP, Acf, MCM, MerCreMer, Tg(Myh6-cre/Esr1*)1Jmk, mer"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037831	69953	2810025M15Rik	http://www.ncbi.nlm.nih.gov/gene/?term=69953	AI429618	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037832	71373	Prr16	http://www.ncbi.nlm.nih.gov/gene/?term=71373	"5430406M13Rik, AI607429"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037833	73941	4930412L05Rik	http://www.ncbi.nlm.nih.gov/gene/?term=73941	LeXis	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037834	74184	2310065F04Rik	http://www.ncbi.nlm.nih.gov/gene/?term=74184	linc-Myh	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037835	75745	Rian	http://www.ncbi.nlm.nih.gov/gene/?term=75745	"Meg8, 5530401N18Rik, C130089L09Rik"	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037836	76100	5830454E08Rik	http://www.ncbi.nlm.nih.gov/gene/?term=76100		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037837	76626	Msi2	http://www.ncbi.nlm.nih.gov/gene/?term=76626	"1700105C15Rik, AI451722, AI563628, AW489193h, Msi2"	mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037838	77866	E130102H24Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77866		lncRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037839	AK018559	AK018559	https://www.ncbi.nlm.nih.gov/nuccore/AK018559		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037840	AK032777	AK032777	https://www.ncbi.nlm.nih.gov/nuccore/AK032777		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037841	AK033161	AK033161	https://www.ncbi.nlm.nih.gov/nuccore/AK033161		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037842	AK033985	AK033985	https://www.ncbi.nlm.nih.gov/nuccore/AK033985		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037843	AK035692	AK035692	https://www.ncbi.nlm.nih.gov/nuccore/AK035692		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037844	AK038224	AK038224	https://www.ncbi.nlm.nih.gov/nuccore/AK038224		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037845	AK039341	AK039341	https://www.ncbi.nlm.nih.gov/nuccore/AK039341		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037846	AK039686	AK039686	https://www.ncbi.nlm.nih.gov/nuccore/AK039686		mRNA	Mus musculus	18184812	Cytoplasm	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. The possibility that these intronic ncRNAs are solely a consequence of persevering nonfunctional lariats is unlikely because we also observe (i) intronic ncRNAs expressed in the cytoplasm, (ii) nonexpressed intronic ncRNAs of highly expressed host protein-coding genes, and (iii) intronic ncRNAs that exhibit a discordant expression profile to their host protein-coding gene."
RLID00037847	AK046764	AK046764	https://www.ncbi.nlm.nih.gov/nuccore/AK046764		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037848	AK046779	AK046779	https://www.ncbi.nlm.nih.gov/nuccore/AK046779		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037849	AK052663	AK052663	https://www.ncbi.nlm.nih.gov/nuccore/AK052663		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037850	AK053343	AK053343	https://www.ncbi.nlm.nih.gov/nuccore/AK053343		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037851	AK076684	AK076684	https://www.ncbi.nlm.nih.gov/nuccore/AK076684		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037852	AK078603	AK078603	https://www.ncbi.nlm.nih.gov/nuccore/AK078603		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037853	AK082015	AK082015	https://www.ncbi.nlm.nih.gov/nuccore/AK082015		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037854	BE649186	BE649186	https://www.ncbi.nlm.nih.gov/nuccore/BE649186		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037855	DV657041	DV657041	https://www.ncbi.nlm.nih.gov/nuccore/DV657041		mRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. We used previously characterized ncRNAs and mRNAs with known subcellular expression profiles as crude markers of subcellular compartments. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037856	ENSMUSG00000087615	Pnpla1os	http://www.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000087615	Gm16190	lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037857	ENSMUSG00000093385	A330044P14Rik	http://www.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000093385		lncRNA	Mus musculus	18184812	Nucleus	Cerebellar Purkinje cell	ISH	"Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Data were collected from supplemental meterial SI Table 1. From the 88 (10% of expressed ncRNAs) that were expressed in Purkinje cells, 25 (29%) showed a nuclear restricted expression profile, a further 54 (61%) appeared as foci or speckles, and the remaining 9 (10%) were diffusely expressed throughout the soma."
RLID00037858	101101691	Hm629797	http://www.ncbi.nlm.nih.gov/gene/?term=101101691	Mrhl	lncRNA	Mus musculus	18515546	Nucleus	Testis and liver	RT-PCR	"The nuclear localization of mrhl RNA was not surprising, as many noncoding RNAs have been shown earlier to exhibit definite nuclear-localization patterns mediating potent regulatory events such as regulation of coding genes (CTN), imprinting (H19, Air), and dosage compensation (Xist, roX)."
RLID00037859	66961	Neat1	http://www.ncbi.nlm.nih.gov/gene/?term=66961	"VINC, 2310043N10Rik"	lncRNA	Mus musculus	19106332	Nucleus	C2C12	RNA-FISH	The Men ¦Å/¦Â (also known as Neat1) transcripts are localized to nuclear paraspeckles and directly interact with NONO.
RLID00037860	55384	MEG3	http://www.ncbi.nlm.nih.gov/gene/?term=55384	"FP504, GTL2, LINC00023, NCRNA00023, PRO0518, PRO2160, onco-lncRNA-83, prebp1"	lncRNA	Homo sapiens	20404130	Nucleus	Fibroblast  cells	qPCR	"Interestingly, we have identified two intergenic CARs in the DLK1-DIO3-imprinted domain; one of them overlaps with the maternally expressed ncRNA MEG3, indicating that, like Kcnq1ot1 and Airn ncRNAs, MEG3 may play a role in regulation of imprinting of flanking genes in the DLK1-DIO3 domain. We also investigated the subcellular localization of the validated CARs and found that all transcripts except one were clearly localized to the nuclear compartment, which is in agreement with the chromatin-associated functions of these transcripts."
RLID00037861	10178876	yar	http://www.ncbi.nlm.nih.gov/gene/?term=10178876	anon-1Be; CR42744; Dmel\CR42744	lncRNA	Drosophila melanogaster	21775470	Cytoplasm	Embryos	RNA-FISH	"The function of lncRNAs depends upon their subcellular location. As lncRNAs can localize to the nucleus and cytoplasm, we determined which subcellular compartment contains yar. Finally, these data imply that spliced yar RNAs are cytoplasmic, a conclusion that is supported by analyses of Ras64B RNA."
RLID00037862	100129387	GABPB1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100129387		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037863	100505881	MAGI2-AS3	http://www.ncbi.nlm.nih.gov/gene/?term=100505881		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037864	100506965	PWAR6	http://www.ncbi.nlm.nih.gov/gene/?term=100506965	"HBT8, PAR-6"	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037865	11336	EXOC3	http://www.ncbi.nlm.nih.gov/gene/?term=11336	"SEC6, SEC6L1, Sec6p"	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037866	148189	LINC00662	http://www.ncbi.nlm.nih.gov/gene/?term=148189		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037867	148189	LINC00662	http://www.ncbi.nlm.nih.gov/gene/?term=148189		lncRNA	Homo sapiens	22532836	Cytoplasm	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037868	157627	LINC00599	http://www.ncbi.nlm.nih.gov/gene/?term=157627	Rncr3	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037869	267017	HLA-Z	http://www.ncbi.nlm.nih.gov/gene/?term=267017	HLA-Z1	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037870	267017	HLA-Z	http://www.ncbi.nlm.nih.gov/gene/?term=267017	HLA-Z1	lncRNA	Homo sapiens	22532836	Cytoplasm	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037871	339290	LINC00667	http://www.ncbi.nlm.nih.gov/gene/?term=339290		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037872	375035	SFT2D2	http://www.ncbi.nlm.nih.gov/gene/?term=375035	"UNQ512, dJ747L4.C1.2"	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037873	378805	LINC-PINT	http://www.ncbi.nlm.nih.gov/gene/?term=378805	"LincRNA-Pint, MKLN1-AS1, PINT"	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037874	4026	LPP	http://www.ncbi.nlm.nih.gov/gene/?term=4026		mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037875	414777	HCG18	http://www.ncbi.nlm.nih.gov/gene/?term=414777		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037876	4719	NDUFS1	http://www.ncbi.nlm.nih.gov/gene/?term=4719	CI-75k; CI-75Kd; PRO1304	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037877	492311	IGIP	http://www.ncbi.nlm.nih.gov/gene/?term=492311	C5orf53	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037878	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, C14orf67, DHRS4AS1, PRO1488"	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037879	55449	DHRS4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=55449	"AS1DHRS4, C14orf167, C14orf67, DHRS4AS1, PRO1488"	lncRNA	Homo sapiens	22532836	Cytoplasm	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037880	55819	RNF130	http://www.ncbi.nlm.nih.gov/gene/?term=55819	"G1RZFP, GOLIATH, GP"	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037881	644873	LINC01184	http://www.ncbi.nlm.nih.gov/gene/?term=644873		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037882	7273	TTN	http://www.ncbi.nlm.nih.gov/gene/?term=7273	"CMD1G, CMH9, CMPD4, EOMFC, HMERF, LGMD2J, MYLK5, SALMY, TMD"	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037883	729082	OIP5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=729082	"cyrano, linc-OIP5"	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037884	729678	LINC00847	http://www.ncbi.nlm.nih.gov/gene/?term=729678		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037885	729678	LINC00847	http://www.ncbi.nlm.nih.gov/gene/?term=729678		lncRNA	Homo sapiens	22532836	Cytoplasm	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037886	84281	C2orf88	http://www.ncbi.nlm.nih.gov/gene/?term=84281	smAKAP	mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037887	84981	MIR22HG	http://www.ncbi.nlm.nih.gov/gene/?term=84981	C17orf91	lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037888	ENSG00000174093	RP11-1407O15.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000174093		mRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We excluded the 23,241 clusters that were predicted to be protein-coding mRNAs, and also removed the 4,888 clusters for which the gene locus was covered by sequence information available only from the RefSeq or the Ensembl, or by just one 5¡ä-EST. Ultimately, we obtained 3,180 clusters as candidates likely to encode ncRNAs. Data were collected from supplemental meterial Table S2. we defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5¨C2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Among the 29 candidates, 25 were localized in the nucleus Data were collected from supplemental meterial Table S4."
RLID00037889	ENSG00000216775	RP1-152L7.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000216775		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037890	ENSG00000223745	RP4-717I23.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223745		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037891	ENSG00000233137	RP11-220I1.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233137		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037892	ENSG00000259976	RP11-553L6.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259976		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037893	ENSG00000268205	CTC-444N24.11	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268205		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037894	ENSG00000272761	RP11-572C15.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272761		lncRNA	Homo sapiens	22532836	Nucleus	HeLa cells	qRT-PCR	"We identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Data can be seen from Table 1. We defined the subcellular localization of the transcripts as: N/C ratio >2, nuclear localization; N/C ratio 0.5-2, nuclear and cytoplasmic localization; and N/C ratio <0.5, cytoplasmic localization. Data were collected from supplemental meterial Table S4."
RLID00037895	50652	PCA3	http://www.ncbi.nlm.nih.gov/gene/?term=50652	"DD3, NCRNA00019, PCAT3"	lncRNA	Homo sapiens	23130941	Nucleus	Prostate cancer cell lines	qRT-PCR	We determined the cell compartment localization of PCA3 in LNCaP cells by differential centrifugation and qRT-PCR. Our data showed that PCA3 expression was mainly restricted to the nuclear and microsomal compartments of LNCaP cells.
RLID00037896	37820	PPP1R15	http://www.ncbi.nlm.nih.gov/gene/?term=37820	"Dmel_CG3825, CG3825, Dm-GADD34, Dmel\CG3825, GADD34, Gadd34, dGADD34, dPPP1R15, gadd34"	mRNA	Drosophila melanogaster	23135994	Endoplasmic Reticulum 	Drosophila S2 cells	RT-PCR	"The vast majority of mRNAs that were strongly associated with the ER were degraded faster during ER stress in an Ire1-dependent manner, suggesting that RIDD is the default pathway for ER-localized mRNAs during stress.Data were collected from supplemental meterials."
RLID00037897	41983	Manf	http://www.ncbi.nlm.nih.gov/gene/?term=41983	"Dmel_CG7013, ARP-like, CG7013, DmMANF, DmManf, Dmel\CG7013, MANF, anon-EST:ParkEST188"	mRNA	Drosophila melanogaster	23135994	Endoplasmic Reticulum 	Drosophila S2 cells	RT-PCR	"The vast majority of mRNAs that were strongly associated with the ER were degraded faster during ER stress in an Ire2-dependent manner, suggesting that RIDD is the default pathway for ER-localized mRNAs during stress.Data were collected from supplemental meterials."
RLID00037898	43832	PlexA	http://www.ncbi.nlm.nih.gov/gene/?term=43832	"Dmel_CG11081, BcDNA:GM05237, CG11081, D-Plex A, DPlexA, Dmel\CG11081, Plex11, lincRNA.927, plex, plex A, plexA, PlexA"	mRNA	Drosophila melanogaster	23135994	Endoplasmic Reticulum 	Drosophila S2 cells	RT-PCR	"The vast majority of mRNAs that were strongly associated with the ER were degraded faster during ER stress in an Ire3-dependent manner, suggesting that RIDD is the default pathway for ER-localized mRNAs during stress.Data were collected from supplemental meterials."
RLID00037899	100289178	GNG12-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100289178		lncRNA	Homo sapiens	23871723	Nucleus	HB2 cells	RT-qPCR	We also investigated the cellular localization of GNG12-AS1 and found that it is predominantly present in the nucleus.
RLID00037900	103012	Firre	http://www.ncbi.nlm.nih.gov/gene/?term=103012	"AW048145, 5830467J12Rik, 6720401G13Rik"	lncRNA	Mus musculus	24463464	Nucleus	Lung fibroblast cell lines	RNA-FISH	"Notably, Firre exhibits strong expression foci near its site of transcription in both male and female mouse and human ESCs (mESCs, hESCs). Thus, Firre is nuclear-localized and forms expression foci on both X-chromosomes prior to, and after X-chromosome inactivation."
RLID00037901	286467	FIRRE	http://www.ncbi.nlm.nih.gov/gene/?term=286467	LINC01200	lncRNA	Homo sapiens	24463464	Nucleus	Lung fibroblast cell lines	RNA-FISH	"Notably, Firre exhibits strong expression foci near its site of transcription in both male and female mouse and human ESCs (mESCs, hESCs). Thus, Firre is nuclear-localized and forms expression foci on both X-chromosomes prior to, and after X-chromosome inactivation."
RLID00037902	103164605	Paupar	http://www.ncbi.nlm.nih.gov/gene/?term=103164605		lncRNA	Mus musculus	24488179	Nucleus	N2A cells	qRT-PCR	"In these cells, we found Paupar RNA, but not a control mRNA, to be nuclear-enriched and located mainly in the chromatin fraction, and noted that ENCODE data show human Paupar to be similarly present in the nucleus and chromatin."
RLID00037903	100507056	CCAT1	http://www.ncbi.nlm.nih.gov/gene/?term=CCAT1	CARLo-5; onco-lncRNA-40	lncRNA	Homo sapiens	24662484	Cytoplasm	Colorectal cancers	RNA fractionation	"In contrast, when a probe recognizing both isoforms of CCAT1 was used in the ISH, we found that fluorescent signals appeared in both cytoplasm and nucleus, suggesting that CCAT1-S is located in the cytoplasm."
RLID00037904	100507056	CCAT1	http://www.ncbi.nlm.nih.gov/gene/?term=CCAT1	CARLo-5; onco-lncRNA-40	lncRNA	Homo sapiens	24662484	Cytoplasm	Colorectal cancers	RNA-FISH	"In contrast, when a probe recognizing both isoforms of CCAT1 was used in the ISH, we found that fluorescent signals appeared in both cytoplasm and nucleus, suggesting that CCAT1-S is located in the cytoplasm."
RLID00037905	83729	INHBE	http://www.ncbi.nlm.nih.gov/gene/?term=83729		mRNA	Homo sapiens	24726458	Nucleus	Rh36 cell	RT-PCR	"Through nuclear/cytoplasmic fractionation of Rh36 and CCA cells, followed by RNA isolation and real©\time RT/PCR, we found that the unspliced GLI1AS RNAs are preferentially retained in the nucleus, while the spliced GLI1AS RNAs transported to the cytoplasm."
RLID00037906	83729	INHBE	http://www.ncbi.nlm.nih.gov/gene/?term=83729		mRNA	Homo sapiens	24726458	Cytoplasm	Rh36 cell	RT-PCR	"Through nuclear/cytoplasmic fractionation of Rh36 and CCA cells, followed by RNA isolation and real©\time RT/PCR, we found that the unspliced GLI1AS RNAs are preferentially retained in the nucleus, while the spliced GLI1AS RNAs transported to the cytoplasm."
RLID00037907	100048912	CDKN2B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100048912	"ANRIL, CDKN2B-AS, CDKN2BAS, NCRNA00089, PCAT12, p15AS"	lncRNA	Homo sapiens	24810364	Nucleus	BGC-823	qRT-PCR	"We found a considerable increase in ANRIL expression in the nucleus versus the cytosol, thus suggesting that ANRIL is mainly localized in the nucleus and play a major regulatory function at the transcriptional level."
RLID00037908	100048912	CDKN2B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100048912	"ANRIL, CDKN2B-AS, CDKN2BAS, NCRNA00089, PCAT12, p15AS"	lncRNA	Homo sapiens	24810364	Nucleus	SGC-7901	qRT-PCR	"We found a considerable increase in ANRIL expression in the nucleus versus the cytosol, thus suggesting that ANRIL is mainly localized in the nucleus and play a major regulatory function at the transcriptional level."
RLID00037909	283131	NEAT1	http://www.ncbi.nlm.nih.gov/gene/?term=283131	"LINC00084, NCRNA00084, TncRNA, VINC"	lncRNA	Homo sapiens	25155612	Nucleus	BJ cell	RNA-FISH	"RNA FISH in BJ cells confirmed the punctate, nuclear localization of NEAT1 RNA."
RLID00037910	400500	BCAR4	http://www.ncbi.nlm.nih.gov/gene/?term=400500		lncRNA	Homo sapiens	25416949	Nucleus	MDA-MB-231	RNA-FISH	"We next examined the subcellular localization of BCAR4 by RNA FISH and real-time RT-qPCR analyses on fractionated RNA, finding that the BCAR4 transcript is predominately localized in the nucleus."
RLID00037911	400500	BCAR4	http://www.ncbi.nlm.nih.gov/gene/?term=400500		lncRNA	Homo sapiens	25416949	Nucleus	MDA-MB-231	RT-qPCR	"We next examined the subcellular localization of BCAR4 by RNA FISH and real-time RT-qPCR analyses on fractionated RNA, finding that the BCAR4 transcript is predominately localized in the nucleus."
RLID00037912	147093	LINC00974	http://www.ncbi.nlm.nih.gov/gene/?term=147093		lncRNA	Homo sapiens	25476897	Cytoplasm	Huh7 cell lines/HepG2 cell lines	RT-PCR	The transcript for Linc00974 was located primarily in the cytoplasm of Huh7 and HepG2 cell lines according to the results of RT-PCR amplified with separated cytoplasm RNA and nuclear RNA.
RLID00037913	23576	DDAH1	http://www.ncbi.nlm.nih.gov/gene/?term=23576	"DDAH, DDAH-1, DDAHI, HEL-S-16"	mRNA	Homo sapiens	25601475	Cytoplasm	WI38-derived cells IMR90 and IMR90 hTERT MEK1-ER cell line	qRT-PCR	"Cell fractionation experiments showed that VAD was almost exclusively found in the chromatin fraction both in proliferative and senescent cells, whereas, as expected, mRNAs, such as the DDAH1-S mRNAs, were predominantly cytoplasmic."
RLID00037914	105221694	BISPR	http://www.ncbi.nlm.nih.gov/gene/?term=105221694	lncBST2	lncRNA	Homo sapiens	25688240	Nucleus	Primary human keratinocytes absence of IFN	RT-qPCR	"We analyzed the subcellular localization of BISPR, which showed that in the absence of IFN it was predominantly nuclear, while after IFN induction the RNA was present in both compartments."
RLID00037915	105416157	NKILA	http://www.ncbi.nlm.nih.gov/gene/?term=105416157		lncRNA	Homo sapiens	25759022	Cytoplasm	Breast Cancer Cells	qRT-PCR	"Confocal microscopy for fluorescent in situ hybridization (FISH) showed that NKILA located primarily in the cytoplasm, which was confirmed by nuclear/cytoplasm fractionation, suggesting that NKILA may exert its biological function in the cytoplasm."
RLID00037916	105500046	Gm30731	http://www.ncbi.nlm.nih.gov/gene/?term=105500046	"Pnky, lnc-pou3f2"	lncRNA	Mus musculus	25800779	Nucleus	Embryonic tissue	RNA-FISH	"Consistent with the nuclear fractionation studies, in situ hybridization (ISH) for Pnky demonstrated predominantly nuclear localization of the transcript."
RLID00037917	283460	HNF1A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=283460	"C12orf27, HAS1, NCRNA00262"	lncRNA	Homo sapiens	25863539	Nucleus	NSCLC cell lines( including both adenocarcinoma and squamous carcinoma subtypes)	qRT-PCR	"We observed a considerable increase in HNF1A-AS1 expression in the nucleus versus the cytosol, thus suggesting that HNF1A-AS1 was mainly localized in the nucleus and maybe played a major regulatory function at the transcriptional level."
RLID00037918	54485	Dll4	http://www.ncbi.nlm.nih.gov/gene/?term=54485	Delta4	mRNA	Mus musculus	25914805	Nucleus	"Endothelial cell line,"	RT-PCR	Dll4-AS transcripts were localized in both cytoplasm and nucleus of mouse Ecs.
RLID00037919	54485	Dll4	http://www.ncbi.nlm.nih.gov/gene/?term=54485	Delta4	mRNA	Mus musculus	25914805	Cytoplasm	"Endothelial cell line,"	RT-PCR	Dll4-AS transcripts were localized in both cytoplasm and nucleus of mouse Ecs.
RLID00037920	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072"	lncRNA	Homo sapiens	26136075	Nucleus	Gastric cancer tissues	qRT-PCR	"Furthermore, we verified that HOTAIR was located both in the nucleus and cytoplasm of gastric cancer cells, and RNA immunoprecipitation (RIP) assays showed that HOTAIR could bind to PRC2."
RLID00037921	100124700	HOTAIR	http://www.ncbi.nlm.nih.gov/gene/?term=100124700	"HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072"	lncRNA	Homo sapiens	26136075	Cytoplasm	Gastric cancer tissues	qRT-PCR	"Furthermore, we verified that HOTAIR was located both in the nucleus and cytoplasm of gastric cancer cells, and RNA immunoprecipitation (RIP) assays showed that HOTAIR could bind to PRC2."
RLID00037922	1000	CDH2	http://www.ncbi.nlm.nih.gov/gene/?term=1000	"CD325, CDHN, CDw325, NCAD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037923	10005	ACOT8	http://www.ncbi.nlm.nih.gov/gene/?term=10005	"HNAACTE, NAP1, PTE-1, PTE-2, PTE1, PTE2, hACTE-III, hTE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037924	10005	ACOT8	http://www.ncbi.nlm.nih.gov/gene/?term=10005	"HNAACTE, NAP1, PTE-1, PTE-2, PTE1, PTE2, hACTE-III, hTE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037925	1001	CDH3	http://www.ncbi.nlm.nih.gov/gene/?term=1001	"CDHP, HJMD, PCAD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037926	1001	CDH3	http://www.ncbi.nlm.nih.gov/gene/?term=1001	"CDHP, HJMD, PCAD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037927	10010	TANK	http://www.ncbi.nlm.nih.gov/gene/?term=10010	"I-TRAF, ITRAF, TRAF2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037928	100101467	ZSCAN30	http://www.ncbi.nlm.nih.gov/gene/?term=100101467	"ZNF-WYM, ZNF397OS, ZNF917"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037929	100128494	LOC100128494	http://www.ncbi.nlm.nih.gov/gene/?term=100128494		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037930	100128494	LOC100128494	http://www.ncbi.nlm.nih.gov/gene/?term=100128494		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037931	100129518	SOD2-OT1	http://www.ncbi.nlm.nih.gov/gene/?term=100129518		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037932	100129917	LOC100129917	http://www.ncbi.nlm.nih.gov/gene/?term=100129917		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037933	100129917	LOC100129917	http://www.ncbi.nlm.nih.gov/gene/?term=100129917		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037934	100129961	CCNT2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100129961		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037935	100131713	RPL29P11	http://www.ncbi.nlm.nih.gov/gene/?term=100131713	RPL29_2_362	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037936	100131713	RPL29P11	http://www.ncbi.nlm.nih.gov/gene/?term=100131713	RPL29_2_362	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037937	100132618	ZRANB2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100132618		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037938	100132891	MSC-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100132891		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037939	100134713	NDUFB2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100134713		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037940	100134713	NDUFB2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100134713		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037941	10018	BCL2L11	http://www.ncbi.nlm.nih.gov/gene/?term=10018	"BAM, BIM, BOD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037942	10018	BCL2L11	http://www.ncbi.nlm.nih.gov/gene/?term=10018	"BAM, BIM, BOD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037943	10019	SH2B3	http://www.ncbi.nlm.nih.gov/gene/?term=10019	"IDDM20, LNK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037944	10019	SH2B3	http://www.ncbi.nlm.nih.gov/gene/?term=10019	"IDDM20, LNK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037945	100271358	RPS15AP16	http://www.ncbi.nlm.nih.gov/gene/?term=100271358	RPS15A_7_402	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037946	100271358	RPS15AP16	http://www.ncbi.nlm.nih.gov/gene/?term=100271358	RPS15A_7_402	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037947	100288831	SRGAP3-AS3	http://www.ncbi.nlm.nih.gov/gene/?term=100288831		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037948	100288831	SRGAP3-AS3	http://www.ncbi.nlm.nih.gov/gene/?term=100288831		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037949	10040	TOM1L1	http://www.ncbi.nlm.nih.gov/gene/?term=10040	SRCASM	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037950	10043	TOM1	http://www.ncbi.nlm.nih.gov/gene/?term=10043		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037951	10043	TOM1	http://www.ncbi.nlm.nih.gov/gene/?term=10043		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037952	10046	MAMLD1	http://www.ncbi.nlm.nih.gov/gene/?term=10046	"CG1, CXorf6, F18, HYSP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037953	10048	RANBP9	http://www.ncbi.nlm.nih.gov/gene/?term=10048	"BPM-L, BPM90, RANBPM, RanBP7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037954	10048	RANBP9	http://www.ncbi.nlm.nih.gov/gene/?term=10048	"BPM-L, BPM90, RANBPM, RanBP7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037955	10049	DNAJB6	http://www.ncbi.nlm.nih.gov/gene/?term=10049	"DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037956	10049	DNAJB6	http://www.ncbi.nlm.nih.gov/gene/?term=10049	"DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037957	100505585	LOC100505585	http://www.ncbi.nlm.nih.gov/gene/?term=100505585		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037958	100505585	LOC100505585	http://www.ncbi.nlm.nih.gov/gene/?term=100505585		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037959	100505624	GTF3C2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505624		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037960	100505624	GTF3C2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505624		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037961	100505876	CEBPZOS	http://www.ncbi.nlm.nih.gov/gene/?term=100505876	CEBPZ-AS1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037962	100505876	CEBPZOS	http://www.ncbi.nlm.nih.gov/gene/?term=100505876	CEBPZ-AS1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037963	100506020	ARAP1-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=100506020		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037964	100506020	ARAP1-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=100506020		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037965	100506100	LOC100506100	http://www.ncbi.nlm.nih.gov/gene/?term=100506100		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037966	100506100	LOC100506100	http://www.ncbi.nlm.nih.gov/gene/?term=100506100		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037967	100506243	KRBOX1	http://www.ncbi.nlm.nih.gov/gene/?term=100506243		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037968	100506403	LOC100506403	http://www.ncbi.nlm.nih.gov/gene/?term=100506403		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037969	100506403	LOC100506403	http://www.ncbi.nlm.nih.gov/gene/?term=100506403		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037970	100506779	TSPOAP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506779	BZRAP1-AS1	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037971	100506779	TSPOAP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506779	BZRAP1-AS1	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037972	100507582	BHLHE40-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507582		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037973	100507582	BHLHE40-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507582		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037974	10051	SMC4	http://www.ncbi.nlm.nih.gov/gene/?term=10051	"CAP-C, CAPC, SMC-4L1, SMC4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037975	10081	PDCD7	http://www.ncbi.nlm.nih.gov/gene/?term=10081	"ES18, HES18"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037976	10082	GPC6	http://www.ncbi.nlm.nih.gov/gene/?term=10082	OMIMD1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037977	10082	GPC6	http://www.ncbi.nlm.nih.gov/gene/?term=10082	OMIMD1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037978	10085	EDIL3	http://www.ncbi.nlm.nih.gov/gene/?term=10085	DEL1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037979	10085	EDIL3	http://www.ncbi.nlm.nih.gov/gene/?term=10085	DEL1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037980	100873952	SZT2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100873952		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037981	100873952	SZT2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100873952		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037982	100874040	PEX5L-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874040		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037983	100874040	PEX5L-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874040		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037984	100874048	DGUOK-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874048		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037985	100874048	DGUOK-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874048		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037986	100874075	ARAP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874075		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037987	100874075	ARAP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874075		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037988	100874108	A2ML1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874108		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037989	100874108	A2ML1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874108		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037990	100874212	MYCBP2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874212		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037991	100874212	MYCBP2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874212		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037992	100874515	POLR2KP1	http://www.ncbi.nlm.nih.gov/gene/?term=100874515		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037993	10098	TSPAN5	http://www.ncbi.nlm.nih.gov/gene/?term=10098	"NET-4, NET4, TM4SF9, TSPAN-5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037994	10098	TSPAN5	http://www.ncbi.nlm.nih.gov/gene/?term=10098	"NET-4, NET4, TM4SF9, TSPAN-5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037995	100996485	C5orf66	http://www.ncbi.nlm.nih.gov/gene/?term=100996485		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00037996	100996485	C5orf66	http://www.ncbi.nlm.nih.gov/gene/?term=100996485		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00037997	100996693	LOC100996693	http://www.ncbi.nlm.nih.gov/gene/?term=100996693		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00037998	100996693	LOC100996693	http://www.ncbi.nlm.nih.gov/gene/?term=100996693		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00037999	10111	RAD50	http://www.ncbi.nlm.nih.gov/gene/?term=10111	"NBSLD2, hRad50, RAD50"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038000	10114	HIPK3	http://www.ncbi.nlm.nih.gov/gene/?term=10114	"DYRK6, FIST3, PKY, YAK1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038001	1012	CDH13	http://www.ncbi.nlm.nih.gov/gene/?term=1012	"CDHH, P105"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038002	1012	CDH13	http://www.ncbi.nlm.nih.gov/gene/?term=1012	"CDHH, P105"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038003	10138	YAF2	http://www.ncbi.nlm.nih.gov/gene/?term=10138		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038004	10138	YAF2	http://www.ncbi.nlm.nih.gov/gene/?term=10138		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038005	10142	AKAP9	http://www.ncbi.nlm.nih.gov/gene/?term=10142	"AKAP-9, AKAP350, AKAP450, CG-NAP, HYPERION, LQT11, MU-RMS-40.16A, PPP1R45, PRKA9, YOTIAO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038006	10142	AKAP9	http://www.ncbi.nlm.nih.gov/gene/?term=10142	"AKAP-9, AKAP350, AKAP450, CG-NAP, HYPERION, LQT11, MU-RMS-40.16A, PPP1R45, PRKA9, YOTIAO"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038007	10144	FAM13A	http://www.ncbi.nlm.nih.gov/gene/?term=10144	"ARHGAP481, FAM13A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038008	10144	FAM13A	http://www.ncbi.nlm.nih.gov/gene/?term=10144	"ARHGAP481, FAM13A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038009	10149	ADGRG2	http://www.ncbi.nlm.nih.gov/gene/?term=10149	"CBAVDX, EDDM6, GPR64, HE6, TM7LN2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038010	10149	ADGRG2	http://www.ncbi.nlm.nih.gov/gene/?term=10149	"CBAVDX, EDDM6, GPR64, HE6, TM7LN2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038011	10150	MBNL2	http://www.ncbi.nlm.nih.gov/gene/?term=10150	"MBLL, MBLL39, PRO2032"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038012	10150	MBNL2	http://www.ncbi.nlm.nih.gov/gene/?term=10150	"MBLL, MBLL39, PRO2032"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038013	10159	ATP6AP2	http://www.ncbi.nlm.nih.gov/gene/?term=10159	"APT6M8-9, ATP6IP2, ATP6M8-9, ELDF10, HT028, M8-9, MRXE, MRXSH, MSTP009, PRR, RENR, XMRE, XPDS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038014	10160	FARP1	http://www.ncbi.nlm.nih.gov/gene/?term=10160	"CDEP-IT1, PLEKHC2, PPP1R75, FARP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038015	10160	FARP1	http://www.ncbi.nlm.nih.gov/gene/?term=10160	"CDEP-IT1, PLEKHC2, PPP1R75, FARP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038016	10165	SLC25A13	http://www.ncbi.nlm.nih.gov/gene/?term=10165	"ARALAR2, CITRIN, CTLN2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038017	10165	SLC25A13	http://www.ncbi.nlm.nih.gov/gene/?term=10165	"ARALAR2, CITRIN, CTLN2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038018	10180	RBM6	http://www.ncbi.nlm.nih.gov/gene/?term=10180	"3G2, DEF-3, DEF3, HLC-11, NY-LU-12, g16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038019	10180	RBM6	http://www.ncbi.nlm.nih.gov/gene/?term=10180	"3G2, DEF-3, DEF3, HLC-11, NY-LU-12, g16"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038020	10181	RBM5	http://www.ncbi.nlm.nih.gov/gene/?term=10181	"G15, H37, LUCA15, RMB5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038021	10181	RBM5	http://www.ncbi.nlm.nih.gov/gene/?term=10181	"G15, H37, LUCA15, RMB5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038022	10186	LHFPL6	http://www.ncbi.nlm.nih.gov/gene/?term=10186	LHFP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038023	10186	LHFPL6	http://www.ncbi.nlm.nih.gov/gene/?term=10186	LHFP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038024	10188	TNK2	http://www.ncbi.nlm.nih.gov/gene/?term=10188	"ACK, ACK-1, ACK1, p21cdc42Hs"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038025	101926987	DLGAP4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101926987	CCAT7	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038026	101926987	DLGAP4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101926987	CCAT7	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038027	101927267	LOC101927267	http://www.ncbi.nlm.nih.gov/gene/?term=101927267		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038028	101927267	LOC101927267	http://www.ncbi.nlm.nih.gov/gene/?term=101927267		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038029	101927492	UTAT33	http://www.ncbi.nlm.nih.gov/gene/?term=101927492		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038030	101927550	LOC101927550	http://www.ncbi.nlm.nih.gov/gene/?term=101927550		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038031	101927550	LOC101927550	http://www.ncbi.nlm.nih.gov/gene/?term=101927550		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038032	101927718	DSG1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101927718		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038033	101927751	LOC101927751	http://www.ncbi.nlm.nih.gov/gene/?term=101927751		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038034	101928069	LOC101928069	http://www.ncbi.nlm.nih.gov/gene/?term=101928069		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038035	101928069	LOC101928069	http://www.ncbi.nlm.nih.gov/gene/?term=101928069		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038036	101928168	LOC101928168	http://www.ncbi.nlm.nih.gov/gene/?term=101928168		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038037	101928168	LOC101928168	http://www.ncbi.nlm.nih.gov/gene/?term=101928168		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038038	101928168	LOC101928168	http://www.ncbi.nlm.nih.gov/gene/?term=101928168		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038039	101928731	LOC101928731	http://www.ncbi.nlm.nih.gov/gene/?term=101928731		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038040	101928731	LOC101928731	http://www.ncbi.nlm.nih.gov/gene/?term=101928731		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038041	101928988	LOC101928988	http://www.ncbi.nlm.nih.gov/gene/?term=101928988		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038042	101928988	LOC101928988	http://www.ncbi.nlm.nih.gov/gene/?term=101928988		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038043	101929315	LOC101929315	http://www.ncbi.nlm.nih.gov/gene/?term=101929315		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038044	101929315	LOC101929315	http://www.ncbi.nlm.nih.gov/gene/?term=101929315		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038045	101929335	ADAMTS9-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101929335		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038046	101929335	ADAMTS9-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101929335		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038047	101929529	LOC101929529	http://www.ncbi.nlm.nih.gov/gene/?term=101929529		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038048	101929529	LOC101929529	http://www.ncbi.nlm.nih.gov/gene/?term=101929529		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038049	101929760	PIK3IP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101929760		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038050	101929760	PIK3IP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101929760		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038051	101930123	LOC101930123	http://www.ncbi.nlm.nih.gov/gene/?term=101930123		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038052	10196	PRMT3	http://www.ncbi.nlm.nih.gov/gene/?term=10196	HRMT1L3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038053	10196	PRMT3	http://www.ncbi.nlm.nih.gov/gene/?term=10196	HRMT1L3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038054	10207	PATJ	http://www.ncbi.nlm.nih.gov/gene/?term=10207	"Cipp, INADL, InaD-like, hINADL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038055	10217	CTDSPL	http://www.ncbi.nlm.nih.gov/gene/?term=10217	"C3orf8, HYA22, PSR1, RBSP3, SCP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038056	10217	CTDSPL	http://www.ncbi.nlm.nih.gov/gene/?term=10217	"C3orf8, HYA22, PSR1, RBSP3, SCP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038057	1022	CDK7	http://www.ncbi.nlm.nih.gov/gene/?term=1022	"CAK, CAK1, CDKN7, HCAK, MO15, STK1, p39MO15"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038058	10235	RASGRP2	http://www.ncbi.nlm.nih.gov/gene/?term=10235	"CALDAG-GEFI, CDC25L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038059	10235	RASGRP2	http://www.ncbi.nlm.nih.gov/gene/?term=10235	"CALDAG-GEFI, CDC25L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038060	10260	DENND4A	http://www.ncbi.nlm.nih.gov/gene/?term=10260	"IRLB, MYCPBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038061	1027	CDKN1B	http://www.ncbi.nlm.nih.gov/gene/?term=1027	"CDKN4, KIP1, MEN1B, MEN4, P27KIP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038062	1027	CDKN1B	http://www.ncbi.nlm.nih.gov/gene/?term=1027	"CDKN4, KIP1, MEN1B, MEN4, P27KIP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038063	102723465	ELF3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=102723465		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038064	102723465	ELF3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=102723465		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038065	102723566	LOC102723566	http://www.ncbi.nlm.nih.gov/gene/?term=102723566		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038066	102723566	LOC102723566	http://www.ncbi.nlm.nih.gov/gene/?term=102723566		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038067	102725138	LOC102725138	http://www.ncbi.nlm.nih.gov/gene/?term=102725138		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038068	102725138	LOC102725138	http://www.ncbi.nlm.nih.gov/gene/?term=102725138		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038069	10274	STAG1	http://www.ncbi.nlm.nih.gov/gene/?term=10274	"SA1, SCC3A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038070	10277	UBE4B	http://www.ncbi.nlm.nih.gov/gene/?term=10277	"E4, HDNB1, UBOX3, UFD2, UFD2A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038071	10277	UBE4B	http://www.ncbi.nlm.nih.gov/gene/?term=10277	"E4, HDNB1, UBOX3, UFD2, UFD2A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038072	10283	CWC27	http://www.ncbi.nlm.nih.gov/gene/?term=10283	"NY-CO-10, RPSKA, SDCCAG-10, SDCCAG10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038073	10283	CWC27	http://www.ncbi.nlm.nih.gov/gene/?term=10283	"NY-CO-10, RPSKA, SDCCAG-10, SDCCAG10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038074	10290	SPEG	http://www.ncbi.nlm.nih.gov/gene/?term=10290	"APEG-1, APEG1, BPEG, CNM5alpha, SPEGbeta, SPEG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038075	10290	SPEG	http://www.ncbi.nlm.nih.gov/gene/?term=10290	"APEG-1, APEG1, BPEG, CNM5alpha, SPEGbeta, SPEG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038076	10299	MARCH6	http://www.ncbi.nlm.nih.gov/gene/?term=10299	"DOA10, MARCH-VI, RNF176, TEB4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038077	10299	MARCH6	http://www.ncbi.nlm.nih.gov/gene/?term=10299	"DOA10, MARCH-VI, RNF176, TEB4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038078	1030	CDKN2B	http://www.ncbi.nlm.nih.gov/gene/?term=1030	"CDK4I, INK4B, MTS2, P15, TP15, p15INK4b"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038079	10313	RTN3	http://www.ncbi.nlm.nih.gov/gene/?term=10313	"ASYIP, HAP, NSPL2, NSPLII-A1, RTN3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038080	10313	RTN3	http://www.ncbi.nlm.nih.gov/gene/?term=10313	"ASYIP, HAP, NSPL2, NSPLII-A1, RTN3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038081	10314	LANCL1	http://www.ncbi.nlm.nih.gov/gene/?term=10314	"GPR69A, p40"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038082	10318	TNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10318	"ABIN-1, NAF1, VAN, nip40-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038083	10318	TNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=10318	"ABIN-1, NAF1, VAN, nip40-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038084	10327	AKR1A1	http://www.ncbi.nlm.nih.gov/gene/?term=10327	"ALDR1, ALR, ARM, DD3, HEL-S-6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038085	10336	PCGF3	http://www.ncbi.nlm.nih.gov/gene/?term=10336	"DONG1, RNF3, RNF3A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038086	10336	PCGF3	http://www.ncbi.nlm.nih.gov/gene/?term=10336	"DONG1, RNF3, RNF3A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038087	10371	SEMA3A	http://www.ncbi.nlm.nih.gov/gene/?term=10371	"COLL1, HH16, Hsema-I, Hsema-III, SEMA1, SEMAD, SEMAIII, SEMAL, SemD, coll-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038088	10390	CEPT1	http://www.ncbi.nlm.nih.gov/gene/?term=10390		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038089	10392	NOD1	http://www.ncbi.nlm.nih.gov/gene/?term=10392	"CARD4, CLR7.1, NLRC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038090	10392	NOD1	http://www.ncbi.nlm.nih.gov/gene/?term=10392	"CARD4, CLR7.1, NLRC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038091	10393	ANAPC10	http://www.ncbi.nlm.nih.gov/gene/?term=10393	"APC10, DOC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038092	10395	DLC1	http://www.ncbi.nlm.nih.gov/gene/?term=10395	"ARHGAP7, HP, STARD12, p122-RhoGAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038093	10397	NDRG1	http://www.ncbi.nlm.nih.gov/gene/?term=10397	"CAP43, CMT4D, DRG-1, DRG1, GC4, HMSNL, NDR1, NMSL, PROXY1, RIT42, RTP, TARG1, TDD5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038094	10397	NDRG1	http://www.ncbi.nlm.nih.gov/gene/?term=10397	"CAP43, CMT4D, DRG-1, DRG1, GC4, HMSNL, NDR1, NMSL, PROXY1, RIT42, RTP, TARG1, TDD5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038095	10402	ST3GAL6	http://www.ncbi.nlm.nih.gov/gene/?term=10402	"SIAT10, ST3GALVI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038096	10402	ST3GAL6	http://www.ncbi.nlm.nih.gov/gene/?term=10402	"SIAT10, ST3GALVI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038097	10404	CPQ	http://www.ncbi.nlm.nih.gov/gene/?term=10404	"LDP, PGCP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038098	10404	CPQ	http://www.ncbi.nlm.nih.gov/gene/?term=10404	"LDP, PGCP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038099	10406	WFDC2	http://www.ncbi.nlm.nih.gov/gene/?term=10406	"EDDM4, HE4, WAP5, dJ461P17.6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038100	10406	WFDC2	http://www.ncbi.nlm.nih.gov/gene/?term=10406	"EDDM4, HE4, WAP5, dJ461P17.6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038101	10408	MYCNOS	http://www.ncbi.nlm.nih.gov/gene/?term=10408	"MYCN-AS1, N-CYM, NCYM, NYCM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038102	10408	MYCNOS	http://www.ncbi.nlm.nih.gov/gene/?term=10408	"MYCN-AS1, N-CYM, NCYM, NYCM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038103	10409	BASP1	http://www.ncbi.nlm.nih.gov/gene/?term=10409	"CAP-23, CAP23, NAP-22, NAP22"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038104	10409	BASP1	http://www.ncbi.nlm.nih.gov/gene/?term=10409	"CAP-23, CAP23, NAP-22, NAP22"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038105	10425	ARIH2	http://www.ncbi.nlm.nih.gov/gene/?term=10425	"ARI2, TRIAD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038106	10425	ARIH2	http://www.ncbi.nlm.nih.gov/gene/?term=10425	"ARI2, TRIAD1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038107	10428	CFDP1	http://www.ncbi.nlm.nih.gov/gene/?term=10428	"BCNT, BUCENTAUR, CENP-29, CP27, SWC5, Yeti, p97"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038108	10428	CFDP1	http://www.ncbi.nlm.nih.gov/gene/?term=10428	"BCNT, BUCENTAUR, CENP-29, CP27, SWC5, Yeti, p97"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038109	10447	FAM3C	http://www.ncbi.nlm.nih.gov/gene/?term=10447	"GS3786, ILEI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038110	10447	FAM3C	http://www.ncbi.nlm.nih.gov/gene/?term=10447	"GS3786, ILEI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038111	10449	ACAA2	http://www.ncbi.nlm.nih.gov/gene/?term=10449	DSAEC	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038112	10451	VAV3	http://www.ncbi.nlm.nih.gov/gene/?term=10451		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038113	10451	VAV3	http://www.ncbi.nlm.nih.gov/gene/?term=10451		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038114	10452	TOMM40	http://www.ncbi.nlm.nih.gov/gene/?term=10452	"C19orf1, D19S1177E, PER-EC1, PEREC1, TOM40"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038115	10452	TOMM40	http://www.ncbi.nlm.nih.gov/gene/?term=10452	"C19orf1, D19S1177E, PER-EC1, PEREC1, TOM40"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038116	10460	TACC3	http://www.ncbi.nlm.nih.gov/gene/?term=10460	"ERIC-1, ERIC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038117	10460	TACC3	http://www.ncbi.nlm.nih.gov/gene/?term=10460	"ERIC-1, ERIC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038118	10463	SLC30A9	http://www.ncbi.nlm.nih.gov/gene/?term=10463	"BILAPES, C4orf1, GAC63, HUEL, ZNT9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038119	10463	SLC30A9	http://www.ncbi.nlm.nih.gov/gene/?term=10463	"BILAPES, C4orf1, GAC63, HUEL, ZNT9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038120	10465	PPIH	http://www.ncbi.nlm.nih.gov/gene/?term=10465	"CYP-20, CYPH, SnuCyp-20, USA-CYP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038121	10465	PPIH	http://www.ncbi.nlm.nih.gov/gene/?term=10465	"CYP-20, CYPH, SnuCyp-20, USA-CYP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038122	10466	COG5	http://www.ncbi.nlm.nih.gov/gene/?term=10466	"CDG2I, GOLTC1, GTC90"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038123	10466	COG5	http://www.ncbi.nlm.nih.gov/gene/?term=10466	"CDG2I, GOLTC1, GTC90"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038124	10483	SEC23B	http://www.ncbi.nlm.nih.gov/gene/?term=10483	"CDA-II, CDAII, CDAN2, CWS7, HEMPAS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038125	10483	SEC23B	http://www.ncbi.nlm.nih.gov/gene/?term=10483	"CDA-II, CDAII, CDAN2, CWS7, HEMPAS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038126	10489	LRRC41	http://www.ncbi.nlm.nih.gov/gene/?term=10489	"MUF1, PP7759"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038127	10489	LRRC41	http://www.ncbi.nlm.nih.gov/gene/?term=10489	"MUF1, PP7759"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038128	10499	NCOA2	http://www.ncbi.nlm.nih.gov/gene/?term=10499	"GRIP1, KAT13C, NCoA-2, SRC2, TIF2, bHLHe75"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038129	10512	SEMA3C	http://www.ncbi.nlm.nih.gov/gene/?term=10512	"SEMAE, SemE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038130	10512	SEMA3C	http://www.ncbi.nlm.nih.gov/gene/?term=10512	"SEMAE, SemE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038131	10513	APPBP2	http://www.ncbi.nlm.nih.gov/gene/?term=10513	"APP-BP2, HS.84084, PAT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038132	10521	DDX17	http://www.ncbi.nlm.nih.gov/gene/?term=10521	"P72, RH70"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038133	10521	DDX17	http://www.ncbi.nlm.nih.gov/gene/?term=10521	"P72, RH70"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038134	10522	DEAF1	http://www.ncbi.nlm.nih.gov/gene/?term=10522	"MRD24, NUDR, SPN, ZMYND5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038135	10522	DEAF1	http://www.ncbi.nlm.nih.gov/gene/?term=10522	"MRD24, NUDR, SPN, ZMYND5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038136	10533	ATG7	http://www.ncbi.nlm.nih.gov/gene/?term=10533	"APG7-LIKE, APG7L, GSA7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038137	10533	ATG7	http://www.ncbi.nlm.nih.gov/gene/?term=10533	"APG7-LIKE, APG7L, GSA7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038138	105375095	LOC105375095	http://www.ncbi.nlm.nih.gov/gene/?term=105375095		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038139	105375095	LOC105375095	http://www.ncbi.nlm.nih.gov/gene/?term=105375095		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038140	10539	GLRX3	http://www.ncbi.nlm.nih.gov/gene/?term=10539	"GLRX4, GRX3, GRX4, PICOT, TXNL2, TXNL3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038141	10539	GLRX3	http://www.ncbi.nlm.nih.gov/gene/?term=10539	"GLRX4, GRX3, GRX4, PICOT, TXNL2, TXNL3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038142	10549	PRDX4	http://www.ncbi.nlm.nih.gov/gene/?term=10549	"AOE37-2, AOE372, HEL-S-97n, PRX-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038143	10564	ARFGEF2	http://www.ncbi.nlm.nih.gov/gene/?term=10564	"BIG2, PVNH2, dJ1164I10.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038144	10564	ARFGEF2	http://www.ncbi.nlm.nih.gov/gene/?term=10564	"BIG2, PVNH2, dJ1164I10.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038145	10565	ARFGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=10565	"ARFGEP1, BIG1, P200"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038146	10576	CCT2	http://www.ncbi.nlm.nih.gov/gene/?term=10576	"99D8.1, CCT-beta, CCTB, HEL-S-100n, PRO1633, TCP-1-beta"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038147	10576	CCT2	http://www.ncbi.nlm.nih.gov/gene/?term=10576	"99D8.1, CCT-beta, CCTB, HEL-S-100n, PRO1633, TCP-1-beta"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038148	10579	TACC2	http://www.ncbi.nlm.nih.gov/gene/?term=10579	"AZU-1, ECTACC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038149	10579	TACC2	http://www.ncbi.nlm.nih.gov/gene/?term=10579	"AZU-1, ECTACC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038150	10580	SORBS1	http://www.ncbi.nlm.nih.gov/gene/?term=10580	"CAP, FLAF2, R85FL, SH3D5, SH3P12, SORB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038151	10580	SORBS1	http://www.ncbi.nlm.nih.gov/gene/?term=10580	"CAP, FLAF2, R85FL, SH3D5, SH3P12, SORB1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038152	1060	CENPC	http://www.ncbi.nlm.nih.gov/gene/?term=1060	"CENP-C1, MIF2, hcp-4, CENPC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038153	1060	CENPC	http://www.ncbi.nlm.nih.gov/gene/?term=1060	"CENP-C1, MIF2, hcp-4, CENPC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038154	10602	CDC42EP3	http://www.ncbi.nlm.nih.gov/gene/?term=10602	"BORG2, CEP3, UB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038155	10602	CDC42EP3	http://www.ncbi.nlm.nih.gov/gene/?term=10602	"BORG2, CEP3, UB1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038156	106144526	PLA2G4C-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=106144526		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038157	106144526	PLA2G4C-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=106144526		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038158	10620	ARID3B	http://www.ncbi.nlm.nih.gov/gene/?term=10620	"BDP, DRIL2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038159	10640	EXOC5	http://www.ncbi.nlm.nih.gov/gene/?term=10640	"HSEC10, PRO1912, SEC10, SEC10L1, SEC10P"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038160	10643	IGF2BP3	http://www.ncbi.nlm.nih.gov/gene/?term=10643	"CT98, IMP-3, IMP3, KOC, KOC1, VICKZ3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038161	10658	CELF1	http://www.ncbi.nlm.nih.gov/gene/?term=10658	"BRUNOL2, CUG-BP, CUGBP, CUGBP1, EDEN-BP, NAB50, NAPOR, hNab50"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038162	10659	CELF2	http://www.ncbi.nlm.nih.gov/gene/?term=10659	"BRUNOL3, CELF-2, CUG-BP2, CUGBP2, ETR-3, ETR3, NAPOR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038163	10659	CELF2	http://www.ncbi.nlm.nih.gov/gene/?term=10659	"BRUNOL3, CELF-2, CUG-BP2, CUGBP2, ETR-3, ETR3, NAPOR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038164	10667	FARS2	http://www.ncbi.nlm.nih.gov/gene/?term=10667	"COXPD14, FARS1, HSPC320, PheRS, SPG77"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038165	10678	B3GNT2	http://www.ncbi.nlm.nih.gov/gene/?term=10678	"3-Gn-T1, 3-Gn-T2, B3GN-T2, B3GNT, B3GNT-2, B3GNT1, BETA3GNT, BGNT2, BGnT-2, beta-1, beta3Gn-T1, beta3Gn-T2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038166	10678	B3GNT2	http://www.ncbi.nlm.nih.gov/gene/?term=10678	"3-Gn-T1, 3-Gn-T2, B3GN-T2, B3GNT, B3GNT-2, B3GNT1, BETA3GNT, BGNT2, BGnT-2, beta-1, beta3Gn-T1, beta3Gn-T2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038167	107	ADCY1	http://www.ncbi.nlm.nih.gov/gene/?term=107	"AC1, DFNB44"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038168	107	ADCY1	http://www.ncbi.nlm.nih.gov/gene/?term=107	"AC1, DFNB44"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038169	10721	POLQ	http://www.ncbi.nlm.nih.gov/gene/?term=10721	PRO0327	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038170	10721	POLQ	http://www.ncbi.nlm.nih.gov/gene/?term=10721	PRO0327	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038171	10725	NFAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10725	"NF-AT5, NFATL1, NFATZ, OREBP, TONEBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038172	10725	NFAT5	http://www.ncbi.nlm.nih.gov/gene/?term=10725	"NF-AT5, NFATL1, NFATZ, OREBP, TONEBP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038173	10735	STAG2	http://www.ncbi.nlm.nih.gov/gene/?term=10735	"SA-2, SA2, SCC3B, bA517O1.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038174	10735	STAG2	http://www.ncbi.nlm.nih.gov/gene/?term=10735	"SA-2, SA2, SCC3B, bA517O1.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038175	10745	PHTF1	http://www.ncbi.nlm.nih.gov/gene/?term=10745	PHTF	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038176	10745	PHTF1	http://www.ncbi.nlm.nih.gov/gene/?term=10745	PHTF	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038177	10758	TRAF3IP2	http://www.ncbi.nlm.nih.gov/gene/?term=10758	"ACT1, C6orf2, C6orf4, C6orf5, C6orf6, CANDF8, CIKS, PSORS13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038178	10758	TRAF3IP2	http://www.ncbi.nlm.nih.gov/gene/?term=10758	"ACT1, C6orf2, C6orf4, C6orf5, C6orf6, CANDF8, CIKS, PSORS13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038179	10771	ZMYND11	http://www.ncbi.nlm.nih.gov/gene/?term=10771	"BRAM1, BS69, MRD30"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038180	10771	ZMYND11	http://www.ncbi.nlm.nih.gov/gene/?term=10771	"BRAM1, BS69, MRD30"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038181	10776	ARPP19	http://www.ncbi.nlm.nih.gov/gene/?term=10776	"ARPP-16, ARPP-19, ARPP16, ENSAL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038182	10776	ARPP19	http://www.ncbi.nlm.nih.gov/gene/?term=10776	"ARPP-16, ARPP-19, ARPP16, ENSAL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038183	10777	ARPP21	http://www.ncbi.nlm.nih.gov/gene/?term=10777	"ARPP-21, R3HDM3, RCS, TARPP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038184	10777	ARPP21	http://www.ncbi.nlm.nih.gov/gene/?term=10777	"ARPP-21, R3HDM3, RCS, TARPP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038185	10783	NEK6	http://www.ncbi.nlm.nih.gov/gene/?term=10783	SID6-1512	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038186	10783	NEK6	http://www.ncbi.nlm.nih.gov/gene/?term=10783	SID6-1512	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038187	10785	WDR4	http://www.ncbi.nlm.nih.gov/gene/?term=10785	"TRM82, TRMT82"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038188	10785	WDR4	http://www.ncbi.nlm.nih.gov/gene/?term=10785	"TRM82, TRMT82"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038189	107986404	LOC107986404	http://www.ncbi.nlm.nih.gov/gene/?term=107986404		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038190	10801	SEPT9	http://www.ncbi.nlm.nih.gov/gene/?term=10801	"AF17q25, MSF, MSF1, NAPB, PNUTL4, SINT1, SeptD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038191	10801	SEPT9	http://www.ncbi.nlm.nih.gov/gene/?term=10801	"AF17q25, MSF, MSF1, NAPB, PNUTL4, SINT1, SeptD1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038192	10818	FRS2	http://www.ncbi.nlm.nih.gov/gene/?term=10818	"FRS1AA, FRS2alpha, SNT, SNT-1, SNT1, FRS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038193	10818	FRS2	http://www.ncbi.nlm.nih.gov/gene/?term=10818	"FRS1AA, FRS2alpha, SNT, SNT-1, SNT1, FRS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038194	10825	NEU3	http://www.ncbi.nlm.nih.gov/gene/?term=10825	SIAL3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038195	10825	NEU3	http://www.ncbi.nlm.nih.gov/gene/?term=10825	SIAL3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038196	10847	SRCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10847	"DOMO1, EAF1, FLHS, SWR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038197	10847	SRCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10847	"DOMO1, EAF1, FLHS, SWR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038198	10867	TSPAN9	http://www.ncbi.nlm.nih.gov/gene/?term=10867	"NET-5, NET5, PP1057"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038199	10867	TSPAN9	http://www.ncbi.nlm.nih.gov/gene/?term=10867	"NET-5, NET5, PP1057"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038200	10873	ME3	http://www.ncbi.nlm.nih.gov/gene/?term=10873	NADP-ME	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038201	10873	ME3	http://www.ncbi.nlm.nih.gov/gene/?term=10873	NADP-ME	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038202	10890	RAB10	http://www.ncbi.nlm.nih.gov/gene/?term=10890		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038203	10890	RAB10	http://www.ncbi.nlm.nih.gov/gene/?term=10890		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038204	10892	MALT1	http://www.ncbi.nlm.nih.gov/gene/?term=10892	"IMD12, MLT, MLT1, PCASP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038205	10904	BLCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10904	BC10	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038206	10904	BLCAP	http://www.ncbi.nlm.nih.gov/gene/?term=10904	BC10	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038207	10905	MAN1A2	http://www.ncbi.nlm.nih.gov/gene/?term=10905	MAN1B	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038208	10905	MAN1A2	http://www.ncbi.nlm.nih.gov/gene/?term=10905	MAN1B	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038209	10907	TXNL4A	http://www.ncbi.nlm.nih.gov/gene/?term=10907	"BMKS, DIB1, DIM1, SNRNP15, TXNL4, U5-15kD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038210	10915	TCERG1	http://www.ncbi.nlm.nih.gov/gene/?term=10915	"CA150, TAF2S, Urn1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038211	10927	SPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=10927	"SPIN, TDRD24"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038212	10927	SPIN1	http://www.ncbi.nlm.nih.gov/gene/?term=10927	"SPIN, TDRD24"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038213	10933	MORF4L1	http://www.ncbi.nlm.nih.gov/gene/?term=10933	"Eaf3, FWP006, HsT17725, MEAF3, MORFRG15, MRG15, S863-6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038214	10945	KDELR1	http://www.ncbi.nlm.nih.gov/gene/?term=10945	"ERD2, ERD2.1, HDEL, PM23"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038215	10972	TMED10	http://www.ncbi.nlm.nih.gov/gene/?term=10972	"P24(DELTA), S31I125, S31III125, TMP21, Tmp-21-I, p23, p24d1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038216	109864269	LOC109864269	http://www.ncbi.nlm.nih.gov/gene/?term=109864269		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038217	109864269	LOC109864269	http://www.ncbi.nlm.nih.gov/gene/?term=109864269		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038218	11010	GLIPR1	http://www.ncbi.nlm.nih.gov/gene/?term=11010	"CRISP7, GLIPR, RTVP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038219	11010	GLIPR1	http://www.ncbi.nlm.nih.gov/gene/?term=11010	"CRISP7, GLIPR, RTVP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038220	11011	TLK2	http://www.ncbi.nlm.nih.gov/gene/?term=11011	"HsHPK, PKU-ALPHA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038221	11014	KDELR2	http://www.ncbi.nlm.nih.gov/gene/?term=11014	"ELP-1, ERD2.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038222	11014	KDELR2	http://www.ncbi.nlm.nih.gov/gene/?term=11014	"ELP-1, ERD2.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038223	11016	ATF7	http://www.ncbi.nlm.nih.gov/gene/?term=11016	ATFA	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038224	1102	RCBTB2	http://www.ncbi.nlm.nih.gov/gene/?term=1102	"CHC1L, RLG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038225	1102	RCBTB2	http://www.ncbi.nlm.nih.gov/gene/?term=1102	"CHC1L, RLG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038226	11030	RBPMS	http://www.ncbi.nlm.nih.gov/gene/?term=11030	HERMES	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038227	11030	RBPMS	http://www.ncbi.nlm.nih.gov/gene/?term=11030	HERMES	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038228	11031	RAB31	http://www.ncbi.nlm.nih.gov/gene/?term=11031	Rab22B	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038229	11034	DSTN	http://www.ncbi.nlm.nih.gov/gene/?term=11034	"ACTDP, ADF, HEL32, bA462D18.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038230	11034	DSTN	http://www.ncbi.nlm.nih.gov/gene/?term=11034	"ACTDP, ADF, HEL32, bA462D18.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038231	11044	PAPD7	http://www.ncbi.nlm.nih.gov/gene/?term=11044	"LAK-1, LAK1, POLK, POLS, TRF4, TRF4-1, TRF41, TUTASE5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038232	11044	PAPD7	http://www.ncbi.nlm.nih.gov/gene/?term=11044	"LAK-1, LAK1, POLK, POLS, TRF4, TRF4-1, TRF41, TUTASE5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038233	1105	CHD1	http://www.ncbi.nlm.nih.gov/gene/?term=1105		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038234	11052	CPSF6	http://www.ncbi.nlm.nih.gov/gene/?term=11052	"CFIM, CFIM68, CFIM72, HPBRII-4, HPBRII-7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038235	11052	CPSF6	http://www.ncbi.nlm.nih.gov/gene/?term=11052	"CFIM, CFIM68, CFIM72, HPBRII-4, HPBRII-7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038236	11054	OGFR	http://www.ncbi.nlm.nih.gov/gene/?term=11054		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038237	11054	OGFR	http://www.ncbi.nlm.nih.gov/gene/?term=11054		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038238	11057	ABHD2	http://www.ncbi.nlm.nih.gov/gene/?term=11057	"HS1-2, LABH2, PHPS1-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038239	11057	ABHD2	http://www.ncbi.nlm.nih.gov/gene/?term=11057	"HS1-2, LABH2, PHPS1-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038240	11059	WWP1	http://www.ncbi.nlm.nih.gov/gene/?term=11059	"AIP5, Tiul1, hSDRP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038241	1106	CHD2	http://www.ncbi.nlm.nih.gov/gene/?term=1106	EEOC	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038242	1106	CHD2	http://www.ncbi.nlm.nih.gov/gene/?term=1106	EEOC	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038243	11083	DIDO1	http://www.ncbi.nlm.nih.gov/gene/?term=11083	"BYE1, C20orf158, DATF-1, DATF1, DIDO2, DIDO3, DIO-1, DIO1, dJ885L7.8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038244	11083	DIDO1	http://www.ncbi.nlm.nih.gov/gene/?term=11083	"BYE1, C20orf158, DATF-1, DATF1, DIDO2, DIDO3, DIO-1, DIO1, dJ885L7.8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038245	11094	CACFD1	http://www.ncbi.nlm.nih.gov/gene/?term=11094	"C9orf7, D9S2135, FLOWER"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038246	11097	NUPL2	http://www.ncbi.nlm.nih.gov/gene/?term=11097	"CG1, NLP-1, NLP_1, hCG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038247	11103	KRR1	http://www.ncbi.nlm.nih.gov/gene/?term=11103	"HRB2, RIP-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038248	11107	PRDM5	http://www.ncbi.nlm.nih.gov/gene/?term=11107	"BCS2, PFM2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038249	11113	CIT	http://www.ncbi.nlm.nih.gov/gene/?term=11113	"CITK, CRIK, MCPH17, STK21"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038250	11113	CIT	http://www.ncbi.nlm.nih.gov/gene/?term=11113	"CITK, CRIK, MCPH17, STK21"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038251	1112	FOXN3	http://www.ncbi.nlm.nih.gov/gene/?term=1112	"C14orf116, CHES1, PRO1635"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038252	1112	FOXN3	http://www.ncbi.nlm.nih.gov/gene/?term=1112	"C14orf116, CHES1, PRO1635"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038253	11124	FAF1	http://www.ncbi.nlm.nih.gov/gene/?term=11124	"CGI-03, HFAF1s, UBXD12, UBXN3A, hFAF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038254	11127	KIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=11127	"FLA10, KLP-20"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038255	11127	KIF3A	http://www.ncbi.nlm.nih.gov/gene/?term=11127	"FLA10, KLP-20"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038256	11138	TBC1D8	http://www.ncbi.nlm.nih.gov/gene/?term=11138	"AD3, GRAMD8, HBLP1A, VRP, TBC1D8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038257	11138	TBC1D8	http://www.ncbi.nlm.nih.gov/gene/?term=11138	"AD3, GRAMD8, HBLP1A, VRP, TBC1D8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038258	11146	GLMN	http://www.ncbi.nlm.nih.gov/gene/?term=11146	"FAP, FAP48, FAP68, FKBPAP, GLML, GVM, VMGLOM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038259	11157	LSM6	http://www.ncbi.nlm.nih.gov/gene/?term=11157	YDR378C	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038260	11157	LSM6	http://www.ncbi.nlm.nih.gov/gene/?term=11157	YDR378C	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038261	11167	FSTL1	http://www.ncbi.nlm.nih.gov/gene/?term=11167	"FRP, FSL1, MIR198, OCC-1, OCC1, tsc36"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038262	11167	FSTL1	http://www.ncbi.nlm.nih.gov/gene/?term=11167	"FRP, FSL1, MIR198, OCC-1, OCC1, tsc36"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038263	11177	BAZ1A	http://www.ncbi.nlm.nih.gov/gene/?term=11177	"ACF1, WALp1, WCRF180, hACF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038264	11177	BAZ1A	http://www.ncbi.nlm.nih.gov/gene/?term=11177	"ACF1, WALp1, WCRF180, hACF1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038265	11183	MAP4K5	http://www.ncbi.nlm.nih.gov/gene/?term=11183	"GCKR, KHS, KHS1, MAPKKKK5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038266	11183	MAP4K5	http://www.ncbi.nlm.nih.gov/gene/?term=11183	"GCKR, KHS, KHS1, MAPKKKK5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038267	11186	RASSF1	http://www.ncbi.nlm.nih.gov/gene/?term=11186	"123F2, NORE2AA, RDA32, REH3P21, RASSF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038268	11186	RASSF1	http://www.ncbi.nlm.nih.gov/gene/?term=11186	"123F2, NORE2AA, RDA32, REH3P21, RASSF1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038269	11196	SEC23IP	http://www.ncbi.nlm.nih.gov/gene/?term=11196	"MSTP053, P125, P125A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038270	11198	SUPT16H	http://www.ncbi.nlm.nih.gov/gene/?term=11198	"CDC68, FACTP140, SPT16, SPT16/CDC68"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038271	11198	SUPT16H	http://www.ncbi.nlm.nih.gov/gene/?term=11198	"CDC68, FACTP140, SPT16, SPT16/CDC68"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038272	11200	CHEK2	http://www.ncbi.nlm.nih.gov/gene/?term=11200	"CDS1, CHK2, HuCds1, LFS2, PP1425, RAD53, hCds1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038273	11214	AKAP13	http://www.ncbi.nlm.nih.gov/gene/?term=11214	"AKAP-13, AKAP-Lbc, ARHGEF13, BRX, HA-3, Ht31, LBC, PRKA13, PROTO-LB, PROTO-LBC, c-lbc, p47"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038274	11214	AKAP13	http://www.ncbi.nlm.nih.gov/gene/?term=11214	"AKAP-13, AKAP-Lbc, ARHGEF13, BRX, HA-3, Ht31, LBC, PRKA13, PROTO-LB, PROTO-LBC, c-lbc, p47"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038275	11215	AKAP11	http://www.ncbi.nlm.nih.gov/gene/?term=11215	"AKAP-11, AKAP220, PPP1R44, PRKA11"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038276	11216	AKAP10	http://www.ncbi.nlm.nih.gov/gene/?term=11216	"AKAP-10, D-AKAP-2, D-AKAP2, PRKA10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038277	11216	AKAP10	http://www.ncbi.nlm.nih.gov/gene/?term=11216	"AKAP-10, D-AKAP-2, D-AKAP2, PRKA10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038278	11228	RASSF8	http://www.ncbi.nlm.nih.gov/gene/?term=11228	"C12orf2, HOJ1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038279	11228	RASSF8	http://www.ncbi.nlm.nih.gov/gene/?term=11228	"C12orf2, HOJ1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038280	11234	HPS5	http://www.ncbi.nlm.nih.gov/gene/?term=11234	"AIBP63, BLOC2S2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038281	11234	HPS5	http://www.ncbi.nlm.nih.gov/gene/?term=11234	"AIBP63, BLOC2S2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038282	11238	CA5B	http://www.ncbi.nlm.nih.gov/gene/?term=11238	CA-VB	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038283	11238	CA5B	http://www.ncbi.nlm.nih.gov/gene/?term=11238	CA-VB	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038284	1124	CHN2	http://www.ncbi.nlm.nih.gov/gene/?term=1124	"ARHGAP3, BCH-3, RHOGAP3, CHN2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038285	1124	CHN2	http://www.ncbi.nlm.nih.gov/gene/?term=1124	"ARHGAP3, BCH-3, RHOGAP3, CHN2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038286	112479	ERI2	http://www.ncbi.nlm.nih.gov/gene/?term=112479	"EXOD1, ZGRF5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038287	112479	ERI2	http://www.ncbi.nlm.nih.gov/gene/?term=112479	"EXOD1, ZGRF5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038288	112752	IFT43	http://www.ncbi.nlm.nih.gov/gene/?term=112752	"C14orf179, CED3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038289	11276	SYNRG	http://www.ncbi.nlm.nih.gov/gene/?term=11276	"SYNG, AP1GBP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038290	11278	KLF12	http://www.ncbi.nlm.nih.gov/gene/?term=11278	"AP-2rep, AP2REP, HSPC122"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038291	1130	LYST	http://www.ncbi.nlm.nih.gov/gene/?term=1130	"CHS, CHS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038292	11311	VPS45	http://www.ncbi.nlm.nih.gov/gene/?term=11311	"H1, H1VPS45, SCN5A, VPS45B, VPS54A, VSP45, VSP45A, VPS45"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038293	113174	SAAL1	http://www.ncbi.nlm.nih.gov/gene/?term=113174	SPACIA1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038294	113174	SAAL1	http://www.ncbi.nlm.nih.gov/gene/?term=113174	SPACIA1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038295	113251	LARP4	http://www.ncbi.nlm.nih.gov/gene/?term=113251	PP13296	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038296	113251	LARP4	http://www.ncbi.nlm.nih.gov/gene/?term=113251	PP13296	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038297	11329	STK38	http://www.ncbi.nlm.nih.gov/gene/?term=11329	"NDR, NDR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038298	11332	ACOT7	http://www.ncbi.nlm.nih.gov/gene/?term=11332	"ACH1, ACT, BACH, CTE-II, LACH, LACH1, hBACH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038299	11332	ACOT7	http://www.ncbi.nlm.nih.gov/gene/?term=11332	"ACH1, ACT, BACH, CTE-II, LACH, LACH1, hBACH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038300	11336	EXOC3	http://www.ncbi.nlm.nih.gov/gene/?term=11336	"SEC6, SEC6L1, Sec6p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038301	11343	MGLL	http://www.ncbi.nlm.nih.gov/gene/?term=11343	"HU-K5, HUK5, MAGL, MGL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038302	11343	MGLL	http://www.ncbi.nlm.nih.gov/gene/?term=11343	"HU-K5, HUK5, MAGL, MGL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038303	113451	AZIN2	http://www.ncbi.nlm.nih.gov/gene/?term=113451	"ADC, AZI2, AZIB1, ODC-p, ODC1L, ODCp"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038304	11346	SYNPO	http://www.ncbi.nlm.nih.gov/gene/?term=11346		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038305	11346	SYNPO	http://www.ncbi.nlm.nih.gov/gene/?term=11346		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038306	114049	BUD23	http://www.ncbi.nlm.nih.gov/gene/?term=114049	"HASJ4442, HUSSY-3, MERM1, PP3381, WBMT, WBSCR22"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038307	114049	BUD23	http://www.ncbi.nlm.nih.gov/gene/?term=114049	"HASJ4442, HUSSY-3, MERM1, PP3381, WBMT, WBSCR22"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038308	114134	SLC2A13	http://www.ncbi.nlm.nih.gov/gene/?term=114134	HMIT	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038309	114327	EFHC1	http://www.ncbi.nlm.nih.gov/gene/?term=114327	"EJM1, dJ304B14.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038310	114327	EFHC1	http://www.ncbi.nlm.nih.gov/gene/?term=114327	"EJM1, dJ304B14.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038311	1147	CHUK	http://www.ncbi.nlm.nih.gov/gene/?term=1147	"IKBKA, IKK-alpha, IKK1, IKKA, NFKBIKA, TCF16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038312	114784	CSMD2	http://www.ncbi.nlm.nih.gov/gene/?term=114784	"dJ1007G16.1, dJ1007G16.2, dJ947L8.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038313	114784	CSMD2	http://www.ncbi.nlm.nih.gov/gene/?term=114784	"dJ1007G16.1, dJ1007G16.2, dJ947L8.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038314	114788	CSMD3	http://www.ncbi.nlm.nih.gov/gene/?term=114788		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038315	114788	CSMD3	http://www.ncbi.nlm.nih.gov/gene/?term=114788		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038316	114793	FMNL2	http://www.ncbi.nlm.nih.gov/gene/?term=114793	FHOD2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038317	114793	FMNL2	http://www.ncbi.nlm.nih.gov/gene/?term=114793	FHOD2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038318	114805	GALNT13	http://www.ncbi.nlm.nih.gov/gene/?term=114805	GalNAc-T13	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038319	114805	GALNT13	http://www.ncbi.nlm.nih.gov/gene/?term=114805	GalNAc-T13	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038320	114879	OSBPL5	http://www.ncbi.nlm.nih.gov/gene/?term=114879	"OBPH1, ORP5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038321	114879	OSBPL5	http://www.ncbi.nlm.nih.gov/gene/?term=114879	"OBPH1, ORP5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038322	114884	OSBPL10	http://www.ncbi.nlm.nih.gov/gene/?term=114884	"ORP10, OSBP9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038323	114884	OSBPL10	http://www.ncbi.nlm.nih.gov/gene/?term=114884	"ORP10, OSBP9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038324	114905	C1QTNF7	http://www.ncbi.nlm.nih.gov/gene/?term=114905	"CTRP7, ZACRP7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038325	114905	C1QTNF7	http://www.ncbi.nlm.nih.gov/gene/?term=114905	"CTRP7, ZACRP7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038326	115	ADCY9	http://www.ncbi.nlm.nih.gov/gene/?term=115	"AC9, ACIX"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038327	115	ADCY9	http://www.ncbi.nlm.nih.gov/gene/?term=115	"AC9, ACIX"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038328	115294	PCMTD1	http://www.ncbi.nlm.nih.gov/gene/?term=115294		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038329	115294	PCMTD1	http://www.ncbi.nlm.nih.gov/gene/?term=115294		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038330	115350	FCRL1	http://www.ncbi.nlm.nih.gov/gene/?term=115350	"CD307a, FCRH1, IFGP1, IRTA5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038331	115350	FCRL1	http://www.ncbi.nlm.nih.gov/gene/?term=115350	"CD307a, FCRH1, IFGP1, IRTA5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038332	115825	WDFY2	http://www.ncbi.nlm.nih.gov/gene/?term=115825	"PROF, WDF2, ZFYVE22"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038333	116159	CYYR1	http://www.ncbi.nlm.nih.gov/gene/?term=116159	C21orf95	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038334	116159	CYYR1	http://www.ncbi.nlm.nih.gov/gene/?term=116159	C21orf95	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038335	116225	ZMYND19	http://www.ncbi.nlm.nih.gov/gene/?term=116225	MIZIP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038336	116225	ZMYND19	http://www.ncbi.nlm.nih.gov/gene/?term=116225	MIZIP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038337	116372	LYPD1	http://www.ncbi.nlm.nih.gov/gene/?term=116372	"LYPDC1, PHTS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038338	116372	LYPD1	http://www.ncbi.nlm.nih.gov/gene/?term=116372	"LYPDC1, PHTS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038339	116461	TSEN15	http://www.ncbi.nlm.nih.gov/gene/?term=116461	"C1orf19, PCH2F, sen15"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038340	116461	TSEN15	http://www.ncbi.nlm.nih.gov/gene/?term=116461	"C1orf19, PCH2F, sen15"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038341	116985	ARAP1	http://www.ncbi.nlm.nih.gov/gene/?term=116985	CENTD2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038342	116985	ARAP1	http://www.ncbi.nlm.nih.gov/gene/?term=116985	CENTD2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038343	116987	AGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=116987	"AGAP-1, CENTG2, GGAP1, cnt-g2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038344	116988	AGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=116988	"AGAP-3, CENTG3, CRAG, MRIP-1, cnt-g3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038345	117583	PARD3B	http://www.ncbi.nlm.nih.gov/gene/?term=117583	"ALS2CR19, PAR3B, PAR3L, PAR3beta"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038346	117583	PARD3B	http://www.ncbi.nlm.nih.gov/gene/?term=117583	"ALS2CR19, PAR3B, PAR3L, PAR3beta"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038347	118812	MORN4	http://www.ncbi.nlm.nih.gov/gene/?term=118812	"C10orf83, bA548K23.4, rtp"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038348	118812	MORN4	http://www.ncbi.nlm.nih.gov/gene/?term=118812	"C10orf83, bA548K23.4, rtp"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038349	119391	GSTO2	http://www.ncbi.nlm.nih.gov/gene/?term=119391	"GSTO 2-2, bA127L20.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038350	1198	CLK3	http://www.ncbi.nlm.nih.gov/gene/?term=1198	"PHCLK3, PHCLK3/152"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038351	1198	CLK3	http://www.ncbi.nlm.nih.gov/gene/?term=1198	"PHCLK3, PHCLK3/152"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038352	120	ADD3	http://www.ncbi.nlm.nih.gov/gene/?term=120	"ADDL, CPSQ3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038353	120	ADD3	http://www.ncbi.nlm.nih.gov/gene/?term=120	"ADDL, CPSQ3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038354	1207	CLNS1A	http://www.ncbi.nlm.nih.gov/gene/?term=1207	"CLCI, CLNS1B, ICln"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038355	1207	CLNS1A	http://www.ncbi.nlm.nih.gov/gene/?term=1207	"CLCI, CLNS1B, ICln"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038356	121260	SLC15A4	http://www.ncbi.nlm.nih.gov/gene/?term=121260	"FP12591, PHT1, PTR4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038357	121260	SLC15A4	http://www.ncbi.nlm.nih.gov/gene/?term=121260	"FP12591, PHT1, PTR4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038358	121665	SPPL3	http://www.ncbi.nlm.nih.gov/gene/?term=121665	"IMP2, MDHV1887, PRO4332, PSH1, PSL4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038359	122945	NOXRED1	http://www.ncbi.nlm.nih.gov/gene/?term=122945	C14orf148	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038360	122945	NOXRED1	http://www.ncbi.nlm.nih.gov/gene/?term=122945	C14orf148	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038361	122953	JDP2	http://www.ncbi.nlm.nih.gov/gene/?term=122953	JUNDM2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038362	122953	JDP2	http://www.ncbi.nlm.nih.gov/gene/?term=122953	JUNDM2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038363	123016	TTC8	http://www.ncbi.nlm.nih.gov/gene/?term=123016	"BBS8, RP51"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038364	123169	LEO1	http://www.ncbi.nlm.nih.gov/gene/?term=123169	RDL	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038365	123169	LEO1	http://www.ncbi.nlm.nih.gov/gene/?term=123169	RDL	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038366	123591	TMEM266	http://www.ncbi.nlm.nih.gov/gene/?term=123591	"C15orf27, HVRP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038367	123591	TMEM266	http://www.ncbi.nlm.nih.gov/gene/?term=123591	"C15orf27, HVRP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038368	1236	CCR7	http://www.ncbi.nlm.nih.gov/gene/?term=1236	"BLR2, CC-CKR-7, CCR-7, CD197, CDw197, CMKBR7, EBI1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038369	1236	CCR7	http://www.ncbi.nlm.nih.gov/gene/?term=1236	"BLR2, CC-CKR-7, CCR-7, CD197, CDw197, CMKBR7, EBI1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038370	123775	C16orf46	http://www.ncbi.nlm.nih.gov/gene/?term=123775		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038371	123775	C16orf46	http://www.ncbi.nlm.nih.gov/gene/?term=123775		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038372	123811	FOPNL	http://www.ncbi.nlm.nih.gov/gene/?term=123811	"C16orf63, FOR20, PHSECRG2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038373	124152	IQCK	http://www.ncbi.nlm.nih.gov/gene/?term=124152		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038374	124152	IQCK	http://www.ncbi.nlm.nih.gov/gene/?term=124152		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038375	124402	UBALD1	http://www.ncbi.nlm.nih.gov/gene/?term=124402	"FAM100A, PP11303"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038376	124402	UBALD1	http://www.ncbi.nlm.nih.gov/gene/?term=124402	"FAM100A, PP11303"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038377	124454	EARS2	http://www.ncbi.nlm.nih.gov/gene/?term=124454	"COXPD12, MSE1, gluRS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038378	124454	EARS2	http://www.ncbi.nlm.nih.gov/gene/?term=124454	"COXPD12, MSE1, gluRS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038379	124460	SNX20	http://www.ncbi.nlm.nih.gov/gene/?term=124460	SLIC1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038380	124460	SNX20	http://www.ncbi.nlm.nih.gov/gene/?term=124460	SLIC1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038381	124540	MSI2	http://www.ncbi.nlm.nih.gov/gene/?term=124540	MSI2H	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038382	124540	MSI2	http://www.ncbi.nlm.nih.gov/gene/?term=124540	MSI2H	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038383	124935	SLC43A2	http://www.ncbi.nlm.nih.gov/gene/?term=124935	LAT4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038384	124935	SLC43A2	http://www.ncbi.nlm.nih.gov/gene/?term=124935	LAT4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038385	124936	CYB5D2	http://www.ncbi.nlm.nih.gov/gene/?term=124936		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038386	124936	CYB5D2	http://www.ncbi.nlm.nih.gov/gene/?term=124936		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038387	124989	EFCAB13	http://www.ncbi.nlm.nih.gov/gene/?term=124989	C17orf57	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038388	125488	TTC39C	http://www.ncbi.nlm.nih.gov/gene/?term=125488	"C18orf17, HsT2697"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038389	1271	CNTFR	http://www.ncbi.nlm.nih.gov/gene/?term=1271		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038390	1271	CNTFR	http://www.ncbi.nlm.nih.gov/gene/?term=1271		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038391	127294	MYOM3	http://www.ncbi.nlm.nih.gov/gene/?term=127294		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038392	127294	MYOM3	http://www.ncbi.nlm.nih.gov/gene/?term=127294		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038393	1281	COL3A1	http://www.ncbi.nlm.nih.gov/gene/?term=1281	EDS4A	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038394	1282	COL4A1	http://www.ncbi.nlm.nih.gov/gene/?term=1282	"BSVD, RATOR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038395	1282	COL4A1	http://www.ncbi.nlm.nih.gov/gene/?term=1282	"BSVD, RATOR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038396	128338	DRAM2	http://www.ncbi.nlm.nih.gov/gene/?term=128338	"CORD21, PRO180, TMEM77, WWFQ154"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038397	1284	COL4A2	http://www.ncbi.nlm.nih.gov/gene/?term=1284	"ICH, POREN2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038398	128553	TSHZ2	http://www.ncbi.nlm.nih.gov/gene/?term=128553	"C20orf17, OVC10-2, TSH2, ZABC2, ZNF218"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038399	128553	TSHZ2	http://www.ncbi.nlm.nih.gov/gene/?term=128553	"C20orf17, OVC10-2, TSH2, ZABC2, ZNF218"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038400	1287	COL4A5	http://www.ncbi.nlm.nih.gov/gene/?term=1287	"ASLN, ATS, CA54"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038401	1287	COL4A5	http://www.ncbi.nlm.nih.gov/gene/?term=1287	"ASLN, ATS, CA54"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038402	1288	COL4A6	http://www.ncbi.nlm.nih.gov/gene/?term=1288	"CXDELq22.3, DELXq22.3, DFNX6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038403	1288	COL4A6	http://www.ncbi.nlm.nih.gov/gene/?term=1288	"CXDELq22.3, DELXq22.3, DFNX6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038404	128866	CHMP4B	http://www.ncbi.nlm.nih.gov/gene/?term=128866	"C20orf178, CHMP4A, CTPP3, CTRCT31, SNF7, SNF7-2, Shax1, VPS32B, Vps32-2, dJ553F4.4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038405	128869	PIGU	http://www.ncbi.nlm.nih.gov/gene/?term=128869	"CDC91L1, GAB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038406	128869	PIGU	http://www.ncbi.nlm.nih.gov/gene/?term=128869	"CDC91L1, GAB1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038407	1289	COL5A1	http://www.ncbi.nlm.nih.gov/gene/?term=1289	EDSC	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038408	1289	COL5A1	http://www.ncbi.nlm.nih.gov/gene/?term=1289	EDSC	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038409	130074	FAM168B	http://www.ncbi.nlm.nih.gov/gene/?term=130074	MANI	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038410	1303	COL12A1	http://www.ncbi.nlm.nih.gov/gene/?term=1303	"BA209D8.1, BTHLM2L, DJ234P15.1, UCMD2, COL12A1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038411	130872	AHSA2	http://www.ncbi.nlm.nih.gov/gene/?term=130872	"AHA1, Hch1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038412	130872	AHSA2	http://www.ncbi.nlm.nih.gov/gene/?term=130872	"AHA1, Hch1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038413	1312	COMT	http://www.ncbi.nlm.nih.gov/gene/?term=1312	HEL-S-98n	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038414	1312	COMT	http://www.ncbi.nlm.nih.gov/gene/?term=1312	HEL-S-98n	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038415	1315	COPB1	http://www.ncbi.nlm.nih.gov/gene/?term=1315	COPB	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038416	1317	SLC31A1	http://www.ncbi.nlm.nih.gov/gene/?term=1317	"COPT1, CTR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038417	1317	SLC31A1	http://www.ncbi.nlm.nih.gov/gene/?term=1317	"COPT1, CTR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038418	132	ADK	http://www.ncbi.nlm.nih.gov/gene/?term=132	AK	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038419	132001	TAMM41	http://www.ncbi.nlm.nih.gov/gene/?term=132001	"C3orf31, RAM41, TAM41"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038420	132864	CPEB2	http://www.ncbi.nlm.nih.gov/gene/?term=132864	"CPE-BP2, CPEB-2, hCPEB-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038421	133015	PACRGL	http://www.ncbi.nlm.nih.gov/gene/?term=133015	C4orf28	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038422	133015	PACRGL	http://www.ncbi.nlm.nih.gov/gene/?term=133015	C4orf28	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038423	134430	WDR36	http://www.ncbi.nlm.nih.gov/gene/?term=134430	"GLC1G, TA-WDRP, TAWDRP, UTP21"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038424	1345	COX6C	http://www.ncbi.nlm.nih.gov/gene/?term=1345		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038425	1345	COX6C	http://www.ncbi.nlm.nih.gov/gene/?term=1345		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038426	134957	STXBP5	http://www.ncbi.nlm.nih.gov/gene/?term=134957	"LGL3, LLGL3, Nbla04300"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038427	1353	COX11	http://www.ncbi.nlm.nih.gov/gene/?term=1353	COX11P	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038428	136	ADORA2B	http://www.ncbi.nlm.nih.gov/gene/?term=136	ADORA2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038429	138241	C9orf85	http://www.ncbi.nlm.nih.gov/gene/?term=138241		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038430	138241	C9orf85	http://www.ncbi.nlm.nih.gov/gene/?term=138241		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038431	138428	PTRH1	http://www.ncbi.nlm.nih.gov/gene/?term=138428	"C9orf115, PTH1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038432	138428	PTRH1	http://www.ncbi.nlm.nih.gov/gene/?term=138428	"C9orf115, PTH1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038433	1387	CREBBP	http://www.ncbi.nlm.nih.gov/gene/?term=1387	"CBP, KAT3A, RSTS, RSTS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038434	1387	CREBBP	http://www.ncbi.nlm.nih.gov/gene/?term=1387	"CBP, KAT3A, RSTS, RSTS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038435	1398	CRK	http://www.ncbi.nlm.nih.gov/gene/?term=1398	"CRKII, p38"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038436	1398	CRK	http://www.ncbi.nlm.nih.gov/gene/?term=1398	"CRKII, p38"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038437	140609	NEK7	http://www.ncbi.nlm.nih.gov/gene/?term=140609		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038438	140609	NEK7	http://www.ncbi.nlm.nih.gov/gene/?term=140609		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038439	1408	CRY2	http://www.ncbi.nlm.nih.gov/gene/?term=1408	"HCRY2, PHLL2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038440	1408	CRY2	http://www.ncbi.nlm.nih.gov/gene/?term=1408	"HCRY2, PHLL2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038441	140885	SIRPA	http://www.ncbi.nlm.nih.gov/gene/?term=140885	"BIT, CD172A, MFR, MYD-1, P84, PTPNS1, SHPS1, SIRP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038442	140885	SIRPA	http://www.ncbi.nlm.nih.gov/gene/?term=140885	"BIT, CD172A, MFR, MYD-1, P84, PTPNS1, SHPS1, SIRP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038443	143187	VTI1A	http://www.ncbi.nlm.nih.gov/gene/?term=143187	"MMDS3, MVti1, VTI1RP2, Vti1-rp2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038444	143187	VTI1A	http://www.ncbi.nlm.nih.gov/gene/?term=143187	"MMDS3, MVti1, VTI1RP2, Vti1-rp2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038445	1432	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=1432	"CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2, PRKM14, PRKM15, RK, SAPK2A, p38, p38ALPHA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038446	1432	MAPK14	http://www.ncbi.nlm.nih.gov/gene/?term=1432	"CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2, PRKM14, PRKM15, RK, SAPK2A, p38, p38ALPHA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038447	143458	LDLRAD3	http://www.ncbi.nlm.nih.gov/gene/?term=143458	LRAD3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038448	143458	LDLRAD3	http://www.ncbi.nlm.nih.gov/gene/?term=143458	LRAD3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038449	143686	SESN3	http://www.ncbi.nlm.nih.gov/gene/?term=143686	SEST3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038450	143686	SESN3	http://www.ncbi.nlm.nih.gov/gene/?term=143686	SEST3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038451	143879	KBTBD3	http://www.ncbi.nlm.nih.gov/gene/?term=143879	BKLHD3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038452	143879	KBTBD3	http://www.ncbi.nlm.nih.gov/gene/?term=143879	BKLHD3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038453	144097	C11orf84	http://www.ncbi.nlm.nih.gov/gene/?term=144097		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038454	144108	SPTY2D1	http://www.ncbi.nlm.nih.gov/gene/?term=144108	Spt2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038455	144108	SPTY2D1	http://www.ncbi.nlm.nih.gov/gene/?term=144108	Spt2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038456	144402	CPNE8	http://www.ncbi.nlm.nih.gov/gene/?term=144402		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038457	1452	CSNK1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1452	"CK1, CK1a, CKIa, HEL-S-77p, HLCDGP1, PRO2975"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038458	1452	CSNK1A1	http://www.ncbi.nlm.nih.gov/gene/?term=1452	"CK1, CK1a, CKIa, HEL-S-77p, HLCDGP1, PRO2975"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038459	1453	CSNK1D	http://www.ncbi.nlm.nih.gov/gene/?term=1453	"ASPS, CKIdelta, FASPS2, HCKID"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038460	1453	CSNK1D	http://www.ncbi.nlm.nih.gov/gene/?term=1453	"ASPS, CKIdelta, FASPS2, HCKID"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038461	145581	LRFN5	http://www.ncbi.nlm.nih.gov/gene/?term=145581	"C14orf146, FIGLER8, SALM5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038462	145581	LRFN5	http://www.ncbi.nlm.nih.gov/gene/?term=145581	"C14orf146, FIGLER8, SALM5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038463	145694	LOC145694	http://www.ncbi.nlm.nih.gov/gene/?term=145694		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00038464	145694	LOC145694	http://www.ncbi.nlm.nih.gov/gene/?term=145694		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00038465	1457	CSNK2A1	http://www.ncbi.nlm.nih.gov/gene/?term=1457	"CK2A1, CKII, CSNK2A3, Cka1, Cka2, OCNDS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038466	1486	CTBS	http://www.ncbi.nlm.nih.gov/gene/?term=1486	CTB	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038467	1488	CTBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1488		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038468	1488	CTBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1488		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038469	149076	ZNF362	http://www.ncbi.nlm.nih.gov/gene/?term=149076	"RN, lin-29"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038470	1491	CTH	http://www.ncbi.nlm.nih.gov/gene/?term=1491		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038471	1491	CTH	http://www.ncbi.nlm.nih.gov/gene/?term=1491		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038472	1495	CTNNA1	http://www.ncbi.nlm.nih.gov/gene/?term=1495	"CAP102, MDPT2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038473	150709	ANKAR	http://www.ncbi.nlm.nih.gov/gene/?term=150709		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038474	151188	ARL6IP6	http://www.ncbi.nlm.nih.gov/gene/?term=151188	"AIP-6, AIP6, PFAAP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038475	151195	CCNYL1	http://www.ncbi.nlm.nih.gov/gene/?term=151195		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038476	151195	CCNYL1	http://www.ncbi.nlm.nih.gov/gene/?term=151195		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038477	1512	CTSH	http://www.ncbi.nlm.nih.gov/gene/?term=1512	"ACC-4, ACC-5, ACC4, ACC5, CPSB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038478	1512	CTSH	http://www.ncbi.nlm.nih.gov/gene/?term=1512	"ACC-4, ACC-5, ACC4, ACC5, CPSB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038479	151963	MB21D2	http://www.ncbi.nlm.nih.gov/gene/?term=151963	C3orf59	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038480	151963	MB21D2	http://www.ncbi.nlm.nih.gov/gene/?term=151963	C3orf59	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038481	152002	XXYLT1	http://www.ncbi.nlm.nih.gov/gene/?term=152002	C3orf21	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038482	152006	RNF38	http://www.ncbi.nlm.nih.gov/gene/?term=152006		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038483	152100	CMC1	http://www.ncbi.nlm.nih.gov/gene/?term=152100	C3orf68	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038484	152185	SPICE1	http://www.ncbi.nlm.nih.gov/gene/?term=152185	"CCDC52, SPICE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038485	152189	CMTM8	http://www.ncbi.nlm.nih.gov/gene/?term=152189	"CKLFSF8, CKLFSF8-V2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038486	152189	CMTM8	http://www.ncbi.nlm.nih.gov/gene/?term=152189	"CKLFSF8, CKLFSF8-V2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038487	1523	CUX1	http://www.ncbi.nlm.nih.gov/gene/?term=1523	"CASP, CDP, CDP/Cut, CDP1, COY1, CUTL1, CUX, Clox, Cux/CDP, GOLIM6, Nbla10317, p100, p110, p200, p75"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038488	1523	CUX1	http://www.ncbi.nlm.nih.gov/gene/?term=1523	"CASP, CDP, CDP/Cut, CDP1, COY1, CUTL1, CUX, Clox, Cux/CDP, GOLIM6, Nbla10317, p100, p110, p200, p75"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038489	152485	ZNF827	http://www.ncbi.nlm.nih.gov/gene/?term=152485		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038490	152485	ZNF827	http://www.ncbi.nlm.nih.gov/gene/?term=152485		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038491	152503	SH3D19	http://www.ncbi.nlm.nih.gov/gene/?term=152503	"EBP, EVE1, Eve-1, Kryn, SH3P19"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038492	152503	SH3D19	http://www.ncbi.nlm.nih.gov/gene/?term=152503	"EBP, EVE1, Eve-1, Kryn, SH3P19"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038493	152579	SCFD2	http://www.ncbi.nlm.nih.gov/gene/?term=152579	STXBP1L1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038494	152579	SCFD2	http://www.ncbi.nlm.nih.gov/gene/?term=152579	STXBP1L1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038495	152789	JAKMIP1	http://www.ncbi.nlm.nih.gov/gene/?term=152789	"Gababrbp, JAMIP1, MARLIN1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038496	152789	JAKMIP1	http://www.ncbi.nlm.nih.gov/gene/?term=152789	"Gababrbp, JAMIP1, MARLIN1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038497	153129	SLC38A9	http://www.ncbi.nlm.nih.gov/gene/?term=153129	URLC11	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038498	153241	CEP120	http://www.ncbi.nlm.nih.gov/gene/?term=153241	"CCDC100, SRTD13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038499	153241	CEP120	http://www.ncbi.nlm.nih.gov/gene/?term=153241	"CCDC100, SRTD13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038500	157570	ESCO2	http://www.ncbi.nlm.nih.gov/gene/?term=157570	"2410004I17Rik, EFO2, RBS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038501	157570	ESCO2	http://www.ncbi.nlm.nih.gov/gene/?term=157570	"2410004I17Rik, EFO2, RBS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038502	157680	VPS13B	http://www.ncbi.nlm.nih.gov/gene/?term=157680	"CHS1, COH1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038503	157680	VPS13B	http://www.ncbi.nlm.nih.gov/gene/?term=157680	"CHS1, COH1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038504	157922	CAMSAP1	http://www.ncbi.nlm.nih.gov/gene/?term=157922		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038505	158135	TTLL11	http://www.ncbi.nlm.nih.gov/gene/?term=158135	"C9orf20, bA244O19.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038506	158158	RASEF	http://www.ncbi.nlm.nih.gov/gene/?term=158158	RAB45	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038507	158158	RASEF	http://www.ncbi.nlm.nih.gov/gene/?term=158158	RAB45	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038508	158358	KIAA2026	http://www.ncbi.nlm.nih.gov/gene/?term=158358		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038509	158358	KIAA2026	http://www.ncbi.nlm.nih.gov/gene/?term=158358		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038510	158399	ZNF483	http://www.ncbi.nlm.nih.gov/gene/?term=158399	"ZKSCAN16, ZSCAN48"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038511	158399	ZNF483	http://www.ncbi.nlm.nih.gov/gene/?term=158399	"ZKSCAN16, ZSCAN48"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038512	158405	KIAA1958	http://www.ncbi.nlm.nih.gov/gene/?term=158405		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038513	1588	CYP19A1	http://www.ncbi.nlm.nih.gov/gene/?term=1588	"ARO, ARO1, CPV1, CYAR, CYP19, CYPXIX, P-450AROM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038514	1588	CYP19A1	http://www.ncbi.nlm.nih.gov/gene/?term=1588	"ARO, ARO1, CPV1, CYAR, CYP19, CYPXIX, P-450AROM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038515	159	ADSS	http://www.ncbi.nlm.nih.gov/gene/?term=159	"ADEH 2, ADSS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038516	159	ADSS	http://www.ncbi.nlm.nih.gov/gene/?term=159	"ADEH 2, ADSS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038517	1601	DAB2	http://www.ncbi.nlm.nih.gov/gene/?term=1601	"DOC-2, DOC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038518	160335	TMTC2	http://www.ncbi.nlm.nih.gov/gene/?term=160335	IBDBP1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038519	160335	TMTC2	http://www.ncbi.nlm.nih.gov/gene/?term=160335	IBDBP1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038520	1604	CD55	http://www.ncbi.nlm.nih.gov/gene/?term=1604	"CHAPLE, CR, CROM, DAF, TC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038521	160518	DENND5B	http://www.ncbi.nlm.nih.gov/gene/?term=160518		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038522	160518	DENND5B	http://www.ncbi.nlm.nih.gov/gene/?term=160518		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038523	1612	DAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=1612	"DAPK, ROCO3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038524	1612	DAPK1	http://www.ncbi.nlm.nih.gov/gene/?term=1612	"DAPK, ROCO3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038525	161742	SPRED1	http://www.ncbi.nlm.nih.gov/gene/?term=161742	"NFLS, PPP1R147, hSpred1, spred-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038526	162514	TRPV3	http://www.ncbi.nlm.nih.gov/gene/?term=162514	"FNEPPK2, OLMS, VRL3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038527	162514	TRPV3	http://www.ncbi.nlm.nih.gov/gene/?term=162514	"FNEPPK2, OLMS, VRL3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038528	163	AP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=163	"ADTB2, AP105B, AP2-BETA, CLAPB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038529	163115	ZNF781	http://www.ncbi.nlm.nih.gov/gene/?term=163115		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038530	1635	DCTD	http://www.ncbi.nlm.nih.gov/gene/?term=1635		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038531	1635	DCTD	http://www.ncbi.nlm.nih.gov/gene/?term=1635		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038532	163702	IFNLR1	http://www.ncbi.nlm.nih.gov/gene/?term=163702	"CRF2/12, IFNLR, IL-28R1, IL28RA, LICR2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038533	1657	DMXL1	http://www.ncbi.nlm.nih.gov/gene/?term=1657		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038534	165918	RNF168	http://www.ncbi.nlm.nih.gov/gene/?term=165918	hRNF168	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038535	1660	DHX9	http://www.ncbi.nlm.nih.gov/gene/?term=1660	"DDX9, LKP, NDH2, NDHII, RHA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038536	1662	DDX10	http://www.ncbi.nlm.nih.gov/gene/?term=1662	"Dbp4, HRH-J8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038537	166614	DCLK2	http://www.ncbi.nlm.nih.gov/gene/?term=166614	"CL2, CLICK-II, CLICK2, CLIK2, DCAMKL2, DCDC3, DCDC3B, DCK2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038538	167153	PAPD4	http://www.ncbi.nlm.nih.gov/gene/?term=167153	"GLD2, TUT2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038539	170463	SSBP4	http://www.ncbi.nlm.nih.gov/gene/?term=170463		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038540	170463	SSBP4	http://www.ncbi.nlm.nih.gov/gene/?term=170463		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038541	171023	ASXL1	http://www.ncbi.nlm.nih.gov/gene/?term=171023	"BOPS, MDS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038542	1738	DLD	http://www.ncbi.nlm.nih.gov/gene/?term=1738	"DLDDH, E3, GCSL, LAD, PHE3, DLD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038543	1738	DLD	http://www.ncbi.nlm.nih.gov/gene/?term=1738	"DLDDH, E3, GCSL, LAD, PHE3, DLD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038544	1739	DLG1	http://www.ncbi.nlm.nih.gov/gene/?term=1739	"DLGH1, SAP-97, SAP97, dJ1061C18.1.1, hdlg"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038545	1760	DMPK	http://www.ncbi.nlm.nih.gov/gene/?term=1760	"DM, DM1, DM1PK, DMK, MDPK, MT-PK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038546	1760	DMPK	http://www.ncbi.nlm.nih.gov/gene/?term=1760	"DM, DM1, DM1PK, DMK, MDPK, MT-PK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038547	1773	DNASE1	http://www.ncbi.nlm.nih.gov/gene/?term=1773	"DNL1, DRNI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038548	1773	DNASE1	http://www.ncbi.nlm.nih.gov/gene/?term=1773	"DNL1, DRNI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038549	1774	DNASE1L1	http://www.ncbi.nlm.nih.gov/gene/?term=1774	"DNAS1L1, DNASEX, DNL1L, G4.8, XIB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038550	1774	DNASE1L1	http://www.ncbi.nlm.nih.gov/gene/?term=1774	"DNAS1L1, DNASEX, DNL1L, G4.8, XIB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038551	1780	DYNC1I1	http://www.ncbi.nlm.nih.gov/gene/?term=1780	"DNCI1, DNCIC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038552	1780	DYNC1I1	http://www.ncbi.nlm.nih.gov/gene/?term=1780	"DNCI1, DNCIC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038553	1781	DYNC1I2	http://www.ncbi.nlm.nih.gov/gene/?term=1781	"DIC74, DNCI2, IC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038554	1785	DNM2	http://www.ncbi.nlm.nih.gov/gene/?term=1785	"CMT2M, CMTDI1, CMTDIB, DI-CMTB, DYN2, DYNII, LCCS5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038555	1785	DNM2	http://www.ncbi.nlm.nih.gov/gene/?term=1785	"CMT2M, CMTDI1, CMTDIB, DI-CMTB, DYN2, DYNII, LCCS5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038556	1788	DNMT3A	http://www.ncbi.nlm.nih.gov/gene/?term=1788	"DNMT3A2, M.HsaIIIA, TBRS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038557	1788	DNMT3A	http://www.ncbi.nlm.nih.gov/gene/?term=1788	"DNMT3A2, M.HsaIIIA, TBRS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038558	1809	DPYSL3	http://www.ncbi.nlm.nih.gov/gene/?term=1809	"CRMP-4, CRMP4, DRP-3, DRP3, LCRMP, ULIP, ULIP-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038559	1809	DPYSL3	http://www.ncbi.nlm.nih.gov/gene/?term=1809	"CRMP-4, CRMP4, DRP-3, DRP3, LCRMP, ULIP, ULIP-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038560	1827	RCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=1827	"ADAPT78, CSP1, DSC1, DSCR1, MCIP1, RCN1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038561	1827	RCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=1827	"ADAPT78, CSP1, DSC1, DSCR1, MCIP1, RCN1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038562	1847	DUSP5	http://www.ncbi.nlm.nih.gov/gene/?term=1847	"DUSP, HVH3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038563	1847	DUSP5	http://www.ncbi.nlm.nih.gov/gene/?term=1847	"DUSP, HVH3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038564	1859	DYRK1A	http://www.ncbi.nlm.nih.gov/gene/?term=1859	"DYRK, DYRK1, HP86, MNB, MNBH, MRD7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038565	1859	DYRK1A	http://www.ncbi.nlm.nih.gov/gene/?term=1859	"DYRK, DYRK1, HP86, MNB, MNBH, MRD7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038566	1870	E2F2	http://www.ncbi.nlm.nih.gov/gene/?term=1870	E2F-2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038567	1870	E2F2	http://www.ncbi.nlm.nih.gov/gene/?term=1870	E2F-2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038568	1879	EBF1	http://www.ncbi.nlm.nih.gov/gene/?term=1879	"COE1, EBF, O/E-1, OLF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038569	1909	EDNRA	http://www.ncbi.nlm.nih.gov/gene/?term=1909	"ET-A, ETA, ETA-R, ETAR, ETRA, MFDA, hET-AR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038570	1912	PHC2	http://www.ncbi.nlm.nih.gov/gene/?term=1912	"EDR2, HPH2, PH2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038571	192669	AGO3	http://www.ncbi.nlm.nih.gov/gene/?term=192669	EIF2C3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038572	192669	AGO3	http://www.ncbi.nlm.nih.gov/gene/?term=192669	EIF2C3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038573	192670	AGO4	http://www.ncbi.nlm.nih.gov/gene/?term=192670	EIF2C4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038574	192670	AGO4	http://www.ncbi.nlm.nih.gov/gene/?term=192670	EIF2C4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038575	1936	EEF1D	http://www.ncbi.nlm.nih.gov/gene/?term=1936	"EF-1D, EF1D, FP1047"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038576	1936	EEF1D	http://www.ncbi.nlm.nih.gov/gene/?term=1936	"EF-1D, EF1D, FP1047"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038577	1946	EFNA5	http://www.ncbi.nlm.nih.gov/gene/?term=1946	"AF1, EFL5, EPLG7, GLC1M, LERK7, RAGS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038578	1946	EFNA5	http://www.ncbi.nlm.nih.gov/gene/?term=1946	"AF1, EFL5, EPLG7, GLC1M, LERK7, RAGS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038579	1956	EGFR	http://www.ncbi.nlm.nih.gov/gene/?term=1956	"ERBB, ERBB1, HER1, NISBD2, PIG61, mENA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038580	195828	ZNF367	http://www.ncbi.nlm.nih.gov/gene/?term=195828	"AFF29, CDC14B, ZFF29"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038581	195828	ZNF367	http://www.ncbi.nlm.nih.gov/gene/?term=195828	"AFF29, CDC14B, ZFF29"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038582	196074	METTL15	http://www.ncbi.nlm.nih.gov/gene/?term=196074	METT5D1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038583	196074	METTL15	http://www.ncbi.nlm.nih.gov/gene/?term=196074	METT5D1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038584	196294	IMMP1L	http://www.ncbi.nlm.nih.gov/gene/?term=196294	"IMMP1, IMP1, IMP1-LIKE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038585	196463	PLBD2	http://www.ncbi.nlm.nih.gov/gene/?term=196463	P76	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038586	196463	PLBD2	http://www.ncbi.nlm.nih.gov/gene/?term=196463	P76	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038587	196740	VSTM4	http://www.ncbi.nlm.nih.gov/gene/?term=196740	C10orf72	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038588	196740	VSTM4	http://www.ncbi.nlm.nih.gov/gene/?term=196740	C10orf72	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038589	196951	FAM227B	http://www.ncbi.nlm.nih.gov/gene/?term=196951	C15orf33	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038590	197131	UBR1	http://www.ncbi.nlm.nih.gov/gene/?term=197131	JBS	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038591	197358	NLRC3	http://www.ncbi.nlm.nih.gov/gene/?term=197358	"CLR16.2, NOD3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038592	197358	NLRC3	http://www.ncbi.nlm.nih.gov/gene/?term=197358	"CLR16.2, NOD3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038593	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP1, EIF4EL1, EIF4F, eIF-4E, EIF4E"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038594	1977	EIF4E	http://www.ncbi.nlm.nih.gov/gene/?term=1977	"AUTS19, CBP1, EIF4EL1, EIF4F, eIF-4E, EIF4E"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038595	1979	EIF4EBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1979	"4EBP2, PHASII"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038596	1979	EIF4EBP2	http://www.ncbi.nlm.nih.gov/gene/?term=1979	"4EBP2, PHASII"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038597	1998	ELF2	http://www.ncbi.nlm.nih.gov/gene/?term=1998	"EU32, NERF, NERF-1A, NERF-1B, NERF-1a,b, NERF-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038598	2004	ELK3	http://www.ncbi.nlm.nih.gov/gene/?term=2004	"ERP, NET, SAP-2, SAP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038599	200734	SPRED2	http://www.ncbi.nlm.nih.gov/gene/?term=200734	Spred-2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038600	200895	DHFR2	http://www.ncbi.nlm.nih.gov/gene/?term=200895	"DHFRL1, DHFRP4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038601	200895	DHFR2	http://www.ncbi.nlm.nih.gov/gene/?term=200895	"DHFRL1, DHFRP4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038602	2009	EML1	http://www.ncbi.nlm.nih.gov/gene/?term=2009	"BH, ELP79, EMAP, EMAPL, HuEMAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038603	2011	MARK2	http://www.ncbi.nlm.nih.gov/gene/?term=2011	"EMK-1, EMK1, PAR-1, Par-1b, Par1b"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038604	2011	MARK2	http://www.ncbi.nlm.nih.gov/gene/?term=2011	"EMK-1, EMK1, PAR-1, Par-1b, Par1b"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038605	201134	CEP112	http://www.ncbi.nlm.nih.gov/gene/?term=201134	"CCDC46, MACOCO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038606	201134	CEP112	http://www.ncbi.nlm.nih.gov/gene/?term=201134	"CCDC46, MACOCO"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038607	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038608	201163	FLCN	http://www.ncbi.nlm.nih.gov/gene/?term=201163	"BHD, FLCL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038609	2012	EMP1	http://www.ncbi.nlm.nih.gov/gene/?term=2012	"CL-20, EMP-1, TMP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038610	201266	SLC39A11	http://www.ncbi.nlm.nih.gov/gene/?term=201266	"C17orf26, ZIP-11, ZIP11"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038611	201266	SLC39A11	http://www.ncbi.nlm.nih.gov/gene/?term=201266	"C17orf26, ZIP-11, ZIP11"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038612	201595	STT3B	http://www.ncbi.nlm.nih.gov/gene/?term=201595	"CDG1X, SIMP, STT3-B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038613	201627	DENND6A	http://www.ncbi.nlm.nih.gov/gene/?term=201627	"AFI1A, FAM116A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038614	2017	CTTN	http://www.ncbi.nlm.nih.gov/gene/?term=2017	EMS1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038615	2017	CTTN	http://www.ncbi.nlm.nih.gov/gene/?term=2017	EMS1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038616	202052	DNAJC18	http://www.ncbi.nlm.nih.gov/gene/?term=202052		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038617	202052	DNAJC18	http://www.ncbi.nlm.nih.gov/gene/?term=202052		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038618	202243	CCDC125	http://www.ncbi.nlm.nih.gov/gene/?term=202243	KENAE	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038619	203238	CCDC171	http://www.ncbi.nlm.nih.gov/gene/?term=203238	"C9orf93, bA536D16.1, bA778P13.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038620	203238	CCDC171	http://www.ncbi.nlm.nih.gov/gene/?term=203238	"C9orf93, bA536D16.1, bA778P13.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038621	2033	EP300	http://www.ncbi.nlm.nih.gov/gene/?term=2033	"KAT3B, RSTS2, p300"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038622	2033	EP300	http://www.ncbi.nlm.nih.gov/gene/?term=2033	"KAT3B, RSTS2, p300"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038623	2034	EPAS1	http://www.ncbi.nlm.nih.gov/gene/?term=2034	"ECYT4, HIF2A, HLF, MOP2, PASD2, bHLHe73"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038624	2034	EPAS1	http://www.ncbi.nlm.nih.gov/gene/?term=2034	"ECYT4, HIF2A, HLF, MOP2, PASD2, bHLHe73"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038625	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038626	2035	EPB41	http://www.ncbi.nlm.nih.gov/gene/?term=2035	"4.1R, EL1, HE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038627	2036	EPB41L1	http://www.ncbi.nlm.nih.gov/gene/?term=2036	"4.1N, MRD11"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038628	2038	EPB42	http://www.ncbi.nlm.nih.gov/gene/?term=2038	"PA, SPH5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038629	2038	EPB42	http://www.ncbi.nlm.nih.gov/gene/?term=2038	"PA, SPH5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038630	204	AK2	http://www.ncbi.nlm.nih.gov/gene/?term=204	ADK2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038631	204	AK2	http://www.ncbi.nlm.nih.gov/gene/?term=204	ADK2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038632	2043	EPHA4	http://www.ncbi.nlm.nih.gov/gene/?term=2043	"HEK8, SEK, TYRO1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038633	2044	EPHA5	http://www.ncbi.nlm.nih.gov/gene/?term=2044	"CEK7, EHK-1, EHK1, EK7, HEK7, TYRO4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038634	2044	EPHA5	http://www.ncbi.nlm.nih.gov/gene/?term=2044	"CEK7, EHK-1, EHK1, EK7, HEK7, TYRO4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038635	2048	EPHB2	http://www.ncbi.nlm.nih.gov/gene/?term=2048	"CAPB, DRT, EK5, EPHT3, ERK, Hek5, PCBC, Tyro5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038636	2048	EPHB2	http://www.ncbi.nlm.nih.gov/gene/?term=2048	"CAPB, DRT, EK5, EPHT3, ERK, Hek5, PCBC, Tyro5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038637	204962	SLC44A5	http://www.ncbi.nlm.nih.gov/gene/?term=204962	CTL5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038638	205564	SENP5	http://www.ncbi.nlm.nih.gov/gene/?term=205564		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038639	2060	EPS15	http://www.ncbi.nlm.nih.gov/gene/?term=2060	"AF-1P, AF1P, MLLT5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038640	2066	ERBB4	http://www.ncbi.nlm.nih.gov/gene/?term=2066	"ALS19, HER4, p180erbB4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038641	2068	ERCC2	http://www.ncbi.nlm.nih.gov/gene/?term=2068	"COFS2, EM9, TFIIH, TTD, TTD1, XPD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038642	2068	ERCC2	http://www.ncbi.nlm.nih.gov/gene/?term=2068	"COFS2, EM9, TFIIH, TTD, TTD1, XPD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038643	2078	ERG	http://www.ncbi.nlm.nih.gov/gene/?term=2078	"erg-3, p55"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038644	2100	ESR2	http://www.ncbi.nlm.nih.gov/gene/?term=2100	"ER-BETA, ESR-BETA, ESRB, ESTRB, Erb, NR3A2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038645	2100	ESR2	http://www.ncbi.nlm.nih.gov/gene/?term=2100	"ER-BETA, ESR-BETA, ESRB, ESTRB, Erb, NR3A2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038646	2103	ESRRB	http://www.ncbi.nlm.nih.gov/gene/?term=2103	"DFNB35, ERR2, ERRb, ESRL2, NR3B2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038647	2103	ESRRB	http://www.ncbi.nlm.nih.gov/gene/?term=2103	"DFNB35, ERR2, ERRb, ESRL2, NR3B2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038648	2107	ETF1	http://www.ncbi.nlm.nih.gov/gene/?term=2107	"D5S1995, ERF, ERF1, RF1, SUP45L1, TB3-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038649	2108	ETFA	http://www.ncbi.nlm.nih.gov/gene/?term=2108	"EMA, GA2, MADD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038650	2114	ETS2	http://www.ncbi.nlm.nih.gov/gene/?term=2114	ETS2IT1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038651	2120	ETV6	http://www.ncbi.nlm.nih.gov/gene/?term=2120	"TEL, TEL/ABL, THC5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038652	2120	ETV6	http://www.ncbi.nlm.nih.gov/gene/?term=2120	"TEL, TEL/ABL, THC5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038653	2121	EVC	http://www.ncbi.nlm.nih.gov/gene/?term=2121	"DWF-11, EVCL, EVC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038654	2121	EVC	http://www.ncbi.nlm.nih.gov/gene/?term=2121	"DWF-11, EVCL, EVC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038655	2131	EXT1	http://www.ncbi.nlm.nih.gov/gene/?term=2131	"EXT, LGCR, LGS, TRPS2, TTV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038656	2131	EXT1	http://www.ncbi.nlm.nih.gov/gene/?term=2131	"EXT, LGCR, LGS, TRPS2, TTV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038657	2132	EXT2	http://www.ncbi.nlm.nih.gov/gene/?term=2132	"SOTV, SSMS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038658	2132	EXT2	http://www.ncbi.nlm.nih.gov/gene/?term=2132	"SOTV, SSMS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038659	214	ALCAM	http://www.ncbi.nlm.nih.gov/gene/?term=214	"CD166, MEMD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038660	214	ALCAM	http://www.ncbi.nlm.nih.gov/gene/?term=214	"CD166, MEMD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038661	2140	EYA3	http://www.ncbi.nlm.nih.gov/gene/?term=2140		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038662	2146	EZH2	http://www.ncbi.nlm.nih.gov/gene/?term=2146	"ENX-1, ENX1b, KMT6, KMT6A, WVS, WVS2, EZH2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038663	2162	F13A1	http://www.ncbi.nlm.nih.gov/gene/?term=2162	F13A	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038664	2162	F13A1	http://www.ncbi.nlm.nih.gov/gene/?term=2162	F13A	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038665	2170	FABP3	http://www.ncbi.nlm.nih.gov/gene/?term=2170	"FABP11, H-FABP, M-FABP, MDGI, O-FABP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038666	2170	FABP3	http://www.ncbi.nlm.nih.gov/gene/?term=2170	"FABP11, H-FABP, M-FABP, MDGI, O-FABP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038667	2176	FANCC	http://www.ncbi.nlm.nih.gov/gene/?term=2176	"FA3, FAC, FACC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038668	2180	ACSL1	http://www.ncbi.nlm.nih.gov/gene/?term=2180	"ACS1, FACL1, FACL2, LACS, LACS1, LACS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038669	2180	ACSL1	http://www.ncbi.nlm.nih.gov/gene/?term=2180	"ACS1, FACL1, FACL2, LACS, LACS1, LACS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038670	2186	BPTF	http://www.ncbi.nlm.nih.gov/gene/?term=2186	"FAC1, FALZ, NURF301"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038671	219333	USP12	http://www.ncbi.nlm.nih.gov/gene/?term=219333	"UBH1L1, USP12"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038672	219333	USP12	http://www.ncbi.nlm.nih.gov/gene/?term=219333	"UBH1L1, USP12"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038673	2195	FAT1	http://www.ncbi.nlm.nih.gov/gene/?term=2195	"CDHF7, CDHR8, FAT, ME5, hFat1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038674	219771	CCNY	http://www.ncbi.nlm.nih.gov/gene/?term=219771	"C10orf9, CBCP1, CCNX, CFP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038675	219771	CCNY	http://www.ncbi.nlm.nih.gov/gene/?term=219771	"C10orf9, CBCP1, CCNX, CFP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038676	220	ALDH1A3	http://www.ncbi.nlm.nih.gov/gene/?term=220	"ALDH1A6, ALDH6, MCOP8, RALDH3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038677	220	ALDH1A3	http://www.ncbi.nlm.nih.gov/gene/?term=220	"ALDH1A6, ALDH6, MCOP8, RALDH3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038678	2200	FBN1	http://www.ncbi.nlm.nih.gov/gene/?term=2200	"ACMICD, ECTOL1, FBN, GPHYSD2, MASS, MFLS, MFS1, OCTD, SGS, SSKS, WMS, WMS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038679	2200	FBN1	http://www.ncbi.nlm.nih.gov/gene/?term=2200	"ACMICD, ECTOL1, FBN, GPHYSD2, MASS, MFLS, MFS1, OCTD, SGS, SSKS, WMS, WMS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038680	220002	CYB561A3	http://www.ncbi.nlm.nih.gov/gene/?term=220002	"CYBASC3, LCYTB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038681	220002	CYB561A3	http://www.ncbi.nlm.nih.gov/gene/?term=220002	"CYBASC3, LCYTB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038682	2201	FBN2	http://www.ncbi.nlm.nih.gov/gene/?term=2201	"CCA, DA9, EOMD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038683	221035	REEP3	http://www.ncbi.nlm.nih.gov/gene/?term=221035	"C10orf74, Yip2b"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038684	221037	JMJD1C	http://www.ncbi.nlm.nih.gov/gene/?term=221037	"KDM3C, TRIP-8, TRIP8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038685	221395	ADGRF5	http://www.ncbi.nlm.nih.gov/gene/?term=221395	"GPR116, KPG_001"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038686	221395	ADGRF5	http://www.ncbi.nlm.nih.gov/gene/?term=221395	"GPR116, KPG_001"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038687	221496	LEMD2	http://www.ncbi.nlm.nih.gov/gene/?term=221496	"CTRCT42, NET25, dJ482C21.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038688	221496	LEMD2	http://www.ncbi.nlm.nih.gov/gene/?term=221496	"CTRCT42, NET25, dJ482C21.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038689	221895	JAZF1	http://www.ncbi.nlm.nih.gov/gene/?term=221895	"TIP27, ZNF802"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038690	221895	JAZF1	http://www.ncbi.nlm.nih.gov/gene/?term=221895	"TIP27, ZNF802"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038691	2222	FDFT1	http://www.ncbi.nlm.nih.gov/gene/?term=2222	"DGPT, ERG9, SQS, SS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038692	222487	ADGRG3	http://www.ncbi.nlm.nih.gov/gene/?term=222487	"GPR97, PB99, PGR26"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038693	222487	ADGRG3	http://www.ncbi.nlm.nih.gov/gene/?term=222487	"GPR97, PB99, PGR26"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038694	222663	SCUBE3	http://www.ncbi.nlm.nih.gov/gene/?term=222663	CEGF3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038695	2241	FER	http://www.ncbi.nlm.nih.gov/gene/?term=2241	"PPP1R74, TYK3, p94-Fer"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038696	2262	GPC5	http://www.ncbi.nlm.nih.gov/gene/?term=2262		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038697	2272	FHIT	http://www.ncbi.nlm.nih.gov/gene/?term=2272	"AP3Aase, FRA3B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038698	2272	FHIT	http://www.ncbi.nlm.nih.gov/gene/?term=2272	"AP3Aase, FRA3B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038699	2274	FHL2	http://www.ncbi.nlm.nih.gov/gene/?term=2274	"AAG11, DRAL, FHL-2, SLIM-3, SLIM3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038700	2274	FHL2	http://www.ncbi.nlm.nih.gov/gene/?term=2274	"AAG11, DRAL, FHL-2, SLIM-3, SLIM3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038701	22800	RRAS2	http://www.ncbi.nlm.nih.gov/gene/?term=22800	TC21	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038702	22821	RASA3	http://www.ncbi.nlm.nih.gov/gene/?term=22821	"GAP1IP4BP, GAPIII"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038703	22828	SCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=22828	RBM16	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038704	22828	SCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=22828	RBM16	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038705	22834	ZNF652	http://www.ncbi.nlm.nih.gov/gene/?term=22834		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038706	22834	ZNF652	http://www.ncbi.nlm.nih.gov/gene/?term=22834		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038707	22836	RHOBTB3	http://www.ncbi.nlm.nih.gov/gene/?term=22836		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038708	22846	VASH1	http://www.ncbi.nlm.nih.gov/gene/?term=22846	KIAA1036	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038709	22859	ADGRL1	http://www.ncbi.nlm.nih.gov/gene/?term=22859	"CIRL1, CL1, LEC2, LPHN1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038710	22859	ADGRL1	http://www.ncbi.nlm.nih.gov/gene/?term=22859	"CIRL1, CL1, LEC2, LPHN1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038711	22862	FNDC3A	http://www.ncbi.nlm.nih.gov/gene/?term=22862	"FNDC3, HUGO, bA203I16.1, bA203I16.5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038712	22862	FNDC3A	http://www.ncbi.nlm.nih.gov/gene/?term=22862	"FNDC3, HUGO, bA203I16.1, bA203I16.5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038713	22864	R3HDM2	http://www.ncbi.nlm.nih.gov/gene/?term=22864	"CAG6, PR01365"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038714	22870	PPP6R1	http://www.ncbi.nlm.nih.gov/gene/?term=22870	"KIAA1115, PP6R1, SAP190, SAPS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038715	22870	PPP6R1	http://www.ncbi.nlm.nih.gov/gene/?term=22870	"KIAA1115, PP6R1, SAP190, SAPS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038716	22872	SEC31A	http://www.ncbi.nlm.nih.gov/gene/?term=22872	"ABP125, ABP130, HSPC275, HSPC334, SEC31L1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038717	22872	SEC31A	http://www.ncbi.nlm.nih.gov/gene/?term=22872	"ABP125, ABP130, HSPC275, HSPC334, SEC31L1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038718	22873	DZIP1	http://www.ncbi.nlm.nih.gov/gene/?term=22873	"DZIP, DZIPt1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038719	22876	INPP5F	http://www.ncbi.nlm.nih.gov/gene/?term=22876	"MSTP007, MSTPO47, SAC2, hSAC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038720	22876	INPP5F	http://www.ncbi.nlm.nih.gov/gene/?term=22876	"MSTP007, MSTPO47, SAC2, hSAC2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038721	22882	ZHX2	http://www.ncbi.nlm.nih.gov/gene/?term=22882	"AFR1, RAF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038722	22887	FOXJ3	http://www.ncbi.nlm.nih.gov/gene/?term=22887		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038723	22887	FOXJ3	http://www.ncbi.nlm.nih.gov/gene/?term=22887		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038724	22898	DENND3	http://www.ncbi.nlm.nih.gov/gene/?term=22898		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038725	22898	DENND3	http://www.ncbi.nlm.nih.gov/gene/?term=22898		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038726	22903	BTBD3	http://www.ncbi.nlm.nih.gov/gene/?term=22903	dJ742J24.1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038727	22905	EPN2	http://www.ncbi.nlm.nih.gov/gene/?term=22905	EHB21	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038728	22905	EPN2	http://www.ncbi.nlm.nih.gov/gene/?term=22905	EHB21	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038729	22909	FAN1	http://www.ncbi.nlm.nih.gov/gene/?term=22909	"KIAA1018, KMIN, MTMR15, hFAN1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038730	22909	FAN1	http://www.ncbi.nlm.nih.gov/gene/?term=22909	"KIAA1018, KMIN, MTMR15, hFAN1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038731	22913	RALY	http://www.ncbi.nlm.nih.gov/gene/?term=22913	"HNRPCL2, P542"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038732	22913	RALY	http://www.ncbi.nlm.nih.gov/gene/?term=22913	"HNRPCL2, P542"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038733	22920	KIFAP3	http://www.ncbi.nlm.nih.gov/gene/?term=22920	"FLA3, KAP-1, KAP-3, KAP3, SMAP, Smg-GDS, dJ190I16.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038734	22920	KIFAP3	http://www.ncbi.nlm.nih.gov/gene/?term=22920	"FLA3, KAP-1, KAP-3, KAP3, SMAP, Smg-GDS, dJ190I16.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038735	22926	ATF6	http://www.ncbi.nlm.nih.gov/gene/?term=22926	"ACHM7A, ATF6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038736	22926	ATF6	http://www.ncbi.nlm.nih.gov/gene/?term=22926	"ACHM7A, ATF6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038737	22936	ELL2	http://www.ncbi.nlm.nih.gov/gene/?term=22936	MRCCAT1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038738	22948	CCT5	http://www.ncbi.nlm.nih.gov/gene/?term=22948	"CCT-epsilon, CCTE, HEL-S-69, PNAS-102, TCP-1-epsilon"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038739	22948	CCT5	http://www.ncbi.nlm.nih.gov/gene/?term=22948	"CCT-epsilon, CCTE, HEL-S-69, PNAS-102, TCP-1-epsilon"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038740	22978	NT5C2	http://www.ncbi.nlm.nih.gov/gene/?term=22978	"GMP, NT5B, PNT5, SPG45, SPG65, cN-II"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038741	22982	DIP2C	http://www.ncbi.nlm.nih.gov/gene/?term=22982	KIAA0934	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038742	22982	DIP2C	http://www.ncbi.nlm.nih.gov/gene/?term=22982	KIAA0934	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038743	22985	ACIN1	http://www.ncbi.nlm.nih.gov/gene/?term=22985	"ACINUS, ACN, fSAP152"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038744	22985	ACIN1	http://www.ncbi.nlm.nih.gov/gene/?term=22985	"ACINUS, ACN, fSAP152"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038745	22998	LIMCH1	http://www.ncbi.nlm.nih.gov/gene/?term=22998	"LIMCH1A, LMO7B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038746	22998	LIMCH1	http://www.ncbi.nlm.nih.gov/gene/?term=22998	"LIMCH1A, LMO7B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038747	23005	MAPKBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23005	"JNKBP-1, JNKBP1, NPHP20"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038748	23011	RAB21	http://www.ncbi.nlm.nih.gov/gene/?term=23011		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038749	23022	PALLD	http://www.ncbi.nlm.nih.gov/gene/?term=23022	"CGI-151, CGI151, MYN, PNCA1, SIH002"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038750	23022	PALLD	http://www.ncbi.nlm.nih.gov/gene/?term=23022	"CGI-151, CGI151, MYN, PNCA1, SIH002"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038751	23023	TMCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23023		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038752	23023	TMCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23023		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038753	23024	PDZRN3	http://www.ncbi.nlm.nih.gov/gene/?term=23024	"LNX3, SEMACAP3, SEMCAP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038754	23024	PDZRN3	http://www.ncbi.nlm.nih.gov/gene/?term=23024	"LNX3, SEMACAP3, SEMCAP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038755	23032	USP33	http://www.ncbi.nlm.nih.gov/gene/?term=23032	VDU1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038756	23041	MON2	http://www.ncbi.nlm.nih.gov/gene/?term=23041		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038757	23043	TNIK	http://www.ncbi.nlm.nih.gov/gene/?term=23043	MRT54	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038758	23043	TNIK	http://www.ncbi.nlm.nih.gov/gene/?term=23043	MRT54	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038759	23048	FNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23048	FBP17	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038760	23048	FNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23048	FBP17	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038761	23049	SMG1	http://www.ncbi.nlm.nih.gov/gene/?term=23049	"61E3.4, ATX, LIP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038762	23054	NCOA6	http://www.ncbi.nlm.nih.gov/gene/?term=23054	"AIB3, ASC2, NRC, PRIP, RAP250, TRBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038763	23054	NCOA6	http://www.ncbi.nlm.nih.gov/gene/?term=23054	"AIB3, ASC2, NRC, PRIP, RAP250, TRBP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038764	23063	WAPL	http://www.ncbi.nlm.nih.gov/gene/?term=23063	"FOE, KIAA0261, WAPAL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038765	23063	WAPL	http://www.ncbi.nlm.nih.gov/gene/?term=23063	"FOE, KIAA0261, WAPAL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038766	23072	HECW1	http://www.ncbi.nlm.nih.gov/gene/?term=23072	NEDL1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038767	23072	HECW1	http://www.ncbi.nlm.nih.gov/gene/?term=23072	NEDL1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038768	23077	MYCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23077	"Myc-bp2, PAM, Phr"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038769	23077	MYCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23077	"Myc-bp2, PAM, Phr"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038770	23080	AVL9	http://www.ncbi.nlm.nih.gov/gene/?term=23080	KIAA0241	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038771	23081	KDM4C	http://www.ncbi.nlm.nih.gov/gene/?term=23081	"GASC1, JHDM3C, JMJD2C, TDRD14C"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038772	23086	EXPH5	http://www.ncbi.nlm.nih.gov/gene/?term=23086	"SLAC2-B, SLAC2B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038773	23086	EXPH5	http://www.ncbi.nlm.nih.gov/gene/?term=23086	"SLAC2-B, SLAC2B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038774	23092	ARHGAP26	http://www.ncbi.nlm.nih.gov/gene/?term=23092	"GRAF, GRAF1, OPHN1L, OPHN1L1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038775	23095	KIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=23095	"CMT2, CMT2A, CMT2A1, HMSNII, KLP, NBLST1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038776	23095	KIF1B	http://www.ncbi.nlm.nih.gov/gene/?term=23095	"CMT2, CMT2A, CMT2A1, HMSNII, KLP, NBLST1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038777	23097	CDK19	http://www.ncbi.nlm.nih.gov/gene/?term=23097	"CDC2L6, CDK11, bA346C16.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038778	23097	CDK19	http://www.ncbi.nlm.nih.gov/gene/?term=23097	"CDC2L6, CDK11, bA346C16.3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038779	23101	MCF2L2	http://www.ncbi.nlm.nih.gov/gene/?term=23101	ARHGEF22	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038780	23101	MCF2L2	http://www.ncbi.nlm.nih.gov/gene/?term=23101	ARHGEF22	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038781	23102	TBC1D2B	http://www.ncbi.nlm.nih.gov/gene/?term=23102		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038782	23102	TBC1D2B	http://www.ncbi.nlm.nih.gov/gene/?term=23102		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038783	23108	RAP1GAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23108	"GARNL4, RAP1GA3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038784	23108	RAP1GAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23108	"GARNL4, RAP1GA3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038785	23111	SPART	http://www.ncbi.nlm.nih.gov/gene/?term=23111	"SPG20, TAHCCP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038786	23111	SPART	http://www.ncbi.nlm.nih.gov/gene/?term=23111	"SPG20, TAHCCP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038787	23118	TAB2	http://www.ncbi.nlm.nih.gov/gene/?term=23118	"CHTD2, MAP3K7IP2, TAB-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038788	23126	POGZ	http://www.ncbi.nlm.nih.gov/gene/?term=23126	"MRD37, WHSUS, ZNF280E, ZNF635, ZNF635m"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038789	23126	POGZ	http://www.ncbi.nlm.nih.gov/gene/?term=23126	"MRD37, WHSUS, ZNF280E, ZNF635, ZNF635m"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038790	23131	GPATCH8	http://www.ncbi.nlm.nih.gov/gene/?term=23131	"GPATC8, KIAA0553"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038791	23131	GPATCH8	http://www.ncbi.nlm.nih.gov/gene/?term=23131	"GPATC8, KIAA0553"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038792	23142	DCUN1D4	http://www.ncbi.nlm.nih.gov/gene/?term=23142		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038793	23142	DCUN1D4	http://www.ncbi.nlm.nih.gov/gene/?term=23142		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038794	23143	LRCH1	http://www.ncbi.nlm.nih.gov/gene/?term=23143	"CHDC1, NP81"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038795	23143	LRCH1	http://www.ncbi.nlm.nih.gov/gene/?term=23143	"CHDC1, NP81"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038796	23144	ZC3H3	http://www.ncbi.nlm.nih.gov/gene/?term=23144	ZC3HDC3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038797	23155	CLCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23155	MCLC	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038798	23155	CLCC1	http://www.ncbi.nlm.nih.gov/gene/?term=23155	MCLC	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038799	23161	SNX13	http://www.ncbi.nlm.nih.gov/gene/?term=23161	RGS-PX1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038800	23168	RTF1	http://www.ncbi.nlm.nih.gov/gene/?term=23168	"GTL7, KIAA0252"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038801	23172	ABRAXAS2	http://www.ncbi.nlm.nih.gov/gene/?term=23172	"ABRO1, FAM175B, KIAA0157"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038802	23174	ZCCHC14	http://www.ncbi.nlm.nih.gov/gene/?term=23174	"BDG-29, BDG29"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038803	23174	ZCCHC14	http://www.ncbi.nlm.nih.gov/gene/?term=23174	"BDG-29, BDG29"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038804	23177	CEP68	http://www.ncbi.nlm.nih.gov/gene/?term=23177	KIAA0582	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038805	23177	CEP68	http://www.ncbi.nlm.nih.gov/gene/?term=23177	KIAA0582	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038806	23178	PASK	http://www.ncbi.nlm.nih.gov/gene/?term=23178	"PASKIN, STK37"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038807	23178	PASK	http://www.ncbi.nlm.nih.gov/gene/?term=23178	"PASKIN, STK37"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038808	23180	RFTN1	http://www.ncbi.nlm.nih.gov/gene/?term=23180	"MIG2, PIB10, PIG9, RAFTLIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038809	23180	RFTN1	http://www.ncbi.nlm.nih.gov/gene/?term=23180	"MIG2, PIB10, PIG9, RAFTLIN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038810	23185	LARP4B	http://www.ncbi.nlm.nih.gov/gene/?term=23185	"KIAA0217, LARP5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038811	23185	LARP4B	http://www.ncbi.nlm.nih.gov/gene/?term=23185	"KIAA0217, LARP5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038812	23187	PHLDB1	http://www.ncbi.nlm.nih.gov/gene/?term=23187	LL5A	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038813	23187	PHLDB1	http://www.ncbi.nlm.nih.gov/gene/?term=23187	LL5A	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038814	23195	MDN1	http://www.ncbi.nlm.nih.gov/gene/?term=23195	Rea1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038815	23195	MDN1	http://www.ncbi.nlm.nih.gov/gene/?term=23195	Rea1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038816	23196	FAM120A	http://www.ncbi.nlm.nih.gov/gene/?term=23196	"C9orf10, HBVPTPAP, OSSA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038817	23196	FAM120A	http://www.ncbi.nlm.nih.gov/gene/?term=23196	"C9orf10, HBVPTPAP, OSSA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038818	23198	PSME4	http://www.ncbi.nlm.nih.gov/gene/?term=23198	PA200	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038819	23198	PSME4	http://www.ncbi.nlm.nih.gov/gene/?term=23198	PA200	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038820	23199	GSE1	http://www.ncbi.nlm.nih.gov/gene/?term=23199	"CRHSP24, KIAA0182"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038821	23199	GSE1	http://www.ncbi.nlm.nih.gov/gene/?term=23199	"CRHSP24, KIAA0182"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038822	23213	SULF1	http://www.ncbi.nlm.nih.gov/gene/?term=23213	SULF-1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038823	23213	SULF1	http://www.ncbi.nlm.nih.gov/gene/?term=23213	SULF-1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038824	23214	XPO6	http://www.ncbi.nlm.nih.gov/gene/?term=23214	"EXP6, RANBP20"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038825	23214	XPO6	http://www.ncbi.nlm.nih.gov/gene/?term=23214	"EXP6, RANBP20"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038826	23216	TBC1D1	http://www.ncbi.nlm.nih.gov/gene/?term=23216	"TBC, TBC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038827	23216	TBC1D1	http://www.ncbi.nlm.nih.gov/gene/?term=23216	"TBC, TBC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038828	23224	SYNE2	http://www.ncbi.nlm.nih.gov/gene/?term=23224	"EDMD5, KASH2, NUA, NUANCE, Nesp2, Nesprin-2, SYNE-2, TROPH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038829	23230	VPS13A	http://www.ncbi.nlm.nih.gov/gene/?term=23230	"CHAC, CHOREIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038830	23230	VPS13A	http://www.ncbi.nlm.nih.gov/gene/?term=23230	"CHAC, CHOREIN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038831	23231	SEL1L3	http://www.ncbi.nlm.nih.gov/gene/?term=23231	Sel-1L3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038832	23231	SEL1L3	http://www.ncbi.nlm.nih.gov/gene/?term=23231	Sel-1L3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038833	23236	PLCB1	http://www.ncbi.nlm.nih.gov/gene/?term=23236	"EIEE12, PI-PLC, PLC-154, PLC-I, PLC-beta-1, PLC154A, PLCB1B, PLCB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038834	23236	PLCB1	http://www.ncbi.nlm.nih.gov/gene/?term=23236	"EIEE12, PI-PLC, PLC-154, PLC-I, PLC-beta-1, PLC154A, PLCB1B, PLCB1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038835	23240	TMEM131L	http://www.ncbi.nlm.nih.gov/gene/?term=23240	KIAA0922	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038836	23240	TMEM131L	http://www.ncbi.nlm.nih.gov/gene/?term=23240	KIAA0922	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038837	23242	COBL	http://www.ncbi.nlm.nih.gov/gene/?term=23242		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038838	23244	PDS5A	http://www.ncbi.nlm.nih.gov/gene/?term=23244	"PIG54, SCC-112, SCC112"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038839	23244	PDS5A	http://www.ncbi.nlm.nih.gov/gene/?term=23244	"PIG54, SCC-112, SCC112"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038840	23247	KIAA0556	http://www.ncbi.nlm.nih.gov/gene/?term=23247	JBTS26	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038841	23247	KIAA0556	http://www.ncbi.nlm.nih.gov/gene/?term=23247	JBTS26	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038842	23248	RPRD2	http://www.ncbi.nlm.nih.gov/gene/?term=23248	"HSPC099, KIAA0460"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038843	23248	RPRD2	http://www.ncbi.nlm.nih.gov/gene/?term=23248	"HSPC099, KIAA0460"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038844	23250	ATP11A	http://www.ncbi.nlm.nih.gov/gene/?term=23250	"ATPIH, ATPIS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038845	23250	ATP11A	http://www.ncbi.nlm.nih.gov/gene/?term=23250	"ATPIH, ATPIS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038846	23253	ANKRD12	http://www.ncbi.nlm.nih.gov/gene/?term=23253	"ANCO-2, ANCO1, GAC-1, Nbla00144"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038847	23255	MTCL1	http://www.ncbi.nlm.nih.gov/gene/?term=23255	"CCDC165, KIAA0802, SOGA2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038848	23255	MTCL1	http://www.ncbi.nlm.nih.gov/gene/?term=23255	"CCDC165, KIAA0802, SOGA2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038849	23256	SCFD1	http://www.ncbi.nlm.nih.gov/gene/?term=23256	"C14orf163, RA410, SLY1, SLY1P, STXBP1L2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038850	23256	SCFD1	http://www.ncbi.nlm.nih.gov/gene/?term=23256	"C14orf163, RA410, SLY1, SLY1P, STXBP1L2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038851	23261	CAMTA1	http://www.ncbi.nlm.nih.gov/gene/?term=23261	CANPMR	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038852	23261	CAMTA1	http://www.ncbi.nlm.nih.gov/gene/?term=23261	CANPMR	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038853	23263	MCF2L	http://www.ncbi.nlm.nih.gov/gene/?term=23263	"ARHGEF14, DBS, OST"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038854	23263	MCF2L	http://www.ncbi.nlm.nih.gov/gene/?term=23263	"ARHGEF14, DBS, OST"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038855	23272	FAM208A	http://www.ncbi.nlm.nih.gov/gene/?term=23272	"C3orf63, RAP140, TASOR, se89-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038856	23275	POFUT2	http://www.ncbi.nlm.nih.gov/gene/?term=23275	"C21orf80, FUT13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038857	23275	POFUT2	http://www.ncbi.nlm.nih.gov/gene/?term=23275	"C21orf80, FUT13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038858	23276	KLHL18	http://www.ncbi.nlm.nih.gov/gene/?term=23276		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038859	23279	NUP160	http://www.ncbi.nlm.nih.gov/gene/?term=23279		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038860	23286	WWC1	http://www.ncbi.nlm.nih.gov/gene/?term=23286	"HBEBP3, HBEBP36, KIBRA, MEMRYQTL, PPP1R168"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038861	23286	WWC1	http://www.ncbi.nlm.nih.gov/gene/?term=23286	"HBEBP3, HBEBP36, KIBRA, MEMRYQTL, PPP1R168"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038862	23291	FBXW11	http://www.ncbi.nlm.nih.gov/gene/?term=23291	"BTRC2, BTRCP2, FBW1B, FBXW1B, Fbw11, Hos"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038863	23291	FBXW11	http://www.ncbi.nlm.nih.gov/gene/?term=23291	"BTRC2, BTRCP2, FBW1B, FBXW1B, Fbw11, Hos"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038864	23294	ANKS1A	http://www.ncbi.nlm.nih.gov/gene/?term=23294	ANKS1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038865	23294	ANKS1A	http://www.ncbi.nlm.nih.gov/gene/?term=23294	ANKS1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038866	23301	EHBP1	http://www.ncbi.nlm.nih.gov/gene/?term=23301	"HPC12, NACSIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038867	23304	UBR2	http://www.ncbi.nlm.nih.gov/gene/?term=23304	"C6orf133, bA49A4.1, dJ242G1.1, dJ392M17.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038868	23304	UBR2	http://www.ncbi.nlm.nih.gov/gene/?term=23304	"C6orf133, bA49A4.1, dJ242G1.1, dJ392M17.3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038869	23315	SLC9A8	http://www.ncbi.nlm.nih.gov/gene/?term=23315	"NHE-8, NHE8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038870	23315	SLC9A8	http://www.ncbi.nlm.nih.gov/gene/?term=23315	"NHE-8, NHE8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038871	23328	SASH1	http://www.ncbi.nlm.nih.gov/gene/?term=23328	"SH3D6A, dJ323M4.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038872	23332	CLASP1	http://www.ncbi.nlm.nih.gov/gene/?term=23332	MAST1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038873	23332	CLASP1	http://www.ncbi.nlm.nih.gov/gene/?term=23332	MAST1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038874	23339	VPS39	http://www.ncbi.nlm.nih.gov/gene/?term=23339	"TLP, VAM6, hVam6p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038875	23345	SYNE1	http://www.ncbi.nlm.nih.gov/gene/?term=23345	"8B, ARCA1, C6orf98, CPG2, EDMD4, KASH1, MYNE1, Nesp1, SCAR8, dJ45H2.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038876	23352	UBR4	http://www.ncbi.nlm.nih.gov/gene/?term=23352	"RBAF600, ZUBR1, p600"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038877	23362	PSD3	http://www.ncbi.nlm.nih.gov/gene/?term=23362	"EFA6D, EFA6R, HCA67"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038878	23362	PSD3	http://www.ncbi.nlm.nih.gov/gene/?term=23362	"EFA6D, EFA6R, HCA67"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038879	23369	PUM2	http://www.ncbi.nlm.nih.gov/gene/?term=23369	"PUMH2, PUML2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038880	23386	NUDCD3	http://www.ncbi.nlm.nih.gov/gene/?term=23386	NudCL	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038881	23386	NUDCD3	http://www.ncbi.nlm.nih.gov/gene/?term=23386	NudCL	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038882	23387	SIK3	http://www.ncbi.nlm.nih.gov/gene/?term=23387	"L19, QSK, SIK-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038883	23389	MED13L	http://www.ncbi.nlm.nih.gov/gene/?term=23389	"MRFACD, PROSIT240, THRAP2, TRAP240L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038884	23389	MED13L	http://www.ncbi.nlm.nih.gov/gene/?term=23389	"MRFACD, PROSIT240, THRAP2, TRAP240L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038885	23394	ADNP	http://www.ncbi.nlm.nih.gov/gene/?term=23394	"ADNP1, HVDAS, MRD28"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038886	23394	ADNP	http://www.ncbi.nlm.nih.gov/gene/?term=23394	"ADNP1, HVDAS, MRD28"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038887	23403	FBXO46	http://www.ncbi.nlm.nih.gov/gene/?term=23403	"20D7-FC4, FBXO34L, Fbx46"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038888	23406	COTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23406	CLP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038889	23406	COTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23406	CLP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038890	23431	AP4E1	http://www.ncbi.nlm.nih.gov/gene/?term=23431	"CPSQ4, SPG51, STUT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038891	23438	HARS2	http://www.ncbi.nlm.nih.gov/gene/?term=23438	"HARSL, HARSR, HO3, PRLTS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038892	23446	SLC44A1	http://www.ncbi.nlm.nih.gov/gene/?term=23446	"CD92, CDW92, CHTL1, CTL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038893	23446	SLC44A1	http://www.ncbi.nlm.nih.gov/gene/?term=23446	"CD92, CDW92, CHTL1, CTL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038894	23468	CBX5	http://www.ncbi.nlm.nih.gov/gene/?term=23468	"HEL25, HP1, HP1A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038895	23468	CBX5	http://www.ncbi.nlm.nih.gov/gene/?term=23468	"HEL25, HP1, HP1A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038896	23473	CAPN7	http://www.ncbi.nlm.nih.gov/gene/?term=23473	"CALPAIN7, PALBH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038897	23473	CAPN7	http://www.ncbi.nlm.nih.gov/gene/?term=23473	"CALPAIN7, PALBH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038898	23478	SEC11A	http://www.ncbi.nlm.nih.gov/gene/?term=23478	"1810012E07Rik, SEC11L1, SPC18, SPCS4A, sid2895"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038899	23484	LEPROTL1	http://www.ncbi.nlm.nih.gov/gene/?term=23484	"HSPC112, Vps55, my047"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038900	23499	MACF1	http://www.ncbi.nlm.nih.gov/gene/?term=23499	"ABP620, ACF7, MACF, OFC4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038901	23499	MACF1	http://www.ncbi.nlm.nih.gov/gene/?term=23499	"ABP620, ACF7, MACF, OFC4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038902	23515	MORC3	http://www.ncbi.nlm.nih.gov/gene/?term=23515	"NXP2, ZCW5, ZCWCC3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038903	23515	MORC3	http://www.ncbi.nlm.nih.gov/gene/?term=23515	"NXP2, ZCW5, ZCWCC3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038904	23517	SKIV2L2	http://www.ncbi.nlm.nih.gov/gene/?term=23517	"Dob1, KIAA0052, Mtr4, fSAP118"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038905	23518	R3HDM1	http://www.ncbi.nlm.nih.gov/gene/?term=23518	R3HDM	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038906	23518	R3HDM1	http://www.ncbi.nlm.nih.gov/gene/?term=23518	R3HDM	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038907	23522	KAT6B	http://www.ncbi.nlm.nih.gov/gene/?term=23522	"GTPTS, MORF, MOZ2, MYST4, ZC2HC6B, qkf, querkopf"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038908	23522	KAT6B	http://www.ncbi.nlm.nih.gov/gene/?term=23522	"GTPTS, MORF, MOZ2, MYST4, ZC2HC6B, qkf, querkopf"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038909	23524	SRRM2	http://www.ncbi.nlm.nih.gov/gene/?term=23524	"300-KD, CWF21, Cwc21, HSPC075, SRL300, SRm300"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038910	23527	ACAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23527	"CENTB2, CNT-B2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038911	23527	ACAP2	http://www.ncbi.nlm.nih.gov/gene/?term=23527	"CENTB2, CNT-B2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038912	23530	NNT	http://www.ncbi.nlm.nih.gov/gene/?term=23530	GCCD4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038913	23530	NNT	http://www.ncbi.nlm.nih.gov/gene/?term=23530	GCCD4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038914	23543	RBFOX2	http://www.ncbi.nlm.nih.gov/gene/?term=23543	"FOX2, Fox-2, HNRBP2, HRNBP2, RBM9, RTA, dJ106I20.3, fxh"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038915	23543	RBFOX2	http://www.ncbi.nlm.nih.gov/gene/?term=23543	"FOX2, Fox-2, HNRBP2, HRNBP2, RBM9, RTA, dJ106I20.3, fxh"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038916	23576	DDAH1	http://www.ncbi.nlm.nih.gov/gene/?term=23576	"DDAH, DDAH-1, DDAHI, HEL-S-16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038917	23576	DDAH1	http://www.ncbi.nlm.nih.gov/gene/?term=23576	"DDAH, DDAH-1, DDAHI, HEL-S-16"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038918	23593	HEBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23593	"C6ORF34B, C6orf34, PP23, SOUL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038919	23597	ACOT9	http://www.ncbi.nlm.nih.gov/gene/?term=23597	"ACATE2, CGI-16, MT-ACT48, MTACT48"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038920	23597	ACOT9	http://www.ncbi.nlm.nih.gov/gene/?term=23597	"ACATE2, CGI-16, MT-ACT48, MTACT48"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038921	23608	MKRN1	http://www.ncbi.nlm.nih.gov/gene/?term=23608	RNF61	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038922	23613	ZMYND8	http://www.ncbi.nlm.nih.gov/gene/?term=23613	"PRKCBP1, PRO2893, RACK7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038923	23613	ZMYND8	http://www.ncbi.nlm.nih.gov/gene/?term=23613	"PRKCBP1, PRO2893, RACK7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038924	23633	KPNA6	http://www.ncbi.nlm.nih.gov/gene/?term=23633	"IPOA7, KPNA7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038925	23633	KPNA6	http://www.ncbi.nlm.nih.gov/gene/?term=23633	"IPOA7, KPNA7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038926	23643	LY96	http://www.ncbi.nlm.nih.gov/gene/?term=23643	"ESOP-1, MD-2, MD2, ly-96"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038927	23643	LY96	http://www.ncbi.nlm.nih.gov/gene/?term=23643	"ESOP-1, MD-2, MD2, ly-96"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038928	23648	SSBP3	http://www.ncbi.nlm.nih.gov/gene/?term=23648	"CSDP, SSDP, SSDP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038929	23648	SSBP3	http://www.ncbi.nlm.nih.gov/gene/?term=23648	"CSDP, SSDP, SSDP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038930	23657	SLC7A11	http://www.ncbi.nlm.nih.gov/gene/?term=23657	"CCBR1, xCT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038931	23657	SLC7A11	http://www.ncbi.nlm.nih.gov/gene/?term=23657	"CCBR1, xCT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038932	23673	STX12	http://www.ncbi.nlm.nih.gov/gene/?term=23673	"STX13, STX14"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038933	23683	PRKD3	http://www.ncbi.nlm.nih.gov/gene/?term=23683	"EPK2, PKC-NU, PKD3, PRKCN, nPKC-NU"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038934	23705	CADM1	http://www.ncbi.nlm.nih.gov/gene/?term=23705	"BL2, IGSF4, IGSF4A, NECL2, Necl-2, RA175, ST17, SYNCAM, TSLC1, sTSLC-1, sgIGSF, synCAM1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038935	23731	TMEM245	http://www.ncbi.nlm.nih.gov/gene/?term=23731	"C9orf5, CG-2, CG2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038936	23731	TMEM245	http://www.ncbi.nlm.nih.gov/gene/?term=23731	"C9orf5, CG-2, CG2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038937	23762	OSBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23762	"HLM, ORP-4, ORP4, OSBPL1, OSBPL4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038938	23762	OSBP2	http://www.ncbi.nlm.nih.gov/gene/?term=23762	"HLM, ORP-4, ORP4, OSBPL1, OSBPL4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038939	23780	APOL2	http://www.ncbi.nlm.nih.gov/gene/?term=23780	"APOL-II, APOL3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038940	23780	APOL2	http://www.ncbi.nlm.nih.gov/gene/?term=23780	"APOL-II, APOL3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038941	23786	BCL2L13	http://www.ncbi.nlm.nih.gov/gene/?term=23786	"BCL-RAMBO, Bcl2-L-13, MIL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038942	23786	BCL2L13	http://www.ncbi.nlm.nih.gov/gene/?term=23786	"BCL-RAMBO, Bcl2-L-13, MIL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038943	23788	MTCH2	http://www.ncbi.nlm.nih.gov/gene/?term=23788	"HSPC032, MIMP, SLC25A50"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038944	23788	MTCH2	http://www.ncbi.nlm.nih.gov/gene/?term=23788	"HSPC032, MIMP, SLC25A50"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038945	238	ALK	http://www.ncbi.nlm.nih.gov/gene/?term=238	"CD246, NBLST3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038946	238	ALK	http://www.ncbi.nlm.nih.gov/gene/?term=238	"CD246, NBLST3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038947	240	ALOX5	http://www.ncbi.nlm.nih.gov/gene/?term=240	"5-LO, 5-LOX, 5LPG, LOG5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038948	240	ALOX5	http://www.ncbi.nlm.nih.gov/gene/?term=240	"5-LO, 5-LOX, 5LPG, LOG5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038949	249	ALPL	http://www.ncbi.nlm.nih.gov/gene/?term=249	"AP-TNAP, APTNAP, HOPS, TNAP, TNSALP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038950	249	ALPL	http://www.ncbi.nlm.nih.gov/gene/?term=249	"AP-TNAP, APTNAP, HOPS, TNAP, TNSALP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038951	2495	FTH1	http://www.ncbi.nlm.nih.gov/gene/?term=2495	"FHC, FTH, FTHL6, HFE5, PIG15, PLIF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038952	2495	FTH1	http://www.ncbi.nlm.nih.gov/gene/?term=2495	"FHC, FTH, FTHL6, HFE5, PIG15, PLIF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038953	25	ABL1	http://www.ncbi.nlm.nih.gov/gene/?term=25	"ABL, CHDSKM, JTK7, bcr/abl, c-ABL, c-ABL1, p150, v-abl"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038954	25	ABL1	http://www.ncbi.nlm.nih.gov/gene/?term=25	"ABL, CHDSKM, JTK7, bcr/abl, c-ABL, c-ABL1, p150, v-abl"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038955	2534	FYN	http://www.ncbi.nlm.nih.gov/gene/?term=2534	"SLK, SYN, p59-FYN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038956	253430	IPMK	http://www.ncbi.nlm.nih.gov/gene/?term=253430		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038957	253559	CADM2	http://www.ncbi.nlm.nih.gov/gene/?term=253559	"IGSF4D, NECL3, Necl-3, SynCAM 2, synCAM2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038958	253769	WDR27	http://www.ncbi.nlm.nih.gov/gene/?term=253769		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038959	253769	WDR27	http://www.ncbi.nlm.nih.gov/gene/?term=253769		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038960	253782	CERS6	http://www.ncbi.nlm.nih.gov/gene/?term=253782	"CERS5, LASS6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038961	253827	MSRB3	http://www.ncbi.nlm.nih.gov/gene/?term=253827	DFNB74	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038962	253827	MSRB3	http://www.ncbi.nlm.nih.gov/gene/?term=253827	DFNB74	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038963	253959	RALGAPA1	http://www.ncbi.nlm.nih.gov/gene/?term=253959	"GARNL1, GRIPE, RalGAPalpha1, TULIP1, p240"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038964	253980	KCTD13	http://www.ncbi.nlm.nih.gov/gene/?term=253980	"BACURD1, FKSG86, PDIP1, POLDIP1, hBACURD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038965	253980	KCTD13	http://www.ncbi.nlm.nih.gov/gene/?term=253980	"BACURD1, FKSG86, PDIP1, POLDIP1, hBACURD1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038966	255967	PAN3	http://www.ncbi.nlm.nih.gov/gene/?term=255967		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038967	2568	GABRP	http://www.ncbi.nlm.nih.gov/gene/?term=2568		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038968	2568	GABRP	http://www.ncbi.nlm.nih.gov/gene/?term=2568		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038969	256949	KANK3	http://www.ncbi.nlm.nih.gov/gene/?term=256949	ANKRD47	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038970	257397	TAB3	http://www.ncbi.nlm.nih.gov/gene/?term=257397	"MAP3K7IP3, NAP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038971	25771	TBC1D22A	http://www.ncbi.nlm.nih.gov/gene/?term=25771	"C22orf4, HSC79E021"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038972	25771	TBC1D22A	http://www.ncbi.nlm.nih.gov/gene/?term=25771	"C22orf4, HSC79E021"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038973	25809	TTLL1	http://www.ncbi.nlm.nih.gov/gene/?term=25809	"C22orf7, HS323M22B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038974	25809	TTLL1	http://www.ncbi.nlm.nih.gov/gene/?term=25809	"C22orf7, HS323M22B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038975	25814	ATXN10	http://www.ncbi.nlm.nih.gov/gene/?term=25814	"E46L, HUMEEP, SCA10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038976	25814	ATXN10	http://www.ncbi.nlm.nih.gov/gene/?term=25814	"E46L, HUMEEP, SCA10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038977	25816	TNFAIP8	http://www.ncbi.nlm.nih.gov/gene/?term=25816	"GG2-1, MDC-3.13, NDED, SCC-S2, SCCS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038978	25816	TNFAIP8	http://www.ncbi.nlm.nih.gov/gene/?term=25816	"GG2-1, MDC-3.13, NDED, SCC-S2, SCCS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038979	25820	ARIH1	http://www.ncbi.nlm.nih.gov/gene/?term=25820	"ARI, HARI, HHARI, UBCH7BP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038980	25825	BACE2	http://www.ncbi.nlm.nih.gov/gene/?term=25825	"AEPLC, ALP56, ASP1, ASP21, BAE2, CDA13, CEAP1, DRAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038981	25825	BACE2	http://www.ncbi.nlm.nih.gov/gene/?term=25825	"AEPLC, ALP56, ASP1, ASP21, BAE2, CDA13, CEAP1, DRAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038982	25829	TMEM184B	http://www.ncbi.nlm.nih.gov/gene/?term=25829	"C22orf5, FM08, HS5O6A, HSPC256"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038983	25829	TMEM184B	http://www.ncbi.nlm.nih.gov/gene/?term=25829	"C22orf5, FM08, HS5O6A, HSPC256"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038984	25831	HECTD1	http://www.ncbi.nlm.nih.gov/gene/?term=25831	EULIR	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038985	25831	HECTD1	http://www.ncbi.nlm.nih.gov/gene/?term=25831	EULIR	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038986	25836	NIPBL	http://www.ncbi.nlm.nih.gov/gene/?term=25836	"CDLS, CDLS1, IDN3, IDN3-B, Scc2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038987	2585	GALK2	http://www.ncbi.nlm.nih.gov/gene/?term=2585	GK2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038988	25862	USP49	http://www.ncbi.nlm.nih.gov/gene/?term=25862		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038989	25884	CHRDL2	http://www.ncbi.nlm.nih.gov/gene/?term=25884	"BNF1, CHL2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038990	25884	CHRDL2	http://www.ncbi.nlm.nih.gov/gene/?term=25884	"BNF1, CHL2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038991	25885	POLR1A	http://www.ncbi.nlm.nih.gov/gene/?term=25885	"A190, RPA1, RPO14, AFDCIN, RPA194, RPO1-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038992	25885	POLR1A	http://www.ncbi.nlm.nih.gov/gene/?term=25885	"A190, RPA1, RPO14, AFDCIN, RPA194, RPO1-4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038993	25896	INTS7	http://www.ncbi.nlm.nih.gov/gene/?term=25896	"C1orf73, INT7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038994	25896	INTS7	http://www.ncbi.nlm.nih.gov/gene/?term=25896	"C1orf73, INT7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038995	2590	GALNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2590	GalNAc-T2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038996	2590	GALNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2590	GalNAc-T2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038997	25911	DPCD	http://www.ncbi.nlm.nih.gov/gene/?term=25911		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00038998	25911	DPCD	http://www.ncbi.nlm.nih.gov/gene/?term=25911		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00038999	25920	NELFB	http://www.ncbi.nlm.nih.gov/gene/?term=25920	"COBRA1, NELF-B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039000	25920	NELFB	http://www.ncbi.nlm.nih.gov/gene/?term=25920	"COBRA1, NELF-B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039001	259230	SGMS1	http://www.ncbi.nlm.nih.gov/gene/?term=259230	"MOB, MOB1, SMS1, TMEM23, hmob33"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039002	259230	SGMS1	http://www.ncbi.nlm.nih.gov/gene/?term=259230	"MOB, MOB1, SMS1, TMEM23, hmob33"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039003	25925	ZNF521	http://www.ncbi.nlm.nih.gov/gene/?term=25925	"EHZF, Evi3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039004	25925	ZNF521	http://www.ncbi.nlm.nih.gov/gene/?term=25925	"EHZF, Evi3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039005	259266	ASPM	http://www.ncbi.nlm.nih.gov/gene/?term=259266	"ASP, Calmbp1, MCPH5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039006	25929	GEMIN5	http://www.ncbi.nlm.nih.gov/gene/?term=25929	GEMIN-5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039007	25929	GEMIN5	http://www.ncbi.nlm.nih.gov/gene/?term=25929	GEMIN-5	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039008	25932	CLIC4	http://www.ncbi.nlm.nih.gov/gene/?term=25932	"CLIC4L, H1, MTCLIC, huH1, p64H1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039009	25932	CLIC4	http://www.ncbi.nlm.nih.gov/gene/?term=25932	"CLIC4L, H1, MTCLIC, huH1, p64H1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039010	25936	NSL1	http://www.ncbi.nlm.nih.gov/gene/?term=25936	"C1orf48, DC8, MIS14"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039011	25936	NSL1	http://www.ncbi.nlm.nih.gov/gene/?term=25936	"C1orf48, DC8, MIS14"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039012	25948	KBTBD2	http://www.ncbi.nlm.nih.gov/gene/?term=25948	BKLHD1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039013	25948	KBTBD2	http://www.ncbi.nlm.nih.gov/gene/?term=25948	BKLHD1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039014	25959	KANK2	http://www.ncbi.nlm.nih.gov/gene/?term=25959	"ANKRD25, MXRA3, PPKWH, SIP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039015	25959	KANK2	http://www.ncbi.nlm.nih.gov/gene/?term=25959	"ANKRD25, MXRA3, PPKWH, SIP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039016	25961	NUDT13	http://www.ncbi.nlm.nih.gov/gene/?term=25961		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039017	25961	NUDT13	http://www.ncbi.nlm.nih.gov/gene/?term=25961		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039018	25966	C2CD2	http://www.ncbi.nlm.nih.gov/gene/?term=25966	"C21orf25, C21orf258, TMEM24L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039019	25966	C2CD2	http://www.ncbi.nlm.nih.gov/gene/?term=25966	"C21orf25, C21orf258, TMEM24L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039020	25984	KRT23	http://www.ncbi.nlm.nih.gov/gene/?term=25984	"CK23, HAIK1, K23"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039021	25984	KRT23	http://www.ncbi.nlm.nih.gov/gene/?term=25984	"CK23, HAIK1, K23"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039022	25999	CLIP3	http://www.ncbi.nlm.nih.gov/gene/?term=25999	"CLIPR-59, CLIPR59, RSNL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039023	25999	CLIP3	http://www.ncbi.nlm.nih.gov/gene/?term=25999	"CLIPR-59, CLIPR59, RSNL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039024	26002	MOXD1	http://www.ncbi.nlm.nih.gov/gene/?term=26002	"MOX, PRO5780, dJ248E1.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039025	26003	GORASP2	http://www.ncbi.nlm.nih.gov/gene/?term=26003	"GOLPH6, GRASP55, GRS2, p59"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039026	26003	GORASP2	http://www.ncbi.nlm.nih.gov/gene/?term=26003	"GOLPH6, GRASP55, GRS2, p59"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039027	26005	C2CD3	http://www.ncbi.nlm.nih.gov/gene/?term=26005	OFD14	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039028	26010	SPATS2L	http://www.ncbi.nlm.nih.gov/gene/?term=26010	"DNAPTP6, SGNP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039029	26013	L3MBTL1	http://www.ncbi.nlm.nih.gov/gene/?term=26013	"H-L(3)MBT, L3MBTL, ZC2HC3, dJ138B7.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039030	26019	UPF2	http://www.ncbi.nlm.nih.gov/gene/?term=26019	"HUPF2, RENT2, smg-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039031	26019	UPF2	http://www.ncbi.nlm.nih.gov/gene/?term=26019	"HUPF2, RENT2, smg-3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039032	26031	OSBPL3	http://www.ncbi.nlm.nih.gov/gene/?term=26031	"ORP-3, ORP3, OSBP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039033	26031	OSBPL3	http://www.ncbi.nlm.nih.gov/gene/?term=26031	"ORP-3, ORP3, OSBP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039034	260425	MAGI3	http://www.ncbi.nlm.nih.gov/gene/?term=260425	"MAGI-3, dJ730K3.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039035	26047	CNTNAP2	http://www.ncbi.nlm.nih.gov/gene/?term=26047	"AUTS15, CASPR2, CDFE, NRXN4, PTHSL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039036	26047	CNTNAP2	http://www.ncbi.nlm.nih.gov/gene/?term=26047	"AUTS15, CASPR2, CDFE, NRXN4, PTHSL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039037	26053	AUTS2	http://www.ncbi.nlm.nih.gov/gene/?term=26053	"FBRSL2, MRD26"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039038	26053	AUTS2	http://www.ncbi.nlm.nih.gov/gene/?term=26053	"FBRSL2, MRD26"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039039	26054	SENP6	http://www.ncbi.nlm.nih.gov/gene/?term=26054	"SSP1, SUSP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039040	26057	ANKRD17	http://www.ncbi.nlm.nih.gov/gene/?term=26057	"GTAR, MASK2, NY-BR-16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039041	26057	ANKRD17	http://www.ncbi.nlm.nih.gov/gene/?term=26057	"GTAR, MASK2, NY-BR-16"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039042	26058	GIGYF2	http://www.ncbi.nlm.nih.gov/gene/?term=26058	"GYF2, PARK11, PERQ2, PERQ3, TNRC15"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039043	26058	GIGYF2	http://www.ncbi.nlm.nih.gov/gene/?term=26058	"GYF2, PARK11, PERQ2, PERQ3, TNRC15"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039044	26059	ERC2	http://www.ncbi.nlm.nih.gov/gene/?term=26059	"CAST, CAST1, ELKSL, SPBC110, Spc110"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039045	26059	ERC2	http://www.ncbi.nlm.nih.gov/gene/?term=26059	"CAST, CAST1, ELKSL, SPBC110, Spc110"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039046	26064	RAI14	http://www.ncbi.nlm.nih.gov/gene/?term=26064	"NORPEG, RAI13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039047	26065	LSM14A	http://www.ncbi.nlm.nih.gov/gene/?term=26065	"C19orf13, FAM61A, RAP55, RAP55A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039048	26065	LSM14A	http://www.ncbi.nlm.nih.gov/gene/?term=26065	"C19orf13, FAM61A, RAP55, RAP55A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039049	26091	HERC4	http://www.ncbi.nlm.nih.gov/gene/?term=26091		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039050	26091	HERC4	http://www.ncbi.nlm.nih.gov/gene/?term=26091		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039051	26133	TRPC4AP	http://www.ncbi.nlm.nih.gov/gene/?term=26133	"C20orf188, PPP1R158, TRRP4AP, TRUSS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039052	26137	ZBTB20	http://www.ncbi.nlm.nih.gov/gene/?term=26137	"DPZF, HOF, ODA-8S, PRIMS, ZNF288"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039053	26137	ZBTB20	http://www.ncbi.nlm.nih.gov/gene/?term=26137	"DPZF, HOF, ODA-8S, PRIMS, ZNF288"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039054	26146	TRAF3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=26146	"IFT54, MIP-T3, MIPT3, SLSN9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039055	26164	MTG2	http://www.ncbi.nlm.nih.gov/gene/?term=26164	"GTPBP5, ObgH1, dJ1005F21.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039056	26164	MTG2	http://www.ncbi.nlm.nih.gov/gene/?term=26164	"GTPBP5, ObgH1, dJ1005F21.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039057	26205	GMEB2	http://www.ncbi.nlm.nih.gov/gene/?term=26205	"GMEB-2, P79PIF, PIF79"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039058	26205	GMEB2	http://www.ncbi.nlm.nih.gov/gene/?term=26205	"GMEB-2, P79PIF, PIF79"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039059	26207	PITPNC1	http://www.ncbi.nlm.nih.gov/gene/?term=26207	"M-RDGB-beta, MRDGBbeta, RDGB-BETA, RDGBB, RDGBB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039060	26207	PITPNC1	http://www.ncbi.nlm.nih.gov/gene/?term=26207	"M-RDGB-beta, MRDGBbeta, RDGB-BETA, RDGBB, RDGBB1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039061	2621	GAS6	http://www.ncbi.nlm.nih.gov/gene/?term=2621	"AXLLG, AXSF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039062	2621	GAS6	http://www.ncbi.nlm.nih.gov/gene/?term=2621	"AXLLG, AXSF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039063	26229	B3GAT3	http://www.ncbi.nlm.nih.gov/gene/?term=26229	"GLCATI, JDSCD, glcUAT-I"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039064	26229	B3GAT3	http://www.ncbi.nlm.nih.gov/gene/?term=26229	"GLCATI, JDSCD, glcUAT-I"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039065	26235	FBXL4	http://www.ncbi.nlm.nih.gov/gene/?term=26235	"FBL4, FBL5, MTDPS13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039066	26256	CABYR	http://www.ncbi.nlm.nih.gov/gene/?term=26256	"CABYRac, CABYRc/d, CABYRe, CBP86, CT88, FSP-2, FSP2, CABYR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039067	26256	CABYR	http://www.ncbi.nlm.nih.gov/gene/?term=26256	"CABYRac, CABYRc/d, CABYRe, CBP86, CT88, FSP-2, FSP2, CABYR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039068	26259	FBXW8	http://www.ncbi.nlm.nih.gov/gene/?term=26259	"FBW6, FBW8, FBX29, FBXO29, FBXW6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039069	26259	FBXW8	http://www.ncbi.nlm.nih.gov/gene/?term=26259	"FBW6, FBW8, FBX29, FBXO29, FBXW6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039070	26268	FBXO9	http://www.ncbi.nlm.nih.gov/gene/?term=26268	"FBX9, NY-REN-57, VCIA1, dJ341E18.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039071	2627	GATA6	http://www.ncbi.nlm.nih.gov/gene/?term=2627		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039072	26275	HIBCH	http://www.ncbi.nlm.nih.gov/gene/?term=26275	HIBYLCOAH	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039073	26276	VPS33B	http://www.ncbi.nlm.nih.gov/gene/?term=26276		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039074	26276	VPS33B	http://www.ncbi.nlm.nih.gov/gene/?term=26276		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039075	26289	AK5	http://www.ncbi.nlm.nih.gov/gene/?term=26289	AK6	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039076	26289	AK5	http://www.ncbi.nlm.nih.gov/gene/?term=26289	AK6	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039077	26297	SERGEF	http://www.ncbi.nlm.nih.gov/gene/?term=26297	"DELGEF, Gnefr"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039078	26297	SERGEF	http://www.ncbi.nlm.nih.gov/gene/?term=26297	"DELGEF, Gnefr"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039079	26505	CNNM3	http://www.ncbi.nlm.nih.gov/gene/?term=26505	ACDP3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039080	26505	CNNM3	http://www.ncbi.nlm.nih.gov/gene/?term=26505	ACDP3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039081	2651	GCNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2651	"CCAT, CTRCT13C, GCNT5, IGNT, II, NACGT1, NAGCT1, ULG3, bA360O19.2, bA421M1.1, GCNT2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039082	2651	GCNT2	http://www.ncbi.nlm.nih.gov/gene/?term=2651	"CCAT, CTRCT13C, GCNT5, IGNT, II, NACGT1, NAGCT1, ULG3, bA360O19.2, bA421M1.1, GCNT2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039083	26512	INTS6	http://www.ncbi.nlm.nih.gov/gene/?term=26512	"DBI-1, DDX26, DDX26A, DICE1, HDB, INT6, Notchl2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039084	26524	LATS2	http://www.ncbi.nlm.nih.gov/gene/?term=26524	KPM	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039085	2661	GDF9	http://www.ncbi.nlm.nih.gov/gene/?term=2661		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039086	2661	GDF9	http://www.ncbi.nlm.nih.gov/gene/?term=2661		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039087	26610	ELP4	http://www.ncbi.nlm.nih.gov/gene/?term=26610	"AN, AN2, C11orf19, PAX6NEB, PAXNEB, dJ68P15A.1, hELP4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039088	26610	ELP4	http://www.ncbi.nlm.nih.gov/gene/?term=26610	"AN, AN2, C11orf19, PAX6NEB, PAXNEB, dJ68P15A.1, hELP4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039089	2669	GEM	http://www.ncbi.nlm.nih.gov/gene/?term=2669	KIR	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039090	2669	GEM	http://www.ncbi.nlm.nih.gov/gene/?term=2669	KIR	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039091	26750	RPS6KC1	http://www.ncbi.nlm.nih.gov/gene/?term=26750	"RPK118, RSKL1, S6K-delta-1, S6PKh1, humS6PKh1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039092	26750	RPS6KC1	http://www.ncbi.nlm.nih.gov/gene/?term=26750	"RPK118, RSKL1, S6K-delta-1, S6PKh1, humS6PKh1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039093	26751	SH3YL1	http://www.ncbi.nlm.nih.gov/gene/?term=26751	RAY	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039094	26751	SH3YL1	http://www.ncbi.nlm.nih.gov/gene/?term=26751	RAY	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039095	2683	B4GALT1	http://www.ncbi.nlm.nih.gov/gene/?term=2683	"B4GAL-T1, CDG2D, GGTB2, GT1, GTB, beta4Gal-T1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039096	26960	NBEA	http://www.ncbi.nlm.nih.gov/gene/?term=26960	"BCL8B, LYST2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039097	26984	SEC22A	http://www.ncbi.nlm.nih.gov/gene/?term=26984	SEC22L2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039098	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039099	26986	PABPC1	http://www.ncbi.nlm.nih.gov/gene/?term=26986	"PAB1, PABP, PABP1, PABPC2, PABPL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039100	27020	NPTN	http://www.ncbi.nlm.nih.gov/gene/?term=27020	"GP55, GP65, SDFR1, SDR1, np55, np65"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039101	27020	NPTN	http://www.ncbi.nlm.nih.gov/gene/?term=27020	"GP55, GP65, SDFR1, SDR1, np55, np65"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039102	27032	ATP2C1	http://www.ncbi.nlm.nih.gov/gene/?term=27032	"ATP2C1A, BCPM, HHD, PMR1, SPCA1, hSPCA1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039103	27044	SND1	http://www.ncbi.nlm.nih.gov/gene/?term=27044	"TDRD11, Tudor-SN, p100"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039104	27044	SND1	http://www.ncbi.nlm.nih.gov/gene/?term=27044	"TDRD11, Tudor-SN, p100"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039105	27067	STAU2	http://www.ncbi.nlm.nih.gov/gene/?term=27067	"39K2, 39K3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039106	27067	STAU2	http://www.ncbi.nlm.nih.gov/gene/?term=27067	"39K2, 39K3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039107	27068	PPA2	http://www.ncbi.nlm.nih.gov/gene/?term=27068	"HSPC124, SCFAI, SCFI, SID6-306"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039108	27068	PPA2	http://www.ncbi.nlm.nih.gov/gene/?term=27068	"HSPC124, SCFAI, SCFI, SID6-306"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039109	27086	FOXP1	http://www.ncbi.nlm.nih.gov/gene/?term=27086	"12CC4, HSPC215, MFH, QRF1, hFKH1B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039110	27086	FOXP1	http://www.ncbi.nlm.nih.gov/gene/?term=27086	"12CC4, HSPC215, MFH, QRF1, hFKH1B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039111	27132	CPNE7	http://www.ncbi.nlm.nih.gov/gene/?term=27132		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039112	27132	CPNE7	http://www.ncbi.nlm.nih.gov/gene/?term=27132		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039113	27136	MORC1	http://www.ncbi.nlm.nih.gov/gene/?term=27136	"CT33, MORC, ZCW6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039114	27183	VPS4A	http://www.ncbi.nlm.nih.gov/gene/?term=27183	"SKD1, SKD1A, SKD2, VPS4, VPS4-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039115	27183	VPS4A	http://www.ncbi.nlm.nih.gov/gene/?term=27183	"SKD1, SKD1A, SKD2, VPS4, VPS4-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039116	27230	SERP1	http://www.ncbi.nlm.nih.gov/gene/?term=27230	RAMP4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039117	27230	SERP1	http://www.ncbi.nlm.nih.gov/gene/?term=27230	RAMP4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039118	27246	RNF115	http://www.ncbi.nlm.nih.gov/gene/?term=27246	"BCA2, ZNF364"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039119	27246	RNF115	http://www.ncbi.nlm.nih.gov/gene/?term=27246	"BCA2, ZNF364"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039120	27250	PDCD4	http://www.ncbi.nlm.nih.gov/gene/?term=27250	H731	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039121	27303	RBMS3	http://www.ncbi.nlm.nih.gov/gene/?term=27303		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039122	27303	RBMS3	http://www.ncbi.nlm.nih.gov/gene/?term=27303		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039123	27327	TNRC6A	http://www.ncbi.nlm.nih.gov/gene/?term=27327	"CAGH26, GW1, GW182, TNRC6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039124	27332	ZNF638	http://www.ncbi.nlm.nih.gov/gene/?term=27332	"NP220, ZFML, Zfp638"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039125	27332	ZNF638	http://www.ncbi.nlm.nih.gov/gene/?term=27332	"NP220, ZFML, Zfp638"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039126	2734	GLG1	http://www.ncbi.nlm.nih.gov/gene/?term=2734	"CFR-1, ESL-1, MG-160, MG160"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039127	2734	GLG1	http://www.ncbi.nlm.nih.gov/gene/?term=2734	"CFR-1, ESL-1, MG-160, MG160"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039128	27347	STK39	http://www.ncbi.nlm.nih.gov/gene/?term=27347	"DCHT, PASK, SPAK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039129	27347	STK39	http://www.ncbi.nlm.nih.gov/gene/?term=27347	"DCHT, PASK, SPAK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039130	2736	GLI2	http://www.ncbi.nlm.nih.gov/gene/?term=2736	"CJS, HPE9, PHS2, THP1, THP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039131	2736	GLI2	http://www.ncbi.nlm.nih.gov/gene/?term=2736	"CJS, HPE9, PHS2, THP1, THP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039132	27436	EML4	http://www.ncbi.nlm.nih.gov/gene/?term=27436	"C2orf2, ELP120, EMAP-4, EMAPL4, ROPP120"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039133	27436	EML4	http://www.ncbi.nlm.nih.gov/gene/?term=27436	"C2orf2, ELP120, EMAP-4, EMAPL4, ROPP120"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039134	2744	GLS	http://www.ncbi.nlm.nih.gov/gene/?term=2744	"AAD20, GAC, GAM1, KGA, GLS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039135	2744	GLS	http://www.ncbi.nlm.nih.gov/gene/?term=2744	"AAD20, GAC, GAM1, KGA, GLS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039136	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039137	2760	GM2A	http://www.ncbi.nlm.nih.gov/gene/?term=2760	"GM2-AP, SAP-3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039138	2762	GMDS	http://www.ncbi.nlm.nih.gov/gene/?term=2762	"GMD, SDR3E1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039139	2762	GMDS	http://www.ncbi.nlm.nih.gov/gene/?term=2762	"GMD, SDR3E1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039140	2768	GNA12	http://www.ncbi.nlm.nih.gov/gene/?term=2768	"NNX3, RMP, gep"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039141	2768	GNA12	http://www.ncbi.nlm.nih.gov/gene/?term=2768	"NNX3, RMP, gep"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039142	2771	GNAI2	http://www.ncbi.nlm.nih.gov/gene/?term=2771	"GIPB, H_LUCA15.1, H_LUCA16.1, GNAI2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039143	2776	GNAQ	http://www.ncbi.nlm.nih.gov/gene/?term=2776	"CMC1, G-ALPHA-q, GAQ, SWS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039144	2782	GNB1	http://www.ncbi.nlm.nih.gov/gene/?term=2782	MRD42	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039145	2782	GNB1	http://www.ncbi.nlm.nih.gov/gene/?term=2782	MRD42	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039146	2820	GPD2	http://www.ncbi.nlm.nih.gov/gene/?term=2820	"GDH2, GPDM, mGPDH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039147	2820	GPD2	http://www.ncbi.nlm.nih.gov/gene/?term=2820	"GDH2, GPDM, mGPDH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039148	28232	SLCO3A1	http://www.ncbi.nlm.nih.gov/gene/?term=28232	"OATP-D, OATP-RP3, OATP3A1, OATPD, OATPRP3, SLC21A11"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039149	28232	SLCO3A1	http://www.ncbi.nlm.nih.gov/gene/?term=28232	"OATP-D, OATP-RP3, OATP3A1, OATPD, OATPRP3, SLC21A11"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039150	283450	HECTD4	http://www.ncbi.nlm.nih.gov/gene/?term=283450	"C12orf51, POTAGE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039151	283450	HECTD4	http://www.ncbi.nlm.nih.gov/gene/?term=283450	"C12orf51, POTAGE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039152	283459	GATC	http://www.ncbi.nlm.nih.gov/gene/?term=283459	15E1.2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039153	283459	GATC	http://www.ncbi.nlm.nih.gov/gene/?term=283459	15E1.2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039154	283635	FAM177A1	http://www.ncbi.nlm.nih.gov/gene/?term=283635	C14orf24	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039155	283635	FAM177A1	http://www.ncbi.nlm.nih.gov/gene/?term=283635	C14orf24	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039156	283807	FBXL22	http://www.ncbi.nlm.nih.gov/gene/?term=283807	Fbl22	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039157	283807	FBXL22	http://www.ncbi.nlm.nih.gov/gene/?term=283807	Fbl22	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039158	284001	CCDC57	http://www.ncbi.nlm.nih.gov/gene/?term=284001		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039159	284001	CCDC57	http://www.ncbi.nlm.nih.gov/gene/?term=284001		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039160	284004	HEXDC	http://www.ncbi.nlm.nih.gov/gene/?term=284004		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039161	284004	HEXDC	http://www.ncbi.nlm.nih.gov/gene/?term=284004		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039162	284119	CAVIN1	http://www.ncbi.nlm.nih.gov/gene/?term=284119	"CAVIN, CGL4, FKSG13, PTRF, cavin-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039163	284119	CAVIN1	http://www.ncbi.nlm.nih.gov/gene/?term=284119	"CAVIN, CGL4, FKSG13, PTRF, cavin-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039164	284273	ZADH2	http://www.ncbi.nlm.nih.gov/gene/?term=284273	PRG-3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039165	284521	OR2L13	http://www.ncbi.nlm.nih.gov/gene/?term=284521	OR2L14	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039166	284521	OR2L13	http://www.ncbi.nlm.nih.gov/gene/?term=284521	OR2L14	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039167	284618	RUSC1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=284618	C1orf104	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00039168	284618	RUSC1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=284618	C1orf104	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00039169	284996	RNF149	http://www.ncbi.nlm.nih.gov/gene/?term=284996	DNAPTP2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039170	284996	RNF149	http://www.ncbi.nlm.nih.gov/gene/?term=284996	DNAPTP2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039171	285	ANGPT2	http://www.ncbi.nlm.nih.gov/gene/?term=285	"AGPT2, ANG2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039172	285148	IAH1	http://www.ncbi.nlm.nih.gov/gene/?term=285148		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039173	285362	SUMF1	http://www.ncbi.nlm.nih.gov/gene/?term=285362	"AAPA3037, FGE, UNQ3037"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039174	285362	SUMF1	http://www.ncbi.nlm.nih.gov/gene/?term=285362	"AAPA3037, FGE, UNQ3037"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039175	285513	GPRIN3	http://www.ncbi.nlm.nih.gov/gene/?term=285513	GRIN3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039176	285943	HOXA-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=285943	HOXA3as	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00039177	285943	HOXA-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=285943	HOXA3as	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00039178	286053	NSMCE2	http://www.ncbi.nlm.nih.gov/gene/?term=286053	"C8orf36, MMS21, NSE2, ZMIZ7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039179	286053	NSMCE2	http://www.ncbi.nlm.nih.gov/gene/?term=286053	"C8orf36, MMS21, NSE2, ZMIZ7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039180	2869	GRK5	http://www.ncbi.nlm.nih.gov/gene/?term=2869	GPRK5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039181	2869	GRK5	http://www.ncbi.nlm.nih.gov/gene/?term=2869	GPRK5	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039182	287	ANK2	http://www.ncbi.nlm.nih.gov/gene/?term=287	"ANK-2, LQT4, brank-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039183	288	ANK3	http://www.ncbi.nlm.nih.gov/gene/?term=288	"ANKYRIN-G, MRT37"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039184	288	ANK3	http://www.ncbi.nlm.nih.gov/gene/?term=288	"ANKYRIN-G, MRT37"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039185	2887	GRB10	http://www.ncbi.nlm.nih.gov/gene/?term=2887	"GRB-IR, Grb-10, IRBP, MEG1, RSS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039186	2887	GRB10	http://www.ncbi.nlm.nih.gov/gene/?term=2887	"GRB-IR, Grb-10, IRBP, MEG1, RSS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039187	2889	RAPGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=2889	"C3G, GRF2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039188	2889	RAPGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=2889	"C3G, GRF2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039189	2892	GRIA3	http://www.ncbi.nlm.nih.gov/gene/?term=2892	"GLUR-C, GLUR-K3, GLUR3, GLURC, GluA3, MRX94"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039190	2892	GRIA3	http://www.ncbi.nlm.nih.gov/gene/?term=2892	"GLUR-C, GLUR-K3, GLUR3, GLURC, GluA3, MRX94"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039191	28955	DEXI	http://www.ncbi.nlm.nih.gov/gene/?term=28955	MYLE	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039192	28955	DEXI	http://www.ncbi.nlm.nih.gov/gene/?term=28955	MYLE	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039193	28957	MRPS28	http://www.ncbi.nlm.nih.gov/gene/?term=28957	"HSPC007, MRP-S28, MRP-S35, MRPS35"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039194	28969	BZW2	http://www.ncbi.nlm.nih.gov/gene/?term=28969	"HSPC028, MST017, MSTP017"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039195	28969	BZW2	http://www.ncbi.nlm.nih.gov/gene/?term=28969	"HSPC028, MST017, MSTP017"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039196	28971	AAMDC	http://www.ncbi.nlm.nih.gov/gene/?term=28971	"C11orf67, CK067, PTD015"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039197	28971	AAMDC	http://www.ncbi.nlm.nih.gov/gene/?term=28971	"C11orf67, CK067, PTD015"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039198	28977	MRPL42	http://www.ncbi.nlm.nih.gov/gene/?term=28977	"HSPC204, L31MT, L42MT, MRP-L31, MRP-L42, MRP-S32, MRPL31, MRPS32, PTD007, RPML31, S32MT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039199	28984	RGCC	http://www.ncbi.nlm.nih.gov/gene/?term=28984	"C13orf15, RGC-32, RGC32, bA157L14.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039200	28984	RGCC	http://www.ncbi.nlm.nih.gov/gene/?term=28984	"C13orf15, RGC-32, RGC32, bA157L14.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039201	28988	DBNL	http://www.ncbi.nlm.nih.gov/gene/?term=28988	"ABP1, HIP-55, HIP55, SH3P7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039202	28988	DBNL	http://www.ncbi.nlm.nih.gov/gene/?term=28988	"ABP1, HIP-55, HIP55, SH3P7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039203	28992	MACROD1	http://www.ncbi.nlm.nih.gov/gene/?term=28992	LRP16	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039204	28992	MACROD1	http://www.ncbi.nlm.nih.gov/gene/?term=28992	LRP16	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039205	28996	HIPK2	http://www.ncbi.nlm.nih.gov/gene/?term=28996	PRO0593	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039206	28996	HIPK2	http://www.ncbi.nlm.nih.gov/gene/?term=28996	PRO0593	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039207	29	ABR	http://www.ncbi.nlm.nih.gov/gene/?term=29	MDB	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039208	29	ABR	http://www.ncbi.nlm.nih.gov/gene/?term=29	MDB	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039209	29028	ATAD2	http://www.ncbi.nlm.nih.gov/gene/?term=29028	"ANCCA, CT137, PRO2000"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039210	29028	ATAD2	http://www.ncbi.nlm.nih.gov/gene/?term=29028	"ANCCA, CT137, PRO2000"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039211	29035	C16orf72	http://www.ncbi.nlm.nih.gov/gene/?term=29035	PRO0149	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039212	29035	C16orf72	http://www.ncbi.nlm.nih.gov/gene/?term=29035	PRO0149	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039213	29062	WDR91	http://www.ncbi.nlm.nih.gov/gene/?term=29062	"HSPC049, SORF-1, SORF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039214	29062	WDR91	http://www.ncbi.nlm.nih.gov/gene/?term=29062	"HSPC049, SORF-1, SORF1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039215	29072	SETD2	http://www.ncbi.nlm.nih.gov/gene/?term=29072	"HBP231, HIF-1, HIP-1, HSPC069, HYPB, KMT3A, LLS, SET2, p231HBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039216	29072	SETD2	http://www.ncbi.nlm.nih.gov/gene/?term=29072	"HBP231, HIF-1, HIP-1, HSPC069, HYPB, KMT3A, LLS, SET2, p231HBP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039217	2908	NR3C1	http://www.ncbi.nlm.nih.gov/gene/?term=2908	"GCCR, GCR, GCRST, GR, GRL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039218	2908	NR3C1	http://www.ncbi.nlm.nih.gov/gene/?term=2908	"GCCR, GCR, GCRST, GR, GRL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039219	29102	DROSHA	http://www.ncbi.nlm.nih.gov/gene/?term=29102	"ETOHI2, HSA242976, RANSE3L, RN3, RNASE3L, RNASEN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039220	29115	SAP30BP	http://www.ncbi.nlm.nih.gov/gene/?term=29115	"HCNGP, HTRG, HTRP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039221	29115	SAP30BP	http://www.ncbi.nlm.nih.gov/gene/?term=29115	"HCNGP, HTRG, HTRP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039222	29116	MYLIP	http://www.ncbi.nlm.nih.gov/gene/?term=29116	"IDOL, MIR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039223	29116	MYLIP	http://www.ncbi.nlm.nih.gov/gene/?term=29116	"IDOL, MIR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039224	29123	ANKRD11	http://www.ncbi.nlm.nih.gov/gene/?term=29123	"ANCO-1, ANCO1, LZ16, T13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039225	29123	ANKRD11	http://www.ncbi.nlm.nih.gov/gene/?term=29123	"ANCO-1, ANCO1, LZ16, T13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039226	2932	GSK3B	http://www.ncbi.nlm.nih.gov/gene/?term=2932		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039227	2932	GSK3B	http://www.ncbi.nlm.nih.gov/gene/?term=2932		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039228	2934	GSN	http://www.ncbi.nlm.nih.gov/gene/?term=2934	"ADF, AGEL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039229	2934	GSN	http://www.ncbi.nlm.nih.gov/gene/?term=2934	"ADF, AGEL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039230	2965	GTF2H1	http://www.ncbi.nlm.nih.gov/gene/?term=2965	"BTF2, P62, TFB1, TFIIH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039231	2965	GTF2H1	http://www.ncbi.nlm.nih.gov/gene/?term=2965	"BTF2, P62, TFB1, TFIIH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039232	2969	GTF2I	http://www.ncbi.nlm.nih.gov/gene/?term=2969	"WBS, DIWS, SPIN, IB291, BAP135, BTKAP1, TFII-I, WBSCR6, GTFII-I"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039233	2971	GTF3A	http://www.ncbi.nlm.nih.gov/gene/?term=2971	"AP2, TFIIIA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039234	2975	GTF3C1	http://www.ncbi.nlm.nih.gov/gene/?term=2975	"TFIIIC, TFIIIC220, TFIIICalpha"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039235	2975	GTF3C1	http://www.ncbi.nlm.nih.gov/gene/?term=2975	"TFIIIC, TFIIIC220, TFIIICalpha"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039236	29766	TMOD3	http://www.ncbi.nlm.nih.gov/gene/?term=29766	UTMOD	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039237	29766	TMOD3	http://www.ncbi.nlm.nih.gov/gene/?term=29766	UTMOD	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039238	2977	GUCY1A2	http://www.ncbi.nlm.nih.gov/gene/?term=2977	"GC-SA2, GUC1A2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039239	2978	GUCA1A	http://www.ncbi.nlm.nih.gov/gene/?term=2978	"C6orf131, COD3, CORD14, GCAP, GCAP1, GUCA, GUCA1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039240	2978	GUCA1A	http://www.ncbi.nlm.nih.gov/gene/?term=2978	"C6orf131, COD3, CORD14, GCAP, GCAP1, GUCA, GUCA1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039241	29780	PARVB	http://www.ncbi.nlm.nih.gov/gene/?term=29780	CGI-56	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039242	29780	PARVB	http://www.ncbi.nlm.nih.gov/gene/?term=29780	CGI-56	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039243	29789	OLA1	http://www.ncbi.nlm.nih.gov/gene/?term=29789	"DOC45, GBP45, GTBP9, GTPBP9, PTD004"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039244	29789	OLA1	http://www.ncbi.nlm.nih.gov/gene/?term=29789	"DOC45, GBP45, GTBP9, GTPBP9, PTD004"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039245	29801	ZDHHC8	http://www.ncbi.nlm.nih.gov/gene/?term=29801	"DHHC8, ZDHHCL1, ZNF378"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039246	29855	UBN1	http://www.ncbi.nlm.nih.gov/gene/?term=29855	"VT, VT4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039247	29855	UBN1	http://www.ncbi.nlm.nih.gov/gene/?term=29855	"VT, VT4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039248	29880	ALG5	http://www.ncbi.nlm.nih.gov/gene/?term=29880	bA421P11.2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039249	29880	ALG5	http://www.ncbi.nlm.nih.gov/gene/?term=29880	bA421P11.2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039250	29894	CPSF1	http://www.ncbi.nlm.nih.gov/gene/?term=29894	"CPSF160, HSU37012, P/cl.18"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039251	29894	CPSF1	http://www.ncbi.nlm.nih.gov/gene/?term=29894	"CPSF160, HSU37012, P/cl.18"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039252	29896	TRA2A	http://www.ncbi.nlm.nih.gov/gene/?term=29896	"AWMS1, HSU53209"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039253	29904	EEF2K	http://www.ncbi.nlm.nih.gov/gene/?term=29904	"HSU93850, eEF-2K"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039254	29906	ST8SIA5	http://www.ncbi.nlm.nih.gov/gene/?term=29906	"SIAT8-E, SIAT8E, ST8SiaV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039255	29956	CERS2	http://www.ncbi.nlm.nih.gov/gene/?term=29956	"L3, LASS2, SP260, TMSG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039256	29956	CERS2	http://www.ncbi.nlm.nih.gov/gene/?term=29956	"L3, LASS2, SP260, TMSG1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039257	29960	MRM2	http://www.ncbi.nlm.nih.gov/gene/?term=29960	"FJH1, FTSJ2, HEL97, RRMJ2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039258	29960	MRM2	http://www.ncbi.nlm.nih.gov/gene/?term=29960	"FJH1, FTSJ2, HEL97, RRMJ2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039259	29966	STRN3	http://www.ncbi.nlm.nih.gov/gene/?term=29966	"PPP2R6B, S/G2NA, SG2NA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039260	29980	DONSON	http://www.ncbi.nlm.nih.gov/gene/?term=29980	"B17, C21orf60, MIMIS, MISSLA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039261	29980	DONSON	http://www.ncbi.nlm.nih.gov/gene/?term=29980	"B17, C21orf60, MIMIS, MISSLA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039262	29990	PILRB	http://www.ncbi.nlm.nih.gov/gene/?term=29990	"FDFACT1, FDFACT2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039263	29990	PILRB	http://www.ncbi.nlm.nih.gov/gene/?term=29990	"FDFACT1, FDFACT2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039264	29992	PILRA	http://www.ncbi.nlm.nih.gov/gene/?term=29992	FDF03	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039265	29992	PILRA	http://www.ncbi.nlm.nih.gov/gene/?term=29992	FDF03	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039266	30	ACAA1	http://www.ncbi.nlm.nih.gov/gene/?term=30	"ACAA, PTHIO, THIO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039267	30001	ERO1A	http://www.ncbi.nlm.nih.gov/gene/?term=30001	"ERO1-L, ERO1-L-alpha, ERO1-alpha, ERO1L, ERO1LA, Ero1alpha"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039268	30001	ERO1A	http://www.ncbi.nlm.nih.gov/gene/?term=30001	"ERO1-L, ERO1-L-alpha, ERO1-alpha, ERO1L, ERO1LA, Ero1alpha"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039269	3017	HIST1H2BD	http://www.ncbi.nlm.nih.gov/gene/?term=3017	"H2B.1B, H2B/b, H2BFB, HIRIP2, dJ221C16.6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039270	302	ANXA2	http://www.ncbi.nlm.nih.gov/gene/?term=302	"ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2, LPC2D, P36, PAP-IV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039271	302	ANXA2	http://www.ncbi.nlm.nih.gov/gene/?term=302	"ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2, LPC2D, P36, PAP-IV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039272	3054	HCFC1	http://www.ncbi.nlm.nih.gov/gene/?term=3054	"CFF, HCF, HCF-1, HCF1, HFC1, MRX3, PPP1R89, VCAF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039273	3055	HCK	http://www.ncbi.nlm.nih.gov/gene/?term=3055	"JTK9, p59Hck, p61Hck"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039274	3055	HCK	http://www.ncbi.nlm.nih.gov/gene/?term=3055	"JTK9, p59Hck, p61Hck"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039275	3064	HTT	http://www.ncbi.nlm.nih.gov/gene/?term=3064	"HD, IT15, LOMARS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039276	3064	HTT	http://www.ncbi.nlm.nih.gov/gene/?term=3064	"HD, IT15, LOMARS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039277	3069	HDLBP	http://www.ncbi.nlm.nih.gov/gene/?term=3069	"HBP, PRO2900, VGL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039278	3069	HDLBP	http://www.ncbi.nlm.nih.gov/gene/?term=3069	"HBP, PRO2900, VGL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039279	3074	HEXB	http://www.ncbi.nlm.nih.gov/gene/?term=3074	"ENC-1AS, HEL-248, HEL-S-111"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039280	30811	HUNK	http://www.ncbi.nlm.nih.gov/gene/?term=30811		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039281	30811	HUNK	http://www.ncbi.nlm.nih.gov/gene/?term=30811		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039282	30833	NT5C	http://www.ncbi.nlm.nih.gov/gene/?term=30833	"DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039283	30833	NT5C	http://www.ncbi.nlm.nih.gov/gene/?term=30833	"DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039284	30844	EHD4	http://www.ncbi.nlm.nih.gov/gene/?term=30844	PAST4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039285	30844	EHD4	http://www.ncbi.nlm.nih.gov/gene/?term=30844	PAST4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039286	3092	HIP1	http://www.ncbi.nlm.nih.gov/gene/?term=3092	"HIP-I, ILWEQ, SHON, SHONbeta, SHONgamma"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039287	3092	HIP1	http://www.ncbi.nlm.nih.gov/gene/?term=3092	"HIP-I, ILWEQ, SHON, SHONbeta, SHONgamma"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039288	3093	UBE2K	http://www.ncbi.nlm.nih.gov/gene/?term=3093	"E2-25K, HIP2, HYPG, LIG, UBC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039289	3093	UBE2K	http://www.ncbi.nlm.nih.gov/gene/?term=3093	"E2-25K, HIP2, HYPG, LIG, UBC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039290	3096	HIVEP1	http://www.ncbi.nlm.nih.gov/gene/?term=3096	"CIRIP, CRYBP1, GAAP, MBP-1, PRDII-BF1, Schnurri-1, ZAS1, ZNF40, ZNF40A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039291	3096	HIVEP1	http://www.ncbi.nlm.nih.gov/gene/?term=3096	"CIRIP, CRYBP1, GAAP, MBP-1, PRDII-BF1, Schnurri-1, ZAS1, ZNF40, ZNF40A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039292	31	ACACA	http://www.ncbi.nlm.nih.gov/gene/?term=31	"ACC, ACAC, ACC1, ACCA, ACACAD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039293	310	ANXA7	http://www.ncbi.nlm.nih.gov/gene/?term=310	"ANX7, SNX, SYNEXIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039294	3104	ZBTB48	http://www.ncbi.nlm.nih.gov/gene/?term=3104	"HKR3, TZAP, ZNF855, pp9964"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039295	3104	ZBTB48	http://www.ncbi.nlm.nih.gov/gene/?term=3104	"HKR3, TZAP, ZNF855, pp9964"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039296	317648	NOP14-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=317648	"C4orf10, RES4-24"	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00039297	317648	NOP14-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=317648	"C4orf10, RES4-24"	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00039298	3183	HNRNPC	http://www.ncbi.nlm.nih.gov/gene/?term=3183	"C1, C2, HNRNP, HNRPC, SNRPC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039299	3184	HNRNPD	http://www.ncbi.nlm.nih.gov/gene/?term=3184	"AUF1, AUF1A, HNRPD, P37, hnRNPD0"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039300	3185	HNRNPF	http://www.ncbi.nlm.nih.gov/gene/?term=3185	"HNRPF, OK/SW-cl.23, mcs94-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039301	3185	HNRNPF	http://www.ncbi.nlm.nih.gov/gene/?term=3185	"HNRPF, OK/SW-cl.23, mcs94-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039302	3213	HOXB3	http://www.ncbi.nlm.nih.gov/gene/?term=3213	"HOX2, HOX2G, Hox-2.7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039303	3213	HOXB3	http://www.ncbi.nlm.nih.gov/gene/?term=3213	"HOX2, HOX2G, Hox-2.7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039304	3216	HOXB6	http://www.ncbi.nlm.nih.gov/gene/?term=3216	"HOX2, HOX2B, HU-2, Hox-2.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039305	3216	HOXB6	http://www.ncbi.nlm.nih.gov/gene/?term=3216	"HOX2, HOX2B, HU-2, Hox-2.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039306	323	APBB2	http://www.ncbi.nlm.nih.gov/gene/?term=323	"FE65L, FE65L1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039307	323	APBB2	http://www.ncbi.nlm.nih.gov/gene/?term=323	"FE65L, FE65L1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039308	3241	HPCAL1	http://www.ncbi.nlm.nih.gov/gene/?term=3241	"BDR1, HLP2, VILIP-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039309	3241	HPCAL1	http://www.ncbi.nlm.nih.gov/gene/?term=3241	"BDR1, HLP2, VILIP-3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039310	3291	HSD11B2	http://www.ncbi.nlm.nih.gov/gene/?term=3291	"AME, AME1, HSD11K, HSD2, SDR9C3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039311	3291	HSD11B2	http://www.ncbi.nlm.nih.gov/gene/?term=3291	"AME, AME1, HSD11K, HSD2, SDR9C3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039312	3339	HSPG2	http://www.ncbi.nlm.nih.gov/gene/?term=3339	"HSPG, PLC, PRCAN, SJA, SJS, SJS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039313	3339	HSPG2	http://www.ncbi.nlm.nih.gov/gene/?term=3339	"HSPG, PLC, PRCAN, SJA, SJS, SJS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039314	334	APLP2	http://www.ncbi.nlm.nih.gov/gene/?term=334	"APLP-2, APPH, APPL2, CDEBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039315	3340	NDST1	http://www.ncbi.nlm.nih.gov/gene/?term=3340	"HSST, MRT46, NST1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039316	3371	TNC	http://www.ncbi.nlm.nih.gov/gene/?term=3371	"150-225, DFNA56, GMEM, GP, HXB, JI, TN, TN-C"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039317	337867	UBAC2	http://www.ncbi.nlm.nih.gov/gene/?term=337867	PHGDHL1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039318	337867	UBAC2	http://www.ncbi.nlm.nih.gov/gene/?term=337867	PHGDHL1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039319	339487	ZBTB8OS	http://www.ncbi.nlm.nih.gov/gene/?term=339487	"ARCH, ARCH2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039320	3418	IDH2	http://www.ncbi.nlm.nih.gov/gene/?term=3418	"D2HGA2, ICD-M, IDH, IDHM, IDP, IDPM, mNADP-IDH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039321	344148	NCKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=344148	"ERIH1, ERIH2, NAP5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039322	3455	IFNAR2	http://www.ncbi.nlm.nih.gov/gene/?term=3455	"IFN-R, IFN-alpha-REC, IFNABR, IFNARB, IMD45"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039323	346389	MACC1	http://www.ncbi.nlm.nih.gov/gene/?term=346389	"7A5, SH3BP4L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039324	3480	IGF1R	http://www.ncbi.nlm.nih.gov/gene/?term=3480	"CD221, IGFIR, IGFR, JTK13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039325	3480	IGF1R	http://www.ncbi.nlm.nih.gov/gene/?term=3480	"CD221, IGFIR, IGFR, JTK13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039326	3482	IGF2R	http://www.ncbi.nlm.nih.gov/gene/?term=3482	"CD222, CI-M6PR, CIMPR, M6P-R, M6P/IGF2R, MPR 300, MPR1, MPR300, MPRI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039327	3482	IGF2R	http://www.ncbi.nlm.nih.gov/gene/?term=3482	"CD222, CI-M6PR, CIMPR, M6P-R, M6P/IGF2R, MPR 300, MPR1, MPR300, MPRI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039328	3487	IGFBP4	http://www.ncbi.nlm.nih.gov/gene/?term=3487	"BP-4, HT29-IGFBP, IBP4, IGFBP-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039329	3487	IGFBP4	http://www.ncbi.nlm.nih.gov/gene/?term=3487	"BP-4, HT29-IGFBP, IBP4, IGFBP-4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039330	348793	WDR53	http://www.ncbi.nlm.nih.gov/gene/?term=348793		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039331	3490	IGFBP7	http://www.ncbi.nlm.nih.gov/gene/?term=3490	"AGM, FSTL2, IBP-7, IGFBP-7, IGFBP-7v, IGFBPRP1, MAC25, PSF, RAMSVPS, TAF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039332	3490	IGFBP7	http://www.ncbi.nlm.nih.gov/gene/?term=3490	"AGM, FSTL2, IBP-7, IGFBP-7, IGFBP-7v, IGFBPRP1, MAC25, PSF, RAMSVPS, TAF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039333	351	APP	http://www.ncbi.nlm.nih.gov/gene/?term=351	"AAA, ABETA, ABPP, AD1I, CTFgamma, CVAP, PN-II, PN2, preA4, APP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039334	3516	RBPJ	http://www.ncbi.nlm.nih.gov/gene/?term=3516	"AOS3, CBF1, IGKJRB, IGKJRB1, KBF2, RBP-JK, RBPSUH, SUH, csl, RBPJ"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039335	3603	IL16	http://www.ncbi.nlm.nih.gov/gene/?term=3603	"LCF, NIL16, PRIL16, prIL-16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039336	3603	IL16	http://www.ncbi.nlm.nih.gov/gene/?term=3603	"LCF, NIL16, PRIL16, prIL-16"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039337	3606	IL18	http://www.ncbi.nlm.nih.gov/gene/?term=3606	"IGIF, IL-18, IL-1g, IL1F4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039338	3606	IL18	http://www.ncbi.nlm.nih.gov/gene/?term=3606	"IGIF, IL-18, IL-1g, IL1F4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039339	3607	FOXK2	http://www.ncbi.nlm.nih.gov/gene/?term=3607	"ILF, ILF-1, ILF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039340	3607	FOXK2	http://www.ncbi.nlm.nih.gov/gene/?term=3607	"ILF, ILF-1, ILF1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039341	3613	IMPA2	http://www.ncbi.nlm.nih.gov/gene/?term=3613		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039342	3613	IMPA2	http://www.ncbi.nlm.nih.gov/gene/?term=3613		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039343	3632	INPP5A	http://www.ncbi.nlm.nih.gov/gene/?term=3632	5PTASE	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039344	3632	INPP5A	http://www.ncbi.nlm.nih.gov/gene/?term=3632	5PTASE	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039345	3643	INSR	http://www.ncbi.nlm.nih.gov/gene/?term=3643	"CD220, HHF5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039346	3643	INSR	http://www.ncbi.nlm.nih.gov/gene/?term=3643	"CD220, HHF5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039347	3646	EIF3E	http://www.ncbi.nlm.nih.gov/gene/?term=3646	"EIF3-P48, EIF3S6, INT6, eIF3-p46"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039348	3655	ITGA6	http://www.ncbi.nlm.nih.gov/gene/?term=3655	"CD49fB, VLA-6, ITGA6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039349	3655	ITGA6	http://www.ncbi.nlm.nih.gov/gene/?term=3655	"CD49fB, VLA-6, ITGA6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039350	3658	IREB2	http://www.ncbi.nlm.nih.gov/gene/?term=3658	"ACO3, IRP2, IRP2AD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039351	3660	IRF2	http://www.ncbi.nlm.nih.gov/gene/?term=3660	IRF-2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039352	3660	IRF2	http://www.ncbi.nlm.nih.gov/gene/?term=3660	IRF-2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039353	3667	IRS1	http://www.ncbi.nlm.nih.gov/gene/?term=3667	HIRS-1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039354	3667	IRS1	http://www.ncbi.nlm.nih.gov/gene/?term=3667	HIRS-1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039355	3675	ITGA3	http://www.ncbi.nlm.nih.gov/gene/?term=3675	"CD49C, FRP-2, GAP-B3, GAPB3, ILNEB, MSK18, VCA-2, VL3A, VLA3a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039356	3675	ITGA3	http://www.ncbi.nlm.nih.gov/gene/?term=3675	"CD49C, FRP-2, GAP-B3, GAPB3, ILNEB, MSK18, VCA-2, VL3A, VLA3a"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039357	3680	ITGA9	http://www.ncbi.nlm.nih.gov/gene/?term=3680	"ALPHA-RLC, ITGA4L, RLC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039358	3680	ITGA9	http://www.ncbi.nlm.nih.gov/gene/?term=3680	"ALPHA-RLC, ITGA4L, RLC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039359	3696	ITGB8	http://www.ncbi.nlm.nih.gov/gene/?term=3696		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039360	3704	ITPA	http://www.ncbi.nlm.nih.gov/gene/?term=3704	"C20orf37, HLC14-06-P, ITPase, My049, NTPase, dJ794I6.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039361	3704	ITPA	http://www.ncbi.nlm.nih.gov/gene/?term=3704	"C20orf37, HLC14-06-P, ITPase, My049, NTPase, dJ794I6.3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039362	3705	ITPK1	http://www.ncbi.nlm.nih.gov/gene/?term=3705	ITRPK1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039363	3705	ITPK1	http://www.ncbi.nlm.nih.gov/gene/?term=3705	ITRPK1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039364	3708	ITPR1	http://www.ncbi.nlm.nih.gov/gene/?term=3708	"ACV, CLA4, INSP3R1, IP3R, IP3R1, PPP1R94, SCA15, SCA16, SCA29"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039365	3709	ITPR2	http://www.ncbi.nlm.nih.gov/gene/?term=3709	"ANHD, CFAP48, INSP3R2, IP3R2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039366	3709	ITPR2	http://www.ncbi.nlm.nih.gov/gene/?term=3709	"ANHD, CFAP48, INSP3R2, IP3R2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039367	3712	IVD	http://www.ncbi.nlm.nih.gov/gene/?term=3712	ACAD2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039368	3712	IVD	http://www.ncbi.nlm.nih.gov/gene/?term=3712	ACAD2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039369	3716	JAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3716	"JAK1AB, JTK3, JAK1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039370	3716	JAK1	http://www.ncbi.nlm.nih.gov/gene/?term=3716	"JAK1AB, JTK3, JAK1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039371	3720	JARID2	http://www.ncbi.nlm.nih.gov/gene/?term=3720	JMJ	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039372	3735	KARS	http://www.ncbi.nlm.nih.gov/gene/?term=3735	"CMTRIB, DFNB891, KARS2, KRS, KARS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039373	3735	KARS	http://www.ncbi.nlm.nih.gov/gene/?term=3735	"CMTRIB, DFNB891, KARS2, KRS, KARS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039374	3737	KCNA2	http://www.ncbi.nlm.nih.gov/gene/?term=3737	"EIEE32, HBK5, HK4, HUKIV, KV1.2, MK2, NGK1, RBK2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039375	3737	KCNA2	http://www.ncbi.nlm.nih.gov/gene/?term=3737	"EIEE32, HBK5, HK4, HUKIV, KV1.2, MK2, NGK1, RBK2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039376	374378	GALNT18	http://www.ncbi.nlm.nih.gov/gene/?term=374378	"GALNACT18, GALNT15, GALNTL4, GalNAc-T15, GalNAc-T18"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039377	374378	GALNT18	http://www.ncbi.nlm.nih.gov/gene/?term=374378	"GALNACT18, GALNT15, GALNTL4, GalNAc-T15, GalNAc-T18"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039378	374618	TEX9	http://www.ncbi.nlm.nih.gov/gene/?term=374618		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039379	374618	TEX9	http://www.ncbi.nlm.nih.gov/gene/?term=374618		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039380	374654	KIF7	http://www.ncbi.nlm.nih.gov/gene/?term=374654	"ACLS, AGBK, HLS2, JBTS12, UNQ340"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039381	374868	ATP9B	http://www.ncbi.nlm.nih.gov/gene/?term=374868	"ATPASEP, ATPIIB, HUSSY-20, NEO1L, hMMR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039382	374868	ATP9B	http://www.ncbi.nlm.nih.gov/gene/?term=374868	"ATPASEP, ATPIIB, HUSSY-20, NEO1L, hMMR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039383	3749	KCNC4	http://www.ncbi.nlm.nih.gov/gene/?term=3749	"C1orf30, HKSHIIIC, KSHIIIC, KV3.4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039384	3749	KCNC4	http://www.ncbi.nlm.nih.gov/gene/?term=3749	"C1orf30, HKSHIIIC, KSHIIIC, KV3.4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039385	375	ARF1	http://www.ncbi.nlm.nih.gov/gene/?term=375		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039386	375190	FAM228B	http://www.ncbi.nlm.nih.gov/gene/?term=375190		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039387	375190	FAM228B	http://www.ncbi.nlm.nih.gov/gene/?term=375190		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039388	378	ARF4	http://www.ncbi.nlm.nih.gov/gene/?term=378	ARF2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039389	3784	KCNQ1	http://www.ncbi.nlm.nih.gov/gene/?term=3784	"ATFB1, ATFB3, JLNS1, KCNA8, KCNA9, KVLQT1, Kv1.9, Kv7.1, LQT, LQT1, RWS, SQT2, WRS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039390	3784	KCNQ1	http://www.ncbi.nlm.nih.gov/gene/?term=3784	"ATFB1, ATFB3, JLNS1, KCNA8, KCNA9, KVLQT1, Kv1.9, Kv7.1, LQT, LQT1, RWS, SQT2, WRS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039391	3786	KCNQ3	http://www.ncbi.nlm.nih.gov/gene/?term=3786	"BFNC2, EBN2, KV7.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039392	3786	KCNQ3	http://www.ncbi.nlm.nih.gov/gene/?term=3786	"BFNC2, EBN2, KV7.3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039393	3796	KIF2A	http://www.ncbi.nlm.nih.gov/gene/?term=3796	"CDCBM3, HK2, KIF2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039394	3796	KIF2A	http://www.ncbi.nlm.nih.gov/gene/?term=3796	"CDCBM3, HK2, KIF2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039395	3831	KLC1	http://www.ncbi.nlm.nih.gov/gene/?term=3831	"KLC, KNS2, KNS2A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039396	3831	KLC1	http://www.ncbi.nlm.nih.gov/gene/?term=3831	"KLC, KNS2, KNS2A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039397	3837	KPNB1	http://www.ncbi.nlm.nih.gov/gene/?term=3837	"IMB1, IPO1, IPOB, Impnb, NTF97"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039398	3837	KPNB1	http://www.ncbi.nlm.nih.gov/gene/?term=3837	"IMB1, IPO1, IPOB, Impnb, NTF97"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039399	3839	KPNA3	http://www.ncbi.nlm.nih.gov/gene/?term=3839	"IPOA4, SRP1, SRP1gamma, SRP4, hSRP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039400	3840	KPNA4	http://www.ncbi.nlm.nih.gov/gene/?term=3840	"IPOA3, QIP1, SRP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039401	3840	KPNA4	http://www.ncbi.nlm.nih.gov/gene/?term=3840	"IPOA3, QIP1, SRP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039402	3842	TNPO1	http://www.ncbi.nlm.nih.gov/gene/?term=3842	"IPO2, KPNB2, MIP, MIP1, TRN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039403	3842	TNPO1	http://www.ncbi.nlm.nih.gov/gene/?term=3842	"IPO2, KPNB2, MIP, MIP1, TRN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039404	3845	KRAS	http://www.ncbi.nlm.nih.gov/gene/?term=3845	"C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A, K-RAS4B, K-Ras, KI-RAS1, KRAS2, NS, NS3, RALD, RASK2, c-Ki-ras2, KRAS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039405	387	RHOA	http://www.ncbi.nlm.nih.gov/gene/?term=387	"ARH12, ARHA, RHO12, RHOH12"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039406	387129	NPSR1	http://www.ncbi.nlm.nih.gov/gene/?term=387129	"ASRT2, GPR154, GPRA, NPSR, PGR14, VRR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039407	387129	NPSR1	http://www.ncbi.nlm.nih.gov/gene/?term=387129	"ASRT2, GPR154, GPRA, NPSR, PGR14, VRR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039408	3899	AFF3	http://www.ncbi.nlm.nih.gov/gene/?term=3899	"LAF4, MLLT2-like"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039409	3899	AFF3	http://www.ncbi.nlm.nih.gov/gene/?term=3899	"LAF4, MLLT2-like"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039410	390	RND3	http://www.ncbi.nlm.nih.gov/gene/?term=390	"ARHE, Rho8, RhoE, memB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039411	3910	LAMA4	http://www.ncbi.nlm.nih.gov/gene/?term=3910	"CMD1JJ, LAMA3*-1, LAMA4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039412	3910	LAMA4	http://www.ncbi.nlm.nih.gov/gene/?term=3910	"CMD1JJ, LAMA3*-1, LAMA4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039413	3912	LAMB1	http://www.ncbi.nlm.nih.gov/gene/?term=3912	"CLM, LIS5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039414	3912	LAMB1	http://www.ncbi.nlm.nih.gov/gene/?term=3912	"CLM, LIS5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039415	3933	LCN1	http://www.ncbi.nlm.nih.gov/gene/?term=3933	"PMFA, TLC, TP, VEGP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039416	3933	LCN1	http://www.ncbi.nlm.nih.gov/gene/?term=3933	"PMFA, TLC, TP, VEGP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039417	3936	LCP1	http://www.ncbi.nlm.nih.gov/gene/?term=3936	"CP64, HEL-S-37, L-PLASTIN, LC64P, LPL, PLS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039418	3936	LCP1	http://www.ncbi.nlm.nih.gov/gene/?term=3936	"CP64, HEL-S-37, L-PLASTIN, LC64P, LPL, PLS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039419	3983	ABLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=3983	"ABLIM, LIMAB1, LIMATIN, abLIM-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039420	3985	LIMK2	http://www.ncbi.nlm.nih.gov/gene/?term=3985		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039421	399665	FAM102A	http://www.ncbi.nlm.nih.gov/gene/?term=399665	"C9orf132, EEIG1, SYM-3A, bA203J24.7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039422	399665	FAM102A	http://www.ncbi.nlm.nih.gov/gene/?term=399665	"C9orf132, EEIG1, SYM-3A, bA203J24.7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039423	3998	LMAN1	http://www.ncbi.nlm.nih.gov/gene/?term=3998	"ERGIC-53, ERGIC53, F5F8D, FMFD1, MCFD1, MR60, gp58"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039424	4008	LMO7	http://www.ncbi.nlm.nih.gov/gene/?term=4008	"FBX20, FBXO20b, LOMP, LMO7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039425	4012	LNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=4012	"CAP, IRAP, P-LAP, PLAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039426	4012	LNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=4012	"CAP, IRAP, P-LAP, PLAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039427	4026	LPP	http://www.ncbi.nlm.nih.gov/gene/?term=4026		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039428	404266	HOXB-AS3	http://www.ncbi.nlm.nih.gov/gene/?term=404266		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00039429	404266	HOXB-AS3	http://www.ncbi.nlm.nih.gov/gene/?term=404266		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00039430	4045	LSAMP	http://www.ncbi.nlm.nih.gov/gene/?term=4045	"IGLON3, LAMP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039431	4045	LSAMP	http://www.ncbi.nlm.nih.gov/gene/?term=4045	"IGLON3, LAMP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039432	404550	C16orf74	http://www.ncbi.nlm.nih.gov/gene/?term=404550		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039433	404550	C16orf74	http://www.ncbi.nlm.nih.gov/gene/?term=404550		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039434	4074	M6PR	http://www.ncbi.nlm.nih.gov/gene/?term=4074	"CD-M6PR, CD-MPR, MPR 46, MPR-46, MPR46, SMPR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039435	4074	M6PR	http://www.ncbi.nlm.nih.gov/gene/?term=4074	"CD-M6PR, CD-MPR, MPR 46, MPR-46, MPR46, SMPR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039436	408	ARRB1	http://www.ncbi.nlm.nih.gov/gene/?term=408	"ARB1, ARR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039437	408	ARRB1	http://www.ncbi.nlm.nih.gov/gene/?term=408	"ARB1, ARR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039438	4084	MXD1	http://www.ncbi.nlm.nih.gov/gene/?term=4084	"BHLHC58, MAD, MAD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039439	4088	SMAD3	http://www.ncbi.nlm.nih.gov/gene/?term=4088	"HSPC193, HsT17436, JV15-2, LDS1C, LDS3, MADH3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039440	4088	SMAD3	http://www.ncbi.nlm.nih.gov/gene/?term=4088	"HSPC193, HsT17436, JV15-2, LDS1C, LDS3, MADH3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039441	4091	SMAD6	http://www.ncbi.nlm.nih.gov/gene/?term=4091	"AOVD2, HsT17432, MADH6, MADH7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039442	4091	SMAD6	http://www.ncbi.nlm.nih.gov/gene/?term=4091	"AOVD2, HsT17432, MADH6, MADH7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039443	4093	SMAD9	http://www.ncbi.nlm.nih.gov/gene/?term=4093	"MADH6, MADH9, PPH2, SMAD8, SMAD8/9, SMAD8A, SMAD8B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039444	4093	SMAD9	http://www.ncbi.nlm.nih.gov/gene/?term=4093	"MADH6, MADH9, PPH2, SMAD8, SMAD8/9, SMAD8A, SMAD8B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039445	4121	MAN1A1	http://www.ncbi.nlm.nih.gov/gene/?term=4121	"HUMM3, HUMM9, MAN9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039446	4121	MAN1A1	http://www.ncbi.nlm.nih.gov/gene/?term=4121	"HUMM3, HUMM9, MAN9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039447	4124	MAN2A1	http://www.ncbi.nlm.nih.gov/gene/?term=4124	"AMan II, GOLIM7, MANA2, MANII"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039448	4133	MAP2	http://www.ncbi.nlm.nih.gov/gene/?term=4133	"MAP2AB, MAP2C, MAP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039449	4140	MARK3	http://www.ncbi.nlm.nih.gov/gene/?term=4140	"CTAK1, KP78, PAR1A, Par-1a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039450	4140	MARK3	http://www.ncbi.nlm.nih.gov/gene/?term=4140	"CTAK1, KP78, PAR1A, Par-1a"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039451	414777	HCG18	http://www.ncbi.nlm.nih.gov/gene/?term=414777		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00039452	414777	HCG18	http://www.ncbi.nlm.nih.gov/gene/?term=414777		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00039453	4149	MAX	http://www.ncbi.nlm.nih.gov/gene/?term=4149	bHLHd4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039454	4154	MBNL1	http://www.ncbi.nlm.nih.gov/gene/?term=4154	"EXP, MBNL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039455	4163	MCC	http://www.ncbi.nlm.nih.gov/gene/?term=4163	MCC1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039456	4163	MCC	http://www.ncbi.nlm.nih.gov/gene/?term=4163	MCC1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039457	4193	MDM2	http://www.ncbi.nlm.nih.gov/gene/?term=4193	"ACTFS, HDMX, hdm2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039458	4194	MDM4	http://www.ncbi.nlm.nih.gov/gene/?term=4194	"HDMX, MDMX, MRP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039459	4204	MECP2	http://www.ncbi.nlm.nih.gov/gene/?term=4204	"AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX, RS, RTS, RTT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039460	4204	MECP2	http://www.ncbi.nlm.nih.gov/gene/?term=4204	"AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX, RS, RTS, RTT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039461	4205	MEF2A	http://www.ncbi.nlm.nih.gov/gene/?term=4205	"ADCAD1, RSRFC4, RSRFC9, mef2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039462	4208	MEF2C	http://www.ncbi.nlm.nih.gov/gene/?term=4208	"C5DELq14.3, DEL5q14.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039463	4209	MEF2D	http://www.ncbi.nlm.nih.gov/gene/?term=4209		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039464	4209	MEF2D	http://www.ncbi.nlm.nih.gov/gene/?term=4209		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039465	4215	MAP3K3	http://www.ncbi.nlm.nih.gov/gene/?term=4215	"MAPKKK3, MEKK3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039466	4217	MAP3K5	http://www.ncbi.nlm.nih.gov/gene/?term=4217	"ASK1, MAPKKK5, MEKK5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039467	4232	MEST	http://www.ncbi.nlm.nih.gov/gene/?term=4232	PEG1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039468	4233	MET	http://www.ncbi.nlm.nih.gov/gene/?term=4233	"AUTS9, DFNB97, HGFR, RCCP2, c-Met"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039469	4255	MGMT	http://www.ncbi.nlm.nih.gov/gene/?term=4255		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039470	4255	MGMT	http://www.ncbi.nlm.nih.gov/gene/?term=4255		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039471	4259	MGST3	http://www.ncbi.nlm.nih.gov/gene/?term=4259	GST-III	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039472	4281	MID1	http://www.ncbi.nlm.nih.gov/gene/?term=4281	"BBBG1, FXY, GBBB1, MIDIN, OGS1, OS, OSX, RNF59, TRIM18, XPRF, ZNFXY"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039473	4289	MKLN1	http://www.ncbi.nlm.nih.gov/gene/?term=4289	TWA2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039474	4289	MKLN1	http://www.ncbi.nlm.nih.gov/gene/?term=4289	TWA2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039475	4292	MLH1	http://www.ncbi.nlm.nih.gov/gene/?term=4292	"COCA2, FCC2, HNPCC, HNPCC2, hMLH1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039476	4292	MLH1	http://www.ncbi.nlm.nih.gov/gene/?term=4292	"COCA2, FCC2, HNPCC, HNPCC2, hMLH1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039477	4299	AFF1	http://www.ncbi.nlm.nih.gov/gene/?term=4299	"AF4, MLLT2, PBM1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039478	4299	AFF1	http://www.ncbi.nlm.nih.gov/gene/?term=4299	"AF4, MLLT2, PBM1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039479	4300	MLLT3	http://www.ncbi.nlm.nih.gov/gene/?term=4300	"AF9, YEATS3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039480	4300	MLLT3	http://www.ncbi.nlm.nih.gov/gene/?term=4300	"AF9, YEATS3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039481	4306	NR3C2	http://www.ncbi.nlm.nih.gov/gene/?term=4306	"MCR, MLR, MRVIT, NR3C2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039482	4306	NR3C2	http://www.ncbi.nlm.nih.gov/gene/?term=4306	"MCR, MLR, MRVIT, NR3C2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039483	4331	MNAT1	http://www.ncbi.nlm.nih.gov/gene/?term=4331	"CAP35, MAT1, RNF66, TFB3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039484	4350	MPG	http://www.ncbi.nlm.nih.gov/gene/?term=4350	"AAG, ADPG, APNG, CRA36.1, MDG, Mid1, PIG11, PIG16, anpg"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039485	4350	MPG	http://www.ncbi.nlm.nih.gov/gene/?term=4350	"AAG, ADPG, APNG, CRA36.1, MDG, Mid1, PIG11, PIG16, anpg"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039486	4353	MPO	http://www.ncbi.nlm.nih.gov/gene/?term=4353		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039487	4353	MPO	http://www.ncbi.nlm.nih.gov/gene/?term=4353		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039488	440957	SMIM4	http://www.ncbi.nlm.nih.gov/gene/?term=440957	C3orf78	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039489	440957	SMIM4	http://www.ncbi.nlm.nih.gov/gene/?term=440957	C3orf78	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039490	442582	STAG3L2	http://www.ncbi.nlm.nih.gov/gene/?term=442582	"STAG3L1, STAG3L3, STAG3L2P"	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00039491	442582	STAG3L2	http://www.ncbi.nlm.nih.gov/gene/?term=442582	"STAG3L1, STAG3L3, STAG3L2P"	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00039492	444	ASPH	http://www.ncbi.nlm.nih.gov/gene/?term=444	"AAH, BAH, CASQ2BP1, FDLAB, HAAH, JCTN, junctin"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039493	445	ASS1	http://www.ncbi.nlm.nih.gov/gene/?term=445	"ASS, CTLN1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039494	445	ASS1	http://www.ncbi.nlm.nih.gov/gene/?term=445	"ASS, CTLN1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039495	4482	MSRA	http://www.ncbi.nlm.nih.gov/gene/?term=4482	PMSR	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039496	4482	MSRA	http://www.ncbi.nlm.nih.gov/gene/?term=4482	PMSR	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039497	4507	MTAP	http://www.ncbi.nlm.nih.gov/gene/?term=4507	"BDMF, DMSFH, DMSMFH, HEL-249, LGMBF, MSAP, c86fus"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039498	4507	MTAP	http://www.ncbi.nlm.nih.gov/gene/?term=4507	"BDMF, DMSFH, DMSMFH, HEL-249, LGMBF, MSAP, c86fus"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039499	4542	MYO1F	http://www.ncbi.nlm.nih.gov/gene/?term=4542		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039500	4542	MYO1F	http://www.ncbi.nlm.nih.gov/gene/?term=4542		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039501	4552	MTRR	http://www.ncbi.nlm.nih.gov/gene/?term=4552	"MSR, cblE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039502	4627	MYH9	http://www.ncbi.nlm.nih.gov/gene/?term=4627	"BDPLT6, DFNA17, EPSTS, FTNS, MHA, NMHC-II-A, NMMHC-IIA, NMMHCA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039503	4627	MYH9	http://www.ncbi.nlm.nih.gov/gene/?term=4627	"BDPLT6, DFNA17, EPSTS, FTNS, MHA, NMHC-II-A, NMMHC-IIA, NMMHCA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039504	4629	MYH11	http://www.ncbi.nlm.nih.gov/gene/?term=4629	"AAT4, FAA4, SMHC, SMMHC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039505	4651	MYO10	http://www.ncbi.nlm.nih.gov/gene/?term=4651		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039506	4651	MYO10	http://www.ncbi.nlm.nih.gov/gene/?term=4651		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039507	4659	PPP1R12A	http://www.ncbi.nlm.nih.gov/gene/?term=4659	"M130, MBS, MYPT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039508	4660	PPP1R12B	http://www.ncbi.nlm.nih.gov/gene/?term=4660	"MYPT2, PP1bp55"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039509	4660	PPP1R12B	http://www.ncbi.nlm.nih.gov/gene/?term=4660	"MYPT2, PP1bp55"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039510	4666	NACA	http://www.ncbi.nlm.nih.gov/gene/?term=4666	"HSD48, NAC-alpha1, skNAC, NACA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039511	4666	NACA	http://www.ncbi.nlm.nih.gov/gene/?term=4666	"HSD48, NAC-alpha1, skNAC, NACA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039512	4670	HNRNPM	http://www.ncbi.nlm.nih.gov/gene/?term=4670	"CEAR4, HNRPM, HNRPM4, HTGR1, NAGR1, hnRNP M, HNRNPM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039513	4670	HNRNPM	http://www.ncbi.nlm.nih.gov/gene/?term=4670	"CEAR4, HNRPM, HNRPM4, HTGR1, NAGR1, hnRNP M, HNRNPM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039514	4678	NASP	http://www.ncbi.nlm.nih.gov/gene/?term=4678	"FLB7527, HMDRA1, PRO1999"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039515	4678	NASP	http://www.ncbi.nlm.nih.gov/gene/?term=4678	"FLB7527, HMDRA1, PRO1999"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039516	4684	NCAM1	http://www.ncbi.nlm.nih.gov/gene/?term=4684	"CD56, MSK39, NCAM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039517	4684	NCAM1	http://www.ncbi.nlm.nih.gov/gene/?term=4684	"CD56, MSK39, NCAM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039518	4685	NCAM2	http://www.ncbi.nlm.nih.gov/gene/?term=4685	NCAM21	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039519	4695	NDUFA2	http://www.ncbi.nlm.nih.gov/gene/?term=4695	"B8, CD14, CIB8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039520	4695	NDUFA2	http://www.ncbi.nlm.nih.gov/gene/?term=4695	"B8, CD14, CIB8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039521	4705	NDUFA10	http://www.ncbi.nlm.nih.gov/gene/?term=4705	"CI-42KD, CI-42k"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039522	4705	NDUFA10	http://www.ncbi.nlm.nih.gov/gene/?term=4705	"CI-42KD, CI-42k"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039523	4716	NDUFB10	http://www.ncbi.nlm.nih.gov/gene/?term=4716	PDSW	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039524	4716	NDUFB10	http://www.ncbi.nlm.nih.gov/gene/?term=4716	PDSW	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039525	4719	NDUFS1	http://www.ncbi.nlm.nih.gov/gene/?term=4719	"CI-75Kd, CI-75k, PRO1304"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039526	4719	NDUFS1	http://www.ncbi.nlm.nih.gov/gene/?term=4719	"CI-75Kd, CI-75k, PRO1304"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039527	4725	NDUFS5	http://www.ncbi.nlm.nih.gov/gene/?term=4725	"CI-15k, CI15K"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039528	473	RERE	http://www.ncbi.nlm.nih.gov/gene/?term=473	"ARG, ARP, ATN1L, DNB1, NEDBEH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039529	473	RERE	http://www.ncbi.nlm.nih.gov/gene/?term=473	"ARG, ARP, ATN1L, DNB1, NEDBEH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039530	4733	DRG1	http://www.ncbi.nlm.nih.gov/gene/?term=4733	NEDD3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039531	4735	SEPT2	http://www.ncbi.nlm.nih.gov/gene/?term=4735	"DIFF6, NEDD-5, NEDD5, Pnutl3, hNedd5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039532	4739	NEDD9	http://www.ncbi.nlm.nih.gov/gene/?term=4739	"CAS-L, CAS2, CASL, CASS2, HEF1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039533	4739	NEDD9	http://www.ncbi.nlm.nih.gov/gene/?term=4739	"CAS-L, CAS2, CASL, CASS2, HEF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039534	4771	NF2	http://www.ncbi.nlm.nih.gov/gene/?term=4771	"ACN, BANF, SCH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039535	4771	NF2	http://www.ncbi.nlm.nih.gov/gene/?term=4771	"ACN, BANF, SCH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039536	4774	NFIA	http://www.ncbi.nlm.nih.gov/gene/?term=4774	"BRMUTD, CTF, NF-I/A, NF1-A, NFI-A, NFI-L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039537	4774	NFIA	http://www.ncbi.nlm.nih.gov/gene/?term=4774	"BRMUTD, CTF, NF-I/A, NF1-A, NFI-A, NFI-L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039538	4781	NFIB	http://www.ncbi.nlm.nih.gov/gene/?term=4781	"CTF, HMGIC/NFIB, NF-I/B, NF1-B, NFI-B, NFI-RED2, NFIB3, NFIB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039539	4784	NFIX	http://www.ncbi.nlm.nih.gov/gene/?term=4784	"CTF, MRSHSS, NF-I/X, NF1-X, NF1A, SOTOS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039540	4784	NFIX	http://www.ncbi.nlm.nih.gov/gene/?term=4784	"CTF, MRSHSS, NF-I/X, NF1-X, NF1A, SOTOS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039541	4799	NFX1	http://www.ncbi.nlm.nih.gov/gene/?term=4799	"NFX2, TEG-42, Tex42"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039542	4802	NFYC	http://www.ncbi.nlm.nih.gov/gene/?term=4802	"CBF-C, CBFC, H1TF2A, HAP5, HSM, NF-YC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039543	4802	NFYC	http://www.ncbi.nlm.nih.gov/gene/?term=4802	"CBF-C, CBFC, H1TF2A, HAP5, HSM, NF-YC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039544	4809	SNU13	http://www.ncbi.nlm.nih.gov/gene/?term=4809	"15.5K, FA-1, FA1, NHP2L1, NHPX, OTK27, SNRNP15-5, SPAG12, SSFA1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039545	4809	SNU13	http://www.ncbi.nlm.nih.gov/gene/?term=4809	"15.5K, FA-1, FA1, NHP2L1, NHPX, OTK27, SNRNP15-5, SPAG12, SSFA1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039546	4814	NINJ1	http://www.ncbi.nlm.nih.gov/gene/?term=4814	"NIN1, NINJURIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039547	4814	NINJ1	http://www.ncbi.nlm.nih.gov/gene/?term=4814	"NIN1, NINJURIN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039548	483	ATP1B3	http://www.ncbi.nlm.nih.gov/gene/?term=483	"ATPB-3, CD298"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039549	483	ATP1B3	http://www.ncbi.nlm.nih.gov/gene/?term=483	"ATPB-3, CD298"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039550	4837	NNMT	http://www.ncbi.nlm.nih.gov/gene/?term=4837		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039551	4837	NNMT	http://www.ncbi.nlm.nih.gov/gene/?term=4837		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039552	4848	CNOT2	http://www.ncbi.nlm.nih.gov/gene/?term=4848	"CDC36, HSPC131, NOT2, NOT2H"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039553	4848	CNOT2	http://www.ncbi.nlm.nih.gov/gene/?term=4848	"CDC36, HSPC131, NOT2, NOT2H"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039554	4850	CNOT4	http://www.ncbi.nlm.nih.gov/gene/?term=4850	"CLONE243, NOT4, NOT4H"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039555	488	ATP2A2	http://www.ncbi.nlm.nih.gov/gene/?term=488	"ATP2B, DAR, DD, SERCA2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039556	488	ATP2A2	http://www.ncbi.nlm.nih.gov/gene/?term=488	"ATP2B, DAR, DD, SERCA2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039557	490	ATP2B1	http://www.ncbi.nlm.nih.gov/gene/?term=490	"PMCA1, PMCA1kb"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039558	4919	ROR1	http://www.ncbi.nlm.nih.gov/gene/?term=4919	"NTRKR1, dJ537F10.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039559	4919	ROR1	http://www.ncbi.nlm.nih.gov/gene/?term=4919	"NTRKR1, dJ537F10.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039560	4927	NUP88	http://www.ncbi.nlm.nih.gov/gene/?term=4927		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039561	4929	NR4A2	http://www.ncbi.nlm.nih.gov/gene/?term=4929	"HZF-3, NOT, NURR1, RNR1, TINUR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039562	4929	NR4A2	http://www.ncbi.nlm.nih.gov/gene/?term=4929	"HZF-3, NOT, NURR1, RNR1, TINUR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039563	4947	OAZ2	http://www.ncbi.nlm.nih.gov/gene/?term=4947	AZ2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039564	4976	OPA1	http://www.ncbi.nlm.nih.gov/gene/?term=4976	"BERHS, MGM1, MTDPS14, NPG, NTG, largeG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039565	4976	OPA1	http://www.ncbi.nlm.nih.gov/gene/?term=4976	"BERHS, MGM1, MTDPS14, NPG, NTG, largeG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039566	5046	PCSK6	http://www.ncbi.nlm.nih.gov/gene/?term=5046	"PACE4, SPC4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039567	5046	PCSK6	http://www.ncbi.nlm.nih.gov/gene/?term=5046	"PACE4, SPC4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039568	5048	PAFAH1B1	http://www.ncbi.nlm.nih.gov/gene/?term=5048	"LIS1, LIS2, MDCR, MDS, NudF, PAFAH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039569	50488	MINK1	http://www.ncbi.nlm.nih.gov/gene/?term=50488	"B55, MAP4K6, MINK, YSK2, ZC3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039570	50515	CHST11	http://www.ncbi.nlm.nih.gov/gene/?term=50515	"C4ST, C4ST-1, C4ST1, HSA269537"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039571	50515	CHST11	http://www.ncbi.nlm.nih.gov/gene/?term=50515	"C4ST, C4ST-1, C4ST1, HSA269537"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039572	5058	PAK1	http://www.ncbi.nlm.nih.gov/gene/?term=5058	PAKalpha	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039573	50618	ITSN2	http://www.ncbi.nlm.nih.gov/gene/?term=50618	"PRO2015, SH3D1B, SH3P18, SWA, SWAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039574	50640	PNPLA8	http://www.ncbi.nlm.nih.gov/gene/?term=50640	"IPLA2-2, IPLA2G, MMLA, PNPLA-gamma, iPLA2gamma"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039575	50650	ARHGEF3	http://www.ncbi.nlm.nih.gov/gene/?term=50650	"GEF3, STA3, XPLN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039576	50650	ARHGEF3	http://www.ncbi.nlm.nih.gov/gene/?term=50650	"GEF3, STA3, XPLN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039577	5066	PAM	http://www.ncbi.nlm.nih.gov/gene/?term=5066	"PAL, PHM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039578	5066	PAM	http://www.ncbi.nlm.nih.gov/gene/?term=5066	"PAL, PHM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039579	5069	PAPPA	http://www.ncbi.nlm.nih.gov/gene/?term=5069	"ASBABP2, DIPLA1, IGFBP-4ase, PAPA, PAPP-A1, PAPPA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039580	5069	PAPPA	http://www.ncbi.nlm.nih.gov/gene/?term=5069	"ASBABP2, DIPLA1, IGFBP-4ase, PAPA, PAPP-A1, PAPPA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039581	50717	DCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=50717	"GAN2, H326, WDR42A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039582	50717	DCAF8	http://www.ncbi.nlm.nih.gov/gene/?term=50717	"GAN2, H326, WDR42A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039583	50807	ASAP1	http://www.ncbi.nlm.nih.gov/gene/?term=50807	"AMAP1, CENTB4, DDEF1, PAG2, PAP, ZG14P"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039584	50807	ASAP1	http://www.ncbi.nlm.nih.gov/gene/?term=50807	"AMAP1, CENTB4, DDEF1, PAG2, PAP, ZG14P"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039585	50810	HDGFL3	http://www.ncbi.nlm.nih.gov/gene/?term=50810	"CGI-142, HDGF-2, HDGF2, HDGFRP3, HRP-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039586	50863	NTM	http://www.ncbi.nlm.nih.gov/gene/?term=50863	"CEPU-1, HNT, IGLON2, NTRI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039587	50863	NTM	http://www.ncbi.nlm.nih.gov/gene/?term=50863	"CEPU-1, HNT, IGLON2, NTRI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039588	5087	PBX1	http://www.ncbi.nlm.nih.gov/gene/?term=5087		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039589	5087	PBX1	http://www.ncbi.nlm.nih.gov/gene/?term=5087		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039590	5090	PBX3	http://www.ncbi.nlm.nih.gov/gene/?term=5090		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039591	5090	PBX3	http://www.ncbi.nlm.nih.gov/gene/?term=5090		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039592	5094	PCBP2	http://www.ncbi.nlm.nih.gov/gene/?term=5094	"HNRNPE2, HNRPE2, hnRNP-E2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039593	5095	PCCA	http://www.ncbi.nlm.nih.gov/gene/?term=5095		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039594	5095	PCCA	http://www.ncbi.nlm.nih.gov/gene/?term=5095		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039595	51010	EXOSC3	http://www.ncbi.nlm.nih.gov/gene/?term=51010	"CGI-102, PCH1B, RRP40, Rrp40p, bA3J10.7, hRrp-40, p10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039596	51053	GMNN	http://www.ncbi.nlm.nih.gov/gene/?term=51053	"Gem, MGORS6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039597	51053	GMNN	http://www.ncbi.nlm.nih.gov/gene/?term=51053	"Gem, MGORS6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039598	51065	RPS27L	http://www.ncbi.nlm.nih.gov/gene/?term=51065		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039599	51065	RPS27L	http://www.ncbi.nlm.nih.gov/gene/?term=51065		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039600	51069	MRPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51069	"CGI-22, MRP-L14, RPML14"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039601	51069	MRPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51069	"CGI-22, MRP-L14, RPML14"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039602	51072	MEMO1	http://www.ncbi.nlm.nih.gov/gene/?term=51072	"C2orf4, CGI-27, MEMO, NS5ATP7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039603	51072	MEMO1	http://www.ncbi.nlm.nih.gov/gene/?term=51072	"C2orf4, CGI-27, MEMO, NS5ATP7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039604	51076	CUTC	http://www.ncbi.nlm.nih.gov/gene/?term=51076	CGI-32	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039605	51076	CUTC	http://www.ncbi.nlm.nih.gov/gene/?term=51076	CGI-32	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039606	51088	KLHL5	http://www.ncbi.nlm.nih.gov/gene/?term=51088		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039607	51112	TRAPPC12	http://www.ncbi.nlm.nih.gov/gene/?term=51112	"CGI-87, TTC-15, TTC15"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039608	51112	TRAPPC12	http://www.ncbi.nlm.nih.gov/gene/?term=51112	"CGI-87, TTC-15, TTC15"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039609	51115	RMDN1	http://www.ncbi.nlm.nih.gov/gene/?term=51115	"CGI-90, FAM82B, RMD-1, RMD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039610	51115	RMDN1	http://www.ncbi.nlm.nih.gov/gene/?term=51115	"CGI-90, FAM82B, RMD-1, RMD1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039611	51124	IER3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=51124	"MEDS, HSPC039, PRO2309"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039612	51124	IER3IP1	http://www.ncbi.nlm.nih.gov/gene/?term=51124	"MEDS, HSPC039, PRO2309"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039613	51222	ZNF219	http://www.ncbi.nlm.nih.gov/gene/?term=51222	ZFP219	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039614	51222	ZNF219	http://www.ncbi.nlm.nih.gov/gene/?term=51222	ZFP219	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039615	51228	GLTP	http://www.ncbi.nlm.nih.gov/gene/?term=51228		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039616	51228	GLTP	http://www.ncbi.nlm.nih.gov/gene/?term=51228		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039617	51230	PHF20	http://www.ncbi.nlm.nih.gov/gene/?term=51230	"C20orf104, GLEA2, HCA58, NZF, TDRD20A, TZP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039618	51230	PHF20	http://www.ncbi.nlm.nih.gov/gene/?term=51230	"C20orf104, GLEA2, HCA58, NZF, TDRD20A, TZP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039619	51232	CRIM1	http://www.ncbi.nlm.nih.gov/gene/?term=51232	"CRIM-1, S52"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039620	51247	PAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=51247	"PAIP-2A, PAIP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039621	51247	PAIP2	http://www.ncbi.nlm.nih.gov/gene/?term=51247	"PAIP-2A, PAIP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039622	51257	MARCH2	http://www.ncbi.nlm.nih.gov/gene/?term=51257	"HSPC240, MARCH-II, RNF172"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039623	51257	MARCH2	http://www.ncbi.nlm.nih.gov/gene/?term=51257	"HSPC240, MARCH-II, RNF172"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039624	51306	FAM13B	http://www.ncbi.nlm.nih.gov/gene/?term=51306	"ARHGAP49, C5orf51, KHCHP, N61, FAM13B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039625	51312	SLC25A37	http://www.ncbi.nlm.nih.gov/gene/?term=51312	"HT015, MFRN, MFRN1, MSC, MSCP, PRO1278, PRO1584, PRO2217"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039626	51312	SLC25A37	http://www.ncbi.nlm.nih.gov/gene/?term=51312	"HT015, MFRN, MFRN1, MSC, MSCP, PRO1278, PRO1584, PRO2217"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039627	51315	KRCC1	http://www.ncbi.nlm.nih.gov/gene/?term=51315	CHBP2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039628	51317	PHF21A	http://www.ncbi.nlm.nih.gov/gene/?term=51317	"BHC80, BM-006"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039629	51317	PHF21A	http://www.ncbi.nlm.nih.gov/gene/?term=51317	"BHC80, BM-006"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039630	51319	RSRC1	http://www.ncbi.nlm.nih.gov/gene/?term=51319	"BM-011, SFRS21, SRrp53"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039631	51322	WAC	http://www.ncbi.nlm.nih.gov/gene/?term=51322	"BM-016, DESSH, PRO1741, Wwp4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039632	51341	ZBTB7A	http://www.ncbi.nlm.nih.gov/gene/?term=51341	"FBI-1, FBI1, LRF, TIP21, ZBTB7, ZNF857A, pokemon"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039633	51341	ZBTB7A	http://www.ncbi.nlm.nih.gov/gene/?term=51341	"FBI-1, FBI1, LRF, TIP21, ZBTB7, ZNF857A, pokemon"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039634	51347	TAOK3	http://www.ncbi.nlm.nih.gov/gene/?term=51347	"DPK, JIK, MAP3K18, hKFC-A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039635	51347	TAOK3	http://www.ncbi.nlm.nih.gov/gene/?term=51347	"DPK, JIK, MAP3K18, hKFC-A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039636	51363	CHST15	http://www.ncbi.nlm.nih.gov/gene/?term=51363	"BRAG, GALNAC4S-6ST"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039637	51363	CHST15	http://www.ncbi.nlm.nih.gov/gene/?term=51363	"BRAG, GALNAC4S-6ST"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039638	51366	UBR5	http://www.ncbi.nlm.nih.gov/gene/?term=51366	"DD5, EDD, EDD1, HYD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039639	51366	UBR5	http://www.ncbi.nlm.nih.gov/gene/?term=51366	"DD5, EDD, EDD1, HYD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039640	51379	CRLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51379	"CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039641	51379	CRLF3	http://www.ncbi.nlm.nih.gov/gene/?term=51379	"CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039642	51382	ATP6V1D	http://www.ncbi.nlm.nih.gov/gene/?term=51382	"ATP6M, VATD, VMA8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039643	51382	ATP6V1D	http://www.ncbi.nlm.nih.gov/gene/?term=51382	"ATP6M, VATD, VMA8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039644	5139	PDE3A	http://www.ncbi.nlm.nih.gov/gene/?term=5139	"CGI-PDE, CGI-PDE A, CGI-PDE-A, HTNB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039645	51397	COMMD10	http://www.ncbi.nlm.nih.gov/gene/?term=51397	PTD002	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039646	51397	COMMD10	http://www.ncbi.nlm.nih.gov/gene/?term=51397	PTD002	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039647	51422	PRKAG2	http://www.ncbi.nlm.nih.gov/gene/?term=51422	"AAKG, AAKG2, CMH6, H91620p, WPWS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039648	51422	PRKAG2	http://www.ncbi.nlm.nih.gov/gene/?term=51422	"AAKG, AAKG2, CMH6, H91620p, WPWS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039649	5144	PDE4D	http://www.ncbi.nlm.nih.gov/gene/?term=5144	"ACRDYS2, DPDE3, HSPDE4D, PDE43N2, STRK1, PDE4D"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039650	5144	PDE4D	http://www.ncbi.nlm.nih.gov/gene/?term=5144	"ACRDYS2, DPDE3, HSPDE4D, PDE43N2, STRK1, PDE4D"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039651	51441	YTHDF2	http://www.ncbi.nlm.nih.gov/gene/?term=51441	"CAHL, HGRG8, NY-REN-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039652	51441	YTHDF2	http://www.ncbi.nlm.nih.gov/gene/?term=51441	"CAHL, HGRG8, NY-REN-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039653	51455	REV1	http://www.ncbi.nlm.nih.gov/gene/?term=51455	"AIBP80L, REV1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039654	5146	PDE6C	http://www.ncbi.nlm.nih.gov/gene/?term=5146	"ACHM5, COD4, PDEA2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039655	5146	PDE6C	http://www.ncbi.nlm.nih.gov/gene/?term=5146	"ACHM5, COD4, PDEA2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039656	51496	CTDSPL2	http://www.ncbi.nlm.nih.gov/gene/?term=51496	"HSPC058, HSPC129"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039657	51497	NELFCD	http://www.ncbi.nlm.nih.gov/gene/?term=51497	"HSPC130, NELF-C, NELF-D, TH1, TH1L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039658	51497	NELFCD	http://www.ncbi.nlm.nih.gov/gene/?term=51497	"HSPC130, NELF-C, NELF-D, TH1, TH1L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039659	51507	RTFDC1	http://www.ncbi.nlm.nih.gov/gene/?term=51507	"C20orf43, CDAO5, HSPC164, SHUJUN-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039660	51507	RTFDC1	http://www.ncbi.nlm.nih.gov/gene/?term=51507	"C20orf43, CDAO5, HSPC164, SHUJUN-3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039661	5152	PDE9A	http://www.ncbi.nlm.nih.gov/gene/?term=5152	HSPDE9A2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039662	5152	PDE9A	http://www.ncbi.nlm.nih.gov/gene/?term=5152	HSPDE9A2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039663	51586	MED15	http://www.ncbi.nlm.nih.gov/gene/?term=51586	"ARC105, CAG7A, CTG7A, PCQAP, TIG-1, TIG1, TNRC7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039664	51586	MED15	http://www.ncbi.nlm.nih.gov/gene/?term=51586	"ARC105, CAG7A, CTG7A, PCQAP, TIG-1, TIG1, TNRC7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039665	51592	TRIM33	http://www.ncbi.nlm.nih.gov/gene/?term=51592	"ECTO, PTC7, RFG7, TF1G, TIF1G, TIF1GAMMA, TIFGAMMA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039666	5160	PDHA1	http://www.ncbi.nlm.nih.gov/gene/?term=5160	"PDHA, PDHAD, PDHCE1A, PHE1A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039667	5160	PDHA1	http://www.ncbi.nlm.nih.gov/gene/?term=5160	"PDHA, PDHAD, PDHCE1A, PHE1A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039668	51602	NOP58	http://www.ncbi.nlm.nih.gov/gene/?term=51602	"HSPC120, NOP5, NOP5/NOP58"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039669	51603	METTL13	http://www.ncbi.nlm.nih.gov/gene/?term=51603	"5630401D24Rik, CGI-01, KIAA0859, feat"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039670	51604	PIGT	http://www.ncbi.nlm.nih.gov/gene/?term=51604	"CGI-06, MCAHS3, NDAP, PNH2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039671	51604	PIGT	http://www.ncbi.nlm.nih.gov/gene/?term=51604	"CGI-06, MCAHS3, NDAP, PNH2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039672	51621	KLF13	http://www.ncbi.nlm.nih.gov/gene/?term=51621	"BTEB3, FKLF2, NSLP1, RFLAT-1, RFLAT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039673	51621	KLF13	http://www.ncbi.nlm.nih.gov/gene/?term=51621	"BTEB3, FKLF2, NSLP1, RFLAT-1, RFLAT1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039674	51646	YPEL5	http://www.ncbi.nlm.nih.gov/gene/?term=51646	CGI-127	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039675	51663	ZFR	http://www.ncbi.nlm.nih.gov/gene/?term=51663	"SPG711, ZFR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039676	51663	ZFR	http://www.ncbi.nlm.nih.gov/gene/?term=51663	"SPG711, ZFR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039677	5168	ENPP2	http://www.ncbi.nlm.nih.gov/gene/?term=5168	"ATX, ATX-X, AUTOTAXIN, LysoPLD, NPP2, PD-IALPHA, PDNP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039678	5168	ENPP2	http://www.ncbi.nlm.nih.gov/gene/?term=5168	"ATX, ATX-X, AUTOTAXIN, LysoPLD, NPP2, PD-IALPHA, PDNP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039679	51701	NLK	http://www.ncbi.nlm.nih.gov/gene/?term=51701		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039680	51704	GPRC5B	http://www.ncbi.nlm.nih.gov/gene/?term=51704	"RAIG-2, RAIG2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039681	51704	GPRC5B	http://www.ncbi.nlm.nih.gov/gene/?term=51704	"RAIG-2, RAIG2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039682	51741	WWOX	http://www.ncbi.nlm.nih.gov/gene/?term=51741	"D16S432E, EIEE28, FOR, FRA16D, HHCMA56, PRO0128, SCAR12, SDR41C1, WOX1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039683	51742	ARID4B	http://www.ncbi.nlm.nih.gov/gene/?term=51742	"BCAA, BRCAA1, RBBP1L1, RBP1L1, SAP180"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039684	51742	ARID4B	http://www.ncbi.nlm.nih.gov/gene/?term=51742	"BCAA, BRCAA1, RBBP1L1, RBP1L1, SAP180"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039685	51762	RAB8B	http://www.ncbi.nlm.nih.gov/gene/?term=51762		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039686	51762	RAB8B	http://www.ncbi.nlm.nih.gov/gene/?term=51762		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039687	51773	RSF1	http://www.ncbi.nlm.nih.gov/gene/?term=51773	"HBXAP, RSF-1, XAP8, p325"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039688	5195	PEX14	http://www.ncbi.nlm.nih.gov/gene/?term=5195	"NAPP2, PBD13A, Pex14p, dJ734G22.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039689	5210	PFKFB4	http://www.ncbi.nlm.nih.gov/gene/?term=5210		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039690	5210	PFKFB4	http://www.ncbi.nlm.nih.gov/gene/?term=5210		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039691	5212	VIT	http://www.ncbi.nlm.nih.gov/gene/?term=5212		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039692	5218	CDK14	http://www.ncbi.nlm.nih.gov/gene/?term=5218	"PFTAIRE1, PFTK1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039693	5218	CDK14	http://www.ncbi.nlm.nih.gov/gene/?term=5218	"PFTAIRE1, PFTK1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039694	523	ATP6V1A	http://www.ncbi.nlm.nih.gov/gene/?term=523	"ARCL2D, ATP6A11, HO68, VA68, VPP2, Vma1, ATP6V1A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039695	5287	PIK3C2B	http://www.ncbi.nlm.nih.gov/gene/?term=5287	C2-PI3K	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039696	5289	PIK3C3	http://www.ncbi.nlm.nih.gov/gene/?term=5289	"VPS34, Vps34, hVps34"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039697	5295	PIK3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5295	"AGM7, GRB1, IMD36, p85, p85-ALPHA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039698	5295	PIK3R1	http://www.ncbi.nlm.nih.gov/gene/?term=5295	"AGM7, GRB1, IMD36, p85, p85-ALPHA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039699	5305	PIP4K2A	http://www.ncbi.nlm.nih.gov/gene/?term=5305	"PI5P4KA, PIP5K2A, PIP5KII-alpha, PIP5KIIA, PIPK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039700	5305	PIP4K2A	http://www.ncbi.nlm.nih.gov/gene/?term=5305	"PI5P4KA, PIP5K2A, PIP5KII-alpha, PIP5KIIA, PIPK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039701	5311	PKD2	http://www.ncbi.nlm.nih.gov/gene/?term=5311	"APKD2, PC2, PKD4, Pc-2, TRPP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039702	5311	PKD2	http://www.ncbi.nlm.nih.gov/gene/?term=5311	"APKD2, PC2, PKD4, Pc-2, TRPP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039703	5321	PLA2G4A	http://www.ncbi.nlm.nih.gov/gene/?term=5321	"PLA2G4, cPLA2, cPLA2-alpha"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039704	5321	PLA2G4A	http://www.ncbi.nlm.nih.gov/gene/?term=5321	"PLA2G4, cPLA2, cPLA2-alpha"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039705	5336	PLCG2	http://www.ncbi.nlm.nih.gov/gene/?term=5336	"APLAID, FCAS3, PLC-IV, PLC-gamma-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039706	5336	PLCG2	http://www.ncbi.nlm.nih.gov/gene/?term=5336	"APLAID, FCAS3, PLC-IV, PLC-gamma-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039707	53371	NUP54	http://www.ncbi.nlm.nih.gov/gene/?term=53371		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039708	53371	NUP54	http://www.ncbi.nlm.nih.gov/gene/?term=53371		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039709	535	ATP6V0A1	http://www.ncbi.nlm.nih.gov/gene/?term=535	"ATP6N1, ATP6N1A, Stv1, VPP1, Vph1, a1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039710	5359	PLSCR1	http://www.ncbi.nlm.nih.gov/gene/?term=5359	MMTRA1B	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039711	53624	Cldn7	http://www.ncbi.nlm.nih.gov/gene/?term=53624		mRNA	Mus musculus	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039712	53624	Cldn7	http://www.ncbi.nlm.nih.gov/gene/?term=53624		mRNA	Mus musculus	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039713	5373	PMM2	http://www.ncbi.nlm.nih.gov/gene/?term=5373	"CDG1, CDG1a, CDGS, PMI, PMI1, PMM 2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039714	5378	PMS1	http://www.ncbi.nlm.nih.gov/gene/?term=5378	"HNPCC3, MLH2, PMSL1, hPMS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039715	5378	PMS1	http://www.ncbi.nlm.nih.gov/gene/?term=5378	"HNPCC3, MLH2, PMSL1, hPMS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039716	5396	PRRX1	http://www.ncbi.nlm.nih.gov/gene/?term=5396	"AGOTC, PHOX1, PMX1, PRX-1, PRX1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039717	5396	PRRX1	http://www.ncbi.nlm.nih.gov/gene/?term=5396	"AGOTC, PHOX1, PMX1, PRX-1, PRX1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039718	54020	SLC37A1	http://www.ncbi.nlm.nih.gov/gene/?term=54020	G3PP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039719	5423	POLB	http://www.ncbi.nlm.nih.gov/gene/?term=5423		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039720	5423	POLB	http://www.ncbi.nlm.nih.gov/gene/?term=5423		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039721	5425	POLD2	http://www.ncbi.nlm.nih.gov/gene/?term=5425		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039722	5425	POLD2	http://www.ncbi.nlm.nih.gov/gene/?term=5425		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039723	5427	POLE2	http://www.ncbi.nlm.nih.gov/gene/?term=5427	DPE2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039724	5427	POLE2	http://www.ncbi.nlm.nih.gov/gene/?term=5427	DPE2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039725	5429	POLH	http://www.ncbi.nlm.nih.gov/gene/?term=5429	"RAD30, RAD30A, XP-V, XPV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039726	54420	Cldn8	http://www.ncbi.nlm.nih.gov/gene/?term=54420	AI648025	mRNA	Mus musculus	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039727	54420	Cldn8	http://www.ncbi.nlm.nih.gov/gene/?term=54420	AI648025	mRNA	Mus musculus	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039728	54434	SSH1	http://www.ncbi.nlm.nih.gov/gene/?term=54434	SSH1L	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039729	54434	SSH1	http://www.ncbi.nlm.nih.gov/gene/?term=54434	SSH1L	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039730	54443	ANLN	http://www.ncbi.nlm.nih.gov/gene/?term=54443	"FSGS8, Scraps, scra"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039731	5445	PON2	http://www.ncbi.nlm.nih.gov/gene/?term=5445		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039732	5445	PON2	http://www.ncbi.nlm.nih.gov/gene/?term=5445		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039733	54453	RIN2	http://www.ncbi.nlm.nih.gov/gene/?term=54453	"MACS, RASSF4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039734	54453	RIN2	http://www.ncbi.nlm.nih.gov/gene/?term=54453	"MACS, RASSF4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039735	54476	RNF216	http://www.ncbi.nlm.nih.gov/gene/?term=54476	"CAHH, TRIAD3, U7I1, UBCE7IP1, ZIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039736	54476	RNF216	http://www.ncbi.nlm.nih.gov/gene/?term=54476	"CAHH, TRIAD3, U7I1, UBCE7IP1, ZIN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039737	54477	PLEKHA5	http://www.ncbi.nlm.nih.gov/gene/?term=54477	"PEPP-2, PEPP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039738	54477	PLEKHA5	http://www.ncbi.nlm.nih.gov/gene/?term=54477	"PEPP-2, PEPP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039739	54495	TMX3	http://www.ncbi.nlm.nih.gov/gene/?term=54495	"PDIA13, TXNDC10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039740	54495	TMX3	http://www.ncbi.nlm.nih.gov/gene/?term=54495	"PDIA13, TXNDC10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039741	54498	SMOX	http://www.ncbi.nlm.nih.gov/gene/?term=54498	"C20orf16, PAO, PAO-1, PAO1, PAOH, PAOH1, SMO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039742	54498	SMOX	http://www.ncbi.nlm.nih.gov/gene/?term=54498	"C20orf16, PAO, PAO-1, PAO1, PAOH, PAOH1, SMO"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039743	545	ATR	http://www.ncbi.nlm.nih.gov/gene/?term=545	"FCTCS, FRP1, MEC1, SCKL, SCKL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039744	545	ATR	http://www.ncbi.nlm.nih.gov/gene/?term=545	"FCTCS, FRP1, MEC1, SCKL, SCKL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039745	54502	RBM47	http://www.ncbi.nlm.nih.gov/gene/?term=54502	NET18	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039746	54502	RBM47	http://www.ncbi.nlm.nih.gov/gene/?term=54502	NET18	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039747	54504	CPVL	http://www.ncbi.nlm.nih.gov/gene/?term=54504	HVLP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039748	54517	PUS7	http://www.ncbi.nlm.nih.gov/gene/?term=54517		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039749	54536	EXOC6	http://www.ncbi.nlm.nih.gov/gene/?term=54536	"EXOC6A, SEC15, SEC15L, SEC15L1, SEC15L3, Sec15p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039750	54536	EXOC6	http://www.ncbi.nlm.nih.gov/gene/?term=54536	"EXOC6A, SEC15, SEC15L, SEC15L1, SEC15L3, Sec15p"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039751	54540	FAM193B	http://www.ncbi.nlm.nih.gov/gene/?term=54540	IRIZIO	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039752	54540	FAM193B	http://www.ncbi.nlm.nih.gov/gene/?term=54540	IRIZIO	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039753	54566	EPB41L4B	http://www.ncbi.nlm.nih.gov/gene/?term=54566	"CG1, EHM2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039754	54566	EPB41L4B	http://www.ncbi.nlm.nih.gov/gene/?term=54566	"CG1, EHM2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039755	54617	INO80	http://www.ncbi.nlm.nih.gov/gene/?term=54617	"INO80A, INOC1, hINO80"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039756	5464	PPA1	http://www.ncbi.nlm.nih.gov/gene/?term=5464	"HEL-S-66p, IOPPP, PP, PP1, SID6-8061"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039757	54677	CROT	http://www.ncbi.nlm.nih.gov/gene/?term=54677	COT	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039758	54677	CROT	http://www.ncbi.nlm.nih.gov/gene/?term=54677	COT	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039759	5468	PPARG	http://www.ncbi.nlm.nih.gov/gene/?term=5468	"CIMT1, GLM1, NR1C31, PPARG2, PPARgamma, PPARG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039760	5468	PPARG	http://www.ncbi.nlm.nih.gov/gene/?term=5468	"CIMT1, GLM1, NR1C31, PPARG2, PPARgamma, PPARG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039761	5471	PPAT	http://www.ncbi.nlm.nih.gov/gene/?term=5471	"ATASE, GPAT, PRAT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039762	54715	RBFOX1	http://www.ncbi.nlm.nih.gov/gene/?term=54715	"2BP1, A2BP1, FOX-1, FOX1, HRNBP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039763	54715	RBFOX1	http://www.ncbi.nlm.nih.gov/gene/?term=54715	"2BP1, A2BP1, FOX-1, FOX1, HRNBP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039764	54726	OTUD4	http://www.ncbi.nlm.nih.gov/gene/?term=54726	"DUBA6, HIN1, HSHIN1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039765	54749	EPDR1	http://www.ncbi.nlm.nih.gov/gene/?term=54749	"EPDR, MERP-1, MERP1, UCC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039766	54751	FBLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=54751	"CAL, FBLP-1, FBLP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039767	54751	FBLIM1	http://www.ncbi.nlm.nih.gov/gene/?term=54751	"CAL, FBLP-1, FBLP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039768	54764	ZRANB1	http://www.ncbi.nlm.nih.gov/gene/?term=54764	TRABID	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039769	54764	ZRANB1	http://www.ncbi.nlm.nih.gov/gene/?term=54764	TRABID	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039770	54765	TRIM44	http://www.ncbi.nlm.nih.gov/gene/?term=54765	"AN3, DIPB, HSA249128, MC7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039771	54765	TRIM44	http://www.ncbi.nlm.nih.gov/gene/?term=54765	"AN3, DIPB, HSA249128, MC7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039772	54776	PPP1R12C	http://www.ncbi.nlm.nih.gov/gene/?term=54776	"AAVS1, LENG3, MBS85, p84, p85"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039773	54776	PPP1R12C	http://www.ncbi.nlm.nih.gov/gene/?term=54776	"AAVS1, LENG3, MBS85, p84, p85"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039774	54778	RNF111	http://www.ncbi.nlm.nih.gov/gene/?term=54778	"ARK, hRNF111"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039775	54778	RNF111	http://www.ncbi.nlm.nih.gov/gene/?term=54778	"ARK, hRNF111"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039776	54796	BNC2	http://www.ncbi.nlm.nih.gov/gene/?term=54796	BSN2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039777	54800	KLHL24	http://www.ncbi.nlm.nih.gov/gene/?term=54800	"DRE1, EBSSH, KRIP6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039778	54800	KLHL24	http://www.ncbi.nlm.nih.gov/gene/?term=54800	"DRE1, EBSSH, KRIP6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039779	54805	CNNM2	http://www.ncbi.nlm.nih.gov/gene/?term=54805	"ACDP2, HOMG6, HOMGSMR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039780	54806	AHI1	http://www.ncbi.nlm.nih.gov/gene/?term=54806	"AHI-1, JBTS3, ORF1, dJ71N10.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039781	54806	AHI1	http://www.ncbi.nlm.nih.gov/gene/?term=54806	"AHI-1, JBTS3, ORF1, dJ71N10.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039782	54808	DYM	http://www.ncbi.nlm.nih.gov/gene/?term=54808	"DMC, SMC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039783	54808	DYM	http://www.ncbi.nlm.nih.gov/gene/?term=54808	"DMC, SMC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039784	54812	AFTPH	http://www.ncbi.nlm.nih.gov/gene/?term=54812	Nbla10388	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039785	54815	GATAD2A	http://www.ncbi.nlm.nih.gov/gene/?term=54815	p66alpha	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039786	54815	GATAD2A	http://www.ncbi.nlm.nih.gov/gene/?term=54815	p66alpha	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039787	54819	ZCCHC10	http://www.ncbi.nlm.nih.gov/gene/?term=54819		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039788	54819	ZCCHC10	http://www.ncbi.nlm.nih.gov/gene/?term=54819		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039789	54828	BCAS3	http://www.ncbi.nlm.nih.gov/gene/?term=54828	"GAOB1, MAAB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039790	54828	BCAS3	http://www.ncbi.nlm.nih.gov/gene/?term=54828	"GAOB1, MAAB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039791	54840	APTX	http://www.ncbi.nlm.nih.gov/gene/?term=54840	"AOA, AOA1, AXA1, EAOH, EOAHA, FHA-HIT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039792	54872	PIGG	http://www.ncbi.nlm.nih.gov/gene/?term=54872	"GPI7, LAS21, MRT53, PRO4405, RLGS1930"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039793	54873	PALMD	http://www.ncbi.nlm.nih.gov/gene/?term=54873	"C1orf11, PALML"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039794	54875	CNTLN	http://www.ncbi.nlm.nih.gov/gene/?term=54875	"C9orf101, C9orf39, bA340N12.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039795	54875	CNTLN	http://www.ncbi.nlm.nih.gov/gene/?term=54875	"C9orf101, C9orf39, bA340N12.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039796	54880	BCOR	http://www.ncbi.nlm.nih.gov/gene/?term=54880	"ANOP2, MAA2, MCOPS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039797	54880	BCOR	http://www.ncbi.nlm.nih.gov/gene/?term=54880	"ANOP2, MAA2, MCOPS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039798	54893	MTMR10	http://www.ncbi.nlm.nih.gov/gene/?term=54893		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039799	54894	RNF43	http://www.ncbi.nlm.nih.gov/gene/?term=54894	"RNF124, SSPCS, URCC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039800	54894	RNF43	http://www.ncbi.nlm.nih.gov/gene/?term=54894	"RNF124, SSPCS, URCC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039801	54897	CASZ1	http://www.ncbi.nlm.nih.gov/gene/?term=54897	"CAS11, CST, SRG, ZNF693, dJ734G22.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039802	54897	CASZ1	http://www.ncbi.nlm.nih.gov/gene/?term=54897	"CAS11, CST, SRG, ZNF693, dJ734G22.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039803	549	AUH	http://www.ncbi.nlm.nih.gov/gene/?term=549		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039804	54901	CDKAL1	http://www.ncbi.nlm.nih.gov/gene/?term=54901		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039805	54902	TTC19	http://www.ncbi.nlm.nih.gov/gene/?term=54902	"2010204O13Rik, MC3DN2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039806	54902	TTC19	http://www.ncbi.nlm.nih.gov/gene/?term=54902	"2010204O13Rik, MC3DN2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039807	54914	FOCAD	http://www.ncbi.nlm.nih.gov/gene/?term=54914	KIAA1797	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039808	54914	FOCAD	http://www.ncbi.nlm.nih.gov/gene/?term=54914	KIAA1797	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039809	54927	CHCHD3	http://www.ncbi.nlm.nih.gov/gene/?term=54927	"MINOS3, Mic19, PPP1R22"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039810	54927	CHCHD3	http://www.ncbi.nlm.nih.gov/gene/?term=54927	"MINOS3, Mic19, PPP1R22"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039811	54947	LPCAT2	http://www.ncbi.nlm.nih.gov/gene/?term=54947	"AGPAT11, AYTL1, LysoPAFAT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039812	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039813	5496	PPM1G	http://www.ncbi.nlm.nih.gov/gene/?term=5496	"PP2CG, PP2CGAMMA, PPP2CG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039814	54995	OXSM	http://www.ncbi.nlm.nih.gov/gene/?term=54995	"CEM1, FASN2D, KASI, KS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039815	54995	OXSM	http://www.ncbi.nlm.nih.gov/gene/?term=54995	"CEM1, FASN2D, KASI, KS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039816	55002	TMCO3	http://www.ncbi.nlm.nih.gov/gene/?term=55002	C13orf11	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039817	55002	TMCO3	http://www.ncbi.nlm.nih.gov/gene/?term=55002	C13orf11	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039818	55003	PAK1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=55003	"MAK11, PIP1, WDR84, bA421M1.5, hPIP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039819	55003	PAK1IP1	http://www.ncbi.nlm.nih.gov/gene/?term=55003	"MAK11, PIP1, WDR84, bA421M1.5, hPIP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039820	55022	PID1	http://www.ncbi.nlm.nih.gov/gene/?term=55022	"HMFN2073, NYGGF4, P-CLI1, PCLI1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039821	55022	PID1	http://www.ncbi.nlm.nih.gov/gene/?term=55022	"HMFN2073, NYGGF4, P-CLI1, PCLI1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039822	55030	FBXO34	http://www.ncbi.nlm.nih.gov/gene/?term=55030	"CGI-301, Fbx34"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039823	55031	USP47	http://www.ncbi.nlm.nih.gov/gene/?term=55031	TRFP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039824	55031	USP47	http://www.ncbi.nlm.nih.gov/gene/?term=55031	TRFP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039825	55034	MOCOS	http://www.ncbi.nlm.nih.gov/gene/?term=55034	"HMCS, MCS, MOS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039826	55034	MOCOS	http://www.ncbi.nlm.nih.gov/gene/?term=55034	"HMCS, MCS, MOS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039827	55040	EPN3	http://www.ncbi.nlm.nih.gov/gene/?term=55040		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039828	55040	EPN3	http://www.ncbi.nlm.nih.gov/gene/?term=55040		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039829	55071	C9orf40	http://www.ncbi.nlm.nih.gov/gene/?term=55071		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039830	55075	UACA	http://www.ncbi.nlm.nih.gov/gene/?term=55075	NUCLING	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039831	55095	SAMD4B	http://www.ncbi.nlm.nih.gov/gene/?term=55095	"SMGB, Smaug2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039832	55095	SAMD4B	http://www.ncbi.nlm.nih.gov/gene/?term=55095	"SMGB, Smaug2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039833	5510	PPP1R7	http://www.ncbi.nlm.nih.gov/gene/?term=5510	SDS22	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039834	5510	PPP1R7	http://www.ncbi.nlm.nih.gov/gene/?term=5510	SDS22	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039835	55100	WDR70	http://www.ncbi.nlm.nih.gov/gene/?term=55100		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039836	55103	RALGPS2	http://www.ncbi.nlm.nih.gov/gene/?term=55103	dJ595C2.1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039837	55103	RALGPS2	http://www.ncbi.nlm.nih.gov/gene/?term=55103	dJ595C2.1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039838	55105	GPATCH2	http://www.ncbi.nlm.nih.gov/gene/?term=55105	"CT110, GPATC2, PPP1R30, Pfa1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039839	55107	ANO1	http://www.ncbi.nlm.nih.gov/gene/?term=55107	"DOG1, ORAOV2, TAOS2, TMEM16A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039840	55107	ANO1	http://www.ncbi.nlm.nih.gov/gene/?term=55107	"DOG1, ORAOV2, TAOS2, TMEM16A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039841	55112	WDR60	http://www.ncbi.nlm.nih.gov/gene/?term=55112	"FAP163, SRPS6, SRTD8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039842	55129	ANO10	http://www.ncbi.nlm.nih.gov/gene/?term=55129	"SCAR10, TMEM16K"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039843	55132	LARP1B	http://www.ncbi.nlm.nih.gov/gene/?term=55132	LARP2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039844	55144	LRRC8D	http://www.ncbi.nlm.nih.gov/gene/?term=55144	LRRC5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039845	55160	ARHGEF10L	http://www.ncbi.nlm.nih.gov/gene/?term=55160	GrinchGEF	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039846	55160	ARHGEF10L	http://www.ncbi.nlm.nih.gov/gene/?term=55160	GrinchGEF	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039847	55164	SHQ1	http://www.ncbi.nlm.nih.gov/gene/?term=55164	"GRIM-1, Shq1p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039848	55164	SHQ1	http://www.ncbi.nlm.nih.gov/gene/?term=55164	"GRIM-1, Shq1p"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039849	55182	RNF220	http://www.ncbi.nlm.nih.gov/gene/?term=55182	C1orf164	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039850	55182	RNF220	http://www.ncbi.nlm.nih.gov/gene/?term=55182	C1orf164	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039851	55183	RIF1	http://www.ncbi.nlm.nih.gov/gene/?term=55183		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039852	55184	DZANK1	http://www.ncbi.nlm.nih.gov/gene/?term=55184	"ANKRD64, C20orf12, C20orf84, bA189K21.1, bA189K21.8, dJ568F9.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039853	55184	DZANK1	http://www.ncbi.nlm.nih.gov/gene/?term=55184	"ANKRD64, C20orf12, C20orf84, bA189K21.1, bA189K21.8, dJ568F9.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039854	55187	VPS13D	http://www.ncbi.nlm.nih.gov/gene/?term=55187		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039855	55187	VPS13D	http://www.ncbi.nlm.nih.gov/gene/?term=55187		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039856	55188	RIC8B	http://www.ncbi.nlm.nih.gov/gene/?term=55188	"RIC8, hSyn"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039857	55193	PBRM1	http://www.ncbi.nlm.nih.gov/gene/?term=55193	"BAF180, PB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039858	55193	PBRM1	http://www.ncbi.nlm.nih.gov/gene/?term=55193	"BAF180, PB1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039859	55195	CCDC198	http://www.ncbi.nlm.nih.gov/gene/?term=55195	C14orf105	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039860	55198	APPL2	http://www.ncbi.nlm.nih.gov/gene/?term=55198	DIP13B	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039861	55198	APPL2	http://www.ncbi.nlm.nih.gov/gene/?term=55198	DIP13B	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039862	55200	PLEKHG6	http://www.ncbi.nlm.nih.gov/gene/?term=55200	MyoGEF	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039863	55200	PLEKHG6	http://www.ncbi.nlm.nih.gov/gene/?term=55200	MyoGEF	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039864	55206	SBNO1	http://www.ncbi.nlm.nih.gov/gene/?term=55206	"MOP3, Sno"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039865	55230	USP40	http://www.ncbi.nlm.nih.gov/gene/?term=55230		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039866	55230	USP40	http://www.ncbi.nlm.nih.gov/gene/?term=55230		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039867	55234	SMU1	http://www.ncbi.nlm.nih.gov/gene/?term=55234	"BWD, SMU-1, fSAP57"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039868	55234	SMU1	http://www.ncbi.nlm.nih.gov/gene/?term=55234	"BWD, SMU-1, fSAP57"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039869	5524	PTPA	http://www.ncbi.nlm.nih.gov/gene/?term=5524	"PP2A, PPP2R4, PR53"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039870	5524	PTPA	http://www.ncbi.nlm.nih.gov/gene/?term=5524	"PP2A, PPP2R4, PR53"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039871	55249	YY1AP1	http://www.ncbi.nlm.nih.gov/gene/?term=55249	"GRNG, HCCA1, HCCA2, YY1AP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039872	55252	ASXL2	http://www.ncbi.nlm.nih.gov/gene/?term=55252	"ASXH2, SHAPNS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039873	55255	WDR41	http://www.ncbi.nlm.nih.gov/gene/?term=55255	MSTP048	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039874	55256	ADI1	http://www.ncbi.nlm.nih.gov/gene/?term=55256	"APL1, ARD, Fe-ARD, HMFT1638, MTCBP1, Ni-ARD, SIPL, mtnD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039875	5527	PPP2R5C	http://www.ncbi.nlm.nih.gov/gene/?term=5527	"B56G, B56gamma, PR61G"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039876	5527	PPP2R5C	http://www.ncbi.nlm.nih.gov/gene/?term=5527	"B56G, B56gamma, PR61G"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039877	55275	VPS53	http://www.ncbi.nlm.nih.gov/gene/?term=55275	"HCCS1, PCH2E, hVps53L, pp13624"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039878	55275	VPS53	http://www.ncbi.nlm.nih.gov/gene/?term=55275	"HCCS1, PCH2E, hVps53L, pp13624"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039879	55284	UBE2W	http://www.ncbi.nlm.nih.gov/gene/?term=55284	"UBC-16, UBC16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039880	5529	PPP2R5E	http://www.ncbi.nlm.nih.gov/gene/?term=5529	"B56E, B56epsilon"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039881	55291	PPP6R3	http://www.ncbi.nlm.nih.gov/gene/?term=55291	"C11orf23, PP6R3, SAP190, SAPL, SAPLa, SAPS3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039882	55291	PPP6R3	http://www.ncbi.nlm.nih.gov/gene/?term=55291	"C11orf23, PP6R3, SAP190, SAPL, SAPLa, SAPS3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039883	55294	FBXW7	http://www.ncbi.nlm.nih.gov/gene/?term=55294	"AGO, CDC4, FBW6, FBW7, FBX30, FBXO30, FBXW6, SEL-10, SEL10, hAgo, hCdc4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039884	55294	FBXW7	http://www.ncbi.nlm.nih.gov/gene/?term=55294	"AGO, CDC4, FBW6, FBW7, FBX30, FBXO30, FBXW6, SEL-10, SEL10, hAgo, hCdc4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039885	55298	RNF121	http://www.ncbi.nlm.nih.gov/gene/?term=55298		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039886	5530	PPP3CA	http://www.ncbi.nlm.nih.gov/gene/?term=5530	"CALN, CALNA, CALNA1, CCN1, CNA1, PPP2B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039887	5530	PPP3CA	http://www.ncbi.nlm.nih.gov/gene/?term=5530	"CALN, CALNA, CALNA1, CCN1, CNA1, PPP2B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039888	553115	PEF1	http://www.ncbi.nlm.nih.gov/gene/?term=553115	"ABP32A, PEF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039889	553115	PEF1	http://www.ncbi.nlm.nih.gov/gene/?term=553115	"ABP32A, PEF1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039890	55339	WDR33	http://www.ncbi.nlm.nih.gov/gene/?term=55339	"NET14, WDC146"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039891	55342	STRBP	http://www.ncbi.nlm.nih.gov/gene/?term=55342	"HEL162, ILF3L, SPNR, p74"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039892	55351	STK32B	http://www.ncbi.nlm.nih.gov/gene/?term=55351	"HSA250839, STK32, STKG6, YANK2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039893	55351	STK32B	http://www.ncbi.nlm.nih.gov/gene/?term=55351	"HSA250839, STK32, STKG6, YANK2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039894	55366	LGR4	http://www.ncbi.nlm.nih.gov/gene/?term=55366	"BNMD17, GPR48"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039895	55422	ZNF331	http://www.ncbi.nlm.nih.gov/gene/?term=55422	"RITA, ZNF361, ZNF463"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039896	55422	ZNF331	http://www.ncbi.nlm.nih.gov/gene/?term=55422	"RITA, ZNF361, ZNF463"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039897	55486	PARL	http://www.ncbi.nlm.nih.gov/gene/?term=55486	"PRO2207, PSARL, PSARL1, PSENIP2, RHBDS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039898	55486	PARL	http://www.ncbi.nlm.nih.gov/gene/?term=55486	"PRO2207, PSARL, PSARL1, PSENIP2, RHBDS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039899	55500	ETNK1	http://www.ncbi.nlm.nih.gov/gene/?term=55500	"EKI, EKI 1, EKI1, Nbla10396"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039900	55506	H2AFY2	http://www.ncbi.nlm.nih.gov/gene/?term=55506	macroH2A2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039901	55534	MAML3	http://www.ncbi.nlm.nih.gov/gene/?term=55534	"CAGH3, ERDA3, GDN, MAM-2, MAM2, TNRC3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039902	55534	MAML3	http://www.ncbi.nlm.nih.gov/gene/?term=55534	"CAGH3, ERDA3, GDN, MAM-2, MAM2, TNRC3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039903	55556	ENOSF1	http://www.ncbi.nlm.nih.gov/gene/?term=55556	"RTS, TYMSAS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039904	55556	ENOSF1	http://www.ncbi.nlm.nih.gov/gene/?term=55556	"RTS, TYMSAS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039905	55561	CDC42BPG	http://www.ncbi.nlm.nih.gov/gene/?term=55561	"DMPK2, HSMDPKIN, KAPPA-200, MRCKG, MRCKgamma"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039906	55561	CDC42BPG	http://www.ncbi.nlm.nih.gov/gene/?term=55561	"DMPK2, HSMDPKIN, KAPPA-200, MRCKG, MRCKgamma"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039907	55565	ZNF821	http://www.ncbi.nlm.nih.gov/gene/?term=55565		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039908	55568	GALNT10	http://www.ncbi.nlm.nih.gov/gene/?term=55568	"GALNACT10, PPGALNACT10, PPGANTASE10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039909	55568	GALNT10	http://www.ncbi.nlm.nih.gov/gene/?term=55568	"GALNACT10, PPGALNACT10, PPGANTASE10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039910	55589	BMP2K	http://www.ncbi.nlm.nih.gov/gene/?term=55589	"BIKE, HRIHFB2017"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039911	55593	OTUD5	http://www.ncbi.nlm.nih.gov/gene/?term=55593	DUBA	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039912	55593	OTUD5	http://www.ncbi.nlm.nih.gov/gene/?term=55593	DUBA	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039913	55614	KIF16B	http://www.ncbi.nlm.nih.gov/gene/?term=55614	"C20orf23, KISC20ORF, SNX23"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039914	55616	ASAP3	http://www.ncbi.nlm.nih.gov/gene/?term=55616	"ACAP4, CENTB6, DDEFL1, UPLC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039915	55616	ASAP3	http://www.ncbi.nlm.nih.gov/gene/?term=55616	"ACAP4, CENTB6, DDEFL1, UPLC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039916	55619	DOCK10	http://www.ncbi.nlm.nih.gov/gene/?term=55619	"DRIP2, Nbla10300, ZIZ3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039917	55619	DOCK10	http://www.ncbi.nlm.nih.gov/gene/?term=55619	"DRIP2, Nbla10300, ZIZ3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039918	55626	AMBRA1	http://www.ncbi.nlm.nih.gov/gene/?term=55626	"DCAF3, WDR94"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039919	55626	AMBRA1	http://www.ncbi.nlm.nih.gov/gene/?term=55626	"DCAF3, WDR94"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039920	55628	ZNF407	http://www.ncbi.nlm.nih.gov/gene/?term=55628		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039921	55634	KRBOX4	http://www.ncbi.nlm.nih.gov/gene/?term=55634	ZNF673	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039922	55634	KRBOX4	http://www.ncbi.nlm.nih.gov/gene/?term=55634	ZNF673	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039923	55651	NHP2	http://www.ncbi.nlm.nih.gov/gene/?term=55651	"DKCB2P, NOLA2, NHP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039924	55651	NHP2	http://www.ncbi.nlm.nih.gov/gene/?term=55651	"DKCB2P, NOLA2, NHP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039925	55652	SLC48A1	http://www.ncbi.nlm.nih.gov/gene/?term=55652	"HRG-1, HRG1, hHRG-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039926	55666	NPLOC4	http://www.ncbi.nlm.nih.gov/gene/?term=55666	NPL4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039927	55666	NPLOC4	http://www.ncbi.nlm.nih.gov/gene/?term=55666	NPL4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039928	55667	DENND4C	http://www.ncbi.nlm.nih.gov/gene/?term=55667	"C9orf55, C9orf55B, RAB10GEF, bA513M16.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039929	55677	IWS1	http://www.ncbi.nlm.nih.gov/gene/?term=55677		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039930	55677	IWS1	http://www.ncbi.nlm.nih.gov/gene/?term=55677		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039931	55680	RUFY2	http://www.ncbi.nlm.nih.gov/gene/?term=55680	"RABIP4R, ZFYVE13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039932	55680	RUFY2	http://www.ncbi.nlm.nih.gov/gene/?term=55680	"RABIP4R, ZFYVE13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039933	55687	TRMU	http://www.ncbi.nlm.nih.gov/gene/?term=55687	"LCAL3, MTO2, MTU1, TRMT, TRMT1, TRNT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039934	55687	TRMU	http://www.ncbi.nlm.nih.gov/gene/?term=55687	"LCAL3, MTO2, MTU1, TRMT, TRMT1, TRNT1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039935	55690	PACS1	http://www.ncbi.nlm.nih.gov/gene/?term=55690	"MRD17, SHMS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039936	55691	FRMD4A	http://www.ncbi.nlm.nih.gov/gene/?term=55691	"CCAFCA, FRMD4, bA295P9.4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039937	55691	FRMD4A	http://www.ncbi.nlm.nih.gov/gene/?term=55691	"CCAFCA, FRMD4, bA295P9.4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039938	55697	VAC14	http://www.ncbi.nlm.nih.gov/gene/?term=55697	"ArPIKfyve, TAX1BP2, TRX"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039939	55697	VAC14	http://www.ncbi.nlm.nih.gov/gene/?term=55697	"ArPIKfyve, TAX1BP2, TRX"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039940	55704	CCDC88A	http://www.ncbi.nlm.nih.gov/gene/?term=55704	"APE, GIRDIN, GIV, GRDN, HkRP1, KIAA1212, PEHO, PEHOL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039941	55720	TSR1	http://www.ncbi.nlm.nih.gov/gene/?term=55720		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039942	55720	TSR1	http://www.ncbi.nlm.nih.gov/gene/?term=55720		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039943	55727	BTBD7	http://www.ncbi.nlm.nih.gov/gene/?term=55727	FUP1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039944	55731	FAM222B	http://www.ncbi.nlm.nih.gov/gene/?term=55731	C17orf63	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039945	55740	ENAH	http://www.ncbi.nlm.nih.gov/gene/?term=55740	"ENA, MENA, NDPP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039946	55740	ENAH	http://www.ncbi.nlm.nih.gov/gene/?term=55740	"ENA, MENA, NDPP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039947	55748	CNDP2	http://www.ncbi.nlm.nih.gov/gene/?term=55748	"CN2, CPGL, HEL-S-13, HsT2298, PEPA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039948	55748	CNDP2	http://www.ncbi.nlm.nih.gov/gene/?term=55748	"CN2, CPGL, HEL-S-13, HsT2298, PEPA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039949	55758	RCOR3	http://www.ncbi.nlm.nih.gov/gene/?term=55758		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039950	55760	DHX32	http://www.ncbi.nlm.nih.gov/gene/?term=55760	"DDX32, DHLP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039951	55760	DHX32	http://www.ncbi.nlm.nih.gov/gene/?term=55760	"DDX32, DHLP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039952	55761	TTC17	http://www.ncbi.nlm.nih.gov/gene/?term=55761		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039953	55763	EXOC1	http://www.ncbi.nlm.nih.gov/gene/?term=55763	"BM-102, SEC3, SEC3L1, SEC3P"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039954	55764	IFT122	http://www.ncbi.nlm.nih.gov/gene/?term=55764	"CED, CED1, SPG, WDR10, WDR10p, WDR140"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039955	55764	IFT122	http://www.ncbi.nlm.nih.gov/gene/?term=55764	"CED, CED1, SPG, WDR10, WDR10p, WDR140"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039956	55768	NGLY1	http://www.ncbi.nlm.nih.gov/gene/?term=55768	"CDDG, CDG1V, PNG1, PNGase"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039957	55769	ZNF83	http://www.ncbi.nlm.nih.gov/gene/?term=55769	"HPF1, ZNF816B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039958	55770	EXOC2	http://www.ncbi.nlm.nih.gov/gene/?term=55770	"SEC5, SEC5L1, Sec5p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039959	55773	TBC1D23	http://www.ncbi.nlm.nih.gov/gene/?term=55773	NS4ATP1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039960	5578	PRKCA	http://www.ncbi.nlm.nih.gov/gene/?term=5578	"AAG6, PKC-alpha, PKCA, PRKACA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039961	5578	PRKCA	http://www.ncbi.nlm.nih.gov/gene/?term=5578	"AAG6, PKC-alpha, PKCA, PRKACA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039962	55789	DEPDC1B	http://www.ncbi.nlm.nih.gov/gene/?term=55789	"BRCC3, XTP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039963	55789	DEPDC1B	http://www.ncbi.nlm.nih.gov/gene/?term=55789	"BRCC3, XTP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039964	55790	CSGALNACT1	http://www.ncbi.nlm.nih.gov/gene/?term=55790	"CSGalNAcT-1, ChGn, ChGn-1, beta4GalNAcT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039965	55790	CSGALNACT1	http://www.ncbi.nlm.nih.gov/gene/?term=55790	"CSGalNAcT-1, ChGn, ChGn-1, beta4GalNAcT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039966	55791	LRIF1	http://www.ncbi.nlm.nih.gov/gene/?term=55791	"C1orf103, RIF1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039967	55796	MBNL3	http://www.ncbi.nlm.nih.gov/gene/?term=55796	"CHCR, MBLX, MBLX39, MBXL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039968	55796	MBNL3	http://www.ncbi.nlm.nih.gov/gene/?term=55796	"CHCR, MBLX, MBLX39, MBXL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039969	55799	CACNA2D3	http://www.ncbi.nlm.nih.gov/gene/?term=55799	HSA272268	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039970	55799	CACNA2D3	http://www.ncbi.nlm.nih.gov/gene/?term=55799	HSA272268	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039971	55800	SCN3B	http://www.ncbi.nlm.nih.gov/gene/?term=55800	"ATFB16, BRGDA7, HSA243396, SCNB3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039972	55800	SCN3B	http://www.ncbi.nlm.nih.gov/gene/?term=55800	"ATFB16, BRGDA7, HSA243396, SCNB3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039973	55806	HR	http://www.ncbi.nlm.nih.gov/gene/?term=55806	"ALUNC, AU, HSA277165, HYPT4, MUHH, MUHH1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039974	55806	HR	http://www.ncbi.nlm.nih.gov/gene/?term=55806	"ALUNC, AU, HSA277165, HYPT4, MUHH, MUHH1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039975	55812	SPATA7	http://www.ncbi.nlm.nih.gov/gene/?term=55812	"HEL-S-296, HSD-3.1, HSD3, LCA3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039976	55812	SPATA7	http://www.ncbi.nlm.nih.gov/gene/?term=55812	"HEL-S-296, HSD-3.1, HSD3, LCA3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039977	55824	PAG1	http://www.ncbi.nlm.nih.gov/gene/?term=55824	"CBP, PAG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039978	55824	PAG1	http://www.ncbi.nlm.nih.gov/gene/?term=55824	"CBP, PAG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039979	55827	DCAF6	http://www.ncbi.nlm.nih.gov/gene/?term=55827	"1200006M05Rik, ARCAP, IQWD1, MSTP055, NRIP, PC326"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039980	55827	DCAF6	http://www.ncbi.nlm.nih.gov/gene/?term=55827	"1200006M05Rik, ARCAP, IQWD1, MSTP055, NRIP, PC326"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039981	5583	PRKCH	http://www.ncbi.nlm.nih.gov/gene/?term=5583	"PKC-L, PKCL, PRKCL, nPKC-eta"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039982	55841	WWC3	http://www.ncbi.nlm.nih.gov/gene/?term=55841	BM042	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039983	55841	WWC3	http://www.ncbi.nlm.nih.gov/gene/?term=55841	BM042	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039984	55857	KIZ	http://www.ncbi.nlm.nih.gov/gene/?term=55857	"C20orf19, HT013, Kizuna, NCRNA00153, PLK1S1, RP69"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039985	55858	TMEM165	http://www.ncbi.nlm.nih.gov/gene/?term=55858	"CDG2K, FT27, GDT1, TMPT27, TPARL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039986	55858	TMEM165	http://www.ncbi.nlm.nih.gov/gene/?term=55858	"CDG2K, FT27, GDT1, TMPT27, TPARL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039987	5586	PKN2	http://www.ncbi.nlm.nih.gov/gene/?term=5586	"PAK2, PRK2, PRKCL2, PRO2042, Pak-2, STK7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039988	5586	PKN2	http://www.ncbi.nlm.nih.gov/gene/?term=5586	"PAK2, PRK2, PRKCL2, PRO2042, Pak-2, STK7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039989	55862	ECHDC1	http://www.ncbi.nlm.nih.gov/gene/?term=55862	"HEL-S-76, MMCD, dJ351K20.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039990	55869	HDAC8	http://www.ncbi.nlm.nih.gov/gene/?term=55869	"CDA07, CDLS5, HD8, HDACL1, MRXS6, RPD3, WTS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039991	55869	HDAC8	http://www.ncbi.nlm.nih.gov/gene/?term=55869	"CDA07, CDLS5, HD8, HDACL1, MRXS6, RPD3, WTS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039992	55884	WSB2	http://www.ncbi.nlm.nih.gov/gene/?term=55884	SBA2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039993	55884	WSB2	http://www.ncbi.nlm.nih.gov/gene/?term=55884	SBA2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039994	55902	ACSS2	http://www.ncbi.nlm.nih.gov/gene/?term=55902	"ACAS2, ACECS, ACS, ACSA, dJ1161H23.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039995	55902	ACSS2	http://www.ncbi.nlm.nih.gov/gene/?term=55902	"ACAS2, ACECS, ACS, ACSA, dJ1161H23.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039996	55904	KMT2E	http://www.ncbi.nlm.nih.gov/gene/?term=55904	"HDCMC04P, MLL5, NKp44L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039997	55920	RCC2	http://www.ncbi.nlm.nih.gov/gene/?term=55920	TD-60	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00039998	55920	RCC2	http://www.ncbi.nlm.nih.gov/gene/?term=55920	TD-60	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00039999	55930	MYO5C	http://www.ncbi.nlm.nih.gov/gene/?term=55930		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040000	55930	MYO5C	http://www.ncbi.nlm.nih.gov/gene/?term=55930		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040001	55967	NDUFA12	http://www.ncbi.nlm.nih.gov/gene/?term=55967	"B17.2, DAP13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040002	55967	NDUFA12	http://www.ncbi.nlm.nih.gov/gene/?term=55967	"B17.2, DAP13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040003	5597	MAPK6	http://www.ncbi.nlm.nih.gov/gene/?term=5597	"ERK3, HsT17250, PRKM6, p97MAPK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040004	55970	GNG12	http://www.ncbi.nlm.nih.gov/gene/?term=55970		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040005	55970	GNG12	http://www.ncbi.nlm.nih.gov/gene/?term=55970		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040006	55973	BCAP29	http://www.ncbi.nlm.nih.gov/gene/?term=55973	BAP29	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040007	56034	PDGFC	http://www.ncbi.nlm.nih.gov/gene/?term=56034	"FALLOTEIN, SCDGF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040008	56034	PDGFC	http://www.ncbi.nlm.nih.gov/gene/?term=56034	"FALLOTEIN, SCDGF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040009	5607	MAP2K5	http://www.ncbi.nlm.nih.gov/gene/?term=5607	"HsT17454, MAPKK5, MEK5, PRKMK5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040010	5607	MAP2K5	http://www.ncbi.nlm.nih.gov/gene/?term=5607	"HsT17454, MAPKK5, MEK5, PRKMK5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040011	5611	DNAJC3	http://www.ncbi.nlm.nih.gov/gene/?term=5611	"ACPHD, ERdj6, HP58, P58, P58IPK, PRKRI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040012	5613	PRKX	http://www.ncbi.nlm.nih.gov/gene/?term=5613	PKX1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040013	56172	ANKH	http://www.ncbi.nlm.nih.gov/gene/?term=56172	"ANK, CCAL2, CMDJ, CPPDD, HANK, MANK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040014	56204	FAM214A	http://www.ncbi.nlm.nih.gov/gene/?term=56204	KIAA1370	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040015	56204	FAM214A	http://www.ncbi.nlm.nih.gov/gene/?term=56204	KIAA1370	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040016	56243	KIAA1217	http://www.ncbi.nlm.nih.gov/gene/?term=56243	"ETL4, SKT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040017	56243	KIAA1217	http://www.ncbi.nlm.nih.gov/gene/?term=56243	"ETL4, SKT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040018	56261	GPCPD1	http://www.ncbi.nlm.nih.gov/gene/?term=56261	"EDI3, GDE5, GDPD6, PREI4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040019	56270	WDR45B	http://www.ncbi.nlm.nih.gov/gene/?term=56270	"WDR45L, WIPI-3, WIPI3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040020	56270	WDR45B	http://www.ncbi.nlm.nih.gov/gene/?term=56270	"WDR45L, WIPI-3, WIPI3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040021	56288	PARD3	http://www.ncbi.nlm.nih.gov/gene/?term=56288	"ASIP, Baz, PAR3, PAR3alpha, PARD-3A, PPP1R118, SE2-5L16, SE2-5LT1, SE2-5T2, PARD3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040022	56288	PARD3	http://www.ncbi.nlm.nih.gov/gene/?term=56288	"ASIP, Baz, PAR3, PAR3alpha, PARD-3A, PPP1R118, SE2-5L16, SE2-5LT1, SE2-5T2, PARD3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040023	56474	CTPS2	http://www.ncbi.nlm.nih.gov/gene/?term=56474		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040024	56474	CTPS2	http://www.ncbi.nlm.nih.gov/gene/?term=56474		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040025	56478	EIF4ENIF1	http://www.ncbi.nlm.nih.gov/gene/?term=56478	"4E-T, Clast4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040026	56478	EIF4ENIF1	http://www.ncbi.nlm.nih.gov/gene/?term=56478	"4E-T, Clast4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040027	5649	RELN	http://www.ncbi.nlm.nih.gov/gene/?term=5649	"ETL7, LIS2, PRO1598, RL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040028	5649	RELN	http://www.ncbi.nlm.nih.gov/gene/?term=5649	"ETL7, LIS2, PRO1598, RL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040029	56623	INPP5E	http://www.ncbi.nlm.nih.gov/gene/?term=56623	"CORS1, CPD4, JBTS1, MORMS, PPI5PIV, pharbin"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040030	56623	INPP5E	http://www.ncbi.nlm.nih.gov/gene/?term=56623	"CORS1, CPD4, JBTS1, MORMS, PPI5PIV, pharbin"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040031	56660	KCNK12	http://www.ncbi.nlm.nih.gov/gene/?term=56660	"K2p12.1, THIK-2, THIK2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040032	5682	PSMA1	http://www.ncbi.nlm.nih.gov/gene/?term=5682	"NU, HC2, PROS30, HEL-S-275"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040033	5682	PSMA1	http://www.ncbi.nlm.nih.gov/gene/?term=5682	"NU, HC2, PROS30, HEL-S-275"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040034	56850	GRIPAP1	http://www.ncbi.nlm.nih.gov/gene/?term=56850	GRASP-1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040035	56850	GRIPAP1	http://www.ncbi.nlm.nih.gov/gene/?term=56850	GRASP-1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040036	56886	UGGT1	http://www.ncbi.nlm.nih.gov/gene/?term=56886	"HUGT1, UGCGL1, UGT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040037	56886	UGGT1	http://www.ncbi.nlm.nih.gov/gene/?term=56886	"HUGT1, UGCGL1, UGT1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040038	56889	TM9SF3	http://www.ncbi.nlm.nih.gov/gene/?term=56889	"EP70-P-iso, SMBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040039	56889	TM9SF3	http://www.ncbi.nlm.nih.gov/gene/?term=56889	"EP70-P-iso, SMBP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040040	56894	AGPAT3	http://www.ncbi.nlm.nih.gov/gene/?term=56894	"LPAAT-GAMMA1, LPAAT3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040041	56894	AGPAT3	http://www.ncbi.nlm.nih.gov/gene/?term=56894	"LPAAT-GAMMA1, LPAAT3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040042	56899	ANKS1B	http://www.ncbi.nlm.nih.gov/gene/?term=56899	"AIDA, AIDA-1, ANKS2, EB-1, EB1, cajalin-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040043	56947	MFF	http://www.ncbi.nlm.nih.gov/gene/?term=56947	"C2orf33, EMPF2, GL004"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040044	56947	MFF	http://www.ncbi.nlm.nih.gov/gene/?term=56947	"C2orf33, EMPF2, GL004"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040045	5695	PSMB7	http://www.ncbi.nlm.nih.gov/gene/?term=5695	Z	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040046	5695	PSMB7	http://www.ncbi.nlm.nih.gov/gene/?term=5695	Z	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040047	56957	OTUD7B	http://www.ncbi.nlm.nih.gov/gene/?term=56957	"ZA20D1, CEZANNE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040048	56987	BBX	http://www.ncbi.nlm.nih.gov/gene/?term=56987	"ARTC1, HBP2, HSPC339, MDS001"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040049	56987	BBX	http://www.ncbi.nlm.nih.gov/gene/?term=56987	"ARTC1, HBP2, HSPC339, MDS001"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040050	56992	KIF15	http://www.ncbi.nlm.nih.gov/gene/?term=56992	"HKLP2, KLP2, KNSL7, NY-BR-62"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040051	56995	TULP4	http://www.ncbi.nlm.nih.gov/gene/?term=56995	TUSP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040052	56995	TULP4	http://www.ncbi.nlm.nih.gov/gene/?term=56995	TUSP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040053	56997	COQ8A	http://www.ncbi.nlm.nih.gov/gene/?term=56997	"ADCK3, ARCA2, CABC1, COQ10D4, COQ8, SCAR9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040054	56997	COQ8A	http://www.ncbi.nlm.nih.gov/gene/?term=56997	"ADCK3, ARCA2, CABC1, COQ10D4, COQ8, SCAR9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040055	57007	ACKR3	http://www.ncbi.nlm.nih.gov/gene/?term=57007	"CMKOR1, CXC-R7, CXCR-7, CXCR7, GPR159, RDC-1, RDC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040056	57020	C16orf62	http://www.ncbi.nlm.nih.gov/gene/?term=57020		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040057	57020	C16orf62	http://www.ncbi.nlm.nih.gov/gene/?term=57020		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040058	57060	PCBP4	http://www.ncbi.nlm.nih.gov/gene/?term=57060	"CBP, LIP4, MCG10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040059	57060	PCBP4	http://www.ncbi.nlm.nih.gov/gene/?term=57060	"CBP, LIP4, MCG10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040060	5707	PSMD1	http://www.ncbi.nlm.nih.gov/gene/?term=5707	"P112, Rpn2, S1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040061	57111	RAB25	http://www.ncbi.nlm.nih.gov/gene/?term=57111	"CATX-8, RAB11C"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040062	57111	RAB25	http://www.ncbi.nlm.nih.gov/gene/?term=57111	"CATX-8, RAB11C"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040063	57142	RTN4	http://www.ncbi.nlm.nih.gov/gene/?term=57142	"ASY, NI220/250, NOGO, NSP, NSP-CL, Nbla00271, Nbla10545, RTN-X-A, RTN4-B1, RTN4-B2, RTN4-C, RTN4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040064	57146	TMEM159	http://www.ncbi.nlm.nih.gov/gene/?term=57146		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040065	57147	SCYL3	http://www.ncbi.nlm.nih.gov/gene/?term=57147	"PACE-1, PACE1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040066	57147	SCYL3	http://www.ncbi.nlm.nih.gov/gene/?term=57147	"PACE-1, PACE1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040067	57154	SMURF1	http://www.ncbi.nlm.nih.gov/gene/?term=57154		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040068	57154	SMURF1	http://www.ncbi.nlm.nih.gov/gene/?term=57154		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040069	57169	ZNFX1	http://www.ncbi.nlm.nih.gov/gene/?term=57169		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040070	57169	ZNFX1	http://www.ncbi.nlm.nih.gov/gene/?term=57169		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040071	57178	ZMIZ1	http://www.ncbi.nlm.nih.gov/gene/?term=57178	"MIZ, RAI17, TRAFIP10, ZIMP10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040072	57178	ZMIZ1	http://www.ncbi.nlm.nih.gov/gene/?term=57178	"MIZ, RAI17, TRAFIP10, ZIMP10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040073	57181	SLC39A10	http://www.ncbi.nlm.nih.gov/gene/?term=57181	LZT-Hs2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040074	57181	SLC39A10	http://www.ncbi.nlm.nih.gov/gene/?term=57181	LZT-Hs2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040075	57217	TTC7A	http://www.ncbi.nlm.nih.gov/gene/?term=57217	"GIDID, MINAT, TTC7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040076	57217	TTC7A	http://www.ncbi.nlm.nih.gov/gene/?term=57217	"GIDID, MINAT, TTC7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040077	57223	PPP4R3B	http://www.ncbi.nlm.nih.gov/gene/?term=57223	"PSY2, smk1, FLFL2, SMEK2, PP4R3B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040078	5728	PTEN	http://www.ncbi.nlm.nih.gov/gene/?term=5728	"10q23del, BZS, CWS1, DEC, GLM2, MHAM, MMAC11, PTENbeta, TEP1, PTEN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040079	57325	KAT14	http://www.ncbi.nlm.nih.gov/gene/?term=57325	"ATAC2, CRP2BP, CSRP2BP, PRO1194, dJ717M23.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040080	57325	KAT14	http://www.ncbi.nlm.nih.gov/gene/?term=57325	"ATAC2, CRP2BP, CSRP2BP, PRO1194, dJ717M23.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040081	57405	SPC25	http://www.ncbi.nlm.nih.gov/gene/?term=57405	"AD024, SPBC25, hSpc25"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040082	57408	LRTM1	http://www.ncbi.nlm.nih.gov/gene/?term=57408	HT017	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040083	57408	LRTM1	http://www.ncbi.nlm.nih.gov/gene/?term=57408	HT017	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040084	57414	RHBDD2	http://www.ncbi.nlm.nih.gov/gene/?term=57414	"NPD007, RHBDL7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040085	57414	RHBDD2	http://www.ncbi.nlm.nih.gov/gene/?term=57414	"NPD007, RHBDL7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040086	57448	BIRC6	http://www.ncbi.nlm.nih.gov/gene/?term=57448	"APOLLON, BRUCE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040087	57448	BIRC6	http://www.ncbi.nlm.nih.gov/gene/?term=57448	"APOLLON, BRUCE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040088	57458	TMCC3	http://www.ncbi.nlm.nih.gov/gene/?term=57458		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040089	57458	TMCC3	http://www.ncbi.nlm.nih.gov/gene/?term=57458		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040090	57459	GATAD2B	http://www.ncbi.nlm.nih.gov/gene/?term=57459	"MRD18, P66beta, p68"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040091	57459	GATAD2B	http://www.ncbi.nlm.nih.gov/gene/?term=57459	"MRD18, P66beta, p68"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040092	5747	PTK2	http://www.ncbi.nlm.nih.gov/gene/?term=5747	"FADK, FAK, FAK1, FRNK, PPP1R71, p125FAK, pp125FAK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040093	5747	PTK2	http://www.ncbi.nlm.nih.gov/gene/?term=5747	"FADK, FAK, FAK1, FRNK, PPP1R71, p125FAK, pp125FAK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040094	57473	ZNF512B	http://www.ncbi.nlm.nih.gov/gene/?term=57473	GM632	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040095	57473	ZNF512B	http://www.ncbi.nlm.nih.gov/gene/?term=57473	GM632	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040096	57478	USP31	http://www.ncbi.nlm.nih.gov/gene/?term=57478		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040097	57488	ESYT2	http://www.ncbi.nlm.nih.gov/gene/?term=57488	"CHR2SYT, E-Syt2, FAM62B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040098	57488	ESYT2	http://www.ncbi.nlm.nih.gov/gene/?term=57488	"CHR2SYT, E-Syt2, FAM62B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040099	57492	ARID1B	http://www.ncbi.nlm.nih.gov/gene/?term=57492	"6A3-5, BAF250B, BRIGHT, CSS1, DAN15, ELD/OSA1, MRD12, OSA2, P250R"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040100	57492	ARID1B	http://www.ncbi.nlm.nih.gov/gene/?term=57492	"6A3-5, BAF250B, BRIGHT, CSS1, DAN15, ELD/OSA1, MRD12, OSA2, P250R"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040101	57498	KIDINS220	http://www.ncbi.nlm.nih.gov/gene/?term=57498	"ARMS, SINO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040102	57507	ZNF608	http://www.ncbi.nlm.nih.gov/gene/?term=57507	NY-REN-36	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040103	57507	ZNF608	http://www.ncbi.nlm.nih.gov/gene/?term=57507	NY-REN-36	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040104	57510	XPO5	http://www.ncbi.nlm.nih.gov/gene/?term=57510	exp5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040105	57510	XPO5	http://www.ncbi.nlm.nih.gov/gene/?term=57510	exp5	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040106	57521	RPTOR	http://www.ncbi.nlm.nih.gov/gene/?term=57521	"KOG1, Mip1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040107	57521	RPTOR	http://www.ncbi.nlm.nih.gov/gene/?term=57521	"KOG1, Mip1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040108	57522	SRGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=57522	"ARHGAP13, NMTC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040109	57522	SRGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=57522	"ARHGAP13, NMTC2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040110	57552	NCEH1	http://www.ncbi.nlm.nih.gov/gene/?term=57552	"AADACL1, NCEH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040111	57552	NCEH1	http://www.ncbi.nlm.nih.gov/gene/?term=57552	"AADACL1, NCEH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040112	57559	STAMBPL1	http://www.ncbi.nlm.nih.gov/gene/?term=57559	"ALMalpha, AMSH-FP, AMSH-LP, bA399O19.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040113	57559	STAMBPL1	http://www.ncbi.nlm.nih.gov/gene/?term=57559	"ALMalpha, AMSH-FP, AMSH-LP, bA399O19.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040114	57563	KLHL8	http://www.ncbi.nlm.nih.gov/gene/?term=57563		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040115	57563	KLHL8	http://www.ncbi.nlm.nih.gov/gene/?term=57563		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040116	57568	SIPA1L2	http://www.ncbi.nlm.nih.gov/gene/?term=57568	SPAL2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040117	57590	WDFY1	http://www.ncbi.nlm.nih.gov/gene/?term=57590	"FENS-1, WDF1, ZFYVE17"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040118	57590	WDFY1	http://www.ncbi.nlm.nih.gov/gene/?term=57590	"FENS-1, WDF1, ZFYVE17"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040119	57591	MKL1	http://www.ncbi.nlm.nih.gov/gene/?term=57591	"BSAC, MAL, MKL, MRTF-A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040120	57591	MKL1	http://www.ncbi.nlm.nih.gov/gene/?term=57591	"BSAC, MAL, MKL, MRTF-A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040121	57609	DIP2B	http://www.ncbi.nlm.nih.gov/gene/?term=57609		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040122	57609	DIP2B	http://www.ncbi.nlm.nih.gov/gene/?term=57609		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040123	57620	STIM2	http://www.ncbi.nlm.nih.gov/gene/?term=57620		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040124	57628	DPP10	http://www.ncbi.nlm.nih.gov/gene/?term=57628	"DPL2, DPPY, DPRP-3, DPRP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040125	57628	DPP10	http://www.ncbi.nlm.nih.gov/gene/?term=57628	"DPL2, DPPY, DPRP-3, DPRP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040126	57630	SH3RF1	http://www.ncbi.nlm.nih.gov/gene/?term=57630	"POSH, RNF142, SH3MD2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040127	57645	POGK	http://www.ncbi.nlm.nih.gov/gene/?term=57645	"BASS2, KRBOX2, LST003"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040128	57654	UVSSA	http://www.ncbi.nlm.nih.gov/gene/?term=57654	"KIAA1530, UVSS3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040129	57654	UVSSA	http://www.ncbi.nlm.nih.gov/gene/?term=57654	"KIAA1530, UVSS3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040130	57669	EPB41L5	http://www.ncbi.nlm.nih.gov/gene/?term=57669	"BE37, YMO1, YRT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040131	57677	ZFP14	http://www.ncbi.nlm.nih.gov/gene/?term=57677	ZNF531	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040132	5768	QSOX1	http://www.ncbi.nlm.nih.gov/gene/?term=5768	"Q6, QSCN6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040133	57693	ZNF317	http://www.ncbi.nlm.nih.gov/gene/?term=57693		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040134	57698	SHTN1	http://www.ncbi.nlm.nih.gov/gene/?term=57698	"KIAA1598, shootin-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040135	57698	SHTN1	http://www.ncbi.nlm.nih.gov/gene/?term=57698	"KIAA1598, shootin-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040136	57706	DENND1A	http://www.ncbi.nlm.nih.gov/gene/?term=57706	"FAM31A, KIAA1608"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040137	57706	DENND1A	http://www.ncbi.nlm.nih.gov/gene/?term=57706	"FAM31A, KIAA1608"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040138	57721	METTL14	http://www.ncbi.nlm.nih.gov/gene/?term=57721	hMETTL14	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040139	57724	EPG5	http://www.ncbi.nlm.nih.gov/gene/?term=57724	"HEEW1, KIAA1632, VICIS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040140	57724	EPG5	http://www.ncbi.nlm.nih.gov/gene/?term=57724	"HEEW1, KIAA1632, VICIS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040141	5775	PTPN4	http://www.ncbi.nlm.nih.gov/gene/?term=5775	"MEG, PTPMEG, PTPMEG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040142	5775	PTPN4	http://www.ncbi.nlm.nih.gov/gene/?term=5775	"MEG, PTPMEG, PTPMEG1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040143	57787	MARK4	http://www.ncbi.nlm.nih.gov/gene/?term=57787	"MARK4LS, MARKL1, MARKL1L, PAR-1D, MARK4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040144	57787	MARK4	http://www.ncbi.nlm.nih.gov/gene/?term=57787	"MARK4LS, MARKL1, MARKL1L, PAR-1D, MARK4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040145	57795	BRINP2	http://www.ncbi.nlm.nih.gov/gene/?term=57795	"DBCCR1L2, FAM5B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040146	57795	BRINP2	http://www.ncbi.nlm.nih.gov/gene/?term=57795	"DBCCR1L2, FAM5B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040147	57799	RAB40C	http://www.ncbi.nlm.nih.gov/gene/?term=57799	"RARL, RASL8C"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040148	5782	PTPN12	http://www.ncbi.nlm.nih.gov/gene/?term=5782	"PTP-PEST, PTPG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040149	57822	GRHL3	http://www.ncbi.nlm.nih.gov/gene/?term=57822	"SOM, TFCP2L4, VWS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040150	57822	GRHL3	http://www.ncbi.nlm.nih.gov/gene/?term=57822	"SOM, TFCP2L4, VWS2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040151	5783	PTPN13	http://www.ncbi.nlm.nih.gov/gene/?term=5783	"FAP-1, PNP1, PTP-BAS, PTP-BL, PTP1E, PTPL1, PTPLE, hPTP1E"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040152	5784	PTPN14	http://www.ncbi.nlm.nih.gov/gene/?term=5784	"PEZ, PTP36"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040153	5789	PTPRD	http://www.ncbi.nlm.nih.gov/gene/?term=5789	"HPTP, HPTPD, HPTPDELTA, PTPD, RPTPDELTA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040154	5789	PTPRD	http://www.ncbi.nlm.nih.gov/gene/?term=5789	"HPTP, HPTPD, HPTPDELTA, PTPD, RPTPDELTA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040155	5791	PTPRE	http://www.ncbi.nlm.nih.gov/gene/?term=5791	"HPTPE, PTPE, R-PTP-EPSILON"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040156	5791	PTPRE	http://www.ncbi.nlm.nih.gov/gene/?term=5791	"HPTPE, PTPE, R-PTP-EPSILON"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040157	5793	PTPRG	http://www.ncbi.nlm.nih.gov/gene/?term=5793	"HPTPG, PTPG, R-PTP-GAMMA, RPTPG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040158	5793	PTPRG	http://www.ncbi.nlm.nih.gov/gene/?term=5793	"HPTPG, PTPG, R-PTP-GAMMA, RPTPG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040159	5795	PTPRJ	http://www.ncbi.nlm.nih.gov/gene/?term=5795	"CD148, DEP1, HPTPeta, R-PTP-ETA, SCC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040160	5795	PTPRJ	http://www.ncbi.nlm.nih.gov/gene/?term=5795	"CD148, DEP1, HPTPeta, R-PTP-ETA, SCC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040161	5796	PTPRK	http://www.ncbi.nlm.nih.gov/gene/?term=5796	R-PTP-kappa	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040162	5797	PTPRM	http://www.ncbi.nlm.nih.gov/gene/?term=5797	"PTPRL1, R-PTP-MU, RPTPM, RPTPU, hR-PTPu"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040163	5797	PTPRM	http://www.ncbi.nlm.nih.gov/gene/?term=5797	"PTPRL1, R-PTP-MU, RPTPM, RPTPU, hR-PTPu"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040164	5799	PTPRN2	http://www.ncbi.nlm.nih.gov/gene/?term=5799	"IA-2beta, IAR, ICAAR, PTPRP, R-PTP-N2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040165	5799	PTPRN2	http://www.ncbi.nlm.nih.gov/gene/?term=5799	"IA-2beta, IAR, ICAAR, PTPRP, R-PTP-N2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040166	58155	PTBP2	http://www.ncbi.nlm.nih.gov/gene/?term=58155	"PTBLP, brPTB, nPTB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040167	58155	PTBP2	http://www.ncbi.nlm.nih.gov/gene/?term=58155	"PTBLP, brPTB, nPTB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040168	5819	NECTIN2	http://www.ncbi.nlm.nih.gov/gene/?term=5819	"CD112, HVEB, PRR2, PVRL2, PVRR2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040169	5819	NECTIN2	http://www.ncbi.nlm.nih.gov/gene/?term=5819	"CD112, HVEB, PRR2, PVRL2, PVRR2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040170	5829	PXN	http://www.ncbi.nlm.nih.gov/gene/?term=5829		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040171	5829	PXN	http://www.ncbi.nlm.nih.gov/gene/?term=5829		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040172	58506	SCAF1	http://www.ncbi.nlm.nih.gov/gene/?term=58506	SRA1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040173	58506	SCAF1	http://www.ncbi.nlm.nih.gov/gene/?term=58506	SRA1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040174	58508	KMT2C	http://www.ncbi.nlm.nih.gov/gene/?term=58508	"HALR, MLL3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040175	58508	KMT2C	http://www.ncbi.nlm.nih.gov/gene/?term=58508	"HALR, MLL3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040176	58513	EPS15L1	http://www.ncbi.nlm.nih.gov/gene/?term=58513	EPS15R	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040177	58513	EPS15L1	http://www.ncbi.nlm.nih.gov/gene/?term=58513	EPS15R	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040178	5862	RAB2A	http://www.ncbi.nlm.nih.gov/gene/?term=5862	"LHX, RAB2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040179	5868	RAB5A	http://www.ncbi.nlm.nih.gov/gene/?term=5868	RAB5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040180	5869	RAB5B	http://www.ncbi.nlm.nih.gov/gene/?term=5869		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040181	5870	RAB6A	http://www.ncbi.nlm.nih.gov/gene/?term=5870	RAB6	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040182	5870	RAB6A	http://www.ncbi.nlm.nih.gov/gene/?term=5870	RAB6	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040183	5887	RAD23B	http://www.ncbi.nlm.nih.gov/gene/?term=5887	"HHR23B, HR23B, P58"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040184	5890	RAD51B	http://www.ncbi.nlm.nih.gov/gene/?term=5890	"R51H2, RAD51L1, REC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040185	5890	RAD51B	http://www.ncbi.nlm.nih.gov/gene/?term=5890	"R51H2, RAD51L1, REC2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040186	5906	RAP1A	http://www.ncbi.nlm.nih.gov/gene/?term=5906	"C21KG, G-22K, KREV-1, KREV1, RAP1, SMGP21"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040187	5910	RAP1GDS1	http://www.ncbi.nlm.nih.gov/gene/?term=5910	"GDS1, SmgGDS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040188	5918	RARRES1	http://www.ncbi.nlm.nih.gov/gene/?term=5918	"LXNL, PERG-1, TIG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040189	5921	RASA1	http://www.ncbi.nlm.nih.gov/gene/?term=5921	"CM-AVM, CMAVM, GAP, PKWS, RASA, RASGAP, p120, p120GAP, p120RASGAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040190	5921	RASA1	http://www.ncbi.nlm.nih.gov/gene/?term=5921	"CM-AVM, CMAVM, GAP, PKWS, RASA, RASGAP, p120, p120GAP, p120RASGAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040191	5924	RASGRF2	http://www.ncbi.nlm.nih.gov/gene/?term=5924	"GRF2, RAS-GRF2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040192	5924	RASGRF2	http://www.ncbi.nlm.nih.gov/gene/?term=5924	"GRF2, RAS-GRF2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040193	5925	RB1	http://www.ncbi.nlm.nih.gov/gene/?term=5925	"OSRC, PPP1R130, RB, p105-Rb, pRb, pp110"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040194	5925	RB1	http://www.ncbi.nlm.nih.gov/gene/?term=5925	"OSRC, PPP1R130, RB, p105-Rb, pRb, pp110"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040195	59271	EVA1C	http://www.ncbi.nlm.nih.gov/gene/?term=59271	"B18, B19, C21orf63, C21orf64, FAM176C, PRED34, SUE21"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040196	59271	EVA1C	http://www.ncbi.nlm.nih.gov/gene/?term=59271	"B18, B19, C21orf63, C21orf64, FAM176C, PRED34, SUE21"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040197	59277	NTN4	http://www.ncbi.nlm.nih.gov/gene/?term=59277	PRO3091	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040198	59277	NTN4	http://www.ncbi.nlm.nih.gov/gene/?term=59277	PRO3091	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040199	59345	GNB4	http://www.ncbi.nlm.nih.gov/gene/?term=59345	CMTD1F	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040200	5937	RBMS1	http://www.ncbi.nlm.nih.gov/gene/?term=5937	"C2orf12, HCC-4, MSSP, MSSP-1, MSSP-2, MSSP-3, SCR2, YC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040201	596	BCL2	http://www.ncbi.nlm.nih.gov/gene/?term=596	"Bcl-2, PPP1R50"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040202	596	BCL2	http://www.ncbi.nlm.nih.gov/gene/?term=596	"Bcl-2, PPP1R50"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040203	5980	REV3L	http://www.ncbi.nlm.nih.gov/gene/?term=5980	"POLZ, REV3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040204	5980	REV3L	http://www.ncbi.nlm.nih.gov/gene/?term=5980	"POLZ, REV3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040205	5991	RFX3	http://www.ncbi.nlm.nih.gov/gene/?term=5991		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040206	5991	RFX3	http://www.ncbi.nlm.nih.gov/gene/?term=5991		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040207	5994	RFXAP	http://www.ncbi.nlm.nih.gov/gene/?term=5994		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040208	5998	RGS3	http://www.ncbi.nlm.nih.gov/gene/?term=5998	"C2PA, RGP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040209	5998	RGS3	http://www.ncbi.nlm.nih.gov/gene/?term=5998	"C2PA, RGP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040210	6009	RHEB	http://www.ncbi.nlm.nih.gov/gene/?term=6009	RHEB2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040211	6009	RHEB	http://www.ncbi.nlm.nih.gov/gene/?term=6009	RHEB2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040212	604	BCL6	http://www.ncbi.nlm.nih.gov/gene/?term=604	"BCL5A, LAZ3, ZBTB27, ZNF51, BCL6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040213	604	BCL6	http://www.ncbi.nlm.nih.gov/gene/?term=604	"BCL5A, LAZ3, ZBTB27, ZNF51, BCL6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040214	60412	EXOC4	http://www.ncbi.nlm.nih.gov/gene/?term=60412	"SEC8, SEC8L1, Sec8p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040215	60412	EXOC4	http://www.ncbi.nlm.nih.gov/gene/?term=60412	"SEC8, SEC8L1, Sec8p"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040216	60468	BACH2	http://www.ncbi.nlm.nih.gov/gene/?term=60468	BTBD25	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040217	60468	BACH2	http://www.ncbi.nlm.nih.gov/gene/?term=60468	BTBD25	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040218	60490	PPCDC	http://www.ncbi.nlm.nih.gov/gene/?term=60490	"MDS018, PPC-DC, coaC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040219	60490	PPCDC	http://www.ncbi.nlm.nih.gov/gene/?term=60490	"MDS018, PPC-DC, coaC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040220	605	BCL7A	http://www.ncbi.nlm.nih.gov/gene/?term=605	BCL7	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040221	605	BCL7A	http://www.ncbi.nlm.nih.gov/gene/?term=605	BCL7	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040222	6051	RNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=6051	"AP-B, APB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040223	6051	RNPEP	http://www.ncbi.nlm.nih.gov/gene/?term=6051	"AP-B, APB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040224	60526	LDAH	http://www.ncbi.nlm.nih.gov/gene/?term=60526	"C2orf43, hLDAH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040225	60526	LDAH	http://www.ncbi.nlm.nih.gov/gene/?term=60526	"C2orf43, hLDAH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040226	60561	RINT1	http://www.ncbi.nlm.nih.gov/gene/?term=60561	RINT-1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040227	60598	KCNK15	http://www.ncbi.nlm.nih.gov/gene/?term=60598	"K2p15.1, KCNK11, KCNK14, KT3.3, TASK-5, TASK5, dJ781B1.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040228	60598	KCNK15	http://www.ncbi.nlm.nih.gov/gene/?term=60598	"K2p15.1, KCNK11, KCNK14, KT3.3, TASK-5, TASK5, dJ781B1.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040229	60684	TRAPPC11	http://www.ncbi.nlm.nih.gov/gene/?term=60684	"C4orf41, FOIGR, GRY, LGMD2S"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040230	60685	ZFAND3	http://www.ncbi.nlm.nih.gov/gene/?term=60685	TEX27	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040231	60685	ZFAND3	http://www.ncbi.nlm.nih.gov/gene/?term=60685	TEX27	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040232	607	BCL9	http://www.ncbi.nlm.nih.gov/gene/?term=607	LGS	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040233	607	BCL9	http://www.ncbi.nlm.nih.gov/gene/?term=607	LGS	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040234	6091	ROBO1	http://www.ncbi.nlm.nih.gov/gene/?term=6091	"DUTT1, SAX3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040235	6093	ROCK1	http://www.ncbi.nlm.nih.gov/gene/?term=6093	"P160ROCK, ROCK-I"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040236	6095	RORA	http://www.ncbi.nlm.nih.gov/gene/?term=6095	"NR1F1, ROR1, ROR2, ROR3, RZR-ALPHA, RZRA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040237	6095	RORA	http://www.ncbi.nlm.nih.gov/gene/?term=6095	"NR1F1, ROR1, ROR2, ROR3, RZR-ALPHA, RZRA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040238	613	BCR	http://www.ncbi.nlm.nih.gov/gene/?term=613	"ALL1, CML, D22S11, D22S662, PHL, BCR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040239	613	BCR	http://www.ncbi.nlm.nih.gov/gene/?term=613	"ALL1, CML, D22S11, D22S662, PHL, BCR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040240	6160	RPL31	http://www.ncbi.nlm.nih.gov/gene/?term=6160	L31	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040241	6164	RPL34	http://www.ncbi.nlm.nih.gov/gene/?term=6164	L34	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040242	6188	RPS3	http://www.ncbi.nlm.nih.gov/gene/?term=6188	S3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040243	6188	RPS3	http://www.ncbi.nlm.nih.gov/gene/?term=6188	S3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040244	6196	RPS6KA2	http://www.ncbi.nlm.nih.gov/gene/?term=6196	"HU-2, MAPKAPK1C, RSK, RSK3, S6K-alpha, S6K-alpha2, p90-RSK3, p90RSK2, pp90RSK3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040245	6196	RPS6KA2	http://www.ncbi.nlm.nih.gov/gene/?term=6196	"HU-2, MAPKAPK1C, RSK, RSK3, S6K-alpha, S6K-alpha2, p90-RSK3, p90RSK2, pp90RSK3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040246	6197	RPS6KA3	http://www.ncbi.nlm.nih.gov/gene/?term=6197	"CLS, HU-3, ISPK-1, MAPKAPK1B, MRX19, RSK, RSK2, S6K-alpha3, p90-RSK2, pp90RSK2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040247	6203	RPS9	http://www.ncbi.nlm.nih.gov/gene/?term=6203	S9	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040248	6203	RPS9	http://www.ncbi.nlm.nih.gov/gene/?term=6203	S9	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040249	6232	RPS27	http://www.ncbi.nlm.nih.gov/gene/?term=6232	"DBA17, MPS-1, MPS1, S27"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040250	6232	RPS27	http://www.ncbi.nlm.nih.gov/gene/?term=6232	"DBA17, MPS-1, MPS1, S27"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040251	6234	RPS28	http://www.ncbi.nlm.nih.gov/gene/?term=6234	"DBA15, S28"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040252	6234	RPS28	http://www.ncbi.nlm.nih.gov/gene/?term=6234	"DBA15, S28"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040253	6259	RYK	http://www.ncbi.nlm.nih.gov/gene/?term=6259	"D3S3195, JTK5, JTK5A1, RYK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040254	6310	ATXN1	http://www.ncbi.nlm.nih.gov/gene/?term=6310	"ATX1, D6S504E, SCA1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040255	6310	ATXN1	http://www.ncbi.nlm.nih.gov/gene/?term=6310	"ATX1, D6S504E, SCA1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040256	6311	ATXN2	http://www.ncbi.nlm.nih.gov/gene/?term=6311	"ATX2, SCA2, TNRC13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040257	6323	SCN1A	http://www.ncbi.nlm.nih.gov/gene/?term=6323	"EIEE6, FEB3, FEB3A, FHM3, GEFSP2, HBSCI, NAC1, Nav1.1, SCN1, SMEI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040258	636	BICD1	http://www.ncbi.nlm.nih.gov/gene/?term=636	BICD	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040259	636	BICD1	http://www.ncbi.nlm.nih.gov/gene/?term=636	BICD	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040260	63877	FAM204A	http://www.ncbi.nlm.nih.gov/gene/?term=63877	"C10orf84, bA319I23.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040261	63877	FAM204A	http://www.ncbi.nlm.nih.gov/gene/?term=63877	"C10orf84, bA319I23.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040262	63893	UBE2O	http://www.ncbi.nlm.nih.gov/gene/?term=63893	E2-230K	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040263	63893	UBE2O	http://www.ncbi.nlm.nih.gov/gene/?term=63893	E2-230K	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040264	63898	SH2D4A	http://www.ncbi.nlm.nih.gov/gene/?term=63898	"PPP1R38, SH2A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040265	6390	SDHB	http://www.ncbi.nlm.nih.gov/gene/?term=6390	"CWS2, IP, PGL4, SDH, SDH1, SDH2, SDHIP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040266	63901	FAM111A	http://www.ncbi.nlm.nih.gov/gene/?term=63901	"GCLEB, KCS2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040267	6392	SDHD	http://www.ncbi.nlm.nih.gov/gene/?term=6392	"PGL, CBT1, CWS3, PGL1, QPs3, SDH4, cybS, CII-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040268	6392	SDHD	http://www.ncbi.nlm.nih.gov/gene/?term=6392	"PGL, CBT1, CWS3, PGL1, QPs3, SDH4, cybS, CII-4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040269	6397	SEC14L1	http://www.ncbi.nlm.nih.gov/gene/?term=6397	"PRELID4A, SEC14L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040270	6397	SEC14L1	http://www.ncbi.nlm.nih.gov/gene/?term=6397	"PRELID4A, SEC14L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040271	63971	KIF13A	http://www.ncbi.nlm.nih.gov/gene/?term=63971	"RBKIN, bA500C11.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040272	63971	KIF13A	http://www.ncbi.nlm.nih.gov/gene/?term=63971	"RBKIN, bA500C11.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040273	63976	PRDM16	http://www.ncbi.nlm.nih.gov/gene/?term=63976	"CMD1LL, KMT8F, LVNC8, MEL1, PFM13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040274	63976	PRDM16	http://www.ncbi.nlm.nih.gov/gene/?term=63976	"CMD1LL, KMT8F, LVNC8, MEL1, PFM13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040275	64067	NPAS3	http://www.ncbi.nlm.nih.gov/gene/?term=64067	"MOP6, PASD6, bHLHe12"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040276	64067	NPAS3	http://www.ncbi.nlm.nih.gov/gene/?term=64067	"MOP6, PASD6, bHLHe12"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040277	64081	PBLD	http://www.ncbi.nlm.nih.gov/gene/?term=64081	"HEL-S-306, MAWBP, MAWDBP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040278	64081	PBLD	http://www.ncbi.nlm.nih.gov/gene/?term=64081	"HEL-S-306, MAWBP, MAWDBP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040279	64083	GOLPH3	http://www.ncbi.nlm.nih.gov/gene/?term=64083	"GOPP1, GPP34, MIDAS, Vps74"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040280	64083	GOLPH3	http://www.ncbi.nlm.nih.gov/gene/?term=64083	"GOPP1, GPP34, MIDAS, Vps74"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040281	64087	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=64087	MCCB	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040282	64087	MCCC2	http://www.ncbi.nlm.nih.gov/gene/?term=64087	MCCB	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040283	64097	EPB41L4A	http://www.ncbi.nlm.nih.gov/gene/?term=64097	"EPB41L4, NBL4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040284	64097	EPB41L4A	http://www.ncbi.nlm.nih.gov/gene/?term=64097	"EPB41L4, NBL4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040285	64101	LRRC4	http://www.ncbi.nlm.nih.gov/gene/?term=64101	"NAG14, NGL-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040286	64101	LRRC4	http://www.ncbi.nlm.nih.gov/gene/?term=64101	"NAG14, NGL-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040287	64115	VSIR	http://www.ncbi.nlm.nih.gov/gene/?term=64115	"B7-H5, B7H5, C10orf54, DD1alpha, GI24, PD-1H, PP2135, SISP1, VISTA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040288	64115	VSIR	http://www.ncbi.nlm.nih.gov/gene/?term=64115	"B7-H5, B7H5, C10orf54, DD1alpha, GI24, PD-1H, PP2135, SISP1, VISTA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040289	64116	SLC39A8	http://www.ncbi.nlm.nih.gov/gene/?term=64116	"BIGM103, CDG2N, LZT-Hs6, PP3105, ZIP8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040290	64116	SLC39A8	http://www.ncbi.nlm.nih.gov/gene/?term=64116	"BIGM103, CDG2N, LZT-Hs6, PP3105, ZIP8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040291	64122	FN3K	http://www.ncbi.nlm.nih.gov/gene/?term=64122		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040292	64122	FN3K	http://www.ncbi.nlm.nih.gov/gene/?term=64122		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040293	6415	SELENOW	http://www.ncbi.nlm.nih.gov/gene/?term=6415	"SEPW1, selW"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040294	6415	SELENOW	http://www.ncbi.nlm.nih.gov/gene/?term=6415	"SEPW1, selW"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040295	64172	OSGEPL1	http://www.ncbi.nlm.nih.gov/gene/?term=64172	"OSGEPL, Qri7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040296	6429	SRSF4	http://www.ncbi.nlm.nih.gov/gene/?term=6429	"SFRS4, SRP75"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040297	6429	SRSF4	http://www.ncbi.nlm.nih.gov/gene/?term=6429	"SFRS4, SRP75"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040298	64324	NSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64324	"ARA267, KMT3B, SOTOS, SOTOS1, STO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040299	64324	NSD1	http://www.ncbi.nlm.nih.gov/gene/?term=64324	"ARA267, KMT3B, SOTOS, SOTOS1, STO"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040300	64327	LMBR1	http://www.ncbi.nlm.nih.gov/gene/?term=64327	"ACHP, C7orf2, DIF14, LSS, PPD2, THYP, TPT, ZRS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040301	64327	LMBR1	http://www.ncbi.nlm.nih.gov/gene/?term=64327	"ACHP, C7orf2, DIF14, LSS, PPD2, THYP, TPT, ZRS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040302	6433	SFSWAP	http://www.ncbi.nlm.nih.gov/gene/?term=6433	"SFRS8, SWAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040303	6433	SFSWAP	http://www.ncbi.nlm.nih.gov/gene/?term=6433	"SFRS8, SWAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040304	643314	KIAA0754	http://www.ncbi.nlm.nih.gov/gene/?term=643314		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040305	643314	KIAA0754	http://www.ncbi.nlm.nih.gov/gene/?term=643314		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040306	64332	NFKBIZ	http://www.ncbi.nlm.nih.gov/gene/?term=64332	"IKBZ, INAP, MAIL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040307	64359	NXN	http://www.ncbi.nlm.nih.gov/gene/?term=64359	"NRX, TRG-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040308	64374	SIL1	http://www.ncbi.nlm.nih.gov/gene/?term=64374	"BAP, MSS, ULG5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040309	64374	SIL1	http://www.ncbi.nlm.nih.gov/gene/?term=64374	"BAP, MSS, ULG5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040310	64398	MPP5	http://www.ncbi.nlm.nih.gov/gene/?term=64398	PALS1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040311	64417	TMEM267	http://www.ncbi.nlm.nih.gov/gene/?term=64417	C5orf28	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040312	64417	TMEM267	http://www.ncbi.nlm.nih.gov/gene/?term=64417	C5orf28	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040313	64419	MTMR14	http://www.ncbi.nlm.nih.gov/gene/?term=64419	C3orf29	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040314	64419	MTMR14	http://www.ncbi.nlm.nih.gov/gene/?term=64419	C3orf29	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040315	64430	PCNX4	http://www.ncbi.nlm.nih.gov/gene/?term=64430	"C14orf135, FBP2, PCNXL4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040316	64430	PCNX4	http://www.ncbi.nlm.nih.gov/gene/?term=64430	"C14orf135, FBP2, PCNXL4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040317	64431	ACTR6	http://www.ncbi.nlm.nih.gov/gene/?term=64431	"ARP6, CDA12, HSPC281, MSTP136, hARP6, hARPX"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040318	64431	ACTR6	http://www.ncbi.nlm.nih.gov/gene/?term=64431	"ARP6, CDA12, HSPC281, MSTP136, hARP6, hARPX"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040319	6446	SGK1	http://www.ncbi.nlm.nih.gov/gene/?term=6446	SGK	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040320	6446	SGK1	http://www.ncbi.nlm.nih.gov/gene/?term=6446	SGK	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040321	6453	ITSN1	http://www.ncbi.nlm.nih.gov/gene/?term=6453	"ITSN, SH3D1A, SH3P17"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040322	645513	LOC645513	http://www.ncbi.nlm.nih.gov/gene/?term=645513		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00040323	645513	LOC645513	http://www.ncbi.nlm.nih.gov/gene/?term=645513		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00040324	64743	WDR13	http://www.ncbi.nlm.nih.gov/gene/?term=64743	MG21	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040325	64743	WDR13	http://www.ncbi.nlm.nih.gov/gene/?term=64743	MG21	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040326	64746	ACBD3	http://www.ncbi.nlm.nih.gov/gene/?term=64746	"GCP60, GOCAP1, GOLPH1, PAP7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040327	64746	ACBD3	http://www.ncbi.nlm.nih.gov/gene/?term=64746	"GCP60, GOCAP1, GOLPH1, PAP7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040328	64754	SMYD3	http://www.ncbi.nlm.nih.gov/gene/?term=64754	"KMT3E, ZMYND1, ZNFN3A1, bA74P14.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040329	64754	SMYD3	http://www.ncbi.nlm.nih.gov/gene/?term=64754	"KMT3E, ZMYND1, ZNFN3A1, bA74P14.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040330	64756	ATPAF1	http://www.ncbi.nlm.nih.gov/gene/?term=64756	"ATP11, ATP11p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040331	64756	ATPAF1	http://www.ncbi.nlm.nih.gov/gene/?term=64756	"ATP11, ATP11p"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040332	64764	CREB3L2	http://www.ncbi.nlm.nih.gov/gene/?term=64764	BBF2H7	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040333	64770	CCDC14	http://www.ncbi.nlm.nih.gov/gene/?term=64770		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040334	64778	FNDC3B	http://www.ncbi.nlm.nih.gov/gene/?term=64778	"FAD104, PRO4979, YVTM2421"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040335	64778	FNDC3B	http://www.ncbi.nlm.nih.gov/gene/?term=64778	"FAD104, PRO4979, YVTM2421"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040336	64779	MTHFSD	http://www.ncbi.nlm.nih.gov/gene/?term=64779		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040337	64779	MTHFSD	http://www.ncbi.nlm.nih.gov/gene/?term=64779		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040338	64786	TBC1D15	http://www.ncbi.nlm.nih.gov/gene/?term=64786	RAB7-GAP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040339	6482	ST3GAL1	http://www.ncbi.nlm.nih.gov/gene/?term=6482	"Gal-NAc6S, SIAT4A, SIATFL, ST3GalA, ST3GalA.1, ST3GalIA, ST3GalIA,1, ST3O"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040340	6482	ST3GAL1	http://www.ncbi.nlm.nih.gov/gene/?term=6482	"Gal-NAc6S, SIAT4A, SIATFL, ST3GalA, ST3GalA.1, ST3GalIA, ST3GalIA,1, ST3O"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040341	6484	ST3GAL4	http://www.ncbi.nlm.nih.gov/gene/?term=6484	"CGS23, NANTA3, SAT3, SIAT4, SIAT4C, ST-4, ST3GalA.2, ST3GalIV, STZ, gal-NAc6S"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040342	6484	ST3GAL4	http://www.ncbi.nlm.nih.gov/gene/?term=6484	"CGS23, NANTA3, SAT3, SIAT4, SIAT4C, ST-4, ST3GalA.2, ST3GalIV, STZ, gal-NAc6S"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040343	64848	YTHDC2	http://www.ncbi.nlm.nih.gov/gene/?term=64848	CAHL	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040344	64848	YTHDC2	http://www.ncbi.nlm.nih.gov/gene/?term=64848	CAHL	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040345	64854	USP46	http://www.ncbi.nlm.nih.gov/gene/?term=64854		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040346	64854	USP46	http://www.ncbi.nlm.nih.gov/gene/?term=64854		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040347	64855	FAM129B	http://www.ncbi.nlm.nih.gov/gene/?term=64855	"C9orf88, MEG-3, MINERVA, OC58, bA356B19.6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040348	64855	FAM129B	http://www.ncbi.nlm.nih.gov/gene/?term=64855	"C9orf88, MEG-3, MINERVA, OC58, bA356B19.6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040349	6487	ST3GAL3	http://www.ncbi.nlm.nih.gov/gene/?term=6487	"EIEE15, MRT12, SIAT6, ST3GALII, ST3Gal III, ST3GalIII, ST3N"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040350	649	BMP1	http://www.ncbi.nlm.nih.gov/gene/?term=649	"OI13, PCOLC, PCP, PCP2, TLD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040351	649	BMP1	http://www.ncbi.nlm.nih.gov/gene/?term=649	"OI13, PCOLC, PCP, PCP2, TLD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040352	64921	CASD1	http://www.ncbi.nlm.nih.gov/gene/?term=64921	"C7orf12, NBLA04196, SOAT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040353	64924	SLC30A5	http://www.ncbi.nlm.nih.gov/gene/?term=64924	"ZNT5, ZNTL1, ZTL1, ZnT-5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040354	6498	SKIL	http://www.ncbi.nlm.nih.gov/gene/?term=6498	"SNO, SnoA, SnoI, SnoN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040355	6498	SKIL	http://www.ncbi.nlm.nih.gov/gene/?term=6498	"SNO, SnoA, SnoI, SnoN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040356	64981	MRPL34	http://www.ncbi.nlm.nih.gov/gene/?term=64981	L34mt	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040357	64981	MRPL34	http://www.ncbi.nlm.nih.gov/gene/?term=64981	L34mt	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040358	6503	SLA	http://www.ncbi.nlm.nih.gov/gene/?term=6503	"SLA1P, SLA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040359	6503	SLA	http://www.ncbi.nlm.nih.gov/gene/?term=6503	"SLA1P, SLA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040360	65055	REEP1	http://www.ncbi.nlm.nih.gov/gene/?term=65055	"C2orf23, HMN5B, SPG31, Yip2a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040361	65055	REEP1	http://www.ncbi.nlm.nih.gov/gene/?term=65055	"C2orf23, HMN5B, SPG31, Yip2a"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040362	65056	GPBP1	http://www.ncbi.nlm.nih.gov/gene/?term=65056	"GPBP, SSH6, VASCULIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040363	6507	SLC1A3	http://www.ncbi.nlm.nih.gov/gene/?term=6507	"EA6, EAAT1, GLAST, GLAST1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040364	6507	SLC1A3	http://www.ncbi.nlm.nih.gov/gene/?term=6507	"EA6, EAAT1, GLAST, GLAST1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040365	65125	WNK1	http://www.ncbi.nlm.nih.gov/gene/?term=65125	"HSAN2, HSN2, KDP, PPP1R167, PRKWNK1, PSK, p65"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040366	6522	SLC4A2	http://www.ncbi.nlm.nih.gov/gene/?term=6522	"AE2, BND3L, EPB3L1, HKB3, NBND3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040367	6522	SLC4A2	http://www.ncbi.nlm.nih.gov/gene/?term=6522	"AE2, BND3L, EPB3L1, HKB3, NBND3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040368	65268	WNK2	http://www.ncbi.nlm.nih.gov/gene/?term=65268	"NY-CO-43, P/OKcl.13, PRKWNK2, SDCCAG43"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040369	654433	PAX8-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=654433		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00040370	654433	PAX8-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=654433		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00040371	6546	SLC8A1	http://www.ncbi.nlm.nih.gov/gene/?term=6546	NCX1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040372	6546	SLC8A1	http://www.ncbi.nlm.nih.gov/gene/?term=6546	NCX1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040373	6558	SLC12A2	http://www.ncbi.nlm.nih.gov/gene/?term=6558	"BSC, BSC2, NKCC1, PPP1R141"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040374	6573	SLC19A1	http://www.ncbi.nlm.nih.gov/gene/?term=6573	"CHMD, FOLT, IFC1, REFC, RFC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040375	659	BMPR2	http://www.ncbi.nlm.nih.gov/gene/?term=659	"BMPR-II, BMPR3, BMR2, BRK-3, POVD1, PPH1, T-ALK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040376	6595	SMARCA2	http://www.ncbi.nlm.nih.gov/gene/?term=6595	"BAF190, BRM, NCBRS, SNF2, SNF2L2, SNF2LA, SWI2, Sth1p, hBRM, hSNF2a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040377	65983	GRAMD2B	http://www.ncbi.nlm.nih.gov/gene/?term=65983	"GRAMD3, NS3TP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040378	65983	GRAMD2B	http://www.ncbi.nlm.nih.gov/gene/?term=65983	"GRAMD3, NS3TP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040379	6599	SMARCC1	http://www.ncbi.nlm.nih.gov/gene/?term=6599	"BAF155, CRACC1, Rsc8, SRG3, SWI3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040380	66005	CHID1	http://www.ncbi.nlm.nih.gov/gene/?term=66005	"GL008, SI-CLP, SICLP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040381	66005	CHID1	http://www.ncbi.nlm.nih.gov/gene/?term=66005	"GL008, SI-CLP, SICLP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040382	664	BNIP3	http://www.ncbi.nlm.nih.gov/gene/?term=664	NIP3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040383	6643	SNX2	http://www.ncbi.nlm.nih.gov/gene/?term=6643	TRG-9	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040384	6646	SOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6646	"ACACT, ACAT, ACAT-1, ACAT1, SOAT, STAT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040385	6646	SOAT1	http://www.ncbi.nlm.nih.gov/gene/?term=6646	"ACACT, ACAT, ACAT-1, ACAT1, SOAT, STAT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040386	6648	SOD2	http://www.ncbi.nlm.nih.gov/gene/?term=6648	"IPO-B, IPOB, MNSOD, MVCD6, Mn-SOD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040387	6651	SON	http://www.ncbi.nlm.nih.gov/gene/?term=6651	"BASS1, C21orf50, DBP-5, NREBP3, TOKIMS, SON"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040388	6651	SON	http://www.ncbi.nlm.nih.gov/gene/?term=6651	"BASS1, C21orf50, DBP-5, NREBP3, TOKIMS, SON"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040389	6687	SPG7	http://www.ncbi.nlm.nih.gov/gene/?term=6687	"CAR, CMAR, PGN, SPG5C"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040390	6687	SPG7	http://www.ncbi.nlm.nih.gov/gene/?term=6687	"CAR, CMAR, PGN, SPG5C"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040391	6688	SPI1	http://www.ncbi.nlm.nih.gov/gene/?term=6688	"OF, PU.1, SFPI1, SPI-1, SPI-A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040392	6688	SPI1	http://www.ncbi.nlm.nih.gov/gene/?term=6688	"OF, PU.1, SFPI1, SPI-1, SPI-A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040393	6695	SPOCK1	http://www.ncbi.nlm.nih.gov/gene/?term=6695	"SPOCK, TESTICAN, TIC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040394	6695	SPOCK1	http://www.ncbi.nlm.nih.gov/gene/?term=6695	"SPOCK, TESTICAN, TIC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040395	671	BPI	http://www.ncbi.nlm.nih.gov/gene/?term=671	"BPIFD1, rBPI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040396	671	BPI	http://www.ncbi.nlm.nih.gov/gene/?term=671	"BPIFD1, rBPI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040397	6711	SPTBN1	http://www.ncbi.nlm.nih.gov/gene/?term=6711	"ELF, HEL102, SPTB2, betaSpII"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040398	6711	SPTBN1	http://www.ncbi.nlm.nih.gov/gene/?term=6711	"ELF, HEL102, SPTB2, betaSpII"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040399	6717	SRI	http://www.ncbi.nlm.nih.gov/gene/?term=6717	"CP-22, CP22, SCN, V19"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040400	6721	SREBF2	http://www.ncbi.nlm.nih.gov/gene/?term=6721	"SREBP-2, SREBP2, bHLHd2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040401	6721	SREBF2	http://www.ncbi.nlm.nih.gov/gene/?term=6721	"SREBP-2, SREBP2, bHLHd2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040402	6729	SRP54	http://www.ncbi.nlm.nih.gov/gene/?term=6729		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040403	6729	SRP54	http://www.ncbi.nlm.nih.gov/gene/?term=6729		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040404	673	BRAF	http://www.ncbi.nlm.nih.gov/gene/?term=673	"B-RAF1, B-raf1, NS7, RAFB1, BRAF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040405	673	BRAF	http://www.ncbi.nlm.nih.gov/gene/?term=673	"B-RAF1, B-raf1, NS7, RAFB1, BRAF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040406	6733	SRPK2	http://www.ncbi.nlm.nih.gov/gene/?term=6733	SFRSK2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040407	6733	SRPK2	http://www.ncbi.nlm.nih.gov/gene/?term=6733	SFRSK2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040408	6777	STAT5B	http://www.ncbi.nlm.nih.gov/gene/?term=6777	STAT5	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040409	6780	STAU1	http://www.ncbi.nlm.nih.gov/gene/?term=6780	"PPP1R150, STAU"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040410	6780	STAU1	http://www.ncbi.nlm.nih.gov/gene/?term=6780	"PPP1R150, STAU"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040411	6790	AURKA	http://www.ncbi.nlm.nih.gov/gene/?term=6790	"AIK, ARK1, AURA, BTAK, PPP1R47, STK15, STK6, STK7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040412	6792	CDKL5	http://www.ncbi.nlm.nih.gov/gene/?term=6792	"CFAP247, EIEE2, ISSX, STK9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040413	6793	STK10	http://www.ncbi.nlm.nih.gov/gene/?term=6793	"LOK, PRO2729"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040414	6793	STK10	http://www.ncbi.nlm.nih.gov/gene/?term=6793	"LOK, PRO2729"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040415	6811	STX5	http://www.ncbi.nlm.nih.gov/gene/?term=6811	"SED5A, STX5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040416	6812	STXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6812	"MUNC18-1, NSEC1, P67, RBSEC1, UNC18"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040417	6812	STXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6812	"MUNC18-1, NSEC1, P67, RBSEC1, UNC18"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040418	6827	SUPT4H1	http://www.ncbi.nlm.nih.gov/gene/?term=6827	"SPT4, SPT4H, SUPT4H, Supt4a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040419	6827	SUPT4H1	http://www.ncbi.nlm.nih.gov/gene/?term=6827	"SPT4, SPT4H, SUPT4H, Supt4a"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040420	683	BST1	http://www.ncbi.nlm.nih.gov/gene/?term=683	CD157	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040421	6840	SVIL	http://www.ncbi.nlm.nih.gov/gene/?term=6840		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040422	6840	SVIL	http://www.ncbi.nlm.nih.gov/gene/?term=6840		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040423	6857	SYT1	http://www.ncbi.nlm.nih.gov/gene/?term=6857	"P65, SVP65, SYT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040424	6865	TACR2	http://www.ncbi.nlm.nih.gov/gene/?term=6865	"NK2R, NKNAR, SKR, TAC2R"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040425	6865	TACR2	http://www.ncbi.nlm.nih.gov/gene/?term=6865	"NK2R, NKNAR, SKR, TAC2R"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040426	6868	ADAM17	http://www.ncbi.nlm.nih.gov/gene/?term=6868	"ADAM18, CD156B, CSVP, NISBD, NISBD1, TACE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040427	6868	ADAM17	http://www.ncbi.nlm.nih.gov/gene/?term=6868	"ADAM18, CD156B, CSVP, NISBD, NISBD1, TACE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040428	6894	TARBP1	http://www.ncbi.nlm.nih.gov/gene/?term=6894	"TRM3, TRMT3, TRP-185, TRP185"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040429	6902	TBCA	http://www.ncbi.nlm.nih.gov/gene/?term=6902		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040430	6902	TBCA	http://www.ncbi.nlm.nih.gov/gene/?term=6902		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040431	6904	TBCD	http://www.ncbi.nlm.nih.gov/gene/?term=6904	"PEBAT, SSD-1, tfcD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040432	6907	TBL1X	http://www.ncbi.nlm.nih.gov/gene/?term=6907	"EBI, SMAP55, TBL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040433	6916	TBXAS1	http://www.ncbi.nlm.nih.gov/gene/?term=6916	"BDPLT14, CYP5, CYP5A1, GHOSAL, THAS, TS, TXAS, TXS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040434	6916	TBXAS1	http://www.ncbi.nlm.nih.gov/gene/?term=6916	"BDPLT14, CYP5, CYP5A1, GHOSAL, THAS, TS, TXAS, TXS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040435	6920	TCEA3	http://www.ncbi.nlm.nih.gov/gene/?term=6920	"TFIIS, TFIIS.H"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040436	6920	TCEA3	http://www.ncbi.nlm.nih.gov/gene/?term=6920	"TFIIS, TFIIS.H"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040437	6934	TCF7L2	http://www.ncbi.nlm.nih.gov/gene/?term=6934	"TCF-4, TCF4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040438	6934	TCF7L2	http://www.ncbi.nlm.nih.gov/gene/?term=6934	"TCF-4, TCF4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040439	6935	ZEB1	http://www.ncbi.nlm.nih.gov/gene/?term=6935	"AREB6, BZP, DELTAEF1, FECD6, NIL2A, PPCD3, TCF8, ZFHEP, ZFHX1A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040440	6936	GCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=6936	"C2orf3, DNABF, GCF, TCF9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040441	6936	GCFC2	http://www.ncbi.nlm.nih.gov/gene/?term=6936	"C2orf3, DNABF, GCF, TCF9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040442	6938	TCF12	http://www.ncbi.nlm.nih.gov/gene/?term=6938	"CRS3, HEB, HTF4, HsT17266, TCF-12, bHLHb20"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040443	6942	TCF20	http://www.ncbi.nlm.nih.gov/gene/?term=6942	"AR1, SPBP, TCF-20"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040444	6942	TCF20	http://www.ncbi.nlm.nih.gov/gene/?term=6942	"AR1, SPBP, TCF-20"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040445	6993	DYNLT1	http://www.ncbi.nlm.nih.gov/gene/?term=6993	"CW-1, TCTEL1, tctex-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040446	6993	DYNLT1	http://www.ncbi.nlm.nih.gov/gene/?term=6993	"CW-1, TCTEL1, tctex-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040447	6996	TDG	http://www.ncbi.nlm.nih.gov/gene/?term=6996	hTDG	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040448	7003	TEAD1	http://www.ncbi.nlm.nih.gov/gene/?term=7003	"AA, NTEF-1, REF1, TCF-13, TCF13, TEAD-1, TEF-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040449	7003	TEAD1	http://www.ncbi.nlm.nih.gov/gene/?term=7003	"AA, NTEF-1, REF1, TCF-13, TCF13, TEAD-1, TEF-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040450	7004	TEAD4	http://www.ncbi.nlm.nih.gov/gene/?term=7004	"EFTR-2, RTEF1, TCF13L1, TEF-3, TEF3, TEFR-1, hRTEF-1B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040451	7009	TMBIM6	http://www.ncbi.nlm.nih.gov/gene/?term=7009	"BAXI1, BI-1, TEGT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040452	7009	TMBIM6	http://www.ncbi.nlm.nih.gov/gene/?term=7009	"BAXI1, BI-1, TEGT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040453	7020	TFAP2A	http://www.ncbi.nlm.nih.gov/gene/?term=7020	"AP-2, AP-2alpha, AP2TF, BOFS, TFAP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040454	7020	TFAP2A	http://www.ncbi.nlm.nih.gov/gene/?term=7020	"AP-2, AP-2alpha, AP2TF, BOFS, TFAP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040455	7024	TFCP2	http://www.ncbi.nlm.nih.gov/gene/?term=7024	"LBP1C, LSF, LSF1D, SEFC, TFCP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040456	7024	TFCP2	http://www.ncbi.nlm.nih.gov/gene/?term=7024	"LBP1C, LSF, LSF1D, SEFC, TFCP2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040457	7038	TG	http://www.ncbi.nlm.nih.gov/gene/?term=7038	"AITD3N, TG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040458	7038	TG	http://www.ncbi.nlm.nih.gov/gene/?term=7038	"AITD3N, TG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040459	7040	TGFB1	http://www.ncbi.nlm.nih.gov/gene/?term=7040	"CED, DPD1, LAP, TGFB, TGFbeta"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040460	7040	TGFB1	http://www.ncbi.nlm.nih.gov/gene/?term=7040	"CED, DPD1, LAP, TGFB, TGFbeta"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040461	7045	TGFBI	http://www.ncbi.nlm.nih.gov/gene/?term=7045	"BIGH3, CDB1, CDG2, CDGG1, CSD, CSD1, CSD2, CSD3, EBMD, LCD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040462	7049	TGFBR3	http://www.ncbi.nlm.nih.gov/gene/?term=7049	"BGCAN, betaglycan"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040463	7049	TGFBR3	http://www.ncbi.nlm.nih.gov/gene/?term=7049	"BGCAN, betaglycan"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040464	7052	TGM2	http://www.ncbi.nlm.nih.gov/gene/?term=7052	"TG(C), TGC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040465	706	TSPO	http://www.ncbi.nlm.nih.gov/gene/?term=706	"BPBS, BZRP, DBI, IBP, MBR, PBR, PBS, PKBS, PTBR, mDRC, pk18"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040466	706	TSPO	http://www.ncbi.nlm.nih.gov/gene/?term=706	"BPBS, BZRP, DBI, IBP, MBR, PBR, PBS, PKBS, PTBR, mDRC, pk18"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040467	7068	THRB	http://www.ncbi.nlm.nih.gov/gene/?term=7068	"C-ERBA-2, C-ERBA-BETA, ERBA2, GRTH, NR1A2, PRTH, THR11, THRB2, THRB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040468	7068	THRB	http://www.ncbi.nlm.nih.gov/gene/?term=7068	"C-ERBA-2, C-ERBA-BETA, ERBA2, GRTH, NR1A2, PRTH, THR11, THRB2, THRB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040469	7072	TIA1	http://www.ncbi.nlm.nih.gov/gene/?term=7072	"TIA-1, WDM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040470	7072	TIA1	http://www.ncbi.nlm.nih.gov/gene/?term=7072	"TIA-1, WDM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040471	7074	TIAM1	http://www.ncbi.nlm.nih.gov/gene/?term=7074	TIAM-1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040472	7074	TIAM1	http://www.ncbi.nlm.nih.gov/gene/?term=7074	TIAM-1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040473	7078	TIMP3	http://www.ncbi.nlm.nih.gov/gene/?term=7078	"HSMRK222, K222, K222TA2, SFD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040474	7078	TIMP3	http://www.ncbi.nlm.nih.gov/gene/?term=7078	"HSMRK222, K222, K222TA2, SFD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040475	7082	TJP1	http://www.ncbi.nlm.nih.gov/gene/?term=7082	ZO-1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040476	7082	TJP1	http://www.ncbi.nlm.nih.gov/gene/?term=7082	ZO-1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040477	7091	TLE4	http://www.ncbi.nlm.nih.gov/gene/?term=7091	"BCE-1, BCE1, E(spI), ESG, ESG4, GRG4, Grg-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040478	7091	TLE4	http://www.ncbi.nlm.nih.gov/gene/?term=7091	"BCE-1, BCE1, E(spI), ESG, ESG4, GRG4, Grg-4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040479	7145	TNS1	http://www.ncbi.nlm.nih.gov/gene/?term=7145	"MST091, MST122, MST127, MSTP091, MSTP122, MSTP127, MXRA6, PPP1R155, TNS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040480	7145	TNS1	http://www.ncbi.nlm.nih.gov/gene/?term=7145	"MST091, MST122, MST127, MSTP091, MSTP122, MSTP127, MXRA6, PPP1R155, TNS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040481	7150	TOP1	http://www.ncbi.nlm.nih.gov/gene/?term=7150	TOPI	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040482	7150	TOP1	http://www.ncbi.nlm.nih.gov/gene/?term=7150	TOPI	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040483	716	C1S	http://www.ncbi.nlm.nih.gov/gene/?term=716	EDSPD2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040484	7163	TPD52	http://www.ncbi.nlm.nih.gov/gene/?term=7163	"D52, N8L, PC-1, PrLZ, hD52"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040485	7163	TPD52	http://www.ncbi.nlm.nih.gov/gene/?term=7163	"D52, N8L, PC-1, PrLZ, hD52"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040486	7168	TPM1	http://www.ncbi.nlm.nih.gov/gene/?term=7168	"C15orf13, CMD1Y, CMH3, HEL-S-265, HTM-alpha, LVNC9, TMSA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040487	7170	TPM3	http://www.ncbi.nlm.nih.gov/gene/?term=7170	"CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040488	7170	TPM3	http://www.ncbi.nlm.nih.gov/gene/?term=7170	"CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040489	7171	TPM4	http://www.ncbi.nlm.nih.gov/gene/?term=7171	HEL-S-108	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040490	7171	TPM4	http://www.ncbi.nlm.nih.gov/gene/?term=7171	HEL-S-108	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040491	7182	NR2C2	http://www.ncbi.nlm.nih.gov/gene/?term=7182	"TAK1, TR4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040492	7182	NR2C2	http://www.ncbi.nlm.nih.gov/gene/?term=7182	"TAK1, TR4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040493	7204	TRIO	http://www.ncbi.nlm.nih.gov/gene/?term=7204	"ARHGEF23, MEBAS, MRD44, tgat"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040494	7204	TRIO	http://www.ncbi.nlm.nih.gov/gene/?term=7204	"ARHGEF23, MEBAS, MRD44, tgat"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040495	7226	TRPM2	http://www.ncbi.nlm.nih.gov/gene/?term=7226	"EREG1, KNP3, LTRPC2, LTrpC-2, NUDT9H, NUDT9L1, TRPC7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040496	7226	TRPM2	http://www.ncbi.nlm.nih.gov/gene/?term=7226	"EREG1, KNP3, LTRPC2, LTrpC-2, NUDT9H, NUDT9L1, TRPC7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040497	7227	TRPS1	http://www.ncbi.nlm.nih.gov/gene/?term=7227	"GC79, LGCR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040498	7227	TRPS1	http://www.ncbi.nlm.nih.gov/gene/?term=7227	"GC79, LGCR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040499	726	CAPN5	http://www.ncbi.nlm.nih.gov/gene/?term=726	"ADNIV, HTRA3, VRNI, nCL-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040500	7265	TTC1	http://www.ncbi.nlm.nih.gov/gene/?term=7265	TPR1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040501	7265	TTC1	http://www.ncbi.nlm.nih.gov/gene/?term=7265	TPR1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040502	7267	TTC3	http://www.ncbi.nlm.nih.gov/gene/?term=7267	"DCRR1, RNF105, TPRDIII"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040503	7294	TXK	http://www.ncbi.nlm.nih.gov/gene/?term=7294	"BTKL, PSCTK5, PTK4, RLK, TKL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040504	7295	TXN	http://www.ncbi.nlm.nih.gov/gene/?term=7295	"TRDX, TRX, TRX1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040505	7297	TYK2	http://www.ncbi.nlm.nih.gov/gene/?term=7297	"IMD35, JTK1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040506	7297	TYK2	http://www.ncbi.nlm.nih.gov/gene/?term=7297	"IMD35, JTK1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040507	730094	C16orf52	http://www.ncbi.nlm.nih.gov/gene/?term=730094		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040508	730094	C16orf52	http://www.ncbi.nlm.nih.gov/gene/?term=730094		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040509	7319	UBE2A	http://www.ncbi.nlm.nih.gov/gene/?term=7319	"HHR6A, MRXS30, MRXSN, RAD6A, UBC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040510	7320	UBE2B	http://www.ncbi.nlm.nih.gov/gene/?term=7320	"E2-17kDa, HHR6B, HR6B, RAD6B, UBC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040511	7323	UBE2D3	http://www.ncbi.nlm.nih.gov/gene/?term=7323	"E2(17)KB3, UBC4/5, UBCH5C"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040512	7328	UBE2H	http://www.ncbi.nlm.nih.gov/gene/?term=7328	"E2-20K, GID3, UBC8, UBCH, UBCH2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040513	7328	UBE2H	http://www.ncbi.nlm.nih.gov/gene/?term=7328	"E2-20K, GID3, UBC8, UBCH, UBCH2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040514	7332	UBE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=7332	"E2-F1, L-UBC, UBCH7, UbcM4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040515	7332	UBE2L3	http://www.ncbi.nlm.nih.gov/gene/?term=7332	"E2-F1, L-UBC, UBCH7, UbcM4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040516	7337	UBE3A	http://www.ncbi.nlm.nih.gov/gene/?term=7337	"ANCR, AS, E6-AP, EPVE6AP, HPVE6A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040517	7360	UGP2	http://www.ncbi.nlm.nih.gov/gene/?term=7360	"UDPG, UDPGP, UDPGP2, UGP1, UGPP1, UGPP2, pHC379"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040518	7371	UCK2	http://www.ncbi.nlm.nih.gov/gene/?term=7371	"TSA903, UK, UMPK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040519	7374	UNG	http://www.ncbi.nlm.nih.gov/gene/?term=7374	"DGU, HIGM4, HIGM5, UDG1, UNG15, UNG2, UNG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040520	7374	UNG	http://www.ncbi.nlm.nih.gov/gene/?term=7374	"DGU, HIGM4, HIGM5, UDG1, UNG15, UNG2, UNG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040521	7388	UQCRH	http://www.ncbi.nlm.nih.gov/gene/?term=7388	"QCR6, UQCR8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040522	7388	UQCRH	http://www.ncbi.nlm.nih.gov/gene/?term=7388	"QCR6, UQCR8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040523	7390	UROS	http://www.ncbi.nlm.nih.gov/gene/?term=7390	UROIIIS	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040524	7390	UROS	http://www.ncbi.nlm.nih.gov/gene/?term=7390	UROIIIS	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040525	7410	VAV2	http://www.ncbi.nlm.nih.gov/gene/?term=7410	VAV-2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040526	7410	VAV2	http://www.ncbi.nlm.nih.gov/gene/?term=7410	VAV-2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040527	7414	VCL	http://www.ncbi.nlm.nih.gov/gene/?term=7414	"CMD1W, CMH15, HEL114, MV, MVCL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040528	7461	CLIP2	http://www.ncbi.nlm.nih.gov/gene/?term=7461	"CLIP, CLIP-115, CYLN2, WBSCR3, WBSCR4, WSCR3, WSCR4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040529	7461	CLIP2	http://www.ncbi.nlm.nih.gov/gene/?term=7461	"CLIP, CLIP-115, CYLN2, WBSCR3, WBSCR4, WSCR3, WSCR4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040530	7468	NSD2	http://www.ncbi.nlm.nih.gov/gene/?term=7468	"KMT3F, KMT3G, MMSET, REIIBP, TRX5, WHS, WHSC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040531	7485	WRB	http://www.ncbi.nlm.nih.gov/gene/?term=7485	"CHD5, GET1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040532	7508	XPC	http://www.ncbi.nlm.nih.gov/gene/?term=7508	"RAD4, XP3C, p125, XPC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040533	7508	XPC	http://www.ncbi.nlm.nih.gov/gene/?term=7508	"RAD4, XP3C, p125, XPC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040534	7520	XRCC5	http://www.ncbi.nlm.nih.gov/gene/?term=7520	"KARP-1, KARP1, KU80, KUB2, Ku86, NFIV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040535	7520	XRCC5	http://www.ncbi.nlm.nih.gov/gene/?term=7520	"KARP-1, KARP1, KU80, KUB2, Ku86, NFIV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040536	7525	YES1	http://www.ncbi.nlm.nih.gov/gene/?term=7525	"HsT441, P61-YES, Yes, c-yes"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040537	7528	YY1	http://www.ncbi.nlm.nih.gov/gene/?term=7528	"DELTA, GADEVS, INO80S, NF-E1, UCRBP, YIN-YANG-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040538	7528	YY1	http://www.ncbi.nlm.nih.gov/gene/?term=7528	"DELTA, GADEVS, INO80S, NF-E1, UCRBP, YIN-YANG-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040539	753	LDLRAD4	http://www.ncbi.nlm.nih.gov/gene/?term=753	C18orf1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040540	753	LDLRAD4	http://www.ncbi.nlm.nih.gov/gene/?term=753	C18orf1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040541	7531	YWHAE	http://www.ncbi.nlm.nih.gov/gene/?term=7531	"14-3-3E, HEL2, KCIP-1, MDCR, MDS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040542	7531	YWHAE	http://www.ncbi.nlm.nih.gov/gene/?term=7531	"14-3-3E, HEL2, KCIP-1, MDCR, MDS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040543	7534	YWHAZ	http://www.ncbi.nlm.nih.gov/gene/?term=7534	"14-3-3-zeta, HEL-S-3, HEL-S-93, HEL4, KCIP-1, YWHAD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040544	7534	YWHAZ	http://www.ncbi.nlm.nih.gov/gene/?term=7534	"14-3-3-zeta, HEL-S-3, HEL-S-93, HEL4, KCIP-1, YWHAD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040545	7541	ZBTB14	http://www.ncbi.nlm.nih.gov/gene/?term=7541	"ZF5, ZFP-161, ZFP-5, ZFP161, ZNF478"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040546	7541	ZBTB14	http://www.ncbi.nlm.nih.gov/gene/?term=7541	"ZF5, ZFP-161, ZFP-5, ZFP161, ZNF478"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040547	7556	ZNF10	http://www.ncbi.nlm.nih.gov/gene/?term=7556	KOX1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040548	7586	ZKSCAN1	http://www.ncbi.nlm.nih.gov/gene/?term=7586	"KOX18, PHZ-37, ZNF139, ZNF36, ZSCAN33"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040549	7629	ZNF76	http://www.ncbi.nlm.nih.gov/gene/?term=7629	"D6S229E, ZNF523, Zfp523"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040550	7629	ZNF76	http://www.ncbi.nlm.nih.gov/gene/?term=7629	"D6S229E, ZNF523, Zfp523"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040551	7678	ZNF124	http://www.ncbi.nlm.nih.gov/gene/?term=7678	"HZF-16, HZF16, ZK7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040552	7678	ZNF124	http://www.ncbi.nlm.nih.gov/gene/?term=7678	"HZF-16, HZF16, ZK7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040553	7704	ZBTB16	http://www.ncbi.nlm.nih.gov/gene/?term=7704	"PLZF, ZNF145"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040554	7704	ZBTB16	http://www.ncbi.nlm.nih.gov/gene/?term=7704	"PLZF, ZNF145"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040555	7706	TRIM25	http://www.ncbi.nlm.nih.gov/gene/?term=7706	"EFP, RNF147, Z147, ZNF147"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040556	7706	TRIM25	http://www.ncbi.nlm.nih.gov/gene/?term=7706	"EFP, RNF147, Z147, ZNF147"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040557	776	CACNA1D	http://www.ncbi.nlm.nih.gov/gene/?term=776	"CACH3, CACN4, CACNL1A2, CCHL1A2, Cav1.3, PASNA, SANDD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040558	776	CACNA1D	http://www.ncbi.nlm.nih.gov/gene/?term=776	"CACH3, CACN4, CACNL1A2, CCHL1A2, Cav1.3, PASNA, SANDD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040559	7776	ZNF236	http://www.ncbi.nlm.nih.gov/gene/?term=7776	"ZNF236AB, ZNF236"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040560	781	CACNA2D1	http://www.ncbi.nlm.nih.gov/gene/?term=781	"CACNA2, CACNL2A, CCHL2A, LINC01112, lncRNA-N3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040561	7869	SEMA3B	http://www.ncbi.nlm.nih.gov/gene/?term=7869	"LUCA-1, SEMA5, SEMAA, SemA, semaV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040562	7869	SEMA3B	http://www.ncbi.nlm.nih.gov/gene/?term=7869	"LUCA-1, SEMA5, SEMAA, SemA, semaV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040563	7871	SLMAP	http://www.ncbi.nlm.nih.gov/gene/?term=7871	SLAP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040564	7871	SLMAP	http://www.ncbi.nlm.nih.gov/gene/?term=7871	SLAP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040565	78991	PCYOX1L	http://www.ncbi.nlm.nih.gov/gene/?term=78991		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040566	78991	PCYOX1L	http://www.ncbi.nlm.nih.gov/gene/?term=78991		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040567	79018	GID4	http://www.ncbi.nlm.nih.gov/gene/?term=79018	"C17orf39, VID24"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040568	79018	GID4	http://www.ncbi.nlm.nih.gov/gene/?term=79018	"C17orf39, VID24"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040569	7905	REEP5	http://www.ncbi.nlm.nih.gov/gene/?term=7905	"C5orf18, D5S346, DP1, TB2, YOP1, Yip2e"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040570	79083	MLPH	http://www.ncbi.nlm.nih.gov/gene/?term=79083	SLAC2-A	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040571	79083	MLPH	http://www.ncbi.nlm.nih.gov/gene/?term=79083	SLAC2-A	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040572	79091	METTL22	http://www.ncbi.nlm.nih.gov/gene/?term=79091	C16orf68	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040573	79091	METTL22	http://www.ncbi.nlm.nih.gov/gene/?term=79091	C16orf68	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040574	79158	GNPTAB	http://www.ncbi.nlm.nih.gov/gene/?term=79158	"GNPTA, ICD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040575	79158	GNPTAB	http://www.ncbi.nlm.nih.gov/gene/?term=79158	"GNPTA, ICD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040576	79573	TTC13	http://www.ncbi.nlm.nih.gov/gene/?term=79573		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040577	79577	CDC73	http://www.ncbi.nlm.nih.gov/gene/?term=79577	"C1orf28, FIHP, HPTJT, HRPT1, HRPT2, HYX"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040578	79577	CDC73	http://www.ncbi.nlm.nih.gov/gene/?term=79577	"C1orf28, FIHP, HPTJT, HRPT1, HRPT2, HYX"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040579	79596	RNF219	http://www.ncbi.nlm.nih.gov/gene/?term=79596	C13orf7	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040580	79596	RNF219	http://www.ncbi.nlm.nih.gov/gene/?term=79596	C13orf7	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040581	79618	HMBOX1	http://www.ncbi.nlm.nih.gov/gene/?term=79618	"HNF1LA, HOT1, PBHNF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040582	79618	HMBOX1	http://www.ncbi.nlm.nih.gov/gene/?term=79618	"HNF1LA, HOT1, PBHNF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040583	79639	TMEM53	http://www.ncbi.nlm.nih.gov/gene/?term=79639	NET4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040584	79639	TMEM53	http://www.ncbi.nlm.nih.gov/gene/?term=79639	NET4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040585	79648	MCPH1	http://www.ncbi.nlm.nih.gov/gene/?term=79648	"BRIT1, MCT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040586	79648	MCPH1	http://www.ncbi.nlm.nih.gov/gene/?term=79648	"BRIT1, MCT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040587	79658	ARHGAP10	http://www.ncbi.nlm.nih.gov/gene/?term=79658	"GRAF2, PS-GAP, PSGAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040588	79658	ARHGAP10	http://www.ncbi.nlm.nih.gov/gene/?term=79658	"GRAF2, PS-GAP, PSGAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040589	79668	PARP8	http://www.ncbi.nlm.nih.gov/gene/?term=79668	"ARTD16, pART16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040590	79675	FASTKD1	http://www.ncbi.nlm.nih.gov/gene/?term=79675		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040591	79677	SMC6	http://www.ncbi.nlm.nih.gov/gene/?term=79677	"SMC-6L1, hSMC6, SMC6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040592	79684	MSANTD2	http://www.ncbi.nlm.nih.gov/gene/?term=79684	C11orf61	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040593	79701	OGFOD3	http://www.ncbi.nlm.nih.gov/gene/?term=79701	C17orf101	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040594	79701	OGFOD3	http://www.ncbi.nlm.nih.gov/gene/?term=79701	C17orf101	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040595	79705	LRRK1	http://www.ncbi.nlm.nih.gov/gene/?term=79705	"RIPK6, Roco1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040596	79705	LRRK1	http://www.ncbi.nlm.nih.gov/gene/?term=79705	"RIPK6, Roco1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040597	79709	COLGALT1	http://www.ncbi.nlm.nih.gov/gene/?term=79709	GLT25D1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040598	79709	COLGALT1	http://www.ncbi.nlm.nih.gov/gene/?term=79709	GLT25D1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040599	79712	GTDC1	http://www.ncbi.nlm.nih.gov/gene/?term=79712	"Hmat-Xa, mat-Xa"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040600	79712	GTDC1	http://www.ncbi.nlm.nih.gov/gene/?term=79712	"Hmat-Xa, mat-Xa"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040601	79718	TBL1XR1	http://www.ncbi.nlm.nih.gov/gene/?term=79718	"C21, DC42, IRA1, MRD41, TBLR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040602	79718	TBL1XR1	http://www.ncbi.nlm.nih.gov/gene/?term=79718	"C21, DC42, IRA1, MRD41, TBLR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040603	79720	VPS37B	http://www.ncbi.nlm.nih.gov/gene/?term=79720		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040604	79720	VPS37B	http://www.ncbi.nlm.nih.gov/gene/?term=79720		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040605	79729	SH3D21	http://www.ncbi.nlm.nih.gov/gene/?term=79729	C1orf113	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040606	79729	SH3D21	http://www.ncbi.nlm.nih.gov/gene/?term=79729	C1orf113	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040607	79731	NARS2	http://www.ncbi.nlm.nih.gov/gene/?term=79731	"DFNB94, SLM5, asnRS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040608	79731	NARS2	http://www.ncbi.nlm.nih.gov/gene/?term=79731	"DFNB94, SLM5, asnRS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040609	79746	ECHDC3	http://www.ncbi.nlm.nih.gov/gene/?term=79746		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040610	79746	ECHDC3	http://www.ncbi.nlm.nih.gov/gene/?term=79746		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040611	79752	ZFAND1	http://www.ncbi.nlm.nih.gov/gene/?term=79752		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040612	79752	ZFAND1	http://www.ncbi.nlm.nih.gov/gene/?term=79752		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040613	79753	SNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=79753	"PML1, PMRED"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040614	79753	SNIP1	http://www.ncbi.nlm.nih.gov/gene/?term=79753	"PML1, PMRED"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040615	79807	GSTCD	http://www.ncbi.nlm.nih.gov/gene/?term=79807		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040616	79807	GSTCD	http://www.ncbi.nlm.nih.gov/gene/?term=79807		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040617	79811	SLTM	http://www.ncbi.nlm.nih.gov/gene/?term=79811	Met	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040618	79811	SLTM	http://www.ncbi.nlm.nih.gov/gene/?term=79811	Met	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040619	79817	MOB3B	http://www.ncbi.nlm.nih.gov/gene/?term=79817	"C9orf35, MOB1D, MOBKL2B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040620	79817	MOB3B	http://www.ncbi.nlm.nih.gov/gene/?term=79817	"C9orf35, MOB1D, MOBKL2B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040621	79823	CAMKMT	http://www.ncbi.nlm.nih.gov/gene/?term=79823	"C2orf34, CLNMT, CaM KMT, Cam, KMT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040622	79823	CAMKMT	http://www.ncbi.nlm.nih.gov/gene/?term=79823	"C2orf34, CLNMT, CaM KMT, Cam, KMT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040623	79832	QSER1	http://www.ncbi.nlm.nih.gov/gene/?term=79832		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040624	79837	PIP4K2C	http://www.ncbi.nlm.nih.gov/gene/?term=79837	PIP5K2C	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040625	79837	PIP4K2C	http://www.ncbi.nlm.nih.gov/gene/?term=79837	PIP5K2C	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040626	79848	CSPP1	http://www.ncbi.nlm.nih.gov/gene/?term=79848	"CSPP, JBTS21"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040627	79866	BORA	http://www.ncbi.nlm.nih.gov/gene/?term=79866	C13orf34	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040628	79866	BORA	http://www.ncbi.nlm.nih.gov/gene/?term=79866	C13orf34	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040629	79873	NUDT18	http://www.ncbi.nlm.nih.gov/gene/?term=79873	MTH3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040630	79873	NUDT18	http://www.ncbi.nlm.nih.gov/gene/?term=79873	MTH3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040631	79875	THSD4	http://www.ncbi.nlm.nih.gov/gene/?term=79875	"ADAMTSL-6, ADAMTSL6, FVSY9334, PRO34005"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040632	79877	DCAKD	http://www.ncbi.nlm.nih.gov/gene/?term=79877		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040633	79877	DCAKD	http://www.ncbi.nlm.nih.gov/gene/?term=79877		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040634	79899	PRR5L	http://www.ncbi.nlm.nih.gov/gene/?term=79899	PROTOR2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040635	79899	PRR5L	http://www.ncbi.nlm.nih.gov/gene/?term=79899	PROTOR2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040636	79906	MORN1	http://www.ncbi.nlm.nih.gov/gene/?term=79906		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040637	79932	KIAA0319L	http://www.ncbi.nlm.nih.gov/gene/?term=79932	"AAVR, AAVRL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040638	79934	COQ8B	http://www.ncbi.nlm.nih.gov/gene/?term=79934	"ADCK4, NPHS9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040639	79934	COQ8B	http://www.ncbi.nlm.nih.gov/gene/?term=79934	"ADCK4, NPHS9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040640	80003	PCNX2	http://www.ncbi.nlm.nih.gov/gene/?term=80003	PCNXL2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040641	80006	TRAPPC13	http://www.ncbi.nlm.nih.gov/gene/?term=80006	C5orf44	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040642	80012	PHC3	http://www.ncbi.nlm.nih.gov/gene/?term=80012	"EDR3, HPH3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040643	80012	PHC3	http://www.ncbi.nlm.nih.gov/gene/?term=80012	"EDR3, HPH3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040644	80014	WWC2	http://www.ncbi.nlm.nih.gov/gene/?term=80014	BOMB	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040645	80014	WWC2	http://www.ncbi.nlm.nih.gov/gene/?term=80014	BOMB	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040646	80017	DGLUCY	http://www.ncbi.nlm.nih.gov/gene/?term=80017	C14orf159	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040647	80017	DGLUCY	http://www.ncbi.nlm.nih.gov/gene/?term=80017	C14orf159	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040648	80036	TRPM3	http://www.ncbi.nlm.nih.gov/gene/?term=80036	"GON-2, LTRPC3, MLSN2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040649	80055	PGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=80055	"Bst1, ISPD3024, MRT42, SPG67"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040650	80108	ZFP2	http://www.ncbi.nlm.nih.gov/gene/?term=80108	"ZNF751, zfp-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040651	80108	ZFP2	http://www.ncbi.nlm.nih.gov/gene/?term=80108	"ZNF751, zfp-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040652	80129	CCDC170	http://www.ncbi.nlm.nih.gov/gene/?term=80129	"C6orf97, bA282P11.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040653	80129	CCDC170	http://www.ncbi.nlm.nih.gov/gene/?term=80129	"C6orf97, bA282P11.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040654	80144	FRAS1	http://www.ncbi.nlm.nih.gov/gene/?term=80144		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040655	80144	FRAS1	http://www.ncbi.nlm.nih.gov/gene/?term=80144		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040656	80145	THOC7	http://www.ncbi.nlm.nih.gov/gene/?term=80145	"NIF3L1BP1, fSAP24, hTREX30"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040657	80149	ZC3H12A	http://www.ncbi.nlm.nih.gov/gene/?term=80149	"MCPIP, MCPIP-1, MCPIP1, Reg1, dJ423B22.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040658	80149	ZC3H12A	http://www.ncbi.nlm.nih.gov/gene/?term=80149	"MCPIP, MCPIP-1, MCPIP1, Reg1, dJ423B22.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040659	80173	IFT74	http://www.ncbi.nlm.nih.gov/gene/?term=80173	"BBS20, CCDC2, CMG-1, CMG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040660	80173	IFT74	http://www.ncbi.nlm.nih.gov/gene/?term=80173	"BBS20, CCDC2, CMG-1, CMG1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040661	80184	CEP290	http://www.ncbi.nlm.nih.gov/gene/?term=80184	"3H11Ag, BBS14, CT87, JBTS5, LCA10, MKS4, NPHP6, POC3, SLSN6, rd16"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040662	80184	CEP290	http://www.ncbi.nlm.nih.gov/gene/?term=80184	"3H11Ag, BBS14, CT87, JBTS5, LCA10, MKS4, NPHP6, POC3, SLSN6, rd16"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040663	80204	FBXO11	http://www.ncbi.nlm.nih.gov/gene/?term=80204	"FBX11, PRMT9, UBR6, UG063H01, VIT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040664	80204	FBXO11	http://www.ncbi.nlm.nih.gov/gene/?term=80204	"FBX11, PRMT9, UBR6, UG063H01, VIT1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040665	80205	CHD9	http://www.ncbi.nlm.nih.gov/gene/?term=80205	"AD013, CHD-9, CReMM, KISH2, PRIC320"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040666	80212	CCDC92	http://www.ncbi.nlm.nih.gov/gene/?term=80212		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040667	80212	CCDC92	http://www.ncbi.nlm.nih.gov/gene/?term=80212		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040668	80218	NAA50	http://www.ncbi.nlm.nih.gov/gene/?term=80218	"MAK3, NAT13, NAT13P, NAT5, NAT5P, SAN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040669	80223	RAB11FIP1	http://www.ncbi.nlm.nih.gov/gene/?term=80223	"NOEL1A, RCP, rab11-FIP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040670	80230	RUFY1	http://www.ncbi.nlm.nih.gov/gene/?term=80230	"RABIP4, ZFYVE12"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040671	80230	RUFY1	http://www.ncbi.nlm.nih.gov/gene/?term=80230	"RABIP4, ZFYVE12"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040672	80232	WDR26	http://www.ncbi.nlm.nih.gov/gene/?term=80232	"CDW2, GID7, MIP2, SKDEAS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040673	80262	C16orf70	http://www.ncbi.nlm.nih.gov/gene/?term=80262	"C16orf6, LIN10, lin-10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040674	80264	ZNF430	http://www.ncbi.nlm.nih.gov/gene/?term=80264		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040675	8028	MLLT10	http://www.ncbi.nlm.nih.gov/gene/?term=8028	AF10	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040676	8028	MLLT10	http://www.ncbi.nlm.nih.gov/gene/?term=8028	AF10	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040677	80314	EPC1	http://www.ncbi.nlm.nih.gov/gene/?term=80314	Epl1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040678	80314	EPC1	http://www.ncbi.nlm.nih.gov/gene/?term=80314	Epl1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040679	80315	CPEB4	http://www.ncbi.nlm.nih.gov/gene/?term=80315	"CPE-BP4, hCPEB-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040680	80315	CPEB4	http://www.ncbi.nlm.nih.gov/gene/?term=80315	"CPE-BP4, hCPEB-4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040681	8034	SLC25A16	http://www.ncbi.nlm.nih.gov/gene/?term=8034	"D10S105E, GDA, GDC, HGT.1, ML7, hML7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040682	8034	SLC25A16	http://www.ncbi.nlm.nih.gov/gene/?term=8034	"D10S105E, GDA, GDC, HGT.1, ML7, hML7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040683	8036	SHOC2	http://www.ncbi.nlm.nih.gov/gene/?term=8036	"SIAA0862, SOC2, SUR8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040684	8036	SHOC2	http://www.ncbi.nlm.nih.gov/gene/?term=8036	"SIAA0862, SOC2, SUR8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040685	8038	ADAM12	http://www.ncbi.nlm.nih.gov/gene/?term=8038	"ADAM12-OT1, CAR10, MCMP, MCMPMltna, MLTN, MLTNA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040686	8038	ADAM12	http://www.ncbi.nlm.nih.gov/gene/?term=8038	"ADAM12-OT1, CAR10, MCMP, MCMPMltna, MLTN, MLTNA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040687	80745	THUMPD2	http://www.ncbi.nlm.nih.gov/gene/?term=80745	C2orf8	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040688	80745	THUMPD2	http://www.ncbi.nlm.nih.gov/gene/?term=80745	C2orf8	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040689	80746	TSEN2	http://www.ncbi.nlm.nih.gov/gene/?term=80746	"PCH2B, SEN2, SEN2L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040690	80746	TSEN2	http://www.ncbi.nlm.nih.gov/gene/?term=80746	"PCH2B, SEN2, SEN2L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040691	80777	CYB5B	http://www.ncbi.nlm.nih.gov/gene/?term=80777	"CYB5-M, CYPB5M, OMB5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040692	80777	CYB5B	http://www.ncbi.nlm.nih.gov/gene/?term=80777	"CYB5-M, CYPB5M, OMB5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040693	80778	ZNF34	http://www.ncbi.nlm.nih.gov/gene/?term=80778	KOX32	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040694	80778	ZNF34	http://www.ncbi.nlm.nih.gov/gene/?term=80778	KOX32	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040695	80790	CMIP	http://www.ncbi.nlm.nih.gov/gene/?term=80790	TCMIP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040696	80790	CMIP	http://www.ncbi.nlm.nih.gov/gene/?term=80790	TCMIP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040697	80824	DUSP16	http://www.ncbi.nlm.nih.gov/gene/?term=80824	"MKP-7, MKP7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040698	80895	ILKAP	http://www.ncbi.nlm.nih.gov/gene/?term=80895	"ILKAP23, PP2C-DELTA, PPM1O, ILKAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040699	80895	ILKAP	http://www.ncbi.nlm.nih.gov/gene/?term=80895	"ILKAP23, PP2C-DELTA, PPM1O, ILKAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040700	8091	HMGA2	http://www.ncbi.nlm.nih.gov/gene/?term=8091	"BABL, HMGI-C, HMGIC, LIPO, STQTL9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040701	8091	HMGA2	http://www.ncbi.nlm.nih.gov/gene/?term=8091	"BABL, HMGI-C, HMGIC, LIPO, STQTL9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040702	81	ACTN4	http://www.ncbi.nlm.nih.gov/gene/?term=81	"ACTININ-4, FSGS, FSGS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040703	81	ACTN4	http://www.ncbi.nlm.nih.gov/gene/?term=81	"ACTININ-4, FSGS, FSGS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040704	8128	ST8SIA2	http://www.ncbi.nlm.nih.gov/gene/?term=8128	"HsT19690, SIAT8-B, SIAT8B, ST8SIA-II, ST8SiaII, STX"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040705	8128	ST8SIA2	http://www.ncbi.nlm.nih.gov/gene/?term=8128	"HsT19690, SIAT8-B, SIAT8B, ST8SIA-II, ST8SiaII, STX"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040706	8131	NPRL3	http://www.ncbi.nlm.nih.gov/gene/?term=8131	"C16orf35, CGTHBA, FFEVF3, HS-40, MARE, NPR3, RMD11"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040707	8148	TAF15	http://www.ncbi.nlm.nih.gov/gene/?term=8148	"Npl3, RBP56, TAF2N, TAFII68"	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00040708	8148	TAF15	http://www.ncbi.nlm.nih.gov/gene/?term=8148	"Npl3, RBP56, TAF2N, TAFII68"	lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00040709	81490	PTDSS2	http://www.ncbi.nlm.nih.gov/gene/?term=81490	PSS2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040710	81490	PTDSS2	http://www.ncbi.nlm.nih.gov/gene/?term=81490	PSS2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040711	81502	HM13	http://www.ncbi.nlm.nih.gov/gene/?term=81502	"H13, IMP1, IMPAS, IMPAS-1, MSTP086, PSENL3, PSL3, SPP, SPPL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040712	81502	HM13	http://www.ncbi.nlm.nih.gov/gene/?term=81502	"H13, IMP1, IMPAS, IMPAS-1, MSTP086, PSENL3, PSL3, SPP, SPPL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040713	81565	NDEL1	http://www.ncbi.nlm.nih.gov/gene/?term=81565	"EOPA, MITAP1, NDE1L1, NDE2, NUDEL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040714	81565	NDEL1	http://www.ncbi.nlm.nih.gov/gene/?term=81565	"EOPA, MITAP1, NDE1L1, NDE2, NUDEL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040715	81603	TRIM8	http://www.ncbi.nlm.nih.gov/gene/?term=81603	"GERP, RNF27"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040716	81603	TRIM8	http://www.ncbi.nlm.nih.gov/gene/?term=81603	"GERP, RNF27"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040717	81605	URM1	http://www.ncbi.nlm.nih.gov/gene/?term=81605	C9orf74	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040718	81605	URM1	http://www.ncbi.nlm.nih.gov/gene/?term=81605	C9orf74	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040719	81606	LBH	http://www.ncbi.nlm.nih.gov/gene/?term=81606		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040720	81606	LBH	http://www.ncbi.nlm.nih.gov/gene/?term=81606		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040721	81607	NECTIN4	http://www.ncbi.nlm.nih.gov/gene/?term=81607	"EDSS1, LNIR, PRR4, PVRL4, nectin-4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040722	81607	NECTIN4	http://www.ncbi.nlm.nih.gov/gene/?term=81607	"EDSS1, LNIR, PRR4, PVRL4, nectin-4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040723	81608	FIP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=81608	"FIP1, Rhe, hFip1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040724	81608	FIP1L1	http://www.ncbi.nlm.nih.gov/gene/?term=81608	"FIP1, Rhe, hFip1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040725	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040726	81609	SNX27	http://www.ncbi.nlm.nih.gov/gene/?term=81609	"MRT1, MY014"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040727	81619	TSPAN14	http://www.ncbi.nlm.nih.gov/gene/?term=81619	"DC-TM4F2, TM4SF14"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040728	81619	TSPAN14	http://www.ncbi.nlm.nih.gov/gene/?term=81619	"DC-TM4F2, TM4SF14"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040729	81688	C6orf62	http://www.ncbi.nlm.nih.gov/gene/?term=81688	"Nbla00237, XTP12, dJ30M3.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040730	81693	AMN	http://www.ncbi.nlm.nih.gov/gene/?term=81693	"PRO1028, amnionless"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040731	81693	AMN	http://www.ncbi.nlm.nih.gov/gene/?term=81693	"PRO1028, amnionless"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040732	817	CAMK2D	http://www.ncbi.nlm.nih.gov/gene/?term=817	CAMKD	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040733	817	CAMK2D	http://www.ncbi.nlm.nih.gov/gene/?term=817	CAMKD	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040734	81790	RNF170	http://www.ncbi.nlm.nih.gov/gene/?term=81790	"ADSA, SNAX1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040735	81790	RNF170	http://www.ncbi.nlm.nih.gov/gene/?term=81790	"ADSA, SNAX1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040736	81846	SBF2	http://www.ncbi.nlm.nih.gov/gene/?term=81846	"CMT4B2, DENND7B, MTMR13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040737	8202	NCOA3	http://www.ncbi.nlm.nih.gov/gene/?term=8202	"ACTR, AIB-1, AIB1, CAGH16, CTG26, KAT13B, RAC3, SRC-3, SRC3, TNRC14, TNRC16, TRAM-1, bHLHe42, pCIP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040738	8202	NCOA3	http://www.ncbi.nlm.nih.gov/gene/?term=8202	"ACTR, AIB-1, AIB1, CAGH16, CTG26, KAT13B, RAC3, SRC-3, SRC3, TNRC14, TNRC16, TRAM-1, bHLHe42, pCIP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040739	8218	CLTCL1	http://www.ncbi.nlm.nih.gov/gene/?term=8218	"CHC22, CLH22, CLTCL, CLTD"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040740	8218	CLTCL1	http://www.ncbi.nlm.nih.gov/gene/?term=8218	"CHC22, CLH22, CLTCL, CLTD"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040741	8224	SYN3	http://www.ncbi.nlm.nih.gov/gene/?term=8224		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040742	8224	SYN3	http://www.ncbi.nlm.nih.gov/gene/?term=8224		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040743	8289	ARID1A	http://www.ncbi.nlm.nih.gov/gene/?term=8289	"B120, BAF250, BAF250a, BM029, C1orf4, CSS2, ELD, MRD14, OSA1, P270, SMARCF1, hELD, hOSA1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040744	8291	DYSF	http://www.ncbi.nlm.nih.gov/gene/?term=8291	"FER1L1, LGMD2B, MMD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040745	8291	DYSF	http://www.ncbi.nlm.nih.gov/gene/?term=8291	"FER1L1, LGMD2B, MMD1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040746	8295	TRRAP	http://www.ncbi.nlm.nih.gov/gene/?term=8295	"PAF350/400, PAF400, STAF40, TR-AP, Tra1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040747	8295	TRRAP	http://www.ncbi.nlm.nih.gov/gene/?term=8295	"PAF350/400, PAF400, STAF40, TR-AP, Tra1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040748	8301	PICALM	http://www.ncbi.nlm.nih.gov/gene/?term=8301	"CALM, CLTH, LAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040749	8301	PICALM	http://www.ncbi.nlm.nih.gov/gene/?term=8301	"CALM, CLTH, LAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040750	831	CAST	http://www.ncbi.nlm.nih.gov/gene/?term=831	"BS-17, PLACK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040751	831	CAST	http://www.ncbi.nlm.nih.gov/gene/?term=831	"BS-17, PLACK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040752	8312	AXIN1	http://www.ncbi.nlm.nih.gov/gene/?term=8312	"AXIN, PPP1R49"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040753	8312	AXIN1	http://www.ncbi.nlm.nih.gov/gene/?term=8312	"AXIN, PPP1R49"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040754	8313	AXIN2	http://www.ncbi.nlm.nih.gov/gene/?term=8313	"AXIL, ODCRCS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040755	8313	AXIN2	http://www.ncbi.nlm.nih.gov/gene/?term=8313	"AXIL, ODCRCS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040756	83439	TCF7L1	http://www.ncbi.nlm.nih.gov/gene/?term=83439	"TCF-3, TCF3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040757	83439	TCF7L1	http://www.ncbi.nlm.nih.gov/gene/?term=83439	"TCF-3, TCF3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040758	83478	ARHGAP24	http://www.ncbi.nlm.nih.gov/gene/?term=83478	"FILGAP, RC-GAP72, RCGAP72, p73, p73RhoGAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040759	83478	ARHGAP24	http://www.ncbi.nlm.nih.gov/gene/?term=83478	"FILGAP, RC-GAP72, RCGAP72, p73, p73RhoGAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040760	83479	DDX59	http://www.ncbi.nlm.nih.gov/gene/?term=83479	"OFD5, ZNHIT5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040761	83479	DDX59	http://www.ncbi.nlm.nih.gov/gene/?term=83479	"OFD5, ZNHIT5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040762	83548	COG3	http://www.ncbi.nlm.nih.gov/gene/?term=83548	SEC34	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040763	83605	CCM2	http://www.ncbi.nlm.nih.gov/gene/?term=83605	"C7orf22, OSM, PP10187"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040764	83605	CCM2	http://www.ncbi.nlm.nih.gov/gene/?term=83605	"C7orf22, OSM, PP10187"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040765	83636	C19orf12	http://www.ncbi.nlm.nih.gov/gene/?term=83636	"MPAN, NBIA3, NBIA4, SPG43"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040766	83636	C19orf12	http://www.ncbi.nlm.nih.gov/gene/?term=83636	"MPAN, NBIA3, NBIA4, SPG43"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040767	83641	FAM107B	http://www.ncbi.nlm.nih.gov/gene/?term=83641	"C10orf45, HITS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040768	83641	FAM107B	http://www.ncbi.nlm.nih.gov/gene/?term=83641	"C10orf45, HITS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040769	83642	SELENOO	http://www.ncbi.nlm.nih.gov/gene/?term=83642	SELO	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040770	83642	SELENOO	http://www.ncbi.nlm.nih.gov/gene/?term=83642	SELO	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040771	83648	FAM167A	http://www.ncbi.nlm.nih.gov/gene/?term=83648	"C8orf13, D8S265"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040772	83648	FAM167A	http://www.ncbi.nlm.nih.gov/gene/?term=83648	"C8orf13, D8S265"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040773	83660	TLN2	http://www.ncbi.nlm.nih.gov/gene/?term=83660	ILWEQ	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040774	83660	TLN2	http://www.ncbi.nlm.nih.gov/gene/?term=83660	ILWEQ	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040775	83667	SESN2	http://www.ncbi.nlm.nih.gov/gene/?term=83667	"HI95, SES2, SEST2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040776	83692	CD99L2	http://www.ncbi.nlm.nih.gov/gene/?term=83692	"CD99B, MIC2L1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040777	83692	CD99L2	http://www.ncbi.nlm.nih.gov/gene/?term=83692	"CD99B, MIC2L1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040778	83696	TRAPPC9	http://www.ncbi.nlm.nih.gov/gene/?term=83696	"IBP, IKBKBBP, MRT13, NIBP, T1, TRS120"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040779	83696	TRAPPC9	http://www.ncbi.nlm.nih.gov/gene/?term=83696	"IBP, IKBKBBP, MRT13, NIBP, T1, TRS120"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040780	83716	CRISPLD2	http://www.ncbi.nlm.nih.gov/gene/?term=83716	"CRISP11, LCRISP2, LGL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040781	83716	CRISPLD2	http://www.ncbi.nlm.nih.gov/gene/?term=83716	"CRISP11, LCRISP2, LGL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040782	83758	RBP5	http://www.ncbi.nlm.nih.gov/gene/?term=83758	"CRBP-III, CRBP3, CRBPIII, HRBPiso"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040783	83758	RBP5	http://www.ncbi.nlm.nih.gov/gene/?term=83758	"CRBP-III, CRBP3, CRBPIII, HRBPiso"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040784	83759	RBM4B	http://www.ncbi.nlm.nih.gov/gene/?term=83759	"RBM30, RBM4L, ZCCHC15, ZCCHC21B, ZCRB3B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040785	83759	RBM4B	http://www.ncbi.nlm.nih.gov/gene/?term=83759	"RBM30, RBM4L, ZCCHC15, ZCCHC21B, ZCRB3B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040786	83878	USHBP1	http://www.ncbi.nlm.nih.gov/gene/?term=83878	"AIEBP, MCC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040787	83878	USHBP1	http://www.ncbi.nlm.nih.gov/gene/?term=83878	"AIEBP, MCC2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040788	83938	LRMDA	http://www.ncbi.nlm.nih.gov/gene/?term=83938	"C10orf11, CDA017"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040789	83938	LRMDA	http://www.ncbi.nlm.nih.gov/gene/?term=83938	"C10orf11, CDA017"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040790	8394	PIP5K1A	http://www.ncbi.nlm.nih.gov/gene/?term=8394		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040791	8394	PIP5K1A	http://www.ncbi.nlm.nih.gov/gene/?term=8394		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040792	8395	PIP5K1B	http://www.ncbi.nlm.nih.gov/gene/?term=8395	"MSS4, STM7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040793	8395	PIP5K1B	http://www.ncbi.nlm.nih.gov/gene/?term=8395	"MSS4, STM7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040794	83989	FAM172A	http://www.ncbi.nlm.nih.gov/gene/?term=83989	C5orf21	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040795	83992	CTTNBP2	http://www.ncbi.nlm.nih.gov/gene/?term=83992	"C7orf8, CORTBP2, Orf4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040796	84002	B3GNT5	http://www.ncbi.nlm.nih.gov/gene/?term=84002	"B3GN-T5, beta3Gn-T5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040797	84033	OBSCN	http://www.ncbi.nlm.nih.gov/gene/?term=84033	"ARHGEF30, UNC89"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040798	84056	KATNAL1	http://www.ncbi.nlm.nih.gov/gene/?term=84056		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040799	84059	ADGRV1	http://www.ncbi.nlm.nih.gov/gene/?term=84059	"FEB4, GPR98, MASS1, USH2B, USH2C, VLGR1, VLGR1b"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040800	84062	DTNBP1	http://www.ncbi.nlm.nih.gov/gene/?term=84062	"BLOC1S8, DBND, HPS7, My031, SDY"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040801	84064	HDHD2	http://www.ncbi.nlm.nih.gov/gene/?term=84064	"3110052N05Rik, HEL-S-301"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040802	84064	HDHD2	http://www.ncbi.nlm.nih.gov/gene/?term=84064	"3110052N05Rik, HEL-S-301"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040803	84081	NSRP1	http://www.ncbi.nlm.nih.gov/gene/?term=84081	"CCDC55, HSPC095, NSrp70"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040804	841	CASP8	http://www.ncbi.nlm.nih.gov/gene/?term=841	"ALPS2B, CAP4, Casp-8, FLICE, MACH, MCH5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040805	841	CASP8	http://www.ncbi.nlm.nih.gov/gene/?term=841	"ALPS2B, CAP4, Casp-8, FLICE, MACH, MCH5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040806	8412	BCAR3	http://www.ncbi.nlm.nih.gov/gene/?term=8412	"NSP2, SH2D3B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040807	8412	BCAR3	http://www.ncbi.nlm.nih.gov/gene/?term=8412	"NSP2, SH2D3B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040808	84138	SLC7A6OS	http://www.ncbi.nlm.nih.gov/gene/?term=84138		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040809	84138	SLC7A6OS	http://www.ncbi.nlm.nih.gov/gene/?term=84138		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040810	84153	RNASEH2C	http://www.ncbi.nlm.nih.gov/gene/?term=84153	"AGS3, AYP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040811	84153	RNASEH2C	http://www.ncbi.nlm.nih.gov/gene/?term=84153	"AGS3, AYP1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040812	84168	ANTXR1	http://www.ncbi.nlm.nih.gov/gene/?term=84168	"ATR, GAPO, TEM8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040813	84168	ANTXR1	http://www.ncbi.nlm.nih.gov/gene/?term=84168	"ATR, GAPO, TEM8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040814	84186	ZCCHC7	http://www.ncbi.nlm.nih.gov/gene/?term=84186	"AIR1, HSPC086"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040815	84186	ZCCHC7	http://www.ncbi.nlm.nih.gov/gene/?term=84186	"AIR1, HSPC086"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040816	84187	TMEM164	http://www.ncbi.nlm.nih.gov/gene/?term=84187	bB360B22.3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040817	84187	TMEM164	http://www.ncbi.nlm.nih.gov/gene/?term=84187	bB360B22.3	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040818	84251	SGIP1	http://www.ncbi.nlm.nih.gov/gene/?term=84251		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040819	84251	SGIP1	http://www.ncbi.nlm.nih.gov/gene/?term=84251		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040820	84253	GARNL3	http://www.ncbi.nlm.nih.gov/gene/?term=84253	bA356B19.1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040821	84253	GARNL3	http://www.ncbi.nlm.nih.gov/gene/?term=84253	bA356B19.1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040822	84254	CAMKK1	http://www.ncbi.nlm.nih.gov/gene/?term=84254	CAMKKA	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040823	84254	CAMKK1	http://www.ncbi.nlm.nih.gov/gene/?term=84254	CAMKKA	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040824	84255	SLC37A3	http://www.ncbi.nlm.nih.gov/gene/?term=84255		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040825	84260	TCHP	http://www.ncbi.nlm.nih.gov/gene/?term=84260	TpMs	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040826	84268	RPAIN	http://www.ncbi.nlm.nih.gov/gene/?term=84268	"HRIP, RIP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040827	84275	SLC25A33	http://www.ncbi.nlm.nih.gov/gene/?term=84275	"BMSC-MCP, PNC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040828	8428	STK24	http://www.ncbi.nlm.nih.gov/gene/?term=8428	"HEL-S-95, MST3, MST3B, STE20, STK3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040829	8428	STK24	http://www.ncbi.nlm.nih.gov/gene/?term=8428	"HEL-S-95, MST3, MST3B, STE20, STK3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040830	84300	UQCC2	http://www.ncbi.nlm.nih.gov/gene/?term=84300	"C6orf125, C6orf126, Cbp6, M19, MNF1, bA6B20.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040831	84300	UQCC2	http://www.ncbi.nlm.nih.gov/gene/?term=84300	"C6orf125, C6orf126, Cbp6, M19, MNF1, bA6B20.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040832	84316	NAA38	http://www.ncbi.nlm.nih.gov/gene/?term=84316	"LSMD1, PFAAP2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040833	84319	CMSS1	http://www.ncbi.nlm.nih.gov/gene/?term=84319	C3orf26	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040834	84320	ACBD6	http://www.ncbi.nlm.nih.gov/gene/?term=84320	MGC2404	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040835	84329	HVCN1	http://www.ncbi.nlm.nih.gov/gene/?term=84329	"HV1, VSOP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040836	84329	HVCN1	http://www.ncbi.nlm.nih.gov/gene/?term=84329	"HV1, VSOP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040837	84333	PCGF5	http://www.ncbi.nlm.nih.gov/gene/?term=84333	RNF159	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040838	84335	AKT1S1	http://www.ncbi.nlm.nih.gov/gene/?term=84335	"Lobe, PRAS40"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040839	84335	AKT1S1	http://www.ncbi.nlm.nih.gov/gene/?term=84335	"Lobe, PRAS40"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040840	8434	RECK	http://www.ncbi.nlm.nih.gov/gene/?term=8434	ST15	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00040841	84340	GFM2	http://www.ncbi.nlm.nih.gov/gene/?term=84340	"EF-G2mt, EFG2, MRRF2, MST027, MSTP027, RRF2, RRF2mt, hEFG2, mEF-G 2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040842	84376	HOOK3	http://www.ncbi.nlm.nih.gov/gene/?term=84376	HK3	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040843	84418	CYSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=84418	"C5orf32, ORF1-FL49"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040844	84418	CYSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=84418	"C5orf32, ORF1-FL49"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040845	84435	ADGRA1	http://www.ncbi.nlm.nih.gov/gene/?term=84435	GPR123	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040846	84435	ADGRA1	http://www.ncbi.nlm.nih.gov/gene/?term=84435	GPR123	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040847	84441	MAML2	http://www.ncbi.nlm.nih.gov/gene/?term=84441	"MAM-3, MAM2, MAM3, MLL-MAML2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040848	84441	MAML2	http://www.ncbi.nlm.nih.gov/gene/?term=84441	"MAM-3, MAM2, MAM3, MLL-MAML2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040849	84449	ZNF333	http://www.ncbi.nlm.nih.gov/gene/?term=84449		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040850	84455	EFCAB7	http://www.ncbi.nlm.nih.gov/gene/?term=84455		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040851	84498	FAM120B	http://www.ncbi.nlm.nih.gov/gene/?term=84498	"CCPG, KIAA1838, PGCC1, dJ894D12.1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040852	84498	FAM120B	http://www.ncbi.nlm.nih.gov/gene/?term=84498	"CCPG, KIAA1838, PGCC1, dJ894D12.1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040853	8451	CUL4A	http://www.ncbi.nlm.nih.gov/gene/?term=8451		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040854	8451	CUL4A	http://www.ncbi.nlm.nih.gov/gene/?term=8451		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040855	8452	CUL3	http://www.ncbi.nlm.nih.gov/gene/?term=8452	"CUL-3, PHA2E"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040856	84524	ZC3H8	http://www.ncbi.nlm.nih.gov/gene/?term=84524	"Fliz1, ZC3HDC8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040857	84530	SRRM4	http://www.ncbi.nlm.nih.gov/gene/?term=84530	"KIAA1853, MU-MB-2.76, nSR100"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040858	84530	SRRM4	http://www.ncbi.nlm.nih.gov/gene/?term=84530	"KIAA1853, MU-MB-2.76, nSR100"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040859	8458	TTF2	http://www.ncbi.nlm.nih.gov/gene/?term=8458	"HuF2, ZGRF6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040860	8458	TTF2	http://www.ncbi.nlm.nih.gov/gene/?term=8458	"HuF2, ZGRF6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040861	84623	KIRREL3	http://www.ncbi.nlm.nih.gov/gene/?term=84623	"KIRRE, MRD4, NEPH2, PRO4502"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040862	84623	KIRREL3	http://www.ncbi.nlm.nih.gov/gene/?term=84623	"KIRRE, MRD4, NEPH2, PRO4502"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040863	84650	EBPL	http://www.ncbi.nlm.nih.gov/gene/?term=84650	EBRP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040864	84650	EBPL	http://www.ncbi.nlm.nih.gov/gene/?term=84650	EBRP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040865	84656	GLYR1	http://www.ncbi.nlm.nih.gov/gene/?term=84656	"BM045, HIBDL, N-PAC, NP60"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040866	84656	GLYR1	http://www.ncbi.nlm.nih.gov/gene/?term=84656	"BM045, HIBDL, N-PAC, NP60"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040867	84668	FAM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84668	"DRCTNNB1A, HCC, HLD5, HYCC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040868	84668	FAM126A	http://www.ncbi.nlm.nih.gov/gene/?term=84668	"DRCTNNB1A, HCC, HLD5, HYCC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040869	84695	LOXL3	http://www.ncbi.nlm.nih.gov/gene/?term=84695	LOXL	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040870	84695	LOXL3	http://www.ncbi.nlm.nih.gov/gene/?term=84695	LOXL	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040871	8470	SORBS2	http://www.ncbi.nlm.nih.gov/gene/?term=8470	"ARGBP2, PRO0618"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040872	8470	SORBS2	http://www.ncbi.nlm.nih.gov/gene/?term=8470	"ARGBP2, PRO0618"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040873	84859	LRCH3	http://www.ncbi.nlm.nih.gov/gene/?term=84859		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040874	84869	CBR4	http://www.ncbi.nlm.nih.gov/gene/?term=84869	SDR45C1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040875	84869	CBR4	http://www.ncbi.nlm.nih.gov/gene/?term=84869	SDR45C1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040876	84893	FBXO18	http://www.ncbi.nlm.nih.gov/gene/?term=84893	"FBH1, Fbx18, hFBH1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040877	84893	FBXO18	http://www.ncbi.nlm.nih.gov/gene/?term=84893	"FBH1, Fbx18, hFBH1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040878	84898	PLXDC2	http://www.ncbi.nlm.nih.gov/gene/?term=84898	TEM7R	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040879	84909	C9orf3	http://www.ncbi.nlm.nih.gov/gene/?term=84909	"AOPEP, AP-O, APO, C90RF3, ONPEP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040880	84909	C9orf3	http://www.ncbi.nlm.nih.gov/gene/?term=84909	"AOPEP, AP-O, APO, C90RF3, ONPEP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040881	8491	MAP4K3	http://www.ncbi.nlm.nih.gov/gene/?term=8491	"GLK, MAPKKKK3, MEKKK 3, MEKKK3, RAB8IPL1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040882	8491	MAP4K3	http://www.ncbi.nlm.nih.gov/gene/?term=8491	"GLK, MAPKKKK3, MEKKK 3, MEKKK3, RAB8IPL1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040883	84910	TMEM87B	http://www.ncbi.nlm.nih.gov/gene/?term=84910		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040884	84910	TMEM87B	http://www.ncbi.nlm.nih.gov/gene/?term=84910		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040885	84918	LRP11	http://www.ncbi.nlm.nih.gov/gene/?term=84918	"MANSC3, bA350J20.3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040886	84918	LRP11	http://www.ncbi.nlm.nih.gov/gene/?term=84918	"MANSC3, bA350J20.3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040887	84942	WDR73	http://www.ncbi.nlm.nih.gov/gene/?term=84942	"GAMOS, HSPC264"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040888	84951	TNS4	http://www.ncbi.nlm.nih.gov/gene/?term=84951	"CTEN, PP14434"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040889	84951	TNS4	http://www.ncbi.nlm.nih.gov/gene/?term=84951	"CTEN, PP14434"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040890	84961	FBXL20	http://www.ncbi.nlm.nih.gov/gene/?term=84961	"Fbl2, Fbl20"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040891	84961	FBXL20	http://www.ncbi.nlm.nih.gov/gene/?term=84961	"Fbl2, Fbl20"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040892	84966	IGSF21	http://www.ncbi.nlm.nih.gov/gene/?term=84966		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040893	84966	IGSF21	http://www.ncbi.nlm.nih.gov/gene/?term=84966		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040894	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040895	8500	PPFIA1	http://www.ncbi.nlm.nih.gov/gene/?term=8500	"LIP.1, LIP1, LIPRIN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040896	8527	DGKD	http://www.ncbi.nlm.nih.gov/gene/?term=8527	"DGKdelta, dgkd-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040897	8527	DGKD	http://www.ncbi.nlm.nih.gov/gene/?term=8527	"DGKdelta, dgkd-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040898	85301	COL27A1	http://www.ncbi.nlm.nih.gov/gene/?term=85301	STLS	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040899	85301	COL27A1	http://www.ncbi.nlm.nih.gov/gene/?term=85301	STLS	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040900	85446	ZFHX2	http://www.ncbi.nlm.nih.gov/gene/?term=85446	"ZFH-5, ZNF409"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040901	85446	ZFHX2	http://www.ncbi.nlm.nih.gov/gene/?term=85446	"ZFH-5, ZNF409"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040902	85456	TNKS1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=85456	TAB182	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040903	85456	TNKS1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=85456	TAB182	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040904	8546	AP3B1	http://www.ncbi.nlm.nih.gov/gene/?term=8546	"ADTB3, ADTB3A, HPS, HPS2, PE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040905	8546	AP3B1	http://www.ncbi.nlm.nih.gov/gene/?term=8546	"ADTB3, ADTB3A, HPS, HPS2, PE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040906	85461	TANC1	http://www.ncbi.nlm.nih.gov/gene/?term=85461	"ROLSB, TANC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040907	85461	TANC1	http://www.ncbi.nlm.nih.gov/gene/?term=85461	"ROLSB, TANC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040908	85464	SSH2	http://www.ncbi.nlm.nih.gov/gene/?term=85464	"SSH-2, SSH-2L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040909	85464	SSH2	http://www.ncbi.nlm.nih.gov/gene/?term=85464	"SSH-2, SSH-2L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040910	85476	GFM1	http://www.ncbi.nlm.nih.gov/gene/?term=85476	"COXPD1, EFG, EFG1, EFGM, EGF1, GFM, hEFG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040911	85476	GFM1	http://www.ncbi.nlm.nih.gov/gene/?term=85476	"COXPD1, EFG, EFG1, EFGM, EGF1, GFM, hEFG1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040912	8554	PIAS1	http://www.ncbi.nlm.nih.gov/gene/?term=8554	"DDXBP1, GBP, GU/RH-II, ZMIZ3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040913	8554	PIAS1	http://www.ncbi.nlm.nih.gov/gene/?term=8554	"DDXBP1, GBP, GU/RH-II, ZMIZ3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040914	8562	DENR	http://www.ncbi.nlm.nih.gov/gene/?term=8562	"DRP, DRP1, SMAP-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040915	8569	MKNK1	http://www.ncbi.nlm.nih.gov/gene/?term=8569	MNK1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040916	8573	CASK	http://www.ncbi.nlm.nih.gov/gene/?term=8573	"CAGH39, CAMGUK, CMG, FGS4, LIN2, MICPCH, MRXSNA, TNRC8, hCASK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040917	8573	CASK	http://www.ncbi.nlm.nih.gov/gene/?term=8573	"CAGH39, CAMGUK, CMG, FGS4, LIN2, MICPCH, MRXSNA, TNRC8, hCASK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040918	861	RUNX1	http://www.ncbi.nlm.nih.gov/gene/?term=861	"AML1, AML1-EVI-1, AMLCR1, CBF2alpha, CBFA2, EVI-1, PEBP2aB, PEBP2alpha"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040919	861	RUNX1	http://www.ncbi.nlm.nih.gov/gene/?term=861	"AML1, AML1-EVI-1, AMLCR1, CBF2alpha, CBFA2, EVI-1, PEBP2aB, PEBP2alpha"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040920	8611	PLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=8611	"LLP1a, LPP1, PAP-2a, PAP2, PPAP2A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040921	8611	PLPP1	http://www.ncbi.nlm.nih.gov/gene/?term=8611	"LLP1a, LPP1, PAP-2a, PAP2, PPAP2A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040922	8614	STC2	http://www.ncbi.nlm.nih.gov/gene/?term=8614	"STC-2, STCRP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040923	8614	STC2	http://www.ncbi.nlm.nih.gov/gene/?term=8614	"STC-2, STCRP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040924	8618	CADPS	http://www.ncbi.nlm.nih.gov/gene/?term=8618	"CADPS1, CAPS, CAPS1, UNC-31"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040925	8618	CADPS	http://www.ncbi.nlm.nih.gov/gene/?term=8618	"CADPS1, CAPS, CAPS1, UNC-31"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040926	862	RUNX1T1	http://www.ncbi.nlm.nih.gov/gene/?term=862	"AML1-MTG8, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040927	8621	CDK13	http://www.ncbi.nlm.nih.gov/gene/?term=8621	"CDC2L, CDC2L5, CHDFIDD, CHED, hCDK13"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040928	8621	CDK13	http://www.ncbi.nlm.nih.gov/gene/?term=8621	"CDC2L, CDC2L5, CHDFIDD, CHED, hCDK13"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040929	8622	PDE8B	http://www.ncbi.nlm.nih.gov/gene/?term=8622	"ADSD, PPNAD3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040930	8648	NCOA1	http://www.ncbi.nlm.nih.gov/gene/?term=8648	"F-SRC-1, KAT13A, RIP160, SRC1, bHLHe42, bHLHe74"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040931	8658	TNKS	http://www.ncbi.nlm.nih.gov/gene/?term=8658	"ARTD5, PARP-5a, PARP5A, PARPL, TIN1, TINF11, pART5, TNKS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040932	8658	TNKS	http://www.ncbi.nlm.nih.gov/gene/?term=8658	"ARTD5, PARP-5a, PARP5A, PARPL, TIN1, TINF11, pART5, TNKS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040933	8660	IRS2	http://www.ncbi.nlm.nih.gov/gene/?term=8660	IRS-2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040934	8665	EIF3F	http://www.ncbi.nlm.nih.gov/gene/?term=8665	"EIF3S5, eIF3-p47"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040935	8672	EIF4G3	http://www.ncbi.nlm.nih.gov/gene/?term=8672	"eIF-4G 3, eIF4G 3, eIF4GII"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040936	8672	EIF4G3	http://www.ncbi.nlm.nih.gov/gene/?term=8672	"eIF-4G 3, eIF4G 3, eIF4GII"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040937	868	CBLB	http://www.ncbi.nlm.nih.gov/gene/?term=868	"Cbl-b, Nbla00127, RNF56"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040938	868	CBLB	http://www.ncbi.nlm.nih.gov/gene/?term=868	"Cbl-b, Nbla00127, RNF56"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040939	8725	URI1	http://www.ncbi.nlm.nih.gov/gene/?term=8725	"C19orf2, NNX3, PPP1R19, RMP, URI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040940	8743	TNFSF10	http://www.ncbi.nlm.nih.gov/gene/?term=8743	"APO2L, Apo-2L, CD253, TL2, TNLG6A, TRAIL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040941	8743	TNFSF10	http://www.ncbi.nlm.nih.gov/gene/?term=8743	"APO2L, Apo-2L, CD253, TL2, TNLG6A, TRAIL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040942	8745	ADAM23	http://www.ncbi.nlm.nih.gov/gene/?term=8745	"MDC-3, MDC3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040943	8763	CD164	http://www.ncbi.nlm.nih.gov/gene/?term=8763	"DFNA66, MGC-24, MGC-24v, MUC-24, endolyn"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040944	8763	CD164	http://www.ncbi.nlm.nih.gov/gene/?term=8763	"DFNA66, MGC-24, MGC-24v, MUC-24, endolyn"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040945	8764	TNFRSF14	http://www.ncbi.nlm.nih.gov/gene/?term=8764	"ATAR, CD270, HVEA, HVEM, LIGHTR, TR2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040946	8764	TNFRSF14	http://www.ncbi.nlm.nih.gov/gene/?term=8764	"ATAR, CD270, HVEA, HVEM, LIGHTR, TR2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040947	8766	RAB11A	http://www.ncbi.nlm.nih.gov/gene/?term=8766	YL8	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040948	8766	RAB11A	http://www.ncbi.nlm.nih.gov/gene/?term=8766	YL8	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040949	8773	SNAP23	http://www.ncbi.nlm.nih.gov/gene/?term=8773	"HsT17016, SNAP-23A, SNAP23B, SNAP23"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040950	8801	SUCLG2	http://www.ncbi.nlm.nih.gov/gene/?term=8801	"G-SCS, GBETA, GTPSCS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040951	8813	DPM1	http://www.ncbi.nlm.nih.gov/gene/?term=8813	"CDGIE, MPDS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040952	8813	DPM1	http://www.ncbi.nlm.nih.gov/gene/?term=8813	"CDGIE, MPDS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040953	8828	NRP2	http://www.ncbi.nlm.nih.gov/gene/?term=8828	"NP2, NPN2, PRO2714, VEGF165R2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040954	8853	ASAP2	http://www.ncbi.nlm.nih.gov/gene/?term=8853	"AMAP2, CENTB3, DDEF2, PAG3, PAP, Pap-alpha, SHAG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040955	8869	ST3GAL5	http://www.ncbi.nlm.nih.gov/gene/?term=8869	"SATI, SIAT9, SIATGM3S, SPDRS, ST3Gal V, ST3GalV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040956	8869	ST3GAL5	http://www.ncbi.nlm.nih.gov/gene/?term=8869	"SATI, SIAT9, SIATGM3S, SPDRS, ST3Gal V, ST3GalV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040957	8878	SQSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=8878	"A170, DMRV, FTDALS3, NADGP, OSIL, PDB3, ZIP3, p60, p62, p62B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040958	8878	SQSTM1	http://www.ncbi.nlm.nih.gov/gene/?term=8878	"A170, DMRV, FTDALS3, NADGP, OSIL, PDB3, ZIP3, p60, p62, p62B"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040959	8883	NAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8883	"A-116A10.1, APPBP1, HPP1, ula-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040960	8883	NAE1	http://www.ncbi.nlm.nih.gov/gene/?term=8883	"A-116A10.1, APPBP1, HPP1, ula-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040961	8887	TAX1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=8887	"CALCOCO3, T6BP, TXBP151"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040962	8887	TAX1BP1	http://www.ncbi.nlm.nih.gov/gene/?term=8887	"CALCOCO3, T6BP, TXBP151"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040963	8925	HERC1	http://www.ncbi.nlm.nih.gov/gene/?term=8925	"MDFPMR, p532, p619"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040964	8925	HERC1	http://www.ncbi.nlm.nih.gov/gene/?term=8925	"MDFPMR, p532, p619"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040965	8932	MBD2	http://www.ncbi.nlm.nih.gov/gene/?term=8932	"DMTase, NY-CO-41"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040966	8935	SKAP2	http://www.ncbi.nlm.nih.gov/gene/?term=8935	"PRAP, RA70, SAPS, SCAP2, SKAP-HOM, SKAP55R"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040967	8942	KYNU	http://www.ncbi.nlm.nih.gov/gene/?term=8942	KYNUU	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040968	8976	WASL	http://www.ncbi.nlm.nih.gov/gene/?term=8976	"N-WASP, NWASP, WASPB"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040969	8976	WASL	http://www.ncbi.nlm.nih.gov/gene/?term=8976	"N-WASP, NWASP, WASPB"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040970	89796	NAV1	http://www.ncbi.nlm.nih.gov/gene/?term=89796	"POMFIL3, STEERIN1, UNC53H1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040971	89797	NAV2	http://www.ncbi.nlm.nih.gov/gene/?term=89797	"HELAD1, POMFIL2, RAINB1, STEERIN2, UNC53H2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040972	89797	NAV2	http://www.ncbi.nlm.nih.gov/gene/?term=89797	"HELAD1, POMFIL2, RAINB1, STEERIN2, UNC53H2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040973	8992	ATP6V0E1	http://www.ncbi.nlm.nih.gov/gene/?term=8992	"ATP6H, ATP6V0E, M9.2, Vma21, Vma21p"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040974	8992	ATP6V0E1	http://www.ncbi.nlm.nih.gov/gene/?term=8992	"ATP6H, ATP6V0E, M9.2, Vma21, Vma21p"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040975	89927	C16orf45	http://www.ncbi.nlm.nih.gov/gene/?term=89927	MINP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040976	89927	C16orf45	http://www.ncbi.nlm.nih.gov/gene/?term=89927	MINP	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040977	8994	LIMD1	http://www.ncbi.nlm.nih.gov/gene/?term=8994		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040978	8994	LIMD1	http://www.ncbi.nlm.nih.gov/gene/?term=8994		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040979	9014	TAF1B	http://www.ncbi.nlm.nih.gov/gene/?term=9014	"MGC:9349, RAF1B, RAFI63, SL1, TAFI63"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040980	90141	EFCAB11	http://www.ncbi.nlm.nih.gov/gene/?term=90141	C14orf143	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040981	90141	EFCAB11	http://www.ncbi.nlm.nih.gov/gene/?term=90141	C14orf143	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040982	90203	SNX21	http://www.ncbi.nlm.nih.gov/gene/?term=90203	"C20orf161, PP3993, SNX-L, dJ337O18.4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040983	90203	SNX21	http://www.ncbi.nlm.nih.gov/gene/?term=90203	"C20orf161, PP3993, SNX-L, dJ337O18.4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040984	90268	OTULIN	http://www.ncbi.nlm.nih.gov/gene/?term=90268	"AIPDS, FAM105B, GUM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040985	9031	BAZ1B	http://www.ncbi.nlm.nih.gov/gene/?term=9031	"WBSCR10, WBSCR9, WSTF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040986	90355	C5orf30	http://www.ncbi.nlm.nih.gov/gene/?term=90355		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040987	90355	C5orf30	http://www.ncbi.nlm.nih.gov/gene/?term=90355		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040988	9039	UBA3	http://www.ncbi.nlm.nih.gov/gene/?term=9039	"NAE2, UBE1C, hUBA3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040989	9039	UBA3	http://www.ncbi.nlm.nih.gov/gene/?term=9039	"NAE2, UBE1C, hUBA3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040990	90427	BMF	http://www.ncbi.nlm.nih.gov/gene/?term=90427		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040991	90427	BMF	http://www.ncbi.nlm.nih.gov/gene/?term=90427		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040992	9044	BTAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9044	"MOT1, TAF(II)170, TAF172, TAFII170"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040993	9044	BTAF1	http://www.ncbi.nlm.nih.gov/gene/?term=9044	"MOT1, TAF(II)170, TAF172, TAFII170"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00040994	9052	GPRC5A	http://www.ncbi.nlm.nih.gov/gene/?term=9052	"GPCR5A, PEIG-1, RAI3, RAIG1, TIG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040995	9057	SLC7A6	http://www.ncbi.nlm.nih.gov/gene/?term=9057	"LAT-2, LAT3, y+LAT-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040996	9061	PAPSS1	http://www.ncbi.nlm.nih.gov/gene/?term=9061	"ATPSK1, PAPSS, SK1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040997	90627	STARD13	http://www.ncbi.nlm.nih.gov/gene/?term=90627	"ARHGAP37, DLC2, GT650, LINC00464"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040998	9063	PIAS2	http://www.ncbi.nlm.nih.gov/gene/?term=9063	"ARIP3, DIP, MIZ1, PIASX, SIZ2, ZMIZ4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00040999	90799	CEP95	http://www.ncbi.nlm.nih.gov/gene/?term=90799	CCDC45	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041000	90799	CEP95	http://www.ncbi.nlm.nih.gov/gene/?term=90799	CCDC45	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041001	91	ACVR1B	http://www.ncbi.nlm.nih.gov/gene/?term=91	"ACTRIB, ACVRLK4, ALK4, SKR2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041002	91	ACVR1B	http://www.ncbi.nlm.nih.gov/gene/?term=91	"ACTRIB, ACVRLK4, ALK4, SKR2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041003	9100	USP10	http://www.ncbi.nlm.nih.gov/gene/?term=9100	UBPO	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041004	9100	USP10	http://www.ncbi.nlm.nih.gov/gene/?term=9100	UBPO	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041005	9101	USP8	http://www.ncbi.nlm.nih.gov/gene/?term=9101	"HumORF8, SPG59, UBPY"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041006	9101	USP8	http://www.ncbi.nlm.nih.gov/gene/?term=9101	"HumORF8, SPG59, UBPY"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041007	91012	CERS5	http://www.ncbi.nlm.nih.gov/gene/?term=91012	"LASS5, Trh4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041008	91012	CERS5	http://www.ncbi.nlm.nih.gov/gene/?term=91012	"LASS5, Trh4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041009	9112	MTA1	http://www.ncbi.nlm.nih.gov/gene/?term=9112		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041010	9112	MTA1	http://www.ncbi.nlm.nih.gov/gene/?term=9112		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041011	9113	LATS1	http://www.ncbi.nlm.nih.gov/gene/?term=9113	"WARTS, wts"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041012	9113	LATS1	http://www.ncbi.nlm.nih.gov/gene/?term=9113	"WARTS, wts"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041013	9125	CNOT9	http://www.ncbi.nlm.nih.gov/gene/?term=9125	"CAF40, CT129, RCD-1, RCD1, RQCD1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041014	9129	PRPF3	http://www.ncbi.nlm.nih.gov/gene/?term=9129	"HPRP3, HPRP3P, PRP3, Prp3p, RP18, SNRNP90"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041015	9129	PRPF3	http://www.ncbi.nlm.nih.gov/gene/?term=9129	"HPRP3, HPRP3P, PRP3, Prp3p, RP18, SNRNP90"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041016	9131	AIFM1	http://www.ncbi.nlm.nih.gov/gene/?term=9131	"AIF, CMT2D, CMTX4, COWCK, COXPD6, DFNX5, NADMR, NAMSD, PDCD8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041017	9131	AIFM1	http://www.ncbi.nlm.nih.gov/gene/?term=9131	"AIF, CMT2D, CMTX4, COWCK, COXPD6, DFNX5, NADMR, NAMSD, PDCD8"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041018	9135	RABEP1	http://www.ncbi.nlm.nih.gov/gene/?term=9135	"RAB5EP, RABPT5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041019	9135	RABEP1	http://www.ncbi.nlm.nih.gov/gene/?term=9135	"RAB5EP, RABPT5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041020	9138	ARHGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=9138	"GEF1, LBCL2, LSC, P115-RHOGEF, SUB1.5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041021	9138	ARHGEF1	http://www.ncbi.nlm.nih.gov/gene/?term=9138	"GEF1, LBCL2, LSC, P115-RHOGEF, SUB1.5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041022	9147	NEMF	http://www.ncbi.nlm.nih.gov/gene/?term=9147	"NY-CO-1, SDCCAG1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041023	9148	NEURL1	http://www.ncbi.nlm.nih.gov/gene/?term=9148	"NEUR1, NEURL, RNF67, bA416N2.1, neu, neu-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041024	9148	NEURL1	http://www.ncbi.nlm.nih.gov/gene/?term=9148	"NEUR1, NEURL, RNF67, bA416N2.1, neu, neu-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041025	91523	PCED1B	http://www.ncbi.nlm.nih.gov/gene/?term=91523	FAM113B	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041026	91523	PCED1B	http://www.ncbi.nlm.nih.gov/gene/?term=91523	FAM113B	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041027	9159	PCSK7	http://www.ncbi.nlm.nih.gov/gene/?term=9159	"LPC, PC7, PC8, SPC7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041028	9159	PCSK7	http://www.ncbi.nlm.nih.gov/gene/?term=9159	"LPC, PC7, PC8, SPC7"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041029	9169	SCAF11	http://www.ncbi.nlm.nih.gov/gene/?term=9169	"CASP11, SFRS2IP, SIP1, SRRP129, SRSF2IP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041030	9169	SCAF11	http://www.ncbi.nlm.nih.gov/gene/?term=9169	"CASP11, SFRS2IP, SIP1, SRRP129, SRSF2IP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041031	9173	IL1RL1	http://www.ncbi.nlm.nih.gov/gene/?term=9173	"DER4, FIT-1, IL33R, ST2, ST2L, ST2V, T1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041032	9173	IL1RL1	http://www.ncbi.nlm.nih.gov/gene/?term=9173	"DER4, FIT-1, IL33R, ST2, ST2L, ST2V, T1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041033	9180	OSMR	http://www.ncbi.nlm.nih.gov/gene/?term=9180	"IL-31R-beta, IL-31RBB, PLCA1, OSMR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041034	9180	OSMR	http://www.ncbi.nlm.nih.gov/gene/?term=9180	"IL-31R-beta, IL-31RBB, PLCA1, OSMR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041035	91833	WDR20	http://www.ncbi.nlm.nih.gov/gene/?term=91833	DMR	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041036	91833	WDR20	http://www.ncbi.nlm.nih.gov/gene/?term=91833	DMR	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041037	91949	COG7	http://www.ncbi.nlm.nih.gov/gene/?term=91949	CDG2E	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041038	91949	COG7	http://www.ncbi.nlm.nih.gov/gene/?term=91949	CDG2E	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041039	92	ACVR2A	http://www.ncbi.nlm.nih.gov/gene/?term=92	"ACTRII, ACVR2"	lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041040	9200	HACD1	http://www.ncbi.nlm.nih.gov/gene/?term=9200	"CAP, PTPLA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041041	9200	HACD1	http://www.ncbi.nlm.nih.gov/gene/?term=9200	"CAP, PTPLA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041042	92017	SNX29	http://www.ncbi.nlm.nih.gov/gene/?term=92017	"A-388D4.1, RUNDC2A"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041043	92017	SNX29	http://www.ncbi.nlm.nih.gov/gene/?term=92017	"A-388D4.1, RUNDC2A"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041044	9202	ZMYM4	http://www.ncbi.nlm.nih.gov/gene/?term=9202	"CDIR, MYM, ZNF198L3, ZNF262"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041045	9202	ZMYM4	http://www.ncbi.nlm.nih.gov/gene/?term=9202	"CDIR, MYM, ZNF198L3, ZNF262"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041046	9208	LRRFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=9208	"FLAP-1, FLAP1, FLIIAP1, GCF-2, GCF2, HUFI-1, TRIP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041047	9208	LRRFIP1	http://www.ncbi.nlm.nih.gov/gene/?term=9208	"FLAP-1, FLAP1, FLIIAP1, GCF-2, GCF2, HUFI-1, TRIP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041048	92106	OXNAD1	http://www.ncbi.nlm.nih.gov/gene/?term=92106		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041049	92106	OXNAD1	http://www.ncbi.nlm.nih.gov/gene/?term=92106		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041050	9218	VAPA	http://www.ncbi.nlm.nih.gov/gene/?term=9218	"VAP-33, VAP-A, VAP33, hVAP-33"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041051	9223	MAGI1	http://www.ncbi.nlm.nih.gov/gene/?term=9223	"AIP-3, AIP3, BAIAP1, BAP-1, BAP1, MAGI-1, Magi1d, TNRC19, WWP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041052	9223	MAGI1	http://www.ncbi.nlm.nih.gov/gene/?term=9223	"AIP-3, AIP3, BAIAP1, BAP-1, BAP1, MAGI-1, Magi1d, TNRC19, WWP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041053	92259	MRPS36	http://www.ncbi.nlm.nih.gov/gene/?term=92259	"DC47, MRP-S36"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041054	92259	MRPS36	http://www.ncbi.nlm.nih.gov/gene/?term=92259	"DC47, MRP-S36"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041055	9229	DLGAP1	http://www.ncbi.nlm.nih.gov/gene/?term=9229	"DAP-1, DAP-1-ALPHA, DAP-1-BETA, DAP1A, DLGAP1B, GKAP, SAPAP1, DLGAP1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041056	9231	DLG5	http://www.ncbi.nlm.nih.gov/gene/?term=9231	"LP-DLG, P-DLG5, PDLG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041057	9231	DLG5	http://www.ncbi.nlm.nih.gov/gene/?term=9231	"LP-DLG, P-DLG5, PDLG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041058	92399	MRRF	http://www.ncbi.nlm.nih.gov/gene/?term=92399	"MRFF, MTRRF, RRF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041059	9249	DHRS3	http://www.ncbi.nlm.nih.gov/gene/?term=9249	"DD83.1, RDH17, Rsdr1, SDR1, SDR16C1, retSDR1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041060	9249	DHRS3	http://www.ncbi.nlm.nih.gov/gene/?term=9249	"DD83.1, RDH17, Rsdr1, SDR1, SDR16C1, retSDR1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041061	9252	RPS6KA5	http://www.ncbi.nlm.nih.gov/gene/?term=9252	"MSK1, MSPK1, RLPK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041062	9252	RPS6KA5	http://www.ncbi.nlm.nih.gov/gene/?term=9252	"MSK1, MSPK1, RLPK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041063	92521	SPECC1	http://www.ncbi.nlm.nih.gov/gene/?term=92521	"CYTSB, HCMOGT-1, HCMOGT1, NSP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041064	92521	SPECC1	http://www.ncbi.nlm.nih.gov/gene/?term=92521	"CYTSB, HCMOGT-1, HCMOGT1, NSP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041065	92591	ASB16	http://www.ncbi.nlm.nih.gov/gene/?term=92591		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041066	92591	ASB16	http://www.ncbi.nlm.nih.gov/gene/?term=92591		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041067	9261	MAPKAPK2	http://www.ncbi.nlm.nih.gov/gene/?term=9261	"MAPKAP-K2, MK-2, MK2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041068	9261	MAPKAPK2	http://www.ncbi.nlm.nih.gov/gene/?term=9261	"MAPKAP-K2, MK-2, MK2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041069	9263	STK17A	http://www.ncbi.nlm.nih.gov/gene/?term=9263	DRAK1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041070	9265	CYTH3	http://www.ncbi.nlm.nih.gov/gene/?term=9265	"ARNO3, GRP1, PSCD3, cytohesin-3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041071	9265	CYTH3	http://www.ncbi.nlm.nih.gov/gene/?term=9265	"ARNO3, GRP1, PSCD3, cytohesin-3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041072	9267	CYTH1	http://www.ncbi.nlm.nih.gov/gene/?term=9267	"B2-1, CYTOHESIN-1, D17S811E, PSCD1, SEC7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041073	92675	DTD1	http://www.ncbi.nlm.nih.gov/gene/?term=92675	"C20orf88, DUE-B, DUEB, HARS2, pqn-68"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041074	92675	DTD1	http://www.ncbi.nlm.nih.gov/gene/?term=92675	"C20orf88, DUE-B, DUEB, HARS2, pqn-68"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041075	92737	DNER	http://www.ncbi.nlm.nih.gov/gene/?term=92737	"UNQ26, bet"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041076	92737	DNER	http://www.ncbi.nlm.nih.gov/gene/?term=92737	"UNQ26, bet"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041077	928	CD9	http://www.ncbi.nlm.nih.gov/gene/?term=928	"BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041078	928	CD9	http://www.ncbi.nlm.nih.gov/gene/?term=928	"BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041079	9282	MED14	http://www.ncbi.nlm.nih.gov/gene/?term=9282	"CRSP150, CRSP2, CSRP, CXorf4, DRIP150, EXLM1, RGR1, TRAP170"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041080	92822	ZNF276	http://www.ncbi.nlm.nih.gov/gene/?term=92822	"CENP-Z, CENPZ, ZADT, ZFP276, ZNF477"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041081	92822	ZNF276	http://www.ncbi.nlm.nih.gov/gene/?term=92822	"CENP-Z, CENPZ, ZADT, ZFP276, ZNF477"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041082	92906	HNRNPLL	http://www.ncbi.nlm.nih.gov/gene/?term=92906	"HNRPLL, SRRF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041083	92906	HNRNPLL	http://www.ncbi.nlm.nih.gov/gene/?term=92906	"HNRPLL, SRRF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041084	9310	ZNF235	http://www.ncbi.nlm.nih.gov/gene/?term=9310	"ANF270, HZF6, ZFP93, ZNF270"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041085	9310	ZNF235	http://www.ncbi.nlm.nih.gov/gene/?term=9310	"ANF270, HZF6, ZFP93, ZNF270"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041086	93145	OLFM2	http://www.ncbi.nlm.nih.gov/gene/?term=93145	"NOE2, NOELIN2, NOELIN2_V1, OlfC"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041087	93145	OLFM2	http://www.ncbi.nlm.nih.gov/gene/?term=93145	"NOE2, NOELIN2, NOELIN2_V1, OlfC"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041088	9320	TRIP12	http://www.ncbi.nlm.nih.gov/gene/?term=9320	"TRIP-12, ULF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041089	9320	TRIP12	http://www.ncbi.nlm.nih.gov/gene/?term=9320	"TRIP-12, ULF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041090	9334	B4GALT5	http://www.ncbi.nlm.nih.gov/gene/?term=9334	"B4Gal-T5, BETA4-GALT-IV, beta4Gal-T5, beta4GalT-V, gt-V"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041091	9352	TXNL1	http://www.ncbi.nlm.nih.gov/gene/?term=9352	"HEL-S-114, TRP32, TXL-1, TXNL, Txl"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041092	9352	TXNL1	http://www.ncbi.nlm.nih.gov/gene/?term=9352	"HEL-S-114, TRP32, TXL-1, TXNL, Txl"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041093	9353	SLIT2	http://www.ncbi.nlm.nih.gov/gene/?term=9353	"SLIL3, Slit-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041094	9360	PPIG	http://www.ncbi.nlm.nih.gov/gene/?term=9360	"CARS-Cyp, CYP, SCAF10, SRCyp"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041095	9360	PPIG	http://www.ncbi.nlm.nih.gov/gene/?term=9360	"CARS-Cyp, CYP, SCAF10, SRCyp"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041096	93611	FBXO44	http://www.ncbi.nlm.nih.gov/gene/?term=93611	"FBG3, FBX30, FBX6A, Fbx44, Fbxo6a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041097	93611	FBXO44	http://www.ncbi.nlm.nih.gov/gene/?term=93611	"FBG3, FBX30, FBX6A, Fbx44, Fbxo6a"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041098	93627	TBCK	http://www.ncbi.nlm.nih.gov/gene/?term=93627	"HSPC302, IHPRF3L, TBCK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041099	93627	TBCK	http://www.ncbi.nlm.nih.gov/gene/?term=93627	"HSPC302, IHPRF3L, TBCK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041100	93664	CADPS2	http://www.ncbi.nlm.nih.gov/gene/?term=93664	CAPS2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041101	93664	CADPS2	http://www.ncbi.nlm.nih.gov/gene/?term=93664	CAPS2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041102	9373	PLAA	http://www.ncbi.nlm.nih.gov/gene/?term=9373	"DOA1, NDMSBA, PLA2P, PLAP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041103	9373	PLAA	http://www.ncbi.nlm.nih.gov/gene/?term=9373	"DOA1, NDMSBA, PLA2P, PLAP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041104	9378	NRXN1	http://www.ncbi.nlm.nih.gov/gene/?term=9378	"Hs.22998, PTHSL2, SCZD17"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041105	9378	NRXN1	http://www.ncbi.nlm.nih.gov/gene/?term=9378	"Hs.22998, PTHSL2, SCZD17"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041106	9397	NMT2	http://www.ncbi.nlm.nih.gov/gene/?term=9397		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041107	9397	NMT2	http://www.ncbi.nlm.nih.gov/gene/?term=9397		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041108	9403	SELENOF	http://www.ncbi.nlm.nih.gov/gene/?term=9403	42993	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041109	9403	SELENOF	http://www.ncbi.nlm.nih.gov/gene/?term=9403	42993	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041110	94104	PAXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=94104	"BM020, C21orf66, FSAP105, GCFC, GCFC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041111	94104	PAXBP1	http://www.ncbi.nlm.nih.gov/gene/?term=94104	"BM020, C21orf66, FSAP105, GCFC, GCFC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041112	94134	ARHGAP12	http://www.ncbi.nlm.nih.gov/gene/?term=94134		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041113	94134	ARHGAP12	http://www.ncbi.nlm.nih.gov/gene/?term=94134		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041114	9414	TJP2	http://www.ncbi.nlm.nih.gov/gene/?term=9414	"C9DUPq21.11, DFNA51, DUP9q21.11, PFIC4, X104, ZO2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041115	94239	H2AFV	http://www.ncbi.nlm.nih.gov/gene/?term=94239	"H2A.Z-2, H2AV"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041116	94239	H2AFV	http://www.ncbi.nlm.nih.gov/gene/?term=94239	"H2A.Z-2, H2AV"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041117	9439	MED23	http://www.ncbi.nlm.nih.gov/gene/?term=9439	"ARC130, CRSP130, CRSP133, CRSP3, DRIP130, MRT18, SUR-2, SUR2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041118	9441	MED26	http://www.ncbi.nlm.nih.gov/gene/?term=9441	"CRSP7, CRSP70"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041119	9441	MED26	http://www.ncbi.nlm.nih.gov/gene/?term=9441	"CRSP7, CRSP70"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041120	9442	MED27	http://www.ncbi.nlm.nih.gov/gene/?term=9442	"CRAP34, CRSP34, CRSP8, MED3, TRAP37"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041121	9442	MED27	http://www.ncbi.nlm.nih.gov/gene/?term=9442	"CRAP34, CRSP34, CRSP8, MED3, TRAP37"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041122	9444	QKI	http://www.ncbi.nlm.nih.gov/gene/?term=9444	"Hqk, QK, QK1, QK3, hqkI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041123	9444	QKI	http://www.ncbi.nlm.nih.gov/gene/?term=9444	"Hqk, QK, QK1, QK3, hqkI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041124	9446	GSTO1	http://www.ncbi.nlm.nih.gov/gene/?term=9446	"GSTO 1-1, GSTTLp28, HEL-S-21, P28, SPG-R"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041125	9451	EIF2AK3	http://www.ncbi.nlm.nih.gov/gene/?term=9451	"PEK, PERK, WRS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041126	9453	GGPS1	http://www.ncbi.nlm.nih.gov/gene/?term=9453	"GGPPS, GGPPS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041127	9462	RASAL2	http://www.ncbi.nlm.nih.gov/gene/?term=9462	NGAP	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041128	9467	SH3BP5	http://www.ncbi.nlm.nih.gov/gene/?term=9467	"SAB, SH3BP-5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041129	9467	SH3BP5	http://www.ncbi.nlm.nih.gov/gene/?term=9467	"SAB, SH3BP-5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041130	9474	ATG5	http://www.ncbi.nlm.nih.gov/gene/?term=9474	"APG5, APG5-LIKE, APG5L, ASP, SCAR25, hAPG5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041131	9474	ATG5	http://www.ncbi.nlm.nih.gov/gene/?term=9474	"APG5, APG5-LIKE, APG5L, ASP, SCAR25, hAPG5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041132	9478	CABP1	http://www.ncbi.nlm.nih.gov/gene/?term=9478	"CALBRAIN, HCALB_BR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041133	9478	CABP1	http://www.ncbi.nlm.nih.gov/gene/?term=9478	"CALBRAIN, HCALB_BR"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041134	949	SCARB1	http://www.ncbi.nlm.nih.gov/gene/?term=949	"CD36L1, CLA-1, CLA1, HDLQTL6, SR-BI, SRB1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041135	9497	SLC4A7	http://www.ncbi.nlm.nih.gov/gene/?term=9497	"NBC2, NBC3, NBCN1, SBC2, SLC4A6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041136	9501	RPH3AL	http://www.ncbi.nlm.nih.gov/gene/?term=9501	NOC2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041137	9501	RPH3AL	http://www.ncbi.nlm.nih.gov/gene/?term=9501	NOC2	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041138	9509	ADAMTS2	http://www.ncbi.nlm.nih.gov/gene/?term=9509	"ADAM-TS2, ADAMTS-2, ADAMTS-3, NPI, PC I-NP, PCI-NP, PCINP, PCPNI, PNPI"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041139	9509	ADAMTS2	http://www.ncbi.nlm.nih.gov/gene/?term=9509	"ADAM-TS2, ADAMTS-2, ADAMTS-3, NPI, PC I-NP, PCI-NP, PCINP, PCPNI, PNPI"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041140	9516	LITAF	http://www.ncbi.nlm.nih.gov/gene/?term=9516	"PIG7, SIMPLE, TP53I7"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041141	9517	SPTLC2	http://www.ncbi.nlm.nih.gov/gene/?term=9517	"HSN1C, LCB2, LCB2A, NSAN1C, SPT2, hLCB2a"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041142	9517	SPTLC2	http://www.ncbi.nlm.nih.gov/gene/?term=9517	"HSN1C, LCB2, LCB2A, NSAN1C, SPT2, hLCB2a"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041143	9524	TECR	http://www.ncbi.nlm.nih.gov/gene/?term=9524	"GPSN2, MRT14, SC2, TER"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041144	9524	TECR	http://www.ncbi.nlm.nih.gov/gene/?term=9524	"GPSN2, MRT14, SC2, TER"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041145	9531	BAG3	http://www.ncbi.nlm.nih.gov/gene/?term=9531	"BAG-3, BIS, CAIR-1, MFM6"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041146	9531	BAG3	http://www.ncbi.nlm.nih.gov/gene/?term=9531	"BAG-3, BIS, CAIR-1, MFM6"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041147	9537	TP53I11	http://www.ncbi.nlm.nih.gov/gene/?term=9537	PIG11	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041148	9542	NRG2	http://www.ncbi.nlm.nih.gov/gene/?term=9542	"DON1, HRG2, NTAK"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041149	9542	NRG2	http://www.ncbi.nlm.nih.gov/gene/?term=9542	"DON1, HRG2, NTAK"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041150	9553	MRPL33	http://www.ncbi.nlm.nih.gov/gene/?term=9553	"C2orf1, L33mt, MRP-L33, RPL33L"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041151	9553	MRPL33	http://www.ncbi.nlm.nih.gov/gene/?term=9553	"C2orf1, L33mt, MRP-L33, RPL33L"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041152	9555	H2AFY	http://www.ncbi.nlm.nih.gov/gene/?term=9555	"H2A.y, H2A/y, H2AF12M, MACROH2A1.1, mH2A1, macroH2A1.2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041153	9555	H2AFY	http://www.ncbi.nlm.nih.gov/gene/?term=9555	"H2A.y, H2A/y, H2AF12M, MACROH2A1.1, mH2A1, macroH2A1.2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041154	9557	CHD1L	http://www.ncbi.nlm.nih.gov/gene/?term=9557	"ALC1, CHDL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041155	9569	GTF2IRD1	http://www.ncbi.nlm.nih.gov/gene/?term=9569	"BEN, CREAM1, GTF3, MUSTRD1, RBAP2, WBS, WBSCR11, WBSCR12, hMusTRD1alpha1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041156	9569	GTF2IRD1	http://www.ncbi.nlm.nih.gov/gene/?term=9569	"BEN, CREAM1, GTF3, MUSTRD1, RBAP2, WBS, WBSCR11, WBSCR12, hMusTRD1alpha1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041157	957	ENTPD5	http://www.ncbi.nlm.nih.gov/gene/?term=957	"CD39L4, NTPDase-5, PCPH"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041158	957	ENTPD5	http://www.ncbi.nlm.nih.gov/gene/?term=957	"CD39L4, NTPDase-5, PCPH"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041159	9577	BABAM2	http://www.ncbi.nlm.nih.gov/gene/?term=9577	"BRCC4, BRCC45, BRE"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041160	9577	BABAM2	http://www.ncbi.nlm.nih.gov/gene/?term=9577	"BRCC4, BRCC45, BRE"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041161	9584	RBM39	http://www.ncbi.nlm.nih.gov/gene/?term=9584	"CAPER, CAPERalpha, FSAP59, HCC1, RNPC2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041162	9584	RBM39	http://www.ncbi.nlm.nih.gov/gene/?term=9584	"CAPER, CAPERalpha, FSAP59, HCC1, RNPC2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041163	9590	AKAP12	http://www.ncbi.nlm.nih.gov/gene/?term=9590	"AKAP250, SSeCKS"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041164	9590	AKAP12	http://www.ncbi.nlm.nih.gov/gene/?term=9590	"AKAP250, SSeCKS"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041165	960	CD44	http://www.ncbi.nlm.nih.gov/gene/?term=960	"CDW44, CSPG8, ECMR-III, HCELL, HUTCH-I, IN, LHR, MC56, MDU2, MDU3, MIC4, Pgp1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041166	9611	NCOR1	http://www.ncbi.nlm.nih.gov/gene/?term=9611	"N-CoR, N-CoR1, PPP1R109, TRAC1, hN-CoR"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041167	9612	NCOR2	http://www.ncbi.nlm.nih.gov/gene/?term=9612	"CTG26, N-CoR2, SMAP270, SMRT, SMRTE, SMRTE-tau, TNRC14, TRAC, TRAC-1, TRAC1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041168	9612	NCOR2	http://www.ncbi.nlm.nih.gov/gene/?term=9612	"CTG26, N-CoR2, SMAP270, SMRT, SMRTE, SMRTE-tau, TNRC14, TRAC, TRAC-1, TRAC1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041169	9628	RGS6	http://www.ncbi.nlm.nih.gov/gene/?term=9628	"GAP, HA117, S914"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041170	9628	RGS6	http://www.ncbi.nlm.nih.gov/gene/?term=9628	"GAP, HA117, S914"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041171	9630	GNA14	http://www.ncbi.nlm.nih.gov/gene/?term=9630		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041172	9630	GNA14	http://www.ncbi.nlm.nih.gov/gene/?term=9630		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041173	9643	MORF4L2	http://www.ncbi.nlm.nih.gov/gene/?term=9643	"MORFL2, MRGX"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041174	9644	SH3PXD2A	http://www.ncbi.nlm.nih.gov/gene/?term=9644	"FISH, SH3MD1, TKS5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041175	9644	SH3PXD2A	http://www.ncbi.nlm.nih.gov/gene/?term=9644	"FISH, SH3MD1, TKS5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041176	9647	PPM1F	http://www.ncbi.nlm.nih.gov/gene/?term=9647	"CAMKP, CaMKPase, FEM-2, POPX2, hFEM-2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041177	9647	PPM1F	http://www.ncbi.nlm.nih.gov/gene/?term=9647	"CAMKP, CaMKPase, FEM-2, POPX2, hFEM-2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041178	9649	RALGPS1	http://www.ncbi.nlm.nih.gov/gene/?term=9649	"RALGEF2A, RALGPS1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041179	9649	RALGPS1	http://www.ncbi.nlm.nih.gov/gene/?term=9649	"RALGEF2A, RALGPS1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041180	965	CD58	http://www.ncbi.nlm.nih.gov/gene/?term=965	"LFA-3, LFA3, ag3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041181	965	CD58	http://www.ncbi.nlm.nih.gov/gene/?term=965	"LFA-3, LFA3, ag3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041182	9650	MTFR1	http://www.ncbi.nlm.nih.gov/gene/?term=9650	"CHPPR, FAM54A2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041183	9650	MTFR1	http://www.ncbi.nlm.nih.gov/gene/?term=9650	"CHPPR, FAM54A2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041184	9657	IQCB1	http://www.ncbi.nlm.nih.gov/gene/?term=9657	"NPHP5, PIQ, SLSN5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041185	9657	IQCB1	http://www.ncbi.nlm.nih.gov/gene/?term=9657	"NPHP5, PIQ, SLSN5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041186	9667	SAFB2	http://www.ncbi.nlm.nih.gov/gene/?term=9667		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041187	9667	SAFB2	http://www.ncbi.nlm.nih.gov/gene/?term=9667		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041188	9675	TTI1	http://www.ncbi.nlm.nih.gov/gene/?term=9675	"KIAA0406, smg-10"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041189	9675	TTI1	http://www.ncbi.nlm.nih.gov/gene/?term=9675	"KIAA0406, smg-10"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041190	96764	TGS1	http://www.ncbi.nlm.nih.gov/gene/?term=96764	"NCOA6IP, PIMT, PIPMT"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041191	96764	TGS1	http://www.ncbi.nlm.nih.gov/gene/?term=96764	"NCOA6IP, PIMT, PIPMT"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041192	9678	PHF14	http://www.ncbi.nlm.nih.gov/gene/?term=9678		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041193	9686	VGLL4	http://www.ncbi.nlm.nih.gov/gene/?term=9686	VGL-4	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041194	9686	VGLL4	http://www.ncbi.nlm.nih.gov/gene/?term=9686	VGL-4	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041195	9687	GREB1	http://www.ncbi.nlm.nih.gov/gene/?term=9687		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041196	9687	GREB1	http://www.ncbi.nlm.nih.gov/gene/?term=9687		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041197	9690	UBE3C	http://www.ncbi.nlm.nih.gov/gene/?term=9690	HECTH2	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041198	9694	EMC2	http://www.ncbi.nlm.nih.gov/gene/?term=9694	"KIAA0103, TTC35"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041199	9695	EDEM1	http://www.ncbi.nlm.nih.gov/gene/?term=9695	EDEM	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041200	9698	PUM1	http://www.ncbi.nlm.nih.gov/gene/?term=9698	"HSPUM, PUMH, PUMH1, PUML1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041201	9698	PUM1	http://www.ncbi.nlm.nih.gov/gene/?term=9698	"HSPUM, PUMH, PUMH1, PUML1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041202	9702	CEP57	http://www.ncbi.nlm.nih.gov/gene/?term=9702	"MVA2, PIG8, TSP57"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041203	9727	RAB11FIP3	http://www.ncbi.nlm.nih.gov/gene/?term=9727	"CART1, Rab11-FIP3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041204	9727	RAB11FIP3	http://www.ncbi.nlm.nih.gov/gene/?term=9727	"CART1, Rab11-FIP3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041205	9734	HDAC9	http://www.ncbi.nlm.nih.gov/gene/?term=9734	"HD7, HD7b, HD9, HDAC, HDAC7, HDAC7BB, HDAC9FL, HDRP, MITR, HDAC9"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041206	9734	HDAC9	http://www.ncbi.nlm.nih.gov/gene/?term=9734	"HD7, HD7b, HD9, HDAC, HDAC7, HDAC7BB, HDAC9FL, HDRP, MITR, HDAC9"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041207	9736	USP34	http://www.ncbi.nlm.nih.gov/gene/?term=9736		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041208	9746	CLSTN3	http://www.ncbi.nlm.nih.gov/gene/?term=9746	"CDHR14, CSTN3, alcbeta"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041209	9746	CLSTN3	http://www.ncbi.nlm.nih.gov/gene/?term=9746	"CDHR14, CSTN3, alcbeta"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041210	9750	RIPOR2	http://www.ncbi.nlm.nih.gov/gene/?term=9750	"C6orf32, DFNB104, DIFF40, DIFF48, FAM65B, MYONAP, PL48"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041211	9750	RIPOR2	http://www.ncbi.nlm.nih.gov/gene/?term=9750	"C6orf32, DFNB104, DIFF40, DIFF48, FAM65B, MYONAP, PL48"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041212	9759	HDAC4	http://www.ncbi.nlm.nih.gov/gene/?term=9759	"AHO3, BDMR, HA6116, HD4, HDAC-4, HDAC-A, HDACA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041213	9759	HDAC4	http://www.ncbi.nlm.nih.gov/gene/?term=9759	"AHO3, BDMR, HA6116, HD4, HDAC-4, HDAC-A, HDACA"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041214	9766	SUSD6	http://www.ncbi.nlm.nih.gov/gene/?term=9766	"DRAGO, KIAA0247"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041215	9768	PCLAF	http://www.ncbi.nlm.nih.gov/gene/?term=9768	"KIAA0101, L5, NS5ATP9, OEATC, OEATC-1, OEATC1, PAF, PAF15, p15(PAF), p15/PAF, p15PAF"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041216	9768	PCLAF	http://www.ncbi.nlm.nih.gov/gene/?term=9768	"KIAA0101, L5, NS5ATP9, OEATC, OEATC-1, OEATC1, PAF, PAF15, p15(PAF), p15/PAF, p15PAF"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041217	9772	TMEM94	http://www.ncbi.nlm.nih.gov/gene/?term=9772	KIAA0195	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041218	9778	KIAA0232	http://www.ncbi.nlm.nih.gov/gene/?term=9778		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041219	9778	KIAA0232	http://www.ncbi.nlm.nih.gov/gene/?term=9778		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041220	9779	TBC1D5	http://www.ncbi.nlm.nih.gov/gene/?term=9779		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041221	9779	TBC1D5	http://www.ncbi.nlm.nih.gov/gene/?term=9779		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041222	9781	RNF144A	http://www.ncbi.nlm.nih.gov/gene/?term=9781	"RNF144, UBCE7IP4, hUIP4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041223	9781	RNF144A	http://www.ncbi.nlm.nih.gov/gene/?term=9781	"RNF144, UBCE7IP4, hUIP4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041224	9782	MATR3	http://www.ncbi.nlm.nih.gov/gene/?term=9782	"ALS21, MPD2, VCPDM"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041225	9782	MATR3	http://www.ncbi.nlm.nih.gov/gene/?term=9782	"ALS21, MPD2, VCPDM"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041226	9783	RIMS3	http://www.ncbi.nlm.nih.gov/gene/?term=9783	"NIM3, RIM3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041227	9783	RIMS3	http://www.ncbi.nlm.nih.gov/gene/?term=9783	"NIM3, RIM3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041228	9786	KIAA0586	http://www.ncbi.nlm.nih.gov/gene/?term=9786	"JBTS23, SRTD14, Talpid3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041229	9786	KIAA0586	http://www.ncbi.nlm.nih.gov/gene/?term=9786	"JBTS23, SRTD14, Talpid3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041230	9791	PTDSS1	http://www.ncbi.nlm.nih.gov/gene/?term=9791	"LMHD, PSS1, PSSA"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041231	9793	CKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9793	"CHTOG, MSPS, TOG, TOGp, ch-TOG"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041232	9793	CKAP5	http://www.ncbi.nlm.nih.gov/gene/?term=9793	"CHTOG, MSPS, TOG, TOGp, ch-TOG"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041233	9794	MAML1	http://www.ncbi.nlm.nih.gov/gene/?term=9794	"Mam-1, Mam1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041234	9794	MAML1	http://www.ncbi.nlm.nih.gov/gene/?term=9794	"Mam-1, Mam1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041235	9798	IST1	http://www.ncbi.nlm.nih.gov/gene/?term=9798	OLC1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041236	9798	IST1	http://www.ncbi.nlm.nih.gov/gene/?term=9798	OLC1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041237	98	ACYP2	http://www.ncbi.nlm.nih.gov/gene/?term=98	"ACYM, ACYP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041238	98	ACYP2	http://www.ncbi.nlm.nih.gov/gene/?term=98	"ACYM, ACYP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041239	9801	MRPL19	http://www.ncbi.nlm.nih.gov/gene/?term=9801	"L19mt, MRP-L15, MRP-L19, MRPL15, RLX1, RPML15"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041240	9805	SCRN1	http://www.ncbi.nlm.nih.gov/gene/?term=9805	SES1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041241	9805	SCRN1	http://www.ncbi.nlm.nih.gov/gene/?term=9805	SES1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041242	9811	CTIF	http://www.ncbi.nlm.nih.gov/gene/?term=9811	"Gm672, KIAA0427"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041243	9811	CTIF	http://www.ncbi.nlm.nih.gov/gene/?term=9811	"Gm672, KIAA0427"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041244	9815	GIT2	http://www.ncbi.nlm.nih.gov/gene/?term=9815	"CAT-2, CAT2, PKL"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041245	9815	GIT2	http://www.ncbi.nlm.nih.gov/gene/?term=9815	"CAT-2, CAT2, PKL"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041246	9819	TSC22D2	http://www.ncbi.nlm.nih.gov/gene/?term=9819	"TILZ4a, TILZ4b, TILZ4c"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041247	9844	ELMO1	http://www.ncbi.nlm.nih.gov/gene/?term=9844	"CED-12, CED12, ELMO-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041248	9844	ELMO1	http://www.ncbi.nlm.nih.gov/gene/?term=9844	"CED-12, CED12, ELMO-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041249	9847	C2CD5	http://www.ncbi.nlm.nih.gov/gene/?term=9847	"CDP138, KIAA0528"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041250	9855	FARP2	http://www.ncbi.nlm.nih.gov/gene/?term=9855	"FIR, FRG, PLEKHC3"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041251	9855	FARP2	http://www.ncbi.nlm.nih.gov/gene/?term=9855	"FIR, FRG, PLEKHC3"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041252	9877	ZC3H11A	http://www.ncbi.nlm.nih.gov/gene/?term=9877	ZC3HDC11A	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041253	9877	ZC3H11A	http://www.ncbi.nlm.nih.gov/gene/?term=9877	ZC3HDC11A	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041254	9882	TBC1D4	http://www.ncbi.nlm.nih.gov/gene/?term=9882	"AS160, NIDDM5"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041255	9882	TBC1D4	http://www.ncbi.nlm.nih.gov/gene/?term=9882	"AS160, NIDDM5"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041256	9886	RHOBTB1	http://www.ncbi.nlm.nih.gov/gene/?term=9886		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041257	9887	SMG7	http://www.ncbi.nlm.nih.gov/gene/?term=9887	"C1orf16, EST1C, SGA56M"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041258	9887	SMG7	http://www.ncbi.nlm.nih.gov/gene/?term=9887	"C1orf16, EST1C, SGA56M"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041259	9895	TECPR2	http://www.ncbi.nlm.nih.gov/gene/?term=9895	"KIAA0329, SPG49"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041260	9897	WASHC5	http://www.ncbi.nlm.nih.gov/gene/?term=9897	"KIAA0196, RTSC, RTSC1, SPG8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041261	9901	SRGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=9901	"ARHGAP14, MEGAP, SRGAP2, WRP"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041262	9901	SRGAP3	http://www.ncbi.nlm.nih.gov/gene/?term=9901	"ARHGAP14, MEGAP, SRGAP2, WRP"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041263	9904	RBM19	http://www.ncbi.nlm.nih.gov/gene/?term=9904	Mrd1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041264	9910	RABGAP1L	http://www.ncbi.nlm.nih.gov/gene/?term=9910	"HHL, TBC1D18"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041265	9912	ARHGAP44	http://www.ncbi.nlm.nih.gov/gene/?term=9912	"NPC-A-10, RICH2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041266	9912	ARHGAP44	http://www.ncbi.nlm.nih.gov/gene/?term=9912	"NPC-A-10, RICH2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041267	9922	IQSEC1	http://www.ncbi.nlm.nih.gov/gene/?term=9922	"ARF-GEP100, ARFGEP100, BRAG2, GEP100"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041268	9922	IQSEC1	http://www.ncbi.nlm.nih.gov/gene/?term=9922	"ARF-GEP100, ARFGEP100, BRAG2, GEP100"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041269	9926	LPGAT1	http://www.ncbi.nlm.nih.gov/gene/?term=9926	"FAM34A, FAM34A1, NET8"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041270	9943	OXSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9943	OSR1	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041271	9943	OXSR1	http://www.ncbi.nlm.nih.gov/gene/?term=9943	OSR1	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041272	9945	GFPT2	http://www.ncbi.nlm.nih.gov/gene/?term=9945	"GFAT, GFAT 2, GFAT2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041273	9945	GFPT2	http://www.ncbi.nlm.nih.gov/gene/?term=9945	"GFAT, GFAT 2, GFAT2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041274	9948	WDR1	http://www.ncbi.nlm.nih.gov/gene/?term=9948	"AIP1, HEL-S-52, NORI-1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041275	9948	WDR1	http://www.ncbi.nlm.nih.gov/gene/?term=9948	"AIP1, HEL-S-52, NORI-1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041276	9949	AMMECR1	http://www.ncbi.nlm.nih.gov/gene/?term=9949	"AMMERC1, MFHIEN"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041277	9949	AMMECR1	http://www.ncbi.nlm.nih.gov/gene/?term=9949	"AMMERC1, MFHIEN"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041278	9953	HS3ST3B1	http://www.ncbi.nlm.nih.gov/gene/?term=9953	"3-OST-3B, 3OST3B1, h3-OST-3B"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041279	9957	HS3ST1	http://www.ncbi.nlm.nih.gov/gene/?term=9957	"3OST, 3OST1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041280	9957	HS3ST1	http://www.ncbi.nlm.nih.gov/gene/?term=9957	"3OST, 3OST1"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041281	9958	USP15	http://www.ncbi.nlm.nih.gov/gene/?term=9958	"UNPH-2, UNPH4"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041282	9958	USP15	http://www.ncbi.nlm.nih.gov/gene/?term=9958	"UNPH-2, UNPH4"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041283	9961	MVP	http://www.ncbi.nlm.nih.gov/gene/?term=9961	"LRP, VAULT1"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041284	9962	SLC23A2	http://www.ncbi.nlm.nih.gov/gene/?term=9962	"NBTL1, SLC23A1, SVCT2, YSPL2, hSVCT2"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041285	9962	SLC23A2	http://www.ncbi.nlm.nih.gov/gene/?term=9962	"NBTL1, SLC23A1, SVCT2, YSPL2, hSVCT2"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041286	9967	THRAP3	http://www.ncbi.nlm.nih.gov/gene/?term=9967	"BCLAF2, TRAP150"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041287	9969	MED13	http://www.ncbi.nlm.nih.gov/gene/?term=9969	"ARC250, DRIP250, HSPC221, THRAP1, TRAP240"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041288	999	CDH1	http://www.ncbi.nlm.nih.gov/gene/?term=999	"Arc-1, CD324, CDHE, ECAD, LCAM, UVO"	mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041289	999	CDH1	http://www.ncbi.nlm.nih.gov/gene/?term=999	"Arc-1, CD324, CDHE, ECAD, LCAM, UVO"	mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041290	ENSG00000178642	AL513477.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000178642		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041291	ENSG00000178642	AL513477.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000178642		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041292	ENSG00000197585	AC107218.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000197585		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041293	ENSG00000197585	AC107218.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000197585		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041294	ENSG00000197604	AC022532.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000197604		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041295	ENSG00000197604	AC022532.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000197604		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041296	ENSG00000203691	AC092811.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000203691		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041297	ENSG00000204044	RP11-465L10.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000204044		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041298	ENSG00000204044	RP11-465L10.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000204044		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041299	ENSG00000204620	AC115618.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000204620		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041300	ENSG00000204620	AC115618.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000204620		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041301	ENSG00000217075	AC007401.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000217075		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041302	ENSG00000217075	AC007401.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000217075		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041303	ENSG00000222007	AC064874.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000222007		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041304	ENSG00000222007	AC064874.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000222007		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041305	ENSG00000223774	RP11-307B6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223774		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041306	ENSG00000223774	RP11-307B6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223774		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041307	ENSG00000224063	AC007319.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224063		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041308	ENSG00000224152	AC009506.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224152		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041309	ENSG00000224152	AC009506.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224152		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041310	ENSG00000225075	RP11-426L16.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225075		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041311	ENSG00000225075	RP11-426L16.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225075		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041312	ENSG00000225138	CTD-2228K2.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225138		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041313	ENSG00000225138	CTD-2228K2.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225138		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041314	ENSG00000225721	RP11-269F19.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225721		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041315	ENSG00000225721	RP11-269F19.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225721		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041316	ENSG00000225798	AC025918.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225798		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041317	ENSG00000225798	AC025918.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225798		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041318	ENSG00000225886	RP11-288L9.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225886		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041319	ENSG00000225886	RP11-288L9.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225886		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041320	ENSG00000226648	RP1-1J6.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226648		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041321	ENSG00000227155	RP11-165F24.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227155		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041322	ENSG00000227155	RP11-165F24.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227155		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041323	ENSG00000228060	RP11-69E11.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228060		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041324	ENSG00000228061	Z83001.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228061		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041325	ENSG00000228061	Z83001.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228061		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041326	ENSG00000228124	RP1-122O8.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228124		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041327	ENSG00000228124	RP1-122O8.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228124		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041328	ENSG00000228274	RP3-508I15.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228274		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041329	ENSG00000228274	RP3-508I15.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228274		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041330	ENSG00000228737	AC008781.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228737		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041331	ENSG00000228737	AC008781.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228737		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041332	ENSG00000229044	RP11-266K22.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229044		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041333	ENSG00000229044	RP11-266K22.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229044		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041334	ENSG00000229821	RP11-567E21.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229821		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041335	ENSG00000229821	RP11-567E21.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229821		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041336	ENSG00000230325	RP11-385F5.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230325		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041337	ENSG00000230325	RP11-385F5.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230325		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041338	ENSG00000230424	RP1-43E13.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230424		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041339	ENSG00000230424	RP1-43E13.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230424		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041340	ENSG00000230733	AC092171.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230733		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041341	ENSG00000230733	AC092171.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230733		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041342	ENSG00000231064	RP11-263K19.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231064		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041343	ENSG00000231064	RP11-263K19.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231064		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041344	ENSG00000231840	AC073342.12	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231840		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041345	ENSG00000231840	AC073342.12	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231840		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041346	ENSG00000231993	RP1-85F18.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231993		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041347	ENSG00000232194	RP1-313L4.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232194		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041348	ENSG00000232194	RP1-313L4.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232194		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041349	ENSG00000232623	AP000266.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232623		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041350	ENSG00000232623	AP000266.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232623		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041351	ENSG00000234055	RP11-247A12.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234055		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041352	ENSG00000234084	RP3-388E23.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234084		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041353	ENSG00000234084	RP3-388E23.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234084		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041354	ENSG00000234136	AC055764.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234136		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041355	ENSG00000234136	AC055764.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234136		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041356	ENSG00000234428	RP11-666F17.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234428		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041357	ENSG00000234428	RP11-666F17.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234428		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041358	ENSG00000234961	RP11-124N14.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234961		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041359	ENSG00000234961	RP11-124N14.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234961		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041360	ENSG00000235085	AC091153.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235085		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041361	ENSG00000235085	AC091153.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235085		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041362	ENSG00000235513	RP4-756G23.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235513		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041363	ENSG00000235790	RP11-73M7.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235790		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041364	ENSG00000235790	RP11-73M7.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235790		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041365	ENSG00000236015	AC011290.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236015		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041366	ENSG00000236015	AC011290.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236015		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041367	ENSG00000236031	RP11-269F20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236031		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041368	ENSG00000236031	RP11-269F20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236031		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041369	ENSG00000236364	RP11-525G13.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236364		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041370	ENSG00000236364	RP11-525G13.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236364		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041371	ENSG00000236432	AC097662.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236432		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041372	ENSG00000236432	AC097662.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236432		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041373	ENSG00000236498	AC107081.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236498		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041374	ENSG00000236498	AC107081.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236498		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041375	ENSG00000236526	RP4-742J24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236526		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041376	ENSG00000236782	RP11-96L14.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236782		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041377	ENSG00000236782	RP11-96L14.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236782		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041378	ENSG00000237234	RP1-142L7.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237234		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041379	ENSG00000237234	RP1-142L7.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237234		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041380	ENSG00000237719	RP1-179N16.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237719		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041381	ENSG00000237781	RP11-54A4.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237781		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041382	ENSG00000237781	RP11-54A4.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237781		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041383	ENSG00000237978	RP11-385J1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237978		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041384	ENSG00000237978	RP11-385J1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237978		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041385	ENSG00000238221	RP11-69L16.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000238221		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041386	ENSG00000238246	RP11-575A19.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000238246		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041387	ENSG00000238279	BX470102.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000238279		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041388	ENSG00000238279	BX470102.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000238279		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041389	ENSG00000240291	RP11-499P20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240291		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041390	ENSG00000240291	RP11-499P20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240291		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041391	ENSG00000240401	AC012358.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240401		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041392	ENSG00000240401	AC012358.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240401		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041393	ENSG00000240449	RP4-584D14.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240449		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041394	ENSG00000240449	RP4-584D14.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240449		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041395	ENSG00000240499	RP5-1101C3.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240499		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041396	ENSG00000240499	RP5-1101C3.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240499		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041397	ENSG00000240553	RP1-184J9.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240553		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041398	ENSG00000240553	RP1-184J9.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240553		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041399	ENSG00000242798	RP11-506M12.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000242798		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041400	ENSG00000242798	RP11-506M12.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000242798		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041401	ENSG00000242861	RP11-285F7.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000242861		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041402	ENSG00000242861	RP11-285F7.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000242861		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041403	ENSG00000243018	RP5-1070G24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000243018		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041404	ENSG00000243018	RP5-1070G24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000243018		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041405	ENSG00000243415	RP11-274H2.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000243415		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041406	ENSG00000244513	CTD-2013N24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244513		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041407	ENSG00000244513	CTD-2013N24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244513		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041408	ENSG00000246889	AP000487.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000246889		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041409	ENSG00000247925	RP3-510L9.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247925		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041410	ENSG00000247925	RP3-510L9.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247925		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041411	ENSG00000248445	CTB-118N6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248445		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041412	ENSG00000248647	RP11-331K21.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248647		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041413	ENSG00000248647	RP11-331K21.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248647		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041414	ENSG00000248710	RP11-432B6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248710		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041415	ENSG00000249084	RP11-376O6.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249084		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041416	ENSG00000250309	CTC-345K18.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250309		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041417	ENSG00000250309	CTC-345K18.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250309		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041418	ENSG00000250751	RP11-613C6.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250751		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041419	ENSG00000250751	RP11-613C6.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250751		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041420	ENSG00000251186	RP11-689P11.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251186		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041421	ENSG00000251186	RP11-689P11.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251186		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041422	ENSG00000251307	RP11-506H20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251307		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041423	ENSG00000251307	RP11-506H20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251307		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041424	ENSG00000253667	RP11-30L15.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253667		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041425	ENSG00000253736	RP11-779O18.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253736		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041426	ENSG00000253921	CTB-113P19.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253921		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041427	ENSG00000253921	CTB-113P19.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253921		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041428	ENSG00000253972	RP11-4K16.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253972		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041429	ENSG00000253972	RP11-4K16.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253972		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041430	ENSG00000254459	RP11-91P24.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254459		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041431	ENSG00000254459	RP11-91P24.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254459		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041432	ENSG00000254548	RP11-429J17.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254548		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041433	ENSG00000254548	RP11-429J17.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254548		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041434	ENSG00000254733	RP11-317J19.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254733		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041435	ENSG00000254733	RP11-317J19.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254733		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041436	ENSG00000254966	RP11-1081L13.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254966		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041437	ENSG00000254966	RP11-1081L13.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254966		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041438	ENSG00000254981	RP11-350N15.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254981		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041439	ENSG00000254981	RP11-350N15.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254981		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041440	ENSG00000255125	RP11-685M7.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255125		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041441	ENSG00000255201	RP11-350N15.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255201		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041442	ENSG00000255201	RP11-350N15.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255201		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041443	ENSG00000255206	RP11-403D15.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255206		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041444	ENSG00000255443	RP1-68D18.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255443		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041445	ENSG00000255443	RP1-68D18.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255443		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041446	ENSG00000255539	CTA-797E19.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255539		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041447	ENSG00000255655	RP11-256L11.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255655		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041448	ENSG00000255692	RP1-127H14.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255692		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041449	ENSG00000255817	RP11-196H14.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255817		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041450	ENSG00000255817	RP11-196H14.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255817		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041451	ENSG00000255872	RP11-613M10.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255872		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041452	ENSG00000255872	RP11-613M10.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255872		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041453	ENSG00000255965	RP11-408I18.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255965		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041454	ENSG00000255965	RP11-408I18.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255965		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041455	ENSG00000256824	RP11-21A7A.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256824		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041456	ENSG00000256824	RP11-21A7A.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256824		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041457	ENSG00000257042	RP11-993B23.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257042		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041458	ENSG00000257042	RP11-993B23.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257042		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041459	ENSG00000257222	RP11-554E23.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257222		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041460	ENSG00000257342	RP11-571M6.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257342		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041461	ENSG00000257342	RP11-571M6.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257342		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041462	ENSG00000257497	RP11-585P4.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257497		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041463	ENSG00000257681	RP11-341G23.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257681		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041464	ENSG00000257681	RP11-341G23.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257681		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041465	ENSG00000258260	RP11-977G19.14	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258260		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041466	ENSG00000258260	RP11-977G19.14	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258260		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041467	ENSG00000258365	RP11-1105G2.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258365		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041468	ENSG00000258365	RP11-1105G2.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258365		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041469	ENSG00000258515	RP11-203M5.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258515		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041470	ENSG00000258646	RP11-950C14.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258646		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041471	ENSG00000258646	RP11-950C14.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258646		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041472	ENSG00000258745	RP11-218E20.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258745		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041473	ENSG00000258789	RP11-507K2.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258789		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041474	ENSG00000258959	RP11-1017G21.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000258959		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041475	ENSG00000259081	RP11-488C13.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259081		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041476	ENSG00000259081	RP11-488C13.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259081		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041477	ENSG00000259088	CTD-2017C7.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259088		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041478	ENSG00000259088	CTD-2017C7.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259088		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041479	ENSG00000259279	CTD-2033D15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259279		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041480	ENSG00000259279	CTD-2033D15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259279		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041481	ENSG00000259322	RP11-762H8.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259322		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041482	ENSG00000259367	RP11-815J21.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259367		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041483	ENSG00000259367	RP11-815J21.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259367		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041484	ENSG00000259407	RP11-158M2.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259407		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041485	ENSG00000259407	RP11-158M2.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259407		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041486	ENSG00000259546	RP11-351M8.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259546		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041487	ENSG00000259577	RP11-430B1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259577		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041488	ENSG00000259577	RP11-430B1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259577		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041489	ENSG00000259627	RP11-244F12.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259627		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041490	ENSG00000259627	RP11-244F12.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259627		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041491	ENSG00000259723	RP5-823G15.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259723		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041492	ENSG00000259723	RP5-823G15.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259723		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041493	ENSG00000259755	RP11-505E24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259755		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041494	ENSG00000259755	RP11-505E24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259755		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041495	ENSG00000259901	RP5-991G20.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259901		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041496	ENSG00000259901	RP5-991G20.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259901		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041497	ENSG00000259939	RP11-77H9.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259939		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041498	ENSG00000259939	RP11-77H9.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259939		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041499	ENSG00000259940	CTD-3203P2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000259940		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041500	ENSG00000260095	RP11-715J22.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260095		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041501	ENSG00000260095	RP11-715J22.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260095		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041502	ENSG00000260121	RP5-1142A6.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260121		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041503	ENSG00000260121	RP5-1142A6.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260121		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041504	ENSG00000260349	RP11-473I1.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260349		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041505	ENSG00000260349	RP11-473I1.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260349		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041506	ENSG00000260350	RP11-152P23.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260350		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041507	ENSG00000260350	RP11-152P23.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260350		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041508	ENSG00000260465	RP11-63M22.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260465		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041509	ENSG00000260465	RP11-63M22.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260465		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041510	ENSG00000260773	RP11-352G18.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260773		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041511	ENSG00000260853	RP11-264B17.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260853		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041512	ENSG00000260853	RP11-264B17.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260853		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041513	ENSG00000260927	RP11-459F6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260927		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041514	ENSG00000260927	RP11-459F6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260927		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041515	ENSG00000261235	RP11-510J16.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261235		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041516	ENSG00000261235	RP11-510J16.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261235		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041517	ENSG00000261669	CTD-2515A14.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261669		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041518	ENSG00000261669	CTD-2515A14.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261669		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041519	ENSG00000261762	RP11-650L12.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261762		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041520	ENSG00000261898	RP11-314A20.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261898		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041521	ENSG00000261898	RP11-314A20.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261898		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041522	ENSG00000262580	RP11-334C17.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000262580		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041523	ENSG00000262580	RP11-334C17.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000262580		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041524	ENSG00000263272	CTC-524C5.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000263272		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041525	ENSG00000263272	CTC-524C5.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000263272		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041526	ENSG00000263300	RP5-1029F21.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000263300		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041527	ENSG00000264031	RP11-68I3.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264031		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041528	ENSG00000264031	RP11-68I3.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264031		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041529	ENSG00000264044	RP11-192H23.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264044		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041530	ENSG00000264044	RP11-192H23.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264044		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041531	ENSG00000265445	RP11-849N15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000265445		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041532	ENSG00000265490	RP11-806L2.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000265490		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041533	ENSG00000265907	RP11-737O24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000265907		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041534	ENSG00000265907	RP11-737O24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000265907		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041535	ENSG00000266903	CTB-171A8.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000266903		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041536	ENSG00000266978	CTD-2369P2.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000266978		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041537	ENSG00000266978	CTD-2369P2.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000266978		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041538	ENSG00000267009	RP11-120M18.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267009		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041539	ENSG00000267009	RP11-120M18.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267009		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041540	ENSG00000267025	AC015849.19	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267025		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041541	ENSG00000267025	AC015849.19	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267025		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041542	ENSG00000267049	AC002398.13	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267049		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041543	ENSG00000267049	AC002398.13	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267049		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041544	ENSG00000267249	RP11-973H7.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267249		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041545	ENSG00000267342	RP11-552F3.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267342		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041546	ENSG00000267342	RP11-552F3.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267342		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041547	ENSG00000267375	CTB-186G2.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267375		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041548	ENSG00000267375	CTB-186G2.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267375		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041549	ENSG00000267379	CTC-548K16.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267379		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041550	ENSG00000267379	CTC-548K16.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267379		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041551	ENSG00000267436	AC005786.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267436		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041552	ENSG00000267436	AC005786.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267436		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041553	ENSG00000267476	RP11-126O1.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267476		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041554	ENSG00000267787	RP11-35G9.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267787		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041555	ENSG00000267954	AP000349.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267954		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041556	ENSG00000268015	CTD-2525I3.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268015		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041557	ENSG00000268015	CTD-2525I3.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268015		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041558	ENSG00000268069	AC004466.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268069		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041559	ENSG00000268069	AC004466.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268069		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041560	ENSG00000268172	AL590452.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268172		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041561	ENSG00000268189	AC005785.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268189		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041562	ENSG00000268189	AC005785.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268189		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041563	ENSG00000268833	AC011513.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268833		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041564	ENSG00000268846	AC018867.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268846		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041565	ENSG00000268846	AC018867.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268846		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041566	ENSG00000268896	RP11-256I23.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268896		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041567	ENSG00000269151	AC007193.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269151		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041568	ENSG00000269151	AC007193.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269151		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041569	ENSG00000269176	RP11-727F15.12	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269176		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041570	ENSG00000269176	RP11-727F15.12	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269176		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041571	ENSG00000269305	AL158147.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269305		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041572	ENSG00000269305	AL158147.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269305		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041573	ENSG00000269496	AC007919.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269496		mRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). We also noted that a considerable fraction of mRNAs (16%) were detected exclusively in the nucleus."
RLID00041574	ENSG00000269496	AC007919.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000269496		mRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). These mRNAs may include transcripts with a very rapid cytoplasmic turnover, those that are inefficiently transported to the cytoplasm, or those that are selectively retained in the nucleus as part of a post-transcriptional mechanism to regulate gene expression."
RLID00041575	ENSG00000270110	RP5-1139B12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000270110		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041576	ENSG00000270110	RP5-1139B12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000270110		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041577	ENSG00000270706	CTD-2301A4.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000270706		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041578	ENSG00000270706	CTD-2301A4.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000270706		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041579	ENSG00000271554	RP4-665N4.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271554		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041580	ENSG00000271554	RP4-665N4.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271554		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041581	ENSG00000271725	RP11-761I4.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271725		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041582	ENSG00000271725	RP11-761I4.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271725		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041583	ENSG00000271774	RP4-678D15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271774		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041584	ENSG00000271774	RP4-678D15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271774		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041585	ENSG00000271795	CTC-251D13.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271795		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041586	ENSG00000271806	RP5-892K4.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271806		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041587	ENSG00000271806	RP5-892K4.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271806		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041588	ENSG00000271870	RP11-97C16.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271870		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041589	ENSG00000271870	RP11-97C16.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271870		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041590	ENSG00000271984	RP3-337O18.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271984		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041591	ENSG00000271984	RP3-337O18.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000271984		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041592	ENSG00000272054	RP11-423P10.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272054		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041593	ENSG00000272072	CTA-363E19.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272072		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041594	ENSG00000272072	CTA-363E19.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272072		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041595	ENSG00000272173	U47924.31	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272173		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041596	ENSG00000272173	U47924.31	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272173		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041597	ENSG00000272182	RP11-802O23.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272182		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041598	ENSG00000272182	RP11-802O23.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272182		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041599	ENSG00000272356	RP5-1112D6.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272356		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041600	ENSG00000272367	CTC-428H11.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272367		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041601	ENSG00000272582	RP5-1039K5.17	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272582		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041602	ENSG00000272582	RP5-1039K5.17	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272582		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041603	ENSG00000272760	RP11-5C23.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272760		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041604	ENSG00000272789	RP11-286H15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272789		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041605	ENSG00000272789	RP11-286H15.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272789		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041606	ENSG00000272910	RP11-15L13.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272910		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041607	ENSG00000272910	RP11-15L13.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272910		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041608	ENSG00000272918	CTB-152G17.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272918		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041609	ENSG00000272918	CTB-152G17.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272918		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041610	ENSG00000272990	RP11-305K5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272990		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041611	ENSG00000272990	RP11-305K5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272990		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041612	ENSG00000273137	RP3-402G11.28	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000273137		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041613	ENSG00000273449	RP11-218F10.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000273449		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041614	ENSG00000273449	RP11-218F10.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000273449		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041615	ENSG00000273466	RP11-548H3.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000273466		lncRNA	Homo sapiens	26151857	Nucleus	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). Forty-one percent of the intronic lncRNAs and 25% of the antisense lncRNAs were detected exclusively in the nuclei of HeLa cells."
RLID00041616	ENSG00000273466	RP11-548H3.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000273466		lncRNA	Homo sapiens	26151857	Cytoplasm	HeLa cells	44k oligoarray	"We used a re-annotated version of a previously described custom-designed 44k intron-exon oligoarray19 that interrogates 6,322 intragenic transcripts with the same orientation as the respective mRNAs (intronic lncRNAs), as well as 10,482 transcripts with an antisense orientation relative to the mRNAs (antisense lncRNAs) and 6,360 protein-coding mRNAs. Data were collected from GEO(GSE62989, GSE62984, GSE62963, GSE62985, GSE62959, GSE62955, and GSE62958). It is interesting to note that the majority of the lncRNAs (58% and 73% of the intronic and antisense lncRNAs, respectively) were also detected in the cytoplasm."
RLID00041617	51352	WT1-AS	http://www.ncbi.nlm.nih.gov/gene/?term=51352	"WIT1, WIT-1, WT1AS, WT1-AS1"	lncRNA	Homo sapiens	26462627	Nucleus	Huh7 and HepG2 cells	FISH	The transcript of WT1-AS was located primarily in the nucleus of Huh7 and HepG2 cells.
RLID00041618	77395	9530018H14Rik	http://www.ncbi.nlm.nih.gov/gene/?term=77395	lncRNA-HIT	mRNA	Mus musculus	26633036	Nucleus	Embryo	RNA-FISH	Analysis of LncRNA-HIT's subcellular localization by single molecule RNA FISH detected the lncRNA in the nucleus where it was distributed diffusely and in larger foci in the limb bud mesenchyme.
RLID00041619	647979	NORAD	http://www.ncbi.nlm.nih.gov/gene/?term=647979	LINC00657	lncRNA	Homo sapiens	26724866	Cytoplasm	cell lines	RT-PCR	"Furthermore, subcellular fractionation and single molecule RNA FISH demonstrated a nearly exclusively cytoplasmic localization of the NORAD RNA."
RLID00041620	100316868	HOTTIP	http://www.ncbi.nlm.nih.gov/gene/?term=100316868	"HOXA-AS6, HOXA13-AS1, NCRNA00213"	lncRNA	Homo sapiens	26807954	Nucleus	HepG2 cell lines/SMMC7721	qRT-PCR	HOTTIP was detected predominantly in the nuclear fraction as U6RNA did in HCC cells.
RLID00041621	100302740	FAS-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100302740	"SAF, FASAS, FAS-AS"	lncRNA	Homo sapiens	26885613	Nucleus	HeLa cells	qPCR	We show that Saf is localized in the nucleus where it interacts with Fas receptor pre-mRNA and human splicing factor 45 (SPF45) to facilitate alternative splicing and exclusion of exon 6.
RLID00041622	100302740	FAS-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100302740	"SAF, FASAS, FAS-AS"	lncRNA	Homo sapiens	26885613	Nucleus	HeLa cells	qPCR	We show that Saf is localized in the nucleus where it interacts with Fas receptor pre-mRNA and human splicing factor 45 (SPF45) to facilitate alternative splicing and exclusion of exon 6.
RLID00041623	4498	MT1JP	http://www.ncbi.nlm.nih.gov/gene/?term=4498	"MT1, MT1J, MT1NP, MTB"	lncRNA	Homo sapiens	26909858	Cytoplasm	L02 cells	RNA-FISH	"We first determined the subcellular distribution of MT1JP by RNA fluorescence in situ hybridization (RNA-FISH), and found that most of the MT1JP transcripts were located in the cytoplasm. "
RLID00041624	4498	MT1JP	http://www.ncbi.nlm.nih.gov/gene/?term=4498	"MT1, MT1J, MT1NP, MTB"	lncRNA	Homo sapiens	26909858	Cytoplasm	L02 cells	qRT-PCR	"Moreover, we confirmed this observation by quantifying the expression ratio of MT1JP in cytoplasmic and nuclear fractions with qRT-PCR."
RLID00041625	100048912	CDKN2B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100048912	"ANRIL, CDKN2B-AS, CDKN2BAS, NCRNA00089, PCAT12, p15AS"	lncRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"We identified 329 lncRNAs with increased and 126 lncRNAs with decreased expression in active UC tissues compared with normal control tissues, including the most significantly upregulated (BC012900, AK001903, and AK023330) and downregulated (BC029135, CDKN2B-AS1, and BC062296) transcripts. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE 72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041626	114041	B3GALT5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=114041	C21orf88	lncRNA	Homo sapiens	26937624	Cytoplasm	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient.The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. Most lncRNAs demonstrate predominant nuclear expression, whereas DIOA3AS and BC062296 demonstrated higher abundance in cytoplasm."
RLID00041627	114041	B3GALT5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=114041	C21orf88	lncRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041628	1846	DUSP4	http://www.ncbi.nlm.nih.gov/gene/?term=1846	"HVH2, MKP-2, MKP2, TYP"	mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041629	301	ANXA1	http://www.ncbi.nlm.nih.gov/gene/?term=301	"ANX1, LPC1"	mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041630	3624	INHBA	http://www.ncbi.nlm.nih.gov/gene/?term=3624	"EDF, FRP"	mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041631	3752	KCND3	http://www.ncbi.nlm.nih.gov/gene/?term=3752	"BRGDA9L, KCND3S, KSHIVB, KV4.3, SCA19, SCA22, KCND3"	mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041632	64150	DIO3OS	http://www.ncbi.nlm.nih.gov/gene/?term=64150	"DIO3-OS, DIO3-AS1, C14orf134, NCRNA00041"	lncRNA	Homo sapiens	26937624	Cytoplasm	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. Most lncRNAs demonstrate predominant nuclear expression, whereas DIOA3AS and BC062296 demonstrated higher abundance in cytoplasm."
RLID00041633	643236	TMEM72	http://www.ncbi.nlm.nih.gov/gene/?term=643236	"C10orf127, KSP37"	mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041634	AK024366	AK024366	https://www.ncbi.nlm.nih.gov/nuccore/AK024366		mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"We identified 329 lncRNAs with increased and 126 lncRNAs with decreased expression in active UC tissues compared with normal control tissues, including the most significantly upregulated (BC012900, AK001903, and AK023330) and downregulated (BC029135, CDKN2B-AS1, and BC062296) transcripts. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041635	BC046210	BC046210	https://www.ncbi.nlm.nih.gov/nuccore/BC046210		mRNA	Homo sapiens	26937624	Nucleus	NCM356	qRT-PCR	"The NCode human noncoding RNA (ncRNA) Microarray V2 (Invitrogen) was used to assess the expression of 17,112 lncRNAs and 22,074 mRNA in individual RNA samples from each patient. The microarray raw data and normalized data have been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE72221. We found that most of the lncRNAs are localized to the nucleus."
RLID00041636	10178800	CR18854	http://www.ncbi.nlm.nih.gov/gene/?term=10178800	CG13122; CG18854; Dmel\CR18854	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041637	10178829	CR32218	http://www.ncbi.nlm.nih.gov/gene/?term=10178829	CG8037; Dmel\CR32218	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041638	10178834	CR42646	http://www.ncbi.nlm.nih.gov/gene/?term=10178834	CR41445; Dmel\CR42646	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041639	10178834	CR42646	http://www.ncbi.nlm.nih.gov/gene/?term=10178834	CR41445; Dmel\CR42646	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041640	10178917	CR31044	http://www.ncbi.nlm.nih.gov/gene/?term=10178917	BcDNA:SD09455; CG31044; Dmel\CR31044; pri-mir-279_mir-996	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041641	10178917	CR31044	http://www.ncbi.nlm.nih.gov/gene/?term=10178917	BcDNA:SD09455; CG31044; Dmel\CR31044; pri-mir-279_mir-996	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 1-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041642	10178937	pncr014:3L	http://www.ncbi.nlm.nih.gov/gene/?term=10178937	BEST:LD13184; CR33944; CR42871; Dmel\CR42871	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041643	10178937	pncr014:3L	http://www.ncbi.nlm.nih.gov/gene/?term=10178937	BEST:LD13184; CR33944; CR42871; Dmel\CR42871	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 6-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041644	10178944	CR32690	http://www.ncbi.nlm.nih.gov/gene/?term=10178944	BEST:LP10814; CG32690; Dmel\CR32690	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041645	10178956	pncr014:3L	http://www.ncbi.nlm.nih.gov/gene/?term=10178956	BEST:LD13184; CR33944; CR42871; Dmel\CR42871	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 8-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041646	10178964	CR42862	http://www.ncbi.nlm.nih.gov/gene/?term=10178964	anon-EST:fe1H7; BcDNA:GH06422; CG13878; CG16971; CG32477; CR32477; Dmel\CR42862	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 4-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041647	12797878	CR43464	http://www.ncbi.nlm.nih.gov/gene/?term=12797878	Dmel\CR43464	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041648	12797878	CR43464	http://www.ncbi.nlm.nih.gov/gene/?term=12797878	Dmel\CR43464	lncRNA	Drosophila melanogaster	26944682	Nucleus	larva intestine	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041649	12797885	CR31386	http://www.ncbi.nlm.nih.gov/gene/?term=12797885	BcDNA:RE39877; CG31386; Dmel\CR31386	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041650	12797909	CR43159	http://www.ncbi.nlm.nih.gov/gene/?term=12797909	Dmel\CR43159	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041651	12797932	CR32194	http://www.ncbi.nlm.nih.gov/gene/?term=12797932	BcDNA:RE06388; CG32194; Dmel\CR32194	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041652	12797935	CR32027	http://www.ncbi.nlm.nih.gov/gene/?term=12797935	BcDNA:RE02231; CG32027; Dmel\CR32027	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041653	12798215	CR43463	http://www.ncbi.nlm.nih.gov/gene/?term=12798215	anon-35Aa; Dmel\CR43463	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041654	12798248	CR31781	http://www.ncbi.nlm.nih.gov/gene/?term=12798248	BcDNA:GH27691; BcDNA:LP04536; CG15131; CG15132; CG31781; Dmel\CR31781	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041655	12798274	CR43476	http://www.ncbi.nlm.nih.gov/gene/?term=12798274	Dmel\CR43476	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041656	12798274	CR43476	http://www.ncbi.nlm.nih.gov/gene/?term=12798274	Dmel\CR43476	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041657	12798336	CR30121	http://www.ncbi.nlm.nih.gov/gene/?term=12798336	BcDNA:GH12850; CG30121; Dmel\CR30121	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 1-3	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041658	12798336	CR30121	http://www.ncbi.nlm.nih.gov/gene/?term=12798336	BcDNA:GH12850; CG30121; Dmel\CR30121	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041659	12798336	CR30121	http://www.ncbi.nlm.nih.gov/gene/?term=12798336	BcDNA:GH12850; CG30121; Dmel\CR30121	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 6-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041660	12798359	CR32252	http://www.ncbi.nlm.nih.gov/gene/?term=12798359	BcDNA:AT23419; CG32252; Dmel\CR32252	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041661	12798366	CR43470	http://www.ncbi.nlm.nih.gov/gene/?term=12798366	Dmel\CR43470	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041662	12798470	CR43426	http://www.ncbi.nlm.nih.gov/gene/?term=12798470	Dmel\CR43426	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 8-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041663	12798483	CR43429	http://www.ncbi.nlm.nih.gov/gene/?term=12798483	Dmel\CR43429	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041664	12798562	CR31647	http://www.ncbi.nlm.nih.gov/gene/?term=12798562	BcDNA:RE16275; CG31647; Dmel\CR31647	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041665	12798562	CR31647	http://www.ncbi.nlm.nih.gov/gene/?term=12798562	BcDNA:RE16275; CG31647; Dmel\CR31647	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041666	12798562	CR31647	http://www.ncbi.nlm.nih.gov/gene/?term=12798562	BcDNA:RE16275; CG31647; Dmel\CR31647	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva muscle	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041667	14462359	CR44029	http://www.ncbi.nlm.nih.gov/gene/?term=14462359	Dmel\CR44029	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041668	14462440	CR42651	http://www.ncbi.nlm.nih.gov/gene/?term=14462440	CG42651; Dmel\CR42651; pri-mir-10	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 4-6	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041669	14462514	CR44052	http://www.ncbi.nlm.nih.gov/gene/?term=14462514	Dmel\CR44052	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041670	14462516	CR44097	http://www.ncbi.nlm.nih.gov/gene/?term=14462516	Dmel\CR44097	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041671	14462604	CR43964	http://www.ncbi.nlm.nih.gov/gene/?term=14462604	Dmel\CR43964	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-3	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041672	14462655	CR43649	http://www.ncbi.nlm.nih.gov/gene/?term=14462655	Dmel\CR43649	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041673	14462890	CR43872	http://www.ncbi.nlm.nih.gov/gene/?term=14462890	CG43872; Dmel\CR43872	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 1-3	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041674	14462890	CR43872	http://www.ncbi.nlm.nih.gov/gene/?term=14462890	CG43872; Dmel\CR43872	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041675	14462918	CR40053	http://www.ncbi.nlm.nih.gov/gene/?term=14462918	BcDNA:AT11374; CG40053; Dmel\CR40053	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041676	14462918	CR40053	http://www.ncbi.nlm.nih.gov/gene/?term=14462918	BcDNA:AT11374; CG40053; Dmel\CR40053	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041677	19835082	CR32111	http://www.ncbi.nlm.nih.gov/gene/?term=19835082	CG32111; Dmel\CR32111	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva ring glands	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041678	19835193	CR44898	http://www.ncbi.nlm.nih.gov/gene/?term=19835193	Dmel\CR44898	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041679	19835321	CR44872	http://www.ncbi.nlm.nih.gov/gene/?term=19835321	Dmel\CR44872	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041680	19835567	CR45018	http://www.ncbi.nlm.nih.gov/gene/?term=19835567	Dmel\CR45018	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041681	19835581	CR45030	http://www.ncbi.nlm.nih.gov/gene/?term=19835581	Dmel\CR45030	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041682	19835588	CR44690	http://www.ncbi.nlm.nih.gov/gene/?term=19835588	Dmel\CR44690	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041683	19835588	CR44690	http://www.ncbi.nlm.nih.gov/gene/?term=19835588	Dmel\CR44690	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041684	19835926	CR44945	http://www.ncbi.nlm.nih.gov/gene/?term=19835926	Dmel\CR44945; lincRNA.798	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva salivary gland	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041685	19835965	CR44931	http://www.ncbi.nlm.nih.gov/gene/?term=19835965	Dmel\CR44931; lincRNA.699	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 4-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041686	26067084	CR32582	http://www.ncbi.nlm.nih.gov/gene/?term=26067084	BcDNA:SD27303; CG32582; Dmel\CR32582; mdcds_55373	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041687	26067100	CR43174	http://www.ncbi.nlm.nih.gov/gene/?term=26067100	CG43173; CG43174; CR43173; Dmel\CR43174; mdcds_28406	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041688	26067356	flam	http://www.ncbi.nlm.nih.gov/gene/?term=26067356	COM; COM/flam; CR46037; Dmel\CR46037; lincRNA.1041	lncRNA	Drosophila melanogaster	26944682	Nucleus	Emrbyo stage 1-17	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041689	26067356	flam	http://www.ncbi.nlm.nih.gov/gene/?term=26067356	COM; COM/flam; CR46037; Dmel\CR46037; lincRNA.1041	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041690	26067356	flam	http://www.ncbi.nlm.nih.gov/gene/?term=26067356	COM; COM/flam; CR46037; Dmel\CR46037; lincRNA.1041	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva intestine	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041691	26067356	flam	http://www.ncbi.nlm.nih.gov/gene/?term=26067356	COM; COM/flam; CR46037; Dmel\CR46037; lincRNA.1041	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva salivary gland	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041692	26067493	CR46179	http://www.ncbi.nlm.nih.gov/gene/?term=26067493	CG12717-related; Dmel\CR46179	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-3	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041693	3772088	pncr002:3R	http://www.ncbi.nlm.nih.gov/gene/?term=3772088	BcDNA:LP03188; CR33938; Dmel\CR33938	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva salivary gland	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041694	3772102	CR32205	http://www.ncbi.nlm.nih.gov/gene/?term=3772102	BcDNA:RE73739; Dmel\CR32205; hp-CR32205	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041695	3772110	iab-4	http://www.ncbi.nlm.nih.gov/gene/?term=3772110	CR31271; Dmel\CR31271; I; iab; pri-mir-iab-4_mir-iab-4as	lncRNA	Drosophila melanogaster	26944682	Nucleus	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041696	3772220	bxd	http://www.ncbi.nlm.nih.gov/gene/?term=3772220	CR31273; CR31277; Dmel\CR31273	lncRNA	Drosophila melanogaster	26944682	Nucleus	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041697	3772292	pncr017:3R	http://www.ncbi.nlm.nih.gov/gene/?term=3772292	BcDNA:SD10988; CR33945; Dmel\CR33945	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041698	3772297	CR32730	http://www.ncbi.nlm.nih.gov/gene/?term=3772297	BcDNA:RE54930; Dmel\CR32730; MRE32	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 4-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041699	3772376	roX1	http://www.ncbi.nlm.nih.gov/gene/?term=3772376	BcDNA:GH10432; chrX:3706836..3706970; CR32777; Dmel\CR32777; EG:EG0002.2; roX; rox-1; rox1; RoX1	lncRNA	Drosophila melanogaster	26944682	Nucleus	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041700	3772405	Cyp9f3Psi	http://www.ncbi.nlm.nih.gov/gene/?term=3772405	9f3p; CG17875; CR17875; Cyp9f3; Cyp9f3p; Dmel\CR17875	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041701	3772463	CR32385	http://www.ncbi.nlm.nih.gov/gene/?term=3772463	anon-WO0118547.23; BcDNA:LD18889; Dmel\CR32385; LD18889	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva salivary gland	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041702	3772538	CR33941	http://www.ncbi.nlm.nih.gov/gene/?term=3772538	BcDNA:GM01028; CG13303; CR33941; CT32596; Dmel\CG33941; MRE3; pncr013:4	mRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 1-3	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041703	3772538	CR33941	http://www.ncbi.nlm.nih.gov/gene/?term=3772538	BcDNA:GM01028; CG13303; CR33941; CT32596; Dmel\CG33941; MRE3; pncr013:4	mRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041704	3772546	CR31969	http://www.ncbi.nlm.nih.gov/gene/?term=3772546		lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-17	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041705	3885572	CR33963	http://www.ncbi.nlm.nih.gov/gene/?term=3885572	BcDNA:GH04518; Dmel\CR33963	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 4-5	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041706	3885572	CR33963	http://www.ncbi.nlm.nih.gov/gene/?term=3885572	BcDNA:GH04518; Dmel\CR33963	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva salivary gland	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041707	3885608	CR33987	http://www.ncbi.nlm.nih.gov/gene/?term=3885608	Dmel\CR33987	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-17	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041708	5740822	CR31032	http://www.ncbi.nlm.nih.gov/gene/?term=5740822	BcDNA:GH15189; CG31032; Dmel\CR31032	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041709	5740822	CR31032	http://www.ncbi.nlm.nih.gov/gene/?term=5740822	BcDNA:GH15189; CG31032; Dmel\CR31032	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Larva salivary gland	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041710	8673968	CR18166	http://www.ncbi.nlm.nih.gov/gene/?term=8673968	BEST:GH02584; CG13372; CG18166; Dmel\CR18166	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	embryo	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041711	8674102	CR42549	http://www.ncbi.nlm.nih.gov/gene/?term=8674102	Dmel\CR42549	lncRNA	Drosophila melanogaster	26944682	Nucleus	Embryo stage 10-17	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041712	8674102	CR42549	http://www.ncbi.nlm.nih.gov/gene/?term=8674102	Dmel\CR42549	lncRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-7	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041713	8674102	CR42549	http://www.ncbi.nlm.nih.gov/gene/?term=8674102	Dmel\CR42549	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva fat body	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041714	8674102	CR42549	http://www.ncbi.nlm.nih.gov/gene/?term=8674102	Dmel\CR42549	lncRNA	Drosophila melanogaster	26944682	Nucleus	Larva intestine	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041715	U80893	U80893	https://www.ncbi.nlm.nih.gov/nuccore/U80893		mRNA	Drosophila melanogaster	26944682	Cytoplasm	Embryo stage 6-9	RNA-FISH	"To see whether this prevalence is unique to early Drosophila embryos, we examined ~8000 transcripts over the full course of embryogenesis and ~800 transcripts in late third instar larval tissues. Data were collected from Fly-FISH database(http://fly-fish.ccbr.utoronto.ca). All were also seen to be redeployed in mesoderm and gut tissues during mid-embryogenesis, but localization at these stages was exclusively cytoplasmic."
RLID00041716	55000	TUG1	http://www.ncbi.nlm.nih.gov/gene/?term=55000	"TI-227H, LINC00080, NCRNA00080"	lncRNA	Homo sapiens	26975529	Cytoplasm	22RV1	RNA-FISH	"Among those sp-lncRNAs that were targeted by more than eight experimentally validated PTEN-regulating miRNAs, we chose two sp-lncRNAs lnc-2 (CTB-89H12.4, ENSG00000230551) and lnc-6 (Taurine Upregulated Gene 1 (TUG1), ENSG00000253352) that showed consistently the highest expression in two prostate cancer cell lines (DU145 and 22RV1) with wild-type PTEN for experimental validation. Indeed, lnc-2 and lnc-6 were predominantly localized in the cytoplasm in the DU145 and 22Rv1 cell lines, whereas lnc-7 was not. Data were collected from supplementary data 5."
RLID00041717	55000	TUG1	http://www.ncbi.nlm.nih.gov/gene/?term=55000	"TI-227H, LINC00080, NCRNA00080"	lncRNA	Homo sapiens	26975529	Cytoplasm	DU145	RNA-FISH	"Among those sp-lncRNAs that were targeted by more than eight experimentally validated PTEN-regulating miRNAs, we chose two sp-lncRNAs lnc-2 (CTB-89H12.4, ENSG00000230551) and lnc-6 (Taurine Upregulated Gene 1 (TUG1), ENSG00000253352) that showed consistently the highest expression in two prostate cancer cell lines (DU145 and 22RV1) with wild-type PTEN for experimental validation. Indeed, lnc-2 and lnc-6 were predominantly localized in the cytoplasm in the DU145 and 22Rv1 cell lines, whereas lnc-7 was not. Data were collected from supplementary data 5."
RLID00041718	ENSG00000230551	CTB-89H12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230551		lncRNA	Homo sapiens	26975529	Cytoplasm	22RV1	RNA-FISH	"Among those sp-lncRNAs that were targeted by more than eight experimentally validated PTEN-regulating miRNAs, we chose two sp-lncRNAs lnc-2 (CTB-89H12.4, ENSG00000230551) and lnc-6 (Taurine Upregulated Gene 1 (TUG1), ENSG00000253352) that showed consistently the highest expression in two prostate cancer cell lines (DU145 and 22RV1) with wild-type PTEN for experimental validation. Indeed, lnc-2 and lnc-6 were predominantly localized in the cytoplasm in the DU145 and 22Rv1 cell lines, whereas lnc-7 was not. Data were collected from supplementary data 5."
RLID00041719	ENSG00000230551	CTB-89H12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230551		lncRNA	Homo sapiens	26975529	Cytoplasm	22RV1	qRT-PCR	"Among those sp-lncRNAs that were targeted by more than eight experimentally validated PTEN-regulating miRNAs, we chose two sp-lncRNAs lnc-2 (CTB-89H12.4, ENSG00000230551) and lnc-6 (Taurine Upregulated Gene 1 (TUG1), ENSG00000253352) that showed consistently the highest expression in two prostate cancer cell lines (DU145 and 22RV1) with wild-type PTEN for experimental validation. Indeed, lnc-2 and lnc-6 were predominantly localized in the cytoplasm in the DU145 and 22Rv1 cell lines, whereas lnc-7 was not. Data were collected from supplementary data 5."
RLID00041720	ENSG00000230551	CTB-89H12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230551		lncRNA	Homo sapiens	26975529	Cytoplasm	DU145	RNA-FISH	"Among those sp-lncRNAs that were targeted by more than eight experimentally validated PTEN-regulating miRNAs, we chose two sp-lncRNAs lnc-2 (CTB-89H12.4, ENSG00000230551) and lnc-6 (Taurine Upregulated Gene 1 (TUG1), ENSG00000253352) that showed consistently the highest expression in two prostate cancer cell lines (DU145 and 22RV1) with wild-type PTEN for experimental validation. Indeed, lnc-2 and lnc-6 were predominantly localized in the cytoplasm in the DU145 and 22Rv1 cell lines, whereas lnc-7 was not. Data were collected from supplementary data 5."
RLID00041721	ENSG00000230551	CTB-89H12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230551		lncRNA	Homo sapiens	26975529	Cytoplasm	DU145	qRT-PCR	"Among those sp-lncRNAs that were targeted by more than eight experimentally validated PTEN-regulating miRNAs, we chose two sp-lncRNAs lnc-2 (CTB-89H12.4, ENSG00000230551) and lnc-6 (Taurine Upregulated Gene 1 (TUG1), ENSG00000253352) that showed consistently the highest expression in two prostate cancer cell lines (DU145 and 22RV1) with wild-type PTEN for experimental validation. Indeed, lnc-2 and lnc-6 were predominantly localized in the cytoplasm in the DU145 and 22Rv1 cell lines, whereas lnc-7 was not. Data were collected from supplementary data 5."
RLID00041722	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Nucleus	22RV1	qRT-PCR	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. One of the validated PTEN sp-lncRNA lnc-6 (TUG1) was previously known to be involved in polycomb repressive complex 2-mediated transcriptional regulation and the three-dimensional organization of the transcription unit in the nucleus."
RLID00041723	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Cytoplasm	22RV1	qRT-PCR	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. Our findings not only suggest an important role of lncRNA-mediated sponge regulation in cancer, but also underscore the critical influence of cytoplasmic localization on the efficacy of a sponge lncRNA."
RLID00041724	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Nucleus	22RV1	RNA-FISH	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. One of the validated PTEN sp-lncRNA lnc-6 (TUG1) was previously known to be involved in polycomb repressive complex 2-mediated transcriptional regulation and the three-dimensional organization of the transcription unit in the nucleus."
RLID00041725	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Cytoplasm	22RV1	RNA-FISH	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. Our findings not only suggest an important role of lncRNA-mediated sponge regulation in cancer, but also underscore the critical influence of cytoplasmic localization on the efficacy of a sponge lncRNA."
RLID00041726	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Nucleus	DU145	RNA-FISH	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. One of the validated PTEN sp-lncRNA lnc-6 (TUG1) was previously known to be involved in polycomb repressive complex 2-mediated transcriptional regulation and the three-dimensional organization of the transcription unit in the nucleus."
RLID00041727	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Cytoplasm	DU145	RNA-FISH	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. Our findings not only suggest an important role of lncRNA-mediated sponge regulation in cancer, but also underscore the critical influence of cytoplasmic localization on the efficacy of a sponge lncRNA."
RLID00041728	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Nucleus	DU145	qRT-PCR	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. One of the validated PTEN sp-lncRNA lnc-6 (TUG1) was previously known to be involved in polycomb repressive complex 2-mediated transcriptional regulation and the three-dimensional organization of the transcription unit in the nucleus."
RLID00041729	ENSG00000267520	RP11-373L24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000267520		lncRNA	Homo sapiens	26975529	Cytoplasm	DU145	qRT-PCR	"Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. Data were collected from supplementary data 5. Our findings not only suggest an important role of lncRNA-mediated sponge regulation in cancer, but also underscore the critical influence of cytoplasmic localization on the efficacy of a sponge lncRNA."
RLID00041730	55611	OTUB1	http://www.ncbi.nlm.nih.gov/gene/?term=55611	"HSPC263, OTB1, OTU1"	mRNA	Homo sapiens	27019636	Nucleus	Gastric cancer tissues	qRT-PCR	OTUB1-isoform 2 was predominantly localized in the cell nucleus.
RLID00041731	100128260	WASIR1	http://www.ncbi.nlm.nih.gov/gene/?term=100128260	NCRNA00286B	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041732	100128292	DLG5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100128292		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041733	100129387	GABPB1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100129387		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041734	100130476	LOC100130476	http://www.ncbi.nlm.nih.gov/gene/?term=100130476		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041735	100130476	LOC100130476	http://www.ncbi.nlm.nih.gov/gene/?term=100130476		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041736	100131067	CKMT2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100131067		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041737	100132077	LOC100132077	http://www.ncbi.nlm.nih.gov/gene/?term=100132077		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041738	100132774	KDM4A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100132774		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041739	100132774	KDM4A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100132774		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041740	100287765	LINC00630	http://www.ncbi.nlm.nih.gov/gene/?term=100287765		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041741	100289098	GS1-124K5.4	http://www.ncbi.nlm.nih.gov/gene/?term=100289098		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041742	100289509	KCNIP2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100289509		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041743	100302692	FTX	http://www.ncbi.nlm.nih.gov/gene/?term=100302692	"LINC00182, MIR374AHG, NCRNA00182"	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041744	100306951	PITPNA-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100306951		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041745	100421432	HNRNPA1P44	http://www.ncbi.nlm.nih.gov/gene/?term=100421432		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041746	100505601	PARD3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505601		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041747	100505636	MALINC1	http://www.ncbi.nlm.nih.gov/gene/?term=100505636	"MA-linc1, LINC01024"	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041748	100505648	RAD51-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505648	TODRA	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041749	100505771	MHENCR	http://www.ncbi.nlm.nih.gov/gene/?term=100505771		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041750	100505854	APTR	http://www.ncbi.nlm.nih.gov/gene/?term=100505854	RSBN1L-AS1	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041751	100505894	TMEM161B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505894	linc-POLR3G-8	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041752	100505894	TMEM161B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100505894	linc-POLR3G-8	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041753	100506025	ISPD-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506025		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041754	100506054	RNASEH1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506054		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041755	100506080	HMGA1P4	http://www.ncbi.nlm.nih.gov/gene/?term=100506080		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041756	100506098	LOC100506098	http://www.ncbi.nlm.nih.gov/gene/?term=100506098		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041757	100506100	LOC100506100	http://www.ncbi.nlm.nih.gov/gene/?term=100506100		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041758	100506211	MIR210HG	http://www.ncbi.nlm.nih.gov/gene/?term=100506211		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041759	100506233	RAB30-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506233		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041760	100506233	RAB30-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506233		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041761	100506305	LINC00958	http://www.ncbi.nlm.nih.gov/gene/?term=100506305		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041762	100506311	HOTAIRM1	http://www.ncbi.nlm.nih.gov/gene/?term=100506311	"HOXA-AS1, HOXA1-AS1, NCRNA00179"	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041763	100506314	LOC100506314	http://www.ncbi.nlm.nih.gov/gene/?term=100506314		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041764	100506314	LOC100506314	http://www.ncbi.nlm.nih.gov/gene/?term=100506314		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041765	100506365	OTUD6B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506365	GS1-251I9.4	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041766	100506365	OTUD6B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506365	GS1-251I9.4	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041767	100506392	SLC16A1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506392		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041768	100506469	TMEM147-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506469		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041769	100506649	PXN-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506649	EyeLinc4	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041770	100506649	PXN-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506649	EyeLinc4	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041771	100506660	DDX11-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100506660	CONCR	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041772	100506691	LOC100506691	http://www.ncbi.nlm.nih.gov/gene/?term=100506691		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041773	100506691	LOC100506691	http://www.ncbi.nlm.nih.gov/gene/?term=100506691		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041774	100507171	BOLA3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507171		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041775	100507194	LINC02525	http://www.ncbi.nlm.nih.gov/gene/?term=100507194		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041776	100507266	STX18-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507266		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041777	100507316	MINCR	http://www.ncbi.nlm.nih.gov/gene/?term=100507316	LINC01604	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041778	100507347	VIM-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507347		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041779	100507475	IDH1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507475		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041780	100507487	LOC100507487	http://www.ncbi.nlm.nih.gov/gene/?term=100507487		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041781	100507584	LINC01016	http://www.ncbi.nlm.nih.gov/gene/?term=100507584		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041782	100507602	TRIM52-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100507602		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041783	100508120	GMDS-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100508120		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041784	100508120	GMDS-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100508120		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041785	100509894	CPB2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100509894		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041786	100533182	SEC24B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100533182	1/2-SBSRNA4	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041787	100652730	LINC00659	http://www.ncbi.nlm.nih.gov/gene/?term=100652730		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041788	100852408	EGFLAM-AS4	http://www.ncbi.nlm.nih.gov/gene/?term=100852408		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041789	100873938	GYG2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100873938		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041790	100873949	IPO9-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100873949		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041791	100873949	IPO9-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100873949		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041792	100874032	PRRT3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874032		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041793	100874048	DGUOK-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874048		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041794	100874052	LINC00534	http://www.ncbi.nlm.nih.gov/gene/?term=100874052		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041795	100874069	STK24-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874069		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041796	100874110	GLYCTK-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874110		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041797	100874216	ZNF385D-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100874216		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041798	100874278	ERI3-IT1	http://www.ncbi.nlm.nih.gov/gene/?term=100874278		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041799	100874322	BACH1-IT2	http://www.ncbi.nlm.nih.gov/gene/?term=100874322		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041800	100874327	DSCR4-IT1	http://www.ncbi.nlm.nih.gov/gene/?term=100874327		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041801	100874364	HOXC-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=100874364		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041802	100996301	FOXD3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=100996301	pasFOXD3	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041803	101060264	FOXP4-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101060264		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041804	101060691	NUTM2B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101060691		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041805	101926888	RALY-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101926888		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041806	101926926	RDH10-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101926926		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041807	101926934	LOC101926934	http://www.ncbi.nlm.nih.gov/gene/?term=101926934		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041808	101927125	ELFN1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101927125	MYCLo-2	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041809	101927221	UBR5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101927221		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041810	101927289	LINC01237	http://www.ncbi.nlm.nih.gov/gene/?term=101927289		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041811	101927420	LOC101927420	http://www.ncbi.nlm.nih.gov/gene/?term=101927420		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041812	101927459	LINC01608	http://www.ncbi.nlm.nih.gov/gene/?term=101927459		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041813	101927621	LINC01534	http://www.ncbi.nlm.nih.gov/gene/?term=101927621		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041814	101927815	LOC101927815	http://www.ncbi.nlm.nih.gov/gene/?term=101927815		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041815	101927851	LOC101927851	http://www.ncbi.nlm.nih.gov/gene/?term=101927851		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041816	101927905	LINC02449	http://www.ncbi.nlm.nih.gov/gene/?term=101927905		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041817	101928000	LOC101928000	http://www.ncbi.nlm.nih.gov/gene/?term=101928000		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041818	101928000	LOC101928000	http://www.ncbi.nlm.nih.gov/gene/?term=101928000		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041819	101928017	UBXN10-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101928017		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041820	101928100	LOC101928100	http://www.ncbi.nlm.nih.gov/gene/?term=101928100		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041821	101928307	LOC101928307	http://www.ncbi.nlm.nih.gov/gene/?term=101928307		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041822	101928402	LOC101928402	http://www.ncbi.nlm.nih.gov/gene/?term=101928402		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041823	101928725	LOC101928725	http://www.ncbi.nlm.nih.gov/gene/?term=101928725		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041824	101928784	RORA-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101928784		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041825	101928834	LOC101928834	http://www.ncbi.nlm.nih.gov/gene/?term=101928834		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041826	101928857	CTD-3080P12.3	http://www.ncbi.nlm.nih.gov/gene/?term=101928857		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041827	101928973	LINC01732	http://www.ncbi.nlm.nih.gov/gene/?term=101928973		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041828	101929128	LOC101929128	http://www.ncbi.nlm.nih.gov/gene/?term=101929128		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041829	101929147	LOC101929147	http://www.ncbi.nlm.nih.gov/gene/?term=101929147		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041830	101929302	RFX3-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=101929302	CVAT7	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041831	101929378	LINC01876	http://www.ncbi.nlm.nih.gov/gene/?term=101929378		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041832	101929736	LINC01372	http://www.ncbi.nlm.nih.gov/gene/?term=101929736		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041833	101930114	LOC101930114	http://www.ncbi.nlm.nih.gov/gene/?term=101930114		mRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"29% (218/755) of protein-coding mRNAs are classified as heavy polysomal, consistent with their being actively translated and in accordance with previous studies. Data were collected from Supplemental Table S1. Potential protein-coding transcripts had a similar global ribosome-association profile to filtered lncRNA, suggesting that they are not translated efficiently, and underlining the stringency of our lncRNA filtering "
RLID00041834	101930370	LOC101930370	http://www.ncbi.nlm.nih.gov/gene/?term=101930370		mRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"29% (218/755) of protein-coding mRNAs are classified as heavy polysomal, consistent with their being actively translated and in accordance with previous studies. Data were collected from Supplemental Table S1. As expected, protein-coding exons have highly elevated conservation. Free cytoplasmic, polysomal, and nuclear lncRNAs exhibit similar rates of nonneutral evolution."
RLID00041835	102723517	LOC102723517	http://www.ncbi.nlm.nih.gov/gene/?term=102723517		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041836	102723828	LINC02506	http://www.ncbi.nlm.nih.gov/gene/?term=102723828		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041837	102723927	LINC01238	http://www.ncbi.nlm.nih.gov/gene/?term=102723927		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041838	102724450	LOC102724450	http://www.ncbi.nlm.nih.gov/gene/?term=102724450		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041839	102724954	LINC01032	http://www.ncbi.nlm.nih.gov/gene/?term=102724954		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041840	103352539	LINC01410	http://www.ncbi.nlm.nih.gov/gene/?term=103352539		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041841	103625681	LLPH-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=103625681		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041842	103695435	BBOX1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=103695435		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041843	103724390	LINC01287	http://www.ncbi.nlm.nih.gov/gene/?term=103724390	TCONS_l2_00027522	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041844	104326051	MAFA-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=104326051	TCONS_00014882	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041845	104355136	LINC01033	http://www.ncbi.nlm.nih.gov/gene/?term=104355136		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041846	104355148	CYP4A22-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=104355148	ncRNA-a3	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041847	104355152	LINC01090	http://www.ncbi.nlm.nih.gov/gene/?term=104355152		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041848	105372840	LINC01694	http://www.ncbi.nlm.nih.gov/gene/?term=105372840		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041849	105374524	LOC105374524	http://www.ncbi.nlm.nih.gov/gene/?term=105374524		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041850	105374524	LOC105374524	http://www.ncbi.nlm.nih.gov/gene/?term=105374524		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041851	105375475	LINC02476	http://www.ncbi.nlm.nih.gov/gene/?term=105375475	LVCAT5	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041852	105375606	MNX1-AS2	http://www.ncbi.nlm.nih.gov/gene/?term=105375606		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041853	105375666	LOC105375666	http://www.ncbi.nlm.nih.gov/gene/?term=105375666		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041854	105376736	LOC105376736	http://www.ncbi.nlm.nih.gov/gene/?term=105376736		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041855	105377348	LOC105377348	http://www.ncbi.nlm.nih.gov/gene/?term=105377348		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041856	105378687	LOC105378687	http://www.ncbi.nlm.nih.gov/gene/?term=105378687		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041857	105378763	LINC01748	http://www.ncbi.nlm.nih.gov/gene/?term=105378763		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041858	106480739	RHOA-IT1	http://www.ncbi.nlm.nih.gov/gene/?term=106480739		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041859	106480743	BRWD1-IT1	http://www.ncbi.nlm.nih.gov/gene/?term=106480743		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041860	107986453	LOC107986453	http://www.ncbi.nlm.nih.gov/gene/?term=107986453		mRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"29% (218/755) of protein-coding mRNAs are classified as heavy polysomal, consistent with their being actively translated and in accordance with previous studies. Data were collected from Supplemental Table S1. As expected, protein-coding exons have highly elevated conservation. Free cytoplasmic, polysomal, and nuclear lncRNAs exhibit similar rates of nonneutral evolution."
RLID00041861	11257	TP53TG1	http://www.ncbi.nlm.nih.gov/gene/?term=11257	"P53TG1, TP53AP1, P53TG1-D, LINC00096, NCRNA00096"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041862	150759	LINC00342	http://www.ncbi.nlm.nih.gov/gene/?term=150759	NCRNA00342	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041863	220906	WAC-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=220906		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041864	23642	SNHG1	http://www.ncbi.nlm.nih.gov/gene/?term=23642	"UHG, U22HG, lncRNA16, LINC00057, NCRNA00057"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041865	23642	SNHG1	http://www.ncbi.nlm.nih.gov/gene/?term=23642	"UHG, U22HG, lncRNA16, LINC00057, NCRNA00057"	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041866	23642	SNHG1	http://www.ncbi.nlm.nih.gov/gene/?term=23642	"UHG, U22HG, lncRNA16, LINC00057, NCRNA00057"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041867	253039	CUTALP	http://www.ncbi.nlm.nih.gov/gene/?term=253039	PSMD5-AS1	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041868	257396	LOC257396	http://www.ncbi.nlm.nih.gov/gene/?term=257396		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041869	283596	SNHG10	http://www.ncbi.nlm.nih.gov/gene/?term=283596	"C14orf62, LINC00063, NCRNA00063"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041870	283981	LINC00685	http://www.ncbi.nlm.nih.gov/gene/?term=283981	"CXYorf10, NCRNA00107, PPP2R3B-AS1"	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041871	284593	FAM41C	http://www.ncbi.nlm.nih.gov/gene/?term=284593		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041872	284930	LOC284930	http://www.ncbi.nlm.nih.gov/gene/?term=284930		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041873	285084	LINC01305	http://www.ncbi.nlm.nih.gov/gene/?term=285084		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041874	340037	PRR7-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=340037		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041875	349408	TLR8-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=349408		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041876	378938	MALAT1	http://www.ncbi.nlm.nih.gov/gene/?term=378938	"HCN, LINC00047, NCRNA00047, NEAT2, PRO2853"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041877	386597	RNF144A-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=386597		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041878	386627	SAP30L-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=386627	GALNT10-AS1	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041879	387066	SNHG5	http://www.ncbi.nlm.nih.gov/gene/?term=387066	"U50HG, C6orf160, LINC00044, bA33E24.2, NCRNA00044"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041880	388796	SNHG17	http://www.ncbi.nlm.nih.gov/gene/?term=388796		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041881	388796	SNHG17	http://www.ncbi.nlm.nih.gov/gene/?term=388796		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041882	388796	SNHG17	http://www.ncbi.nlm.nih.gov/gene/?term=388796		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041883	400618	SOX9-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=400618		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041884	401106	LINC00884	http://www.ncbi.nlm.nih.gov/gene/?term=401106		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041885	401264	TRAM2-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=401264		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041886	401312	LOC401312	http://www.ncbi.nlm.nih.gov/gene/?term=401312		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041887	401588	ZNF674-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=401588		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041888	404663	CT49	http://www.ncbi.nlm.nih.gov/gene/?term=404663	"TAG, CT49"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041889	414765	HCG25	http://www.ncbi.nlm.nih.gov/gene/?term=414765	dJ1033B10.16	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041890	439994	LINC00863	http://www.ncbi.nlm.nih.gov/gene/?term=439994		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041891	440584	SLC2A1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=440584		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041892	441307	HRAT92	http://www.ncbi.nlm.nih.gov/gene/?term=441307		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041893	4478	MSN	http://www.ncbi.nlm.nih.gov/gene/?term=4478	"HEL70, IMD50"	mRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"29% (218/755) of protein-coding mRNAs are classified as heavy polysomal, consistent with their being actively translated and in accordance with previous studies. Data were collected from Supplemental Table S1. Potential protein-coding transcripts had a similar global ribosome-association profile to filtered lncRNA, suggesting that they are not translated efficiently, and underlining the stringency of our lncRNA filtering "
RLID00041894	4478	MSN	http://www.ncbi.nlm.nih.gov/gene/?term=4478	"HEL70, IMD50"	mRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"29% (218/755) of protein-coding mRNAs are classified as heavy polysomal, consistent with their being actively translated and in accordance with previous studies. Data were collected from Supplemental Table S1. As expected, protein-coding exons have highly elevated conservation. Free cytoplasmic, polysomal, and nuclear lncRNAs exhibit similar rates of nonneutral evolution."
RLID00041895	493900	TMEM9B-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=493900	C11orf18	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041896	553103	MIR3936HG	http://www.ncbi.nlm.nih.gov/gene/?term=553103	SLC22A5-AS1	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041897	553103	MIR3936HG	http://www.ncbi.nlm.nih.gov/gene/?term=553103	SLC22A5-AS1	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041898	57291	DANCR	http://www.ncbi.nlm.nih.gov/gene/?term=57291	"AGU2, ANCR, KIAA0114, SNHG13, lncRNA-ANCR"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041899	57291	DANCR	http://www.ncbi.nlm.nih.gov/gene/?term=57291	"AGU2, ANCR, KIAA0114, SNHG13, lncRNA-ANCR"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041900	58160	NFE4	http://www.ncbi.nlm.nih.gov/gene/?term=58160	NF-E4	mRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"29% (218/755) of protein-coding mRNAs are classified as heavy polysomal, consistent with their being actively translated and in accordance with previous studies. Data were collected from Supplemental Table S1. Potential protein-coding transcripts had a similar global ribosome-association profile to filtered lncRNA, suggesting that they are not translated efficiently, and underlining the stringency of our lncRNA filtering "
RLID00041901	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041902	60674	GAS5	http://www.ncbi.nlm.nih.gov/gene/?term=60674	"NCRNA00030, SNHG2"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041903	619423	FAM85A	http://www.ncbi.nlm.nih.gov/gene/?term=619423		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041904	641638	SNHG6	http://www.ncbi.nlm.nih.gov/gene/?term=641638	"U87HG, HBII-276HG, NCRNA00058"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041905	641638	SNHG6	http://www.ncbi.nlm.nih.gov/gene/?term=641638	"U87HG, HBII-276HG, NCRNA00058"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041906	643401	LINC01021	http://www.ncbi.nlm.nih.gov/gene/?term=643401		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041907	643837	LINC01128	http://www.ncbi.nlm.nih.gov/gene/?term=643837		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041908	643837	LINC01128	http://www.ncbi.nlm.nih.gov/gene/?term=643837		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041909	677822	SNORA40	http://www.ncbi.nlm.nih.gov/gene/?term=677822	"ACA40, SNORA40A"	lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041910	692148	SCARNA10	http://www.ncbi.nlm.nih.gov/gene/?term=692148	U85	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041911	728769	SCAMP1-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=728769		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041912	729082	OIP5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=729082	"cyrano, linc-OIP5"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041913	729178	STXBP5-AS1	http://www.ncbi.nlm.nih.gov/gene/?term=729178		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041914	735301	SNHG9	http://www.ncbi.nlm.nih.gov/gene/?term=735301	NCRNA00062	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041915	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66"	lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041916	7503	XIST	http://www.ncbi.nlm.nih.gov/gene/?term=7503	"DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66"	lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041917	ENSG00000115934	RP11-153K16.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000115934		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041918	ENSG00000189229	AC069277.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000189229		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041919	ENSG00000196295	AC005154.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000196295		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041920	ENSG00000205662	RP11-706O15.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205662		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041921	ENSG00000213863	XX-C2158C12.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000213863		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041922	ENSG00000216775	RP1-152L7.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000216775		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041923	ENSG00000223379	RP11-374M1.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223379		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041924	ENSG00000223473	GS1-124K5.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223473		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041925	ENSG00000223473	GS1-124K5.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223473		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041926	ENSG00000223812	RP11-197K6.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223812		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041927	ENSG00000223960	AC009948.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000223960		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041928	ENSG00000224034	RP11-445P17.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224034		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041929	ENSG00000224066	RP4-622L5.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224066		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041930	ENSG00000224303	RP11-327I22.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224303		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041931	ENSG00000224505	AC002117.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224505		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041932	ENSG00000224536	RP11-134G8.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224536		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041933	ENSG00000224616	RP11-305E17.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224616		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041934	ENSG00000224635	RP4-564F22.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224635		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041935	ENSG00000224698	RP11-131J3.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224698		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041936	ENSG00000224699	LAMTOR5-AS1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224699		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041937	ENSG00000224790	AP000704.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224790		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041938	ENSG00000224903	AC005534.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224903		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041939	ENSG00000224934	RP11-441O15.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224934		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041940	ENSG00000224950	RP5-1086K13.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224950		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041941	ENSG00000224959	AC017002.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000224959		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041942	ENSG00000225135	RP11-361F15.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225135		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041943	ENSG00000225173	XXbac-BPG308K3.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225173		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041944	ENSG00000225205	AC093818.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225205		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041945	ENSG00000225265	RP11-378J18.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225265		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041946	ENSG00000225300	RP11-439E19.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225300		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041947	ENSG00000225335	XXbac-B476C20.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225335		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041948	ENSG00000225411	RP11-764K9.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225411		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041949	ENSG00000225450	RP3-508I15.14	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225450		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041950	ENSG00000225490	RP4-610C12.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225490		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041951	ENSG00000225548	AC098973.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225548		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041952	ENSG00000225793	RP1-234P15.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225793		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041953	ENSG00000225889	AC074289.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225889		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041954	ENSG00000225981	AC102953.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000225981		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041955	ENSG00000226043	AP000705.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226043		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041956	ENSG00000226308	RP4-813D12.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226308		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041957	ENSG00000226310	RP3-323P24.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226310		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041958	ENSG00000226328	CTA-217C2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226328		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041959	ENSG00000226465	RP13-401N8.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226465		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041960	ENSG00000226609	RP11-276E15.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226609		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041961	ENSG00000226969	RP11-547D24.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226969		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041962	ENSG00000227070	RP11-191G24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227070		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041963	ENSG00000227332	RP11-38M15.11	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227332		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041964	ENSG00000227598	RP1-167A14.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227598		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041965	ENSG00000227602	RP3-445N2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227602		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041966	ENSG00000227748	RP11-497D6.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227748		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041967	ENSG00000227932	RP13-16H11.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000227932		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041968	ENSG00000228043	AC097721.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228043		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041969	ENSG00000228065	RP11-222A11.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228065		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041970	ENSG00000228100	AC016912.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228100		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041971	ENSG00000228160	RP13-57D9.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228160		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041972	ENSG00000228235	AP001476.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228235		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041973	ENSG00000228327	RP11-206L10.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228327		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041974	ENSG00000228384	AC007040.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228384		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041975	ENSG00000228541	AC093159.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228541		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041976	ENSG00000228649	AC005682.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228649		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041977	ENSG00000228742	RP5-884M6.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228742		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041978	ENSG00000228989	AC133528.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000228989		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041979	ENSG00000229043	AC091729.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229043		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041980	ENSG00000229127	AC007038.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229127		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041981	ENSG00000229299	RP4-583P15.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229299		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041982	ENSG00000229591	RP5-981O7.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229591		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041983	ENSG00000229801	RP11-353N4.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229801		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041984	ENSG00000229832	RP11-384C4.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229832		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041985	ENSG00000229953	RP11-284F21.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000229953		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041986	ENSG00000230074	RP11-195F19.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230074		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041987	ENSG00000230113	AC091177.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230113		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041988	ENSG00000230345	RP13-455A7.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230345		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041989	ENSG00000230648	RP3-406P24.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230648		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041990	ENSG00000230747	AC021188.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230747		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041991	ENSG00000230751	AC007036.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230751		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041992	ENSG00000230880	RP11-417J8.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230880		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041993	ENSG00000230918	AC008063.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230918		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00041994	ENSG00000231025	RP11-175O19.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231025		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00041995	ENSG00000231125	AF129075.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231125		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041996	ENSG00000231481	RP11-292F9.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231481		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041997	ENSG00000231485	RP4-535B20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231485		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041998	ENSG00000231612	RP11-522M21.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231612		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00041999	ENSG00000231709	RP5-857K21.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231709		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042000	ENSG00000231808	RP11-143M1.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231808		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042001	ENSG00000231856	RP11-327P2.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231856		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042002	ENSG00000231937	RP11-329E24.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000231937		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042003	ENSG00000232006	AC005537.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232006		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042004	ENSG00000232019	AC074183.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232019		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042005	ENSG00000232053	AC009784.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232053		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042006	ENSG00000232093	RP11-307C12.11	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232093		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042007	ENSG00000232336	RP11-782C8.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232336		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042008	ENSG00000232874	RP11-135A1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000232874		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042009	ENSG00000233396	RP11-458D21.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233396		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042010	ENSG00000233461	RP11-295G20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233461		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042011	ENSG00000233547	RP11-57H14.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233547		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042012	ENSG00000233654	AC093388.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233654		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042013	ENSG00000233766	AC098617.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233766		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042014	ENSG00000233875	RP11-61L14.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000233875		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042015	ENSG00000234072	AC074117.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234072		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042016	ENSG00000234129	RP11-120D5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234129		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042017	ENSG00000234142	RP11-276E17.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234142		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042018	ENSG00000234147	RP3-460G2.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234147		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042019	ENSG00000234183	AC004854.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234183		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042020	ENSG00000234225	RP4-704D21.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234225		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042021	ENSG00000234245	RP11-94I2.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234245		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042022	ENSG00000234426	RP11-459O1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234426		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042023	ENSG00000234584	AC019186.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234584		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042024	ENSG00000234593	RP4-704D23.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234593		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042025	ENSG00000234869	RP3-439F8.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234869		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042026	ENSG00000234902	AC007879.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234902		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042027	ENSG00000234913	XXbac-B476C20.13	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234913		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042028	ENSG00000234936	AC010883.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234936		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042029	ENSG00000234978	RP11-423O2.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234978		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042030	ENSG00000234986	XX-C2158C12.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000234986		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042031	ENSG00000235151	AC114730.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235151		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042032	ENSG00000235245	RP11-122K13.12	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235245		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042033	ENSG00000235335	AC016723.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235335		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042034	ENSG00000235335	AC016723.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235335		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042035	ENSG00000235781	XXbac-BPG249D20.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000235781		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042036	ENSG00000236140	RP11-89F3.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236140		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042037	ENSG00000236213	AC006369.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236213		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042038	ENSG00000236263	RP11-263K19.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236263		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042039	ENSG00000236519	AL773604.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236519		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042040	ENSG00000236537	RP11-732M18.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236537		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042041	ENSG00000236723	RP5-1024G6.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000236723		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042042	ENSG00000237015	CTA-984G1.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237015		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042043	ENSG00000237181	AC147651.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237181		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042044	ENSG00000237253	RP11-666A1.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237253		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042045	ENSG00000237311	RP6-159A1.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237311		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042046	ENSG00000237343	RP11-763B22.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237343		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042047	ENSG00000237410	AP001092.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237410		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042048	ENSG00000237429	RP1-159A19.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237429		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042049	ENSG00000237436	RP11-312B8.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237436		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042050	ENSG00000237587	RP11-327I22.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237587		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042051	ENSG00000237643	RP11-462G2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237643		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042052	ENSG00000237753	AC079922.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237753		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042053	ENSG00000237886	RP11-611D20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237886		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042054	ENSG00000237950	RP11-7O11.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237950		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042055	ENSG00000237976	RP11-126K1.6	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237976		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042056	ENSG00000237978	RP11-385J1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000237978		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042057	ENSG00000238178	RP11-431J24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000238178		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042058	ENSG00000239213	RP11-85F14.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000239213		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042059	ENSG00000239415	AP001469.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000239415		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042060	ENSG00000239705	RP11-65N13.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000239705		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042061	ENSG00000240015	RP11-90P5.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240015		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042062	ENSG00000240291	RP11-499P20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240291		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042063	ENSG00000240562	RP11-59J16.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000240562		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042064	ENSG00000241732	RP11-38P22.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000241732		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042065	ENSG00000241860	RP11-34P13.13	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000241860		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042066	ENSG00000242622	RP11-18H7.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000242622		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042067	ENSG00000244239	AC007009.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244239		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042068	ENSG00000244625	CTA-211A9.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244625		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042069	ENSG00000244952	RP11-1000B6.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000244952		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042070	ENSG00000245261	RP3-330M21.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000245261		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042071	ENSG00000246493	RP11-68L18.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000246493		lncRNA	Homo sapiens	27090285	Cytoplasm	K570 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042072	ENSG00000246792	RP11-68L18.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000246792		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042073	ENSG00000247137	RP11-727A23.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247137		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042074	ENSG00000247137	RP11-727A23.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247137		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042075	ENSG00000247728	RP11-932O9.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247728		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042076	ENSG00000247765	RP11-32B5.7	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247765		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042077	ENSG00000247810	RP11-103J17.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247810		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042078	ENSG00000247934	RP11-967K21.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000247934		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042079	ENSG00000248667	CTD-2331D11.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248667		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042080	ENSG00000248774	RP11-798M19.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248774		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042081	ENSG00000248783	RP11-308B16.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248783		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042082	ENSG00000248839	RP11-227H4.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000248839		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042083	ENSG00000249174	RP11-124N3.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249174		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042084	ENSG00000249356	RP11-21I10.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249356		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042085	ENSG00000249413	RP11-25H12.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249413		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042086	ENSG00000249502	AC006160.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249502		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042087	ENSG00000249639	CTB-138E5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249639		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042088	ENSG00000249650	RP11-310P5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000249650		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042089	ENSG00000250061	RP11-541P9.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250061		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042090	ENSG00000250081	CTD-2116N20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250081		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042091	ENSG00000250102	RP11-314N14.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250102		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042092	ENSG00000250159	RP11-381K20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250159		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042093	ENSG00000250159	RP11-381K20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250159		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042094	ENSG00000250222	CTC-338M12.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250222		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042095	ENSG00000250410	RP11-714G18.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250410		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042096	ENSG00000250453	CTD-2134P3.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250453		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042097	ENSG00000250501	RP11-98O2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250501		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042098	ENSG00000250604	RP11-597D13.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250604		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042099	ENSG00000250764	CTD-2152M20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250764		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042100	ENSG00000250842	CTC-806A22.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250842		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042101	ENSG00000250874	CTC-480C2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250874		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042102	ENSG00000250950	RP11-33B1.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000250950		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042103	ENSG00000251061	RP11-789C1.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251061		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042104	ENSG00000251141	RP11-53O19.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251141		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042105	ENSG00000251199	RP11-400D2.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251199		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042106	ENSG00000251259	AC004069.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251259		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042107	ENSG00000251387	CTB-35F21.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251387		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042108	ENSG00000251487	RP11-124N3.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251487		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042109	ENSG00000251637	RP11-119D9.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251637		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042110	ENSG00000251661	RP11-326C3.11	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251661		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042111	ENSG00000251676	RP11-614F17.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000251676		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042112	ENSG00000253154	CTA-392E5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253154		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042113	ENSG00000253194	RP11-351A11.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253194		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042114	ENSG00000253235	RP11-434I12.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253235		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042115	ENSG00000253347	CTD-2026D20.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253347		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042116	ENSG00000253376	RP11-44D19.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253376		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042117	ENSG00000253476	RP11-395I14.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253476		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042118	ENSG00000253636	RP11-531A24.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253636		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042119	ENSG00000253753	AC145123.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253753		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042120	ENSG00000253853	GS1-57L11.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253853		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042121	ENSG00000253865	RP11-394O4.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253865		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042122	ENSG00000253931	RP11-909N17.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253931		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042123	ENSG00000253982	CTD-2336O2.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000253982		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042124	ENSG00000254002	RP11-213G6.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254002		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042125	ENSG00000254067	RP11-122L4.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254067		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042126	ENSG00000254165	RP11-503E24.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254165		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042127	ENSG00000254298	CTB-17P3.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254298		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042128	ENSG00000254458	RP11-867G23.13	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254458		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042129	ENSG00000254461	RP11-755F10.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254461		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042130	ENSG00000254477	AP000640.10	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254477		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042131	ENSG00000254518	RP11-347H15.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254518		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042132	ENSG00000254519	CTD-2210P24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254519		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042133	ENSG00000254592	RP5-1173A5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254592		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042134	ENSG00000254639	CTD-2589M5.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254639		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042135	ENSG00000254682	RP11-660L16.2	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254682		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042136	ENSG00000254694	RP11-50B3.4	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254694		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042137	ENSG00000254739	RP13-46H24.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254739		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042138	ENSG00000254760	CTD-2616J11.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254760		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042139	ENSG00000254812	RP11-661A12.12	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254812		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042140	ENSG00000254855	RP11-867G23.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000254855		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042141	ENSG00000255135	RP11-111M22.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255135		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042142	ENSG00000255176	AP002954.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255176		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042143	ENSG00000255224	CTD-3065J16.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255224		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042144	ENSG00000255229	RP11-304M2.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255229		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042145	ENSG00000255237	RP13-317D12.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255237		lncRNA	Homo sapiens	27090285	Cytoplasm	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm."
RLID00042146	ENSG00000255318	RP11-655M14.13	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255318		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042147	ENSG00000255471	RP11-736K20.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255471		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042148	ENSG00000255487	RP11-513D5.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255487		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042149	ENSG00000255655	RP11-256L11.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255655		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042150	ENSG00000255893	RP11-685N10.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255893		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042151	ENSG00000255966	RP5-940J5.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000255966		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042152	ENSG00000256101	RP11-90D4.3	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256101		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042153	ENSG00000256258	RP11-495K9.9	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256258		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042154	ENSG00000256433	RP1-102E24.8	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256433		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042155	ENSG00000256473	RP11-437F6.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256473		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042156	ENSG00000256742	RP13-941N14.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256742		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042157	ENSG00000256922	RP11-749H20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256922		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042158	ENSG00000256940	RP11-783K16.5	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256940		lncRNA	Homo sapiens	27090285	Ribosome	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. Cytoplasmic and ribosomal localization has previously been reported for a number of lncRNA."
RLID00042159	ENSG00000256967	RP11-273B20.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000256967		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042160	ENSG00000272328	RP4-594A5.1	http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000272328		lncRNA	Homo sapiens	27090285	Nucleus	K562 cells	Microarray	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from Supplemental Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042161	21823	Th	http://www.ncbi.nlm.nih.gov/gene/?term=21823		mRNA	Mus musculus	27095027	Axons	Sympathetic Neurons	qRT-PCR	We show that TH mRNA is localized to distal axons.
RLID00042162	90632	LINC00473	http://www.ncbi.nlm.nih.gov/gene/?term=90632	"C6orf176, bA142J11.1"	lncRNA	Homo sapiens	27140397	Nucleus	FFPE human lung cancer specimens	Fractionation assay	"Moreover, exogenous LINC00473 showed similar nuclear localization when overexpressed in LKB1-WT H522 cells."
RLID00042163	90632	LINC00473	http://www.ncbi.nlm.nih.gov/gene/?term=90632	"C6orf176, bA142J11.1"	lncRNA	Homo sapiens	27140397	Nucleus	FFPE human lung cancer specimens	RNA-FISH	"Moreover, exogenous LINC00473 showed similar nuclear localization when overexpressed in LKB1-WT H522 cells."
RLID00042164	394452	vegt	http://www.ncbi.nlm.nih.gov/gene/?term=394452	"Apod, antipodean, brat, tVegT-a, vegt-b, xombi, vegt"	mRNA	Xenopus tropicalis	27140624	Nucleus	Embryo	RT-PCR	"Therefore, nuclear staining with Anti-VegT in cleavage to blastula stages probably demonstrates the nuclear localization of VegT in embryos of these frogs."
RLID00042165	723844	Mir338	http://www.ncbi.nlm.nih.gov/gene/?term=723844	"Mirn338, mir-338, mmu-mir-338"	miRNA	Mus musculus	27229124	Axons	Superior Cervical Ganglion	qRT-PCR	"Using compartmentalized culture chambers, we also observed that labeled pre-miR-338 localized to distal axons and was also associated with axonal mitochondria."
RLID00042166	102635290	Ttc39aos1	http://www.ncbi.nlm.nih.gov/gene/?term=102635290	"Gm12750, lincRNA-EPS"	lncRNA	Mus musculus	27315481	Nucleus	Macrophages	RT-qPCR	The nuclear localization of lincRNA-EPS was also confirmed using single molecule RNA fluorescent in situ hybridization (FISH) in resting primary BMDMs.
RLID00042167	1026	CDKN1A	http://www.ncbi.nlm.nih.gov/gene/?term=1026	"CAP20, CDKN1, CIP1, MDA-6, P21, SDI1, WAF1, p21CIP1"	mRNA	Homo sapiens	27378782	Nucleus	Dermal Fibroblasts	qRT-PCR	"Moreover, the structures formed by IRAlus are involved in the localization of hLincRNA-p21 in the nucleus, where hLincRNA-p21 colocalizes with paraspeckles."
RLID00042168	14714	Gnrh1	http://www.ncbi.nlm.nih.gov/gene/?term=14714	"Gnrh, Gnrh2, LHRH, Lhrh1, Lnrh, hpg"	mRNA	Mus musculus	27389022	Nucleus	cell lines	RT-qPCR	The localization of Gnrh1 mRNA in both the nucleus and cytoplasm is consistent with the robust Gnrh1 expression and GnRH synthesis in GT1-7 neurons.
RLID00042169	14714	Gnrh1	http://www.ncbi.nlm.nih.gov/gene/?term=14714	"Gnrh, Gnrh2, LHRH, Lhrh1, Lnrh, hpg"	mRNA	Mus musculus	27389022	Cytoplasm	cell lines	RT-qPCR	The localization of Gnrh1 mRNA in both the nucleus and cytoplasm is consistent with the robust Gnrh1 expression and GnRH synthesis in GT1-7 neurons.
RLID00042170	27198	B3GNT2	http://www.ncbi.nlm.nih.gov/gene/?term=27198	"B3GNT, BGNT2, B3GNT1, BGnT-2,beta-1, 3-Gn-T1, 3-Gn-T2, B3GN-T2, B3GNT-2, BETA3GNT, beta3Gn-T1, beta3Gn-T2"	mRNA	Homo sapiens	27477284	Axons	DRG neuron	qPCR	"Immunostaining for nucleolin protein concomitantly with FISH for importin ¦Â1 mRNA revealed extensive axonal colocalization, as compared to similar analyses for ¦Â-actin or GAP43 mRNAs."
RLID00042171	400123	LINC00548	http://www.ncbi.nlm.nih.gov/gene/?term=400123		lncRNA	Homo sapiens	27572135	Nucleus	HeLa and HEK293 cells	RNA-FISH	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from supplemental meterial's Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042172	400123	LINC00548	http://www.ncbi.nlm.nih.gov/gene/?term=400123		lncRNA	Homo sapiens	27572135	Nucleus	HeLa and HEK293 cells	qRT-PCR	"Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Data were collected from supplemental meterial's Table S1. From the remaining filtered lncRNA transcripts, an additional 292 transcripts (3.2%, representing 255 or 3.7% genes) were detected in the nucleus based on ENCODE data, and henceforth defined as nuclear-specific."
RLID00042173	646982	LINC00598	http://www.ncbi.nlm.nih.gov/gene/?term=646982	lncFOXO1	lncRNA	Homo sapiens	27572135	Nucleus	HeLa and HEK293 cells	RNA-FISH	"We observed that linc00598 was mainly located in the nuclear compartment, similarly to Xist, a well-known nuclear lncRNA."
RLID00042174	646982	LINC00598	http://www.ncbi.nlm.nih.gov/gene/?term=646982	lncFOXO1	lncRNA	Homo sapiens	27572135	Nucleus	HeLa and HEK293 cells	qRT-PCR	"We observed that linc00598 was mainly located in the nuclear compartment, similarly to Xist, a well-known nuclear lncRNA."
RLID00042175	12310	Calca	http://www.ncbi.nlm.nih.gov/gene/?term=12310	"CA, CGRP-1, CGRP1, Calc, Calc1, Cgrp, Ct, Ctn"	mRNA	Mus musculus	27665741	Paraspeckles	Embryonic Fibroblasts	RT-qPCR	"In WT-MEFs, Ctn RNA is localized to paraspeckles, as confirmed by co-staining of cells with Neat1."
RLID00042176	19782	Rmrp	http://www.ncbi.nlm.nih.gov/gene/?term=19782	"Rmrpr, 1110032O22Rik"	lncRNA	Mus musculus	27699653	Cytoplasm	HeLa and HEK293 cells	PCR	"Our findings indicate that RBPs HuR and GRSF1 govern the cytoplasmic and mitochondrial localization of the lncRNA RMRP, which is encoded by nuclear DNA but has key functions in mitochondria."
RLID00042177	19782	Rmrp	http://www.ncbi.nlm.nih.gov/gene/?term=19782	"Rmrpr, 1110032O22Rik"	lncRNA	Mus musculus	27699653	Mitochondria 	HeLa and HEK293 cells	PCR	"Our findings indicate that RBPs HuR and GRSF1 govern the cytoplasmic and mitochondrial localization of the lncRNA RMRP, which is encoded by nuclear DNA but has key functions in mitochondria."
RLID00042178	57425	U90926	http://www.ncbi.nlm.nih.gov/gene/?term=57425		lncRNA	Mus musculus	27780975	Cytoplasm	Adipose Tissue	FISH	FISH results showed that lnc-U90926 was mainly located in the cytoplasm.
RLID00042179	68949	Zfas1	http://www.ncbi.nlm.nih.gov/gene/?term=68949	"Zfos1, 1500012F01Rik"	mRNA	Mus musculus	27871336	Cytoplasm	Breast Cancer Cells	RT-PCR	"Since cellular location will dictate function of lncRNA, cellular fractionation was performed to identify the subcellular localisation of ZFAS1 in MDA-MB-468 and MDA-MB-231 breast cancer cells. As indicated for MDA-MB-468 cell extracts, ZFAS1 was found in both the cytoplasm and nucleus, indicating that ZFAS1 is not restricted to a specific cellular compartment."
RLID00042180	68949	Zfas1	http://www.ncbi.nlm.nih.gov/gene/?term=68949	"Zfos1, 1500012F01Rik"	mRNA	Mus musculus	27871336	Nucleus	Breast Cancer Cells	RT-PCR	"Since cellular location will dictate function of lncRNA, cellular fractionation was performed to identify the subcellular localisation of ZFAS1 in MDA-MB-468 and MDA-MB-231 breast cancer cells. As indicated for MDA-MB-468 cell extracts, ZFAS1 was found in both the cytoplasm and nucleus, indicating that ZFAS1 is not restricted to a specific cellular compartment."
RLID00042181	38565	HDAC1	http://www.ncbi.nlm.nih.gov/gene/?term=38565	"Dmel_CG7471, CG7471, DHDAC1, DRpd3, DmHDAC1, Dmel\CG7471, E(var)3-64BC, HDAC, HDAC-1, Hdac, Hdac1, RPD3, Rpd3, Rpd3/HDAC, Su(var)3-26, Su(var)326, Su(var)328, dHDAC-1, dHDAC1, dRPD3, dRpd3, dmHDA401, drpd3, hdac1, l(3)04556, l(3)64Cc, rpd3, rpd[3]"	mRNA	Drosophila melanogaster	27907135	Nucleus	Fat bodies	RT-qPCR	"The strong Rpd3 signals clearly merged with the Fibrillarin signals, indicating that Rpd3 mainly localizes in the nucleolus."
RLID00042182	208715	Hmgcs1	http://www.ncbi.nlm.nih.gov/gene/?term=208715	B130032C06Rik	mRNA	Mus musculus	28155669	Peroxisome	Livers	qRT-PCR	"The immunoelectron microscopy of rat liver from the same study has shown that the cytosolic fraction of HMG-CoA synthase 1 is detected in the area surrounding peroxisomes, which is consistent with our data on localization of Hmgcs1 mRNA in the vicinity of peroxisome."
RLID00042183	15569	Elavl2	http://www.ncbi.nlm.nih.gov/gene/?term=15569	"Hub, mel-N1"	mRNA	Mus musculus	28300211	Axons	Neuronal cell	PCR	"As our predictions suggest that Elavl2 mRNA is localized in axons of MN, we sought to characterize its protein and mRNA localization."
RLID00042184	12737	Cldn1	http://www.ncbi.nlm.nih.gov/gene/?term=12737	AI596271	mRNA	Mus musculus	28455726	Tight Junction	Mammary Glands	qRT-PCR	"Here, we briefly review our current understanding of claudin structure and function followed by an examination of changes in claudin mRNA and protein expression and localization through mammary gland development. Claudin-1 is clearly localized to tight junctions in mammary ducts in non-pregnant non-lactating animals."
RLID00042185	12739	Cldn3	http://www.ncbi.nlm.nih.gov/gene/?term=12739	"AI182374, Cpetr2, mRVP1"	mRNA	Mus musculus	28455726	Tight Junction	Mammary Glands	qRT-PCR	"Here, we briefly review our current understanding of claudin structure and function followed by an examination of changes in claudin mRNA and protein expression and localization through mammary gland development. In the lactating mouse both claudin-3 and claudin-8 are localized at the tight junction where they may be important in forming the paracellular barrier."
RLID00042186	1366	CLDN7	http://www.ncbi.nlm.nih.gov/gene/?term=1366	"CLDN-7, CEPTRL2, CPETRL2, Hs.84359, claudin-1"	mRNA	Homo sapiens	28455726	Cytoplasm	Mammary Glands	qRT-PCR	"Here, we briefly review our current understanding of claudin structure and function followed by an examination of changes in claudin mRNA and protein expression and localization through mammary gland development. Claudin-7 remained largely in the soluble fraction after LPS treatment, in keeping with its usual location in cytoplasmic vesicles."
RLID00042187	54420	Cldn8	http://www.ncbi.nlm.nih.gov/gene/?term=54420	AI648025	mRNA	Mus musculus	28455726	Tight Junction	Mammary Glands	qRT-PCR	"Here, we briefly review our current understanding of claudin structure and function followed by an examination of changes in claudin mRNA and protein expression and localization through mammary gland development. In the lactating mouse both claudin-3 and claudin-8 are localized at the tight junction where they may be important in forming the paracellular barrier."
RLID00042188	53413	Exoc7	http://www.ncbi.nlm.nih.gov/gene/?term=53413	"Exo70, sec70"	mRNA	Mus musculus	28536622	Cytoplasm	Vascular Smooth Muscle	qRT-PCR	"The expression of the Exo70 gene in A7r5 cells was detected by RT-PCR and immunofluorescent staining. The results showed that Exo70 was expressed in A7r5 cells. Additionally, Exo70 expression was mainly localized in the cytoplasm and a small amount in the nucleus."
RLID00042189	53413	Exoc7	http://www.ncbi.nlm.nih.gov/gene/?term=53413	"Exo70, sec70"	mRNA	Mus musculus	28536622	Nucleus	Vascular Smooth Muscle	qRT-PCR	"The expression of the Exo70 gene in A7r5 cells was detected by RT-PCR and immunofluorescent staining. The results showed that Exo70 was expressed in A7r5 cells. Additionally, Exo70 expression was mainly localized in the cytoplasm and a small amount in the nucleus."
RLID00042190	724102	SNHG4	http://www.ncbi.nlm.nih.gov/gene/?term=724102	"U19H, NCRNA00059"	lncRNA	Homo sapiens	9630250	Nucleoplasm	HeLa cells	qRT-PCR	"Because the U19H RNA possesses limited potential for protein coding and shows a predominant nucleoplasmic localization, we suggest that the sole function of the U19H gene is to express the U19 intronic snoRNA."